/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://lammps.sandia.gov/, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ // unit tests for pair styles intended for molecular systems #include "error_stats.h" #include "test_config.h" #include "test_config_reader.h" #include "test_main.h" #include "yaml_reader.h" #include "yaml_writer.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include "atom.h" #include "compute.h" #include "fix.h" #include "fmt/format.h" #include "force.h" #include "info.h" #include "input.h" #include "kspace.h" #include "lammps.h" #include "modify.h" #include "pair.h" #include "universe.h" #include "utils.h" #include "variable.h" #include #include #include #include #include #include #include #include #include using ::testing::HasSubstr; using ::testing::StartsWith; using namespace LAMMPS_NS; static void delete_file(const std::string &filename) { remove(filename.c_str()); }; void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg) { delete_file(cfg.basename + ".restart"); delete lmp; lmp = nullptr; } LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool use_respa = false) { LAMMPS *lmp; lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); // check if prerequisite styles are available Info *info = new Info(lmp); int nfail = 0; for (auto &prerequisite : cfg.prerequisites) { std::string style = prerequisite.second; // this is a test for fix styles, so if the suffixed // version is not available, there is no reason to test. if (prerequisite.first == "fix") { if (lmp->suffix_enable) { style += "/"; style += lmp->suffix; } } if (!info->has_style(prerequisite.first, style)) ++nfail; } delete info; if (nfail > 0) { cleanup_lammps(lmp, cfg); return nullptr; } // utility lambda to improve readability auto command = [&](const std::string &line) { lmp->input->one(line.c_str()); }; command("variable input_dir index " + INPUT_FOLDER); for (auto &pre_command : cfg.pre_commands) command(pre_command); std::string input_file = INPUT_FOLDER + PATH_SEP + cfg.input_file; lmp->input->file(input_file.c_str()); if (use_respa) command("run_style respa 2 1 bond 1 pair 2"); // set up molecular system force field command("pair_style lj/cut 8.0"); command("pair_coeff 1 1 0.02 2.5"); command("pair_coeff 2 2 0.005 1.0"); command("pair_coeff 2 4 0.005 0.5"); command("pair_coeff 3 3 0.02 3.2"); command("pair_coeff 4 4 0.015 3.1"); command("pair_coeff 5 5 0.015 3.1"); command("bond_style harmonic"); command("bond_coeff 1 250.0 1.5"); command("bond_coeff 2 300.0 1.1"); command("bond_coeff 3 350.0 1.3"); command("bond_coeff 4 650.0 1.2"); command("bond_coeff 5 450.0 1.0"); command("angle_style harmonic"); command("angle_coeff 1 75.0 110.1"); command("angle_coeff 2 45.0 111.0"); command("angle_coeff 3 50.0 120.0"); command("angle_coeff 4 100.0 108.5"); command("group solute molecule 1:2"); command("group solvent molecule 3:5"); for (auto &post_command : cfg.post_commands) command(post_command); command("timestep 0.25"); command("run 0 post no"); command("thermo 2"); command("run 4 post no start 0 stop 8"); command("write_restart " + cfg.basename + ".restart"); command("run 4 post no start 0 stop 8"); return lmp; } void restart_lammps(LAMMPS *lmp, const TestConfig &cfg, bool use_rmass, bool use_respa) { // utility lambda to improve readability auto command = [&](const std::string &line) { lmp->input->one(line.c_str()); }; command("clear"); command("read_restart " + cfg.basename + ".restart"); if (use_rmass) { command("fix rmass all property/atom rmass ghost yes"); for (int i = 0; i < lmp->atom->ntypes; ++i) command(fmt::format("set type {} mass {}", i + 1, lmp->atom->mass[i + 1])); } if (use_respa) command("run_style respa 2 1 bond 1 pair 2"); for (auto &post_command : cfg.post_commands) command(post_command); command("thermo 2"); command("run 4 post no start 0 stop 8"); } // re-generate yaml file with current settings. void generate_yaml_file(const char *outfile, const TestConfig &config) { // initialize system geometry const char *args[] = {"FixIntegrate", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); LAMMPS *lmp = init_lammps(argc, argv, config); if (!lmp) { std::cerr << "One or more prerequisite styles are not available " "in this LAMMPS configuration:\n"; for (auto prerequisite : config.prerequisites) { std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n"; } return; } const int natoms = lmp->atom->natoms; std::string block(""); YamlWriter