From f3391199e71e606f2de687ed1e842b04c226e8e0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 25 Mar 2024 14:26:39 -0400 Subject: [PATCH 01/40] correct formatting of tables --- doc/src/variable.rst | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 1cd96543f5..483e95045c 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -1174,12 +1174,17 @@ custom atom properties are the same; just replace the leading "i" with +--------+---------------+------------------------------------------+ | equal | i_name[I] | element of per-atom vector (I = atom ID) | ++--------+---------------+------------------------------------------+ | equal | i2_name[I][J] | element of per-atom array (I = atom ID) | +--------+---------------+------------------------------------------+ ++--------+---------------+------------------------------------------+ | vector | i_name[I] | element of per-atom vector (I = atom ID) | ++--------+---------------+------------------------------------------+ | vector | i2_name[I][J] | element of per-atom array (I = atom ID) | +--------+---------------+------------------------------------------+ ++--------+---------------+------------------------------------------+ | atom | i_name | per-atom vector | ++--------+---------------+------------------------------------------+ | atom | i2_name[I] | column of per-atom array | +--------+---------------+------------------------------------------+ @@ -1222,15 +1227,23 @@ table: +--------+------------+------------------------------------------+ | equal | c_ID | global scalar | ++--------+------------+------------------------------------------+ | equal | c_ID[I] | element of global vector | ++--------+------------+------------------------------------------+ | equal | c_ID[I][J] | element of global array | ++--------+------------+------------------------------------------+ | equal | C_ID[I] | element of per-atom vector (I = atom ID) | ++--------+------------+------------------------------------------+ | equal | C_ID[I][J] | element of per-atom array (I = atom ID) | +--------+------------+------------------------------------------+ ++--------+------------+------------------------------------------+ | vector | c_ID | global vector | ++--------+------------+------------------------------------------+ | vector | c_ID[I] | column of global array | +--------+------------+------------------------------------------+ ++--------+------------+------------------------------------------+ | atom | c_ID | per-atom vector | ++--------+------------+------------------------------------------+ | atom | c_ID[I] | column of per-atom array | +--------+------------+------------------------------------------+ @@ -1286,15 +1299,23 @@ and atom-style variables are listed in the following table: +--------+------------+------------------------------------------+ | equal | f_ID | global scalar | ++--------+------------+------------------------------------------+ | equal | f_ID[I] | element of global vector | ++--------+------------+------------------------------------------+ | equal | f_ID[I][J] | element of global array | ++--------+------------+------------------------------------------+ | equal | F_ID[I] | element of per-atom vector (I = atom ID) | ++--------+------------+------------------------------------------+ | equal | F_ID[I][J] | element of per-atom array (I = atom ID) | +--------+------------+------------------------------------------+ ++--------+------------+------------------------------------------+ | vector | f_ID | global vector | ++--------+------------+------------------------------------------+ | vector | f_ID[I] | column of global array | +--------+------------+------------------------------------------+ ++--------+------------+------------------------------------------+ | atom | f_ID | per-atom vector | ++--------+------------+------------------------------------------+ | atom | f_ID[I] | column of per-atom array | +--------+------------+------------------------------------------+ @@ -1365,17 +1386,27 @@ per-atom vector. +--------+-----------+-----------------------------------------------------------------------------------+ | equal | v_name | global scalar from an equal-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | equal | v_name[I] | element of global vector from a vector-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | equal | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable | +--------+-----------+-----------------------------------------------------------------------------------+ ++--------+-----------+-----------------------------------------------------------------------------------+ | vector | v_name | global scalar from an equal-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | vector | v_name | global vector from a vector-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | vector | v_name[I] | element of global vector from a vector-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | vector | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable | +--------+-----------+-----------------------------------------------------------------------------------+ ++--------+-----------+-----------------------------------------------------------------------------------+ | atom | v_name | global scalar from an equal-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | atom | v_name | per-atom vector from an atom-style or atomfile-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | atom | v_name[I] | element of global vector from a vector-style variable | ++--------+-----------+-----------------------------------------------------------------------------------+ | atom | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable | +--------+-----------+-----------------------------------------------------------------------------------+ From 45fbe73f2b6d2d91c52f9b0ef574a72d7fe5fc9f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 25 Mar 2024 22:48:01 -0400 Subject: [PATCH 02/40] Simplify output of windows version. If unknown build number just output "Windows Build #####" --- src/platform.cpp | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/src/platform.cpp b/src/platform.cpp index b324bd0b5c..7e9fa820fa 100644 --- a/src/platform.cpp +++ b/src/platform.cpp @@ -249,12 +249,7 @@ std::string platform::os_info() } else if (build == "22631") { buf = "Windows 11 23H2"; } else { - const char *entry = "ProductName"; - RegGetValue(HKEY_LOCAL_MACHINE, subkey, entry, RRF_RT_REG_SZ, nullptr, &value, - (LPDWORD) &value_length); - // enforce zero termination - value[1023] = '\0'; - buf = value; + buf = "Windows Build " + build; } DWORD fullversion, majorv, minorv, buildv = 0; fullversion = GetVersion(); From c4eadd3a5966a0103afe8236273408a5c68a1df7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Mar 2024 01:52:07 -0400 Subject: [PATCH 03/40] change ordering of eigenvalues in jacobi3() function. update tests. --- examples/micelle/in.micelle | 76 +-- examples/micelle/in.micelle-rigid | 90 ++-- .../micelle/log.25Mar24.micelle-rigid.g++.1 | 272 ++++++++++ .../micelle/log.25Mar24.micelle-rigid.g++.4 | 272 ++++++++++ examples/micelle/log.25Mar24.micelle.g++.1 | 229 +++++++++ examples/micelle/log.25Mar24.micelle.g++.4 | 229 +++++++++ .../micelle/log.29Mar2019.micelle-rigid.g++.1 | 260 ---------- .../micelle/log.29Mar2019.micelle-rigid.g++.4 | 260 ---------- examples/micelle/log.29Mar2019.micelle.g++.1 | 218 -------- examples/micelle/log.29Mar2019.micelle.g++.4 | 218 -------- examples/rigid/log.20Mar22.rigid.infile.g++.1 | 312 ------------ examples/rigid/log.20Mar22.rigid.infile.g++.4 | 312 ------------ .../rigid/log.20Mar22.rigid.molecule.g++.1 | 349 ------------- .../rigid/log.20Mar22.rigid.molecule.g++.4 | 349 ------------- examples/rigid/log.20Mar22.rigid.poems.g++.1 | 328 ------------ examples/rigid/log.20Mar22.rigid.poems.g++.4 | 328 ------------ examples/rigid/log.20Mar22.rigid.poems2.g++.1 | 330 ------------ examples/rigid/log.20Mar22.rigid.poems2.g++.4 | 330 ------------ examples/rigid/log.20Mar22.rigid.poems3.g++.1 | 329 ------------ examples/rigid/log.20Mar22.rigid.poems3.g++.4 | 329 ------------ examples/rigid/log.20Mar22.rigid.poems4.g++.1 | 328 ------------ examples/rigid/log.20Mar22.rigid.poems4.g++.4 | 328 ------------ examples/rigid/log.20Mar22.rigid.poems5.g++.1 | 329 ------------ examples/rigid/log.20Mar22.rigid.poems5.g++.4 | 329 ------------ .../log.20Mar22.rigid.rigid.molecule.g++.1 | 0 .../log.20Mar22.rigid.rigid.molecule.g++.4 | 0 examples/rigid/log.20Mar22.rigid.small.g++.1 | 322 ------------ examples/rigid/log.20Mar22.rigid.small.g++.4 | 322 ------------ .../log.20Mar22.rigid.small.infile.g++.1 | 323 ------------ .../log.20Mar22.rigid.small.infile.g++.4 | 323 ------------ .../rigid/log.25Mar24.rigid.atomfile.g++.1 | 341 +++++++++++++ .../rigid/log.25Mar24.rigid.atomfile.g++.4 | 341 +++++++++++++ .../rigid/log.25Mar24.rigid.atomvar.g++.1 | 341 +++++++++++++ .../rigid/log.25Mar24.rigid.atomvar.g++.4 | 341 +++++++++++++ examples/rigid/log.25Mar24.rigid.early.g++.1 | 340 +++++++++++++ examples/rigid/log.25Mar24.rigid.early.g++.4 | 340 +++++++++++++ examples/rigid/log.25Mar24.rigid.g++.1 | 338 +++++++++++++ examples/rigid/log.25Mar24.rigid.g++.4 | 338 +++++++++++++ .../rigid/log.25Mar24.rigid.gravity.g++.1 | 228 +++++++++ .../rigid/log.25Mar24.rigid.gravity.g++.4 | 228 +++++++++ examples/rigid/log.25Mar24.rigid.infile.g++.1 | 310 ++++++++++++ examples/rigid/log.25Mar24.rigid.infile.g++.4 | 310 ++++++++++++ .../rigid/log.25Mar24.rigid.molecule.g++.1 | 319 ++++++++++++ .../rigid/log.25Mar24.rigid.molecule.g++.4 | 319 ++++++++++++ .../rigid/log.25Mar24.rigid.nve.early.g++.1 | 340 +++++++++++++ .../rigid/log.25Mar24.rigid.nve.early.g++.4 | 340 +++++++++++++ examples/rigid/log.25Mar24.rigid.nve.g++.1 | 338 +++++++++++++ examples/rigid/log.25Mar24.rigid.nve.g++.4 | 338 +++++++++++++ examples/rigid/log.25Mar24.rigid.poems.g++.1 | 328 ++++++++++++ examples/rigid/log.25Mar24.rigid.poems.g++.4 | 328 ++++++++++++ examples/rigid/log.25Mar24.rigid.poems2.g++.1 | 330 ++++++++++++ examples/rigid/log.25Mar24.rigid.poems2.g++.4 | 330 ++++++++++++ examples/rigid/log.25Mar24.rigid.poems3.g++.1 | 329 ++++++++++++ examples/rigid/log.25Mar24.rigid.poems3.g++.4 | 329 ++++++++++++ examples/rigid/log.25Mar24.rigid.poems4.g++.1 | 328 ++++++++++++ examples/rigid/log.25Mar24.rigid.poems4.g++.4 | 328 ++++++++++++ examples/rigid/log.25Mar24.rigid.poems5.g++.1 | 329 ++++++++++++ examples/rigid/log.25Mar24.rigid.poems5.g++.4 | 329 ++++++++++++ .../rigid/log.25Mar24.rigid.property.g++.1 | 343 +++++++++++++ .../rigid/log.25Mar24.rigid.property.g++.4 | 343 +++++++++++++ examples/rigid/log.25Mar24.rigid.small.g++.1 | 321 ++++++++++++ examples/rigid/log.25Mar24.rigid.small.g++.4 | 321 ++++++++++++ .../log.25Mar24.rigid.small.infile.g++.1 | 322 ++++++++++++ .../log.25Mar24.rigid.small.infile.g++.4 | 322 ++++++++++++ examples/rigid/log.25Mar24.rigid.tnr.g++.1 | 475 ++++++++++++++++++ examples/rigid/log.25Mar24.rigid.tnr.g++.4 | 475 ++++++++++++++++++ .../rigid/log.27Nov18.rigid.atomfile.g++.1 | 338 ------------- .../rigid/log.27Nov18.rigid.atomfile.g++.4 | 338 ------------- .../rigid/log.27Nov18.rigid.atomvar.g++.1 | 338 ------------- .../rigid/log.27Nov18.rigid.atomvar.g++.4 | 338 ------------- examples/rigid/log.27Nov18.rigid.early.g++.1 | 337 ------------- examples/rigid/log.27Nov18.rigid.early.g++.4 | 337 ------------- examples/rigid/log.27Nov18.rigid.g++.1 | 335 ------------ examples/rigid/log.27Nov18.rigid.g++.4 | 335 ------------ .../rigid/log.27Nov18.rigid.nve.early.g++.1 | 337 ------------- .../rigid/log.27Nov18.rigid.nve.early.g++.4 | 337 ------------- examples/rigid/log.27Nov18.rigid.nve.g++.1 | 335 ------------ examples/rigid/log.27Nov18.rigid.nve.g++.4 | 335 ------------ .../rigid/log.27Nov18.rigid.property.g++.1 | 340 ------------- .../rigid/log.27Nov18.rigid.property.g++.4 | 340 ------------- examples/rigid/log.27Nov18.rigid.tnr.g++.1 | 458 ----------------- examples/rigid/log.27Nov18.rigid.tnr.g++.4 | 458 ----------------- src/math_eigen.cpp | 4 +- .../tests/fix-timestep-rigid_group.yaml | 113 ++--- .../tests/fix-timestep-rigid_molecule.yaml | 43 +- .../fix-timestep-rigid_molecule_tri.yaml | 37 +- .../tests/fix-timestep-rigid_nph.yaml | 85 ++-- .../tests/fix-timestep-rigid_nph_small.yaml | 85 ++-- .../tests/fix-timestep-rigid_npt.yaml | 119 ++--- .../tests/fix-timestep-rigid_npt_small.yaml | 85 ++-- .../tests/fix-timestep-rigid_nve_group.yaml | 113 ++--- .../fix-timestep-rigid_nve_molecule.yaml | 45 +- .../tests/fix-timestep-rigid_nve_single.yaml | 77 +-- .../tests/fix-timestep-rigid_nve_small.yaml | 45 +- .../tests/fix-timestep-rigid_nvt.yaml | 79 +-- .../tests/fix-timestep-rigid_nvt_small.yaml | 45 +- .../tests/fix-timestep-rigid_single.yaml | 77 +-- .../tests/fix-timestep-rigid_small.yaml | 43 +- unittest/formats/test_atom_styles.cpp | 288 +++++------ 99 files changed, 13772 insertions(+), 13271 deletions(-) create mode 100644 examples/micelle/log.25Mar24.micelle-rigid.g++.1 create mode 100644 examples/micelle/log.25Mar24.micelle-rigid.g++.4 create mode 100644 examples/micelle/log.25Mar24.micelle.g++.1 create mode 100644 examples/micelle/log.25Mar24.micelle.g++.4 delete mode 100644 examples/micelle/log.29Mar2019.micelle-rigid.g++.1 delete mode 100644 examples/micelle/log.29Mar2019.micelle-rigid.g++.4 delete mode 100644 examples/micelle/log.29Mar2019.micelle.g++.1 delete mode 100644 examples/micelle/log.29Mar2019.micelle.g++.4 delete mode 100644 examples/rigid/log.20Mar22.rigid.infile.g++.1 delete mode 100644 examples/rigid/log.20Mar22.rigid.infile.g++.4 delete mode 100644 examples/rigid/log.20Mar22.rigid.molecule.g++.1 delete mode 100644 examples/rigid/log.20Mar22.rigid.molecule.g++.4 delete mode 100644 examples/rigid/log.20Mar22.rigid.poems.g++.1 delete mode 100644 examples/rigid/log.20Mar22.rigid.poems.g++.4 delete mode 100644 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100644 examples/rigid/log.25Mar24.rigid.atomfile.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.atomvar.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.atomvar.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.early.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.early.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.gravity.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.gravity.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.infile.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.infile.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.molecule.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.molecule.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.nve.early.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.nve.early.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.nve.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.nve.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.poems.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.poems.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.poems2.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.poems2.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.poems3.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.poems3.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.poems4.