writer(outfile); // write yaml header write_yaml_header(&writer, &test_config, lmp->version); // natoms writer.emit("natoms", natoms); int ifix = lmp->modify->find_fix("test"); if (ifix < 0) { std::cerr << "ERROR: no fix defined with fix ID 'test'\n"; exit(1); } else { Fix *fix = lmp->modify->fix[ifix]; // run_stress, if enabled if (fix->thermo_virial) { auto stress = fix->virial; block = fmt::format("{:23.16e} {:23.16e} {:23.16e} " "{:23.16e} {:23.16e} {:23.16e}", stress[0], stress[1], stress[2], stress[3], stress[4], stress[5]); writer.emit_block("run_stress", block); } // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); writer.emit("global_scalar", value); } // global vector if (fix->vector_flag) { int num = fix->size_vector; block = std::to_string(num); for (int i = 0; i < num; ++i) block += fmt::format(" {}", fix->compute_vector(i)); writer.emit_block("global_vector", block); } } // run_pos block.clear(); auto x = lmp->atom->x; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, x[j][0], x[j][1], x[j][2]); } writer.emit_block("run_pos", block); // run_vel block.clear(); auto v = lmp->atom->v; for (int i = 1; i <= natoms; ++i) { const int j = lmp->atom->map(i); block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, v[j][0], v[j][1], v[j][2]); } writer.emit_block("run_vel", block); cleanup_lammps(lmp, config); return; } TEST(FixTimestep, plain) { if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite"}; char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); ::testing::internal::CaptureStdout(); LAMMPS *lmp = init_lammps(argc, argv, test_config); std::string output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; if (!lmp) { std::cerr << "One or more prerequisite styles are not available " "in this LAMMPS configuration:\n"; for (auto &prerequisite : test_config.prerequisites) { std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n"; } GTEST_SKIP(); } EXPECT_THAT(output, StartsWith("LAMMPS (")); EXPECT_THAT(output, HasSubstr("Loop time")); // abort if running in parallel and not all atoms are local const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); double epsilon = test_config.epsilon; auto tag = lmp->atom->tag; auto x = lmp->atom->x; auto v = lmp->atom->v; ErrorStats stats; stats.reset(); const std::vector &x_ref = test_config.run_pos; ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, normal run, verlet: " << stats << std::endl; const std::vector &v_ref = test_config.run_vel; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, normal run, verlet: " << stats << std::endl; int ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon); if (print_stats) std::cerr << "run_stress normal run, verlet: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), epsilon); } // check t_target for thermostats int dim = -1; double *ptr = (double *)fix->extract("t_target", dim); if ((ptr != nullptr) && (dim == 0)) { int ivar = lmp->input->variable->find("t_target"); if (ivar >= 0) { double t_ref = atof(lmp->input->variable->retrieve("t_target")); double t_target = *ptr; EXPECT_FP_LE_WITH_EPS(t_target, t_ref, epsilon); } } if (print_stats && stats.has_data()) std::cerr << "global_data, normal run, verlet: " << stats << std::endl; } if (!verbose) ::testing::internal::CaptureStdout(); restart_lammps(lmp, test_config, false, false); if (!verbose) ::testing::internal::GetCapturedStdout(); tag = lmp->atom->tag; x = lmp->atom->x; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, restart, verlet: " << stats << std::endl; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, restart, verlet: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon); if (print_stats) std::cerr << "run_stress restart, verlet: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, restart, verlet: " << stats << std::endl; } if (!verbose) ::testing::internal::CaptureStdout(); restart_lammps(lmp, test_config, true, false); if (!verbose) ::testing::internal::GetCapturedStdout(); x = lmp->atom->x; tag = lmp->atom->tag; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, rmass, verlet: " << stats << std::endl; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, rmass, verlet: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon); if (print_stats) std::cerr << "run_stress rmass, verlet: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, rmass, verlet: " << stats << std::endl; } // rigid fixes need work to test properly with r-RESPA. // fix