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.poems4.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.poems5.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.poems5.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.property.g++.1 create mode 100644 examples/rigid/log.25Mar24.rigid.property.g++.4 create mode 100644 examples/rigid/log.25Mar24.rigid.small.g++.1 create mode 100644 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examples/rigid/log.27Nov18.rigid.nve.g++.1 delete mode 100644 examples/rigid/log.27Nov18.rigid.nve.g++.4 delete mode 100644 examples/rigid/log.27Nov18.rigid.property.g++.1 delete mode 100644 examples/rigid/log.27Nov18.rigid.property.g++.4 delete mode 100644 examples/rigid/log.27Nov18.rigid.tnr.g++.1 delete mode 100644 examples/rigid/log.27Nov18.rigid.tnr.g++.4 diff --git a/examples/micelle/in.micelle b/examples/micelle/in.micelle index 34bc9ad359..1626d09993 100644 --- a/examples/micelle/in.micelle +++ b/examples/micelle/in.micelle @@ -1,72 +1,72 @@ # 2d micelle simulation -dimension 2 +dimension 2 -neighbor 0.3 bin -neigh_modify delay 5 +neighbor 0.33 bin +neigh_modify delay 5 -atom_style bond +atom_style bond # Soft potential push-off -read_data data.micelle -special_bonds fene +read_data data.micelle +special_bonds fene -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 -bond_style harmonic -bond_coeff 1 50.0 0.75 +bond_style harmonic +bond_coeff 1 50.0 0.75 -velocity all create 0.45 2349852 +velocity all create 0.45 2349852 -variable prefactor equal ramp(1.0,20.0) +variable prefactor equal ramp(1.0,20.0) -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d -thermo 50 -run 1000 +thermo 50 +run 1000 -unfix 3 +unfix 3 # Main run -pair_style lj/cut 2.5 +pair_style lj/cut 2.5 # solvent/head - full-size and long-range -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 # tail/tail - size-averaged and long-range -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 # solvent/tail - full-size and repulsive -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 # head/tail - size-averaged and repulsive -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 -thermo 50 +thermo 50 -#dump 1 all atom 2000 dump.micelle +#dump 1 all atom 2000 dump.micelle -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 -reset_timestep 0 -run 1000 +reset_timestep 0 +run 1000 diff --git a/examples/micelle/in.micelle-rigid b/examples/micelle/in.micelle-rigid index 93cb2655f8..21a9cb8a58 100644 --- a/examples/micelle/in.micelle-rigid +++ b/examples/micelle/in.micelle-rigid @@ -1,87 +1,87 @@ # 2d micelle simulation -dimension 2 +dimension 2 -neighbor 0.3 bin -neigh_modify delay 5 +neighbor 0.33 bin +neigh_modify delay 5 -atom_style bond +atom_style bond # Soft potential push-off -read_data data.micelle -special_bonds fene +read_data data.micelle +special_bonds fene -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 -bond_style harmonic -bond_coeff 1 50.0 0.75 +bond_style harmonic +bond_coeff 1 50.0 0.75 -velocity all create 0.45 2349852 +velocity all create 0.45 2349852 -variable prefactor equal ramp(1.0,20.0) +variable prefactor equal ramp(1.0,20.0) -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d -thermo 50 -run 500 +thermo 50 +run 500 -unfix 3 +unfix 3 # Main run -pair_style lj/cut 2.5 +pair_style lj/cut 2.5 # solvent/head - full-size and long-range -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 # tail/tail - size-averaged and long-range -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 # solvent/tail - full-size and repulsive -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 # head/tail - size-averaged and repulsive -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 -thermo 50 +thermo 50 -#dump 1 all atom 2000 dump.micelle +#dump 1 all atom 2000 dump.micelle -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 -reset_timestep 0 +reset_timestep 0 group solvent molecule 0 group solute subtract all solvent unfix 1 unfix 2 unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -fix 4 all enforce2d -run 500 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +fix 4 all enforce2d +run 500 unfix 2 unfix 4 unfix 5 -fix 5 solute rigid/small molecule -fix 4 all enforce2d -run 500 +fix 5 solute rigid/small molecule +fix 4 all enforce2d +run 500 diff --git a/examples/micelle/log.25Mar24.micelle-rigid.g++.1 b/examples/micelle/log.25Mar24.micelle-rigid.g++.1 new file mode 100644 index 0000000000..8008630d76 --- /dev/null +++ b/examples/micelle/log.25Mar24.micelle-rigid.g++.1 @@ -0,0 +1,272 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.33 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +Reading data file ... + orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.45246 + ghost atom cutoff = 1.45246 + binsize = 0.72623, bins = 50 50 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) +Per MPI rank memory allocation (min/avg/max) = 4.148 | 4.148 | 4.148 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.0683956 on 1 procs for 500 steps with 1200 atoms + +Performance: 3158095.858 tau/day, 7310.407 timesteps/s, 8.772 Matom-step/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.042818 | 0.042818 | 0.042818 | 0.0 | 62.60 +Bond | 0.0026205 | 0.0026205 | 0.0026205 | 0.0 | 3.83 +Neigh | 0.011794 | 0.011794 | 0.011794 | 0.0 | 17.24 +Comm | 0.0014012 | 0.0014012 | 0.0014012 | 0.0 | 2.05 +Output | 0.00012752 | 0.00012752 | 0.00012752 | 0.0 | 0.19 +Modify | 0.0078924 | 0.0078924 | 0.0078924 | 0.0 | 11.54 +Other | | 0.001743 | | | 2.55 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 198 ave 198 max 198 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3199 ave 3199 max 3199 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3199 +Ave neighs/atom = 2.6658333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 48 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 + 150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.83 + ghost atom cutoff = 2.83 + binsize = 1.415, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109 + 100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772 + 150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796 + 200 0.49410558 -1.7945459 0.13695201 -1.2565449 3.7958258 + 250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445 + 300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851 + 350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818 + 400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566 + 450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611 + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738 +Loop time of 0.129419 on 1 procs for 500 steps with 1200 atoms + +Performance: 1668996.565 tau/day, 3863.418 timesteps/s, 4.636 Matom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.059482 | 0.059482 | 0.059482 | 0.0 | 45.96 +Bond | 0.0027154 | 0.0027154 | 0.0027154 | 0.0 | 2.10 +Neigh | 0.017086 | 0.017086 | 0.017086 | 0.0 | 13.20 +Comm | 0.0019065 | 0.0019065 | 0.0019065 | 0.0 | 1.47 +Output | 0.00012035 | 0.00012035 | 0.00012035 | 0.0 | 0.09 +Modify | 0.046099 | 0.046099 | 0.046099 | 0.0 | 35.62 +Other | | 0.002009 | | | 1.55 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 413 ave 413 max 413 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8944 ave 8944 max 8944 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8944 +Ave neighs/atom = 7.4533333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 41 +Dangerous builds = 1 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 0.000 seconds + 150 rigid bodies with 450 atoms + 1.3043524 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 9.306 | 9.306 | 9.306 Mbytes + Step Temp E_pair E_mol TotEng Press + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752 + 550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662 + 600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379 + 650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789 + 700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082 + 750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147 + 800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481 + 850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703 + 900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388 + 950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786 + 1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987 +Loop time of 0.119542 on 1 procs for 500 steps with 1200 atoms + +Performance: 1806900.644 tau/day, 4182.640 timesteps/s, 5.019 Matom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.058715 | 0.058715 | 0.058715 | 0.0 | 49.12 +Bond | 0.0028428 | 0.0028428 | 0.0028428 | 0.0 | 2.38 +Neigh | 0.015212 | 0.015212 | 0.015212 | 0.0 | 12.73 +Comm | 0.0019242 | 0.0019242 | 0.0019242 | 0.0 | 1.61 +Output | 0.00018977 | 0.00018977 | 0.00018977 | 0.0 | 0.16 +Modify | 0.038399 | 0.038399 | 0.038399 | 0.0 | 32.12 +Other | | 0.002259 | | | 1.89 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 425 ave 425 max 425 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8846 ave 8846 max 8846 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8846 +Ave neighs/atom = 7.3716667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 36 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.25Mar24.micelle-rigid.g++.4 b/examples/micelle/log.25Mar24.micelle-rigid.g++.4 new file mode 100644 index 0000000000..b5c53e9b05 --- /dev/null +++ b/examples/micelle/log.25Mar24.micelle-rigid.g++.4 @@ -0,0 +1,272 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.33 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +Reading data file ... + orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.45246 + ghost atom cutoff = 1.45246 + binsize = 0.72623, bins = 50 50 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) +Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.0217401 on 4 procs for 500 steps with 1200 atoms + +Performance: 9935551.276 tau/day, 22998.961 timesteps/s, 27.599 Matom-step/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0088539 | 0.0095602 | 0.010452 | 0.6 | 43.97 +Bond | 0.00058476 | 0.00062647 | 0.00070207 | 0.0 | 2.88 +Neigh | 0.0030965 | 0.0031112 | 0.0031222 | 0.0 | 