nve/limit cannot work with r-RESPA ifix = lmp->modify->find_fix("test"); if (!utils::strmatch(lmp->modify->fix[ifix]->style, "^rigid") && !utils::strmatch(lmp->modify->fix[ifix]->style, "^nve/limit")) { if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); ::testing::internal::CaptureStdout(); lmp = init_lammps(argc, argv, test_config, true); output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; // lower required precision by two orders of magnitude to accommodate respa epsilon *= 100.0; tag = lmp->atom->tag; x = lmp->atom->x; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, normal run, respa: " << stats << std::endl; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, normal run, respa: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 1000 * epsilon); if (print_stats) std::cerr << "run_stress normal run, respa: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, normal run, respa: " << stats << std::endl; } if (!verbose) ::testing::internal::CaptureStdout(); restart_lammps(lmp, test_config, false, true); if (!verbose) ::testing::internal::GetCapturedStdout(); tag = lmp->atom->tag; x = lmp->atom->x; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, restart, respa: " << stats << std::endl; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, restart, respa: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 1000 * epsilon); if (print_stats) std::cerr << "run_stress restart, respa: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, restart, respa: " << stats << std::endl; } if (!verbose) ::testing::internal::CaptureStdout(); restart_lammps(lmp, test_config, true, true); if (!verbose) ::testing::internal::GetCapturedStdout(); x = lmp->atom->x; tag = lmp->atom->tag; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, rmass, respa: " << stats << std::endl; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, rmass, respa: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 1000 * epsilon); if (print_stats) std::cerr << "run_stress rmass, respa: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, rmass, respa: " << stats << std::endl; } } if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); }; TEST(FixTimestep, omp) { if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP(); if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP(); const char *args[] = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite", "-pk", "omp", "4", "-sf", "omp"}; char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); ::testing::internal::CaptureStdout(); LAMMPS *lmp = init_lammps(argc, argv, test_config); std::string output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; if (!lmp) { std::cerr << "One or more prerequisite styles are not available " "in this LAMMPS configuration:\n"; for (auto &prerequisite : test_config.prerequisites) { std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n"; } GTEST_SKIP(); } EXPECT_THAT(output, StartsWith("LAMMPS (")); EXPECT_THAT(output, HasSubstr("Loop time")); // abort if running in parallel and not all atoms are local const int nlocal = lmp->atom->nlocal; ASSERT_EQ(lmp->atom->natoms, nlocal); double epsilon = test_config.epsilon; auto tag = lmp->atom->tag; auto x = lmp->atom->x; auto v = lmp->atom->v; ErrorStats stats; stats.reset(); const std::vector &x_ref = test_config.run_pos; ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, normal run, verlet: " << stats << std::endl; const std::vector &v_ref = test_config.run_vel; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, normal run, verlet: " << stats << std::endl; int ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon); if (print_stats) std::cerr << "run_stress normal run, verlet: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), epsilon); } // check t_target for thermostats int dim = -1; double *ptr = (double *)fix->extract("t_target", dim); if ((ptr != nullptr) && (dim == 0)) { int ivar = lmp->input->variable->find("t_target"); if (ivar >= 0) { double t_ref = atof(lmp->input->variable->retrieve("t_target")); double t_target = *ptr; EXPECT_FP_LE_WITH_EPS(t_target, t_ref, epsilon); } } if (print_stats && stats.has_data()) std::cerr << "global_data, normal run, verlet: " << stats << std::endl; } if (!verbose) ::testing::internal::CaptureStdout(); restart_lammps(lmp, test_config, false, false); if (!verbose) ::testing::internal::GetCapturedStdout(); tag = lmp->atom->tag; x = lmp->atom->x; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, restart, verlet: " << stats << std::endl; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, restart, verlet: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon); if (print_stats) std::cerr << "run_stress restart, verlet: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, restart, verlet: " << stats << std::endl; } if (!verbose) ::testing::internal::CaptureStdout(); restart_lammps(lmp, test_config, true, false); if (!verbose) ::testing::internal::GetCapturedStdout(); x = lmp->atom->x; tag = lmp->atom->tag; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, rmass, verlet: " << stats << std::endl; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, rmass, verlet: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon); if (print_stats) std::cerr << "run_stress rmass, verlet: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, rmass, verlet: " << stats << std::endl; } // rigid fixes need work to test properly with r-RESPA ifix = lmp->modify->find_fix("test"); if (!utils::strmatch(lmp->modify->fix[ifix]->style, "^rigid")) { if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); ::testing::internal::CaptureStdout(); lmp = init_lammps(argc, argv, test_config, true); output = ::testing::internal::GetCapturedStdout(); if (verbose) std::cout << output; // lower required precision by two orders of magnitude to accommodate respa epsilon *= 100.0; tag = lmp->atom->tag; x = lmp->atom->x; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, normal run, respa: " << stats << std::endl; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, normal run, respa: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 1000 * epsilon); if (print_stats) std::cerr << "run_stress normal run, respa: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, normal run, respa: " << stats << std::endl; } if (!verbose) ::testing::internal::CaptureStdout(); restart_lammps(lmp, test_config, false, true); if (!verbose) ::testing::internal::GetCapturedStdout(); tag = lmp->atom->tag; x = lmp->atom->x; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, restart, respa: " << stats << std::endl; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, restart, respa: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 1000 * epsilon); if (print_stats) std::cerr << "run_stress restart, respa: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, restart, respa: " << stats << std::endl; } if (!verbose) ::testing::internal::CaptureStdout(); restart_lammps(lmp, test_config, true, true); if (!verbose) ::testing::internal::GetCapturedStdout(); x = lmp->atom->x; tag = lmp->atom->tag; stats.reset(); ASSERT_EQ(nlocal + 1, x_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(x[i][0], x_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][1], x_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(x[i][2], x_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_pos, rmass, respa: " << stats << std::endl; v = lmp->atom->v; stats.reset(); ASSERT_EQ(nlocal + 1, v_ref.size()); for (int i = 0; i < nlocal; ++i) { EXPECT_FP_LE_WITH_EPS(v[i][0], v_ref[tag[i]].x, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][1], v_ref[tag[i]].y, epsilon); EXPECT_FP_LE_WITH_EPS(v[i][2], v_ref[tag[i]].z, epsilon); } if (print_stats) std::cerr << "run_vel, rmass, respa: " << stats << std::endl; ifix = lmp->modify->find_fix("test"); if (ifix < 0) { FAIL() << "ERROR: no fix defined with fix ID 'test'\n"; } else { Fix *fix = lmp->modify->fix[ifix]; if (fix->thermo_virial) { stats.reset(); auto stress = fix->virial; EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 1000 * epsilon); EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 1000 * epsilon); if (print_stats) std::cerr << "run_stress rmass, respa: " << stats << std::endl; } stats.reset(); // global scalar if (fix->scalar_flag) { double value = fix->compute_scalar(); EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, 10 * epsilon); } // global vector if (fix->vector_flag) { int num = fix->size_vector; EXPECT_EQ(num, test_config.global_vector.size()); for (int i = 0; i < num; ++i) EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], fix->compute_vector(i), 10 * epsilon); } if (print_stats && stats.has_data()) std::cerr << "global_data, rmass, respa: " << stats << std::endl; } } if (!verbose) ::testing::internal::CaptureStdout(); cleanup_lammps(lmp, test_config); if (!verbose) ::testing::internal::GetCapturedStdout(); };