14.31 +Comm | 0.0040493 | 0.0050374 | 0.0057508 | 0.9 | 23.17 +Output | 8.0051e-05 | 8.6079e-05 | 0.00010294 | 0.0 | 0.40 +Modify | 0.0024258 | 0.0025227 | 0.0026365 | 0.2 | 11.60 +Other | | 0.0007961 | | | 3.66 + +Nlocal: 300 ave 305 max 292 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Nghost: 105.25 ave 110 max 99 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 799.75 ave 817 max 763 min +Histogram: 1 0 0 0 0 0 0 1 0 2 + +Total # of neighbors = 3199 +Ave neighs/atom = 2.6658333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 48 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 + 150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.83 + ghost atom cutoff = 2.83 + binsize = 1.415, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.375 | 5.375 | 5.375 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109 + 100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772 + 150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796 + 200 0.49410558 -1.7945459 0.13695201 -1.2565449 3.7958258 + 250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445 + 300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851 + 350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818 + 400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566 + 450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611 + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738 +Loop time of 0.0560481 on 4 procs for 500 steps with 1200 atoms + +Performance: 3853834.547 tau/day, 8920.913 timesteps/s, 10.705 Matom-step/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.013556 | 0.013707 | 0.013803 | 0.1 | 24.46 +Bond | 0.00063884 | 0.00066997 | 0.0007103 | 0.0 | 1.20 +Neigh | 0.004707 | 0.0047121 | 0.0047151 | 0.0 | 8.41 +Comm | 0.0060936 | 0.0061963 | 0.006299 | 0.1 | 11.06 +Output | 9.3791e-05 | 0.00010703 | 0.00013426 | 0.0 | 0.19 +Modify | 0.029359 | 0.029467 | 0.029627 | 0.1 | 52.57 +Other | | 0.001189 | | | 2.12 + +Nlocal: 300 ave 303 max 296 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 217.75 ave 220 max 215 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 2236 ave 2264 max 2213 min +Histogram: 1 0 1 0 0 1 0 0 0 1 + +Total # of neighbors = 8944 +Ave neighs/atom = 7.4533333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 41 +Dangerous builds = 1 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 0.000 seconds + 150 rigid bodies with 450 atoms + 1.3043524 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 9.233 | 9.233 | 9.234 Mbytes + Step Temp E_pair E_mol TotEng Press + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752 + 550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662 + 600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379 + 650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789 + 700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082 + 750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147 + 800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481 + 850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703 + 900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388 + 950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786 + 1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987 +Loop time of 0.0401556 on 4 procs for 500 steps with 1200 atoms + +Performance: 5379078.679 tau/day, 12451.571 timesteps/s, 14.942 Matom-step/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.013239 | 0.013488 | 0.013882 | 0.2 | 33.59 +Bond | 0.00064766 | 0.00068403 | 0.00074631 | 0.0 | 1.70 +Neigh | 0.0040808 | 0.0040899 | 0.0041035 | 0.0 | 10.19 +Comm | 0.0056353 | 0.0060663 | 0.0063864 | 0.3 | 15.11 +Output | 0.0001049 | 0.0001153 | 0.00014195 | 0.0 | 0.29 +Modify | 0.014414 | 0.014559 | 0.014753 | 0.1 | 36.26 +Other | | 0.001153 | | | 2.87 + +Nlocal: 300 ave 305 max 295 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Nghost: 226 ave 231 max 220 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Neighs: 2211.5 ave 2313 max 2144 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 8846 +Ave neighs/atom = 7.3716667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 36 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.25Mar24.micelle.g++.1 b/examples/micelle/log.25Mar24.micelle.g++.1 new file mode 100644 index 0000000000..4b519e0ea7 --- /dev/null +++ b/examples/micelle/log.25Mar24.micelle.g++.1 @@ -0,0 +1,229 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.33 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +Reading data file ... + orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.005 seconds +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 1000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.45246 + ghost atom cutoff = 1.45246 + binsize = 0.72623, bins = 50 50 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) +Per MPI rank memory allocation (min/avg/max) = 4.148 | 4.148 | 4.148 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 + 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 + 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 + 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 + 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 + 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 + 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 + 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 + 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 + 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 + 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 + 600 0.45 0.58193041 0.088386617 1.119942 5.131481 + 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 + 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 + 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 + 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 + 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 + 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 + 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 + 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 +Loop time of 0.135036 on 1 procs for 1000 steps with 1200 atoms + +Performance: 3199144.549 tau/day, 7405.427 timesteps/s, 8.887 Matom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.086466 | 0.086466 | 0.086466 | 0.0 | 64.03 +Bond | 0.0052524 | 0.0052524 | 0.0052524 | 0.0 | 3.89 +Neigh | 0.020278 | 0.020278 | 0.020278 | 0.0 | 15.02 +Comm | 0.0026978 | 0.0026978 | 0.0026978 | 0.0 | 2.00 +Output | 0.00032119 | 0.00032119 | 0.00032119 | 0.0 | 0.24 +Modify | 0.016117 | 0.016117 | 0.016117 | 0.0 | 11.94 +Other | | 0.003904 | | | 2.89 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 200 ave 200 max 200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3220 ave 3220 max 3220 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3220 +Ave neighs/atom = 2.6833333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 84 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +run 1000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.83 + ghost atom cutoff = 2.83 + binsize = 1.415, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.141 | 4.141 | 4.141 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 + 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 + 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 + 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 + 200 0.45 -1.8918673 0.082422107 -1.3598201 2.5629655 + 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 + 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 + 350 0.47650026 -1.9313687 0.072115118 -1.3831504 2.1987532 + 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 + 450 0.47220237 -1.9468502 0.065625625 -1.4094157 2.0984288 + 500 0.46846731 -1.9444333 0.076696281 -1.3996601 2.0528682 + 550 0.47683129 -1.958676 0.070589717 -1.4116523 2.0856022 + 600 0.46851244 -1.9338267 0.070605485 -1.3950992 2.2640498 + 650 0.46874143 -1.9462493 0.069134673 -1.4087638 2.1070264 + 700 0.46437375 -1.9309952 0.071977553 -1.3950309 2.2256927 + 750 0.47326219 -1.9484255 0.075435861 -1.4001218 2.0880257 + 800 0.45 -1.9646003 0.064159585 -1.4508158 2.0612708 + 850 0.46748293 -1.9705587 0.060384889 -1.4430805 1.9472917 + 900 0.46909505 -1.9537228 0.06246996 -1.4225487 2.0222946 + 950 0.45631552 -1.9387752 0.067536414 -1.4153035 2.0638412 + 1000 0.45 -1.9727636 0.058608205 -1.4645304 1.9982412 +Loop time of 0.172925 on 1 procs for 1000 steps with 1200 atoms + +Performance: 2498198.117 tau/day, 5782.866 timesteps/s, 6.939 Matom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.11308 | 0.11308 | 0.11308 | 0.0 | 65.39 +Bond | 0.0054036 | 0.0054036 | 0.0054036 | 0.0 | 3.12 +Neigh | 0.032892 | 0.032892 | 0.032892 | 0.0 | 19.02 +Comm | 0.0038268 | 0.0038268 | 0.0038268 | 0.0 | 2.21 +Output | 0.00023892 | 0.00023892 | 0.00023892 | 0.0 | 0.14 +Modify | 0.013461 | 0.013461 | 0.013461 | 0.0 | 7.78 +Other | | 0.004027 | | | 2.33 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 421 ave 421 max 421 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8779 ave 8779 max 8779 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8779 +Ave neighs/atom = 7.3158333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 77 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.25Mar24.micelle.g++.4 b/examples/micelle/log.25Mar24.micelle.g++.4 new file mode 100644 index 0000000000..174cab5f5e --- /dev/null +++ b/examples/micelle/log.25Mar24.micelle.g++.4 @@ -0,0 +1,229 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.33 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +Reading data file ... + orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 1000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.45246 + ghost atom cutoff = 1.45246 + binsize = 0.72623, bins = 50 50 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) +Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 + 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 + 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 + 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 + 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 + 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 + 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 + 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 + 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 + 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 + 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 + 600 0.45 0.58193041 0.088386617 1.119942 5.131481 + 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 + 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 + 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 + 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 + 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 + 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 + 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 + 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 +Loop time of 0.0430044 on 4 procs for 1000 steps with 1200 atoms + +Performance: 10045485.178 tau/day, 23253.438 timesteps/s, 27.904 Matom-step/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.01855 | 0.019447 | 0.019916 | 0.4 | 45.22 +Bond | 0.0011939 | 0.0012689 | 0.0013518 | 0.2 | 2.95 +Neigh | 0.0054396 | 0.0054535 | 0.0054635 | 0.0 | 12.68 +Comm | 0.0093296 | 0.0097958 | 0.010731 | 0.6 | 22.78 +Output | 0.00016417 | 0.00018578 | 0.00024995 | 0.0 | 0.43 +Modify | 0.0049758 | 0.0050749 | 0.005268 | 0.2 | 11.80 +Other | | 0.001778 | | | 4.14 + +Nlocal: 300 ave 306 max 294 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 103 ave 110 max 98 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 805 ave 827 max 768 min +Histogram: 1 0 0 0 0 0 1 0 1 1 + +Total # of neighbors = 3220 +Ave neighs/atom = 2.6833333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 84 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +run 1000 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.83 + ghost atom cutoff = 2.83 + binsize = 1.415, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.125 | 4.125 | 4.125 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 + 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 + 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 + 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 + 200 0.45 -1.8918673 0.082422107 -1.3598201 2.5629655 + 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 + 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 + 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 + 400 0.45 -1.9554318 0.08160394 -1.4242028 2.0787066 + 450 0.47220237 -1.9468502 0.065625625 -1.4094157 2.0984288 + 500 0.46846732 -1.9444333 0.076696282 -1.3996601 2.0528682 + 550 0.47683129 -1.958676 0.070589715 -1.4116523 2.0856023 + 600 0.46851246 -1.9338267 0.070605474 -1.3950992 2.2640497 + 650 0.46874145 -1.9462493 0.069134673 -1.4087638 2.1070263 + 700 0.46437384 -1.9309953 0.071977538 -1.3950309 2.2256921 + 750 0.47326257 -1.9484258 0.075435782 -1.4001218 2.0880238 + 800 0.45 -1.9646002 0.064159564 -1.4508156 2.0612711 + 850 0.46748245 -1.9705585 0.060385282 -1.4430803 1.9472928 + 900 0.46909475 -1.953722 0.062469986 -1.4225482 2.0223017 + 950 0.45631666 -1.9387749 0.067535547 -1.415303 2.0638464 + 1000 0.45 -1.9727662 0.058608374 -1.4645328 1.9982544 +Loop time of 0.0580559 on 4 procs for 1000 steps with 1200 atoms + +Performance: 7441102.030 tau/day, 17224.773 timesteps/s, 20.670 Matom-step/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.025537 | 0.026849 | 0.0293 | 0.9 | 46.25 +Bond | 0.0012241 | 0.0013287 | 0.0015123 | 0.3 | 2.29 +Neigh | 0.0093194 | 0.0093648 | 0.0093978 | 0.0 | 16.13 +Comm | 0.011992 | 0.014606 | 0.015998 | 1.3 | 25.16 +Output | 0.00018318 | 0.0001963 | 0.0002352 | 0.0 | 0.34 +Modify | 0.003441 | 0.0035887 | 0.0037522 | 0.2 | 6.18 +Other | | 0.002122 | | | 3.66 + +Nlocal: 300 ave 305 max 294 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 222.25 ave 231 max 215 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 2195 ave 2233 max 2150 min +Histogram: 1 0 0 0 0 2 0 0 0 1 + +Total # of neighbors = 8780 +Ave neighs/atom = 7.3166667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 77 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 deleted file mode 100644 index f1001e6cea..0000000000 --- a/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 +++ /dev/null @@ -1,260 +0,0 @@ -LAMMPS (29 Mar 2019) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000473022 secs - read_data CPU = 0.0024147 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.00022316 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 - 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 - 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 - 200 0.45 1.01454 0.10663502 1.5708 4.7598476 - 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 - 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 - 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 - 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 - 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 - 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 -Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms - -Performance: 2093802.885 tau/day, 4846.766 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21 -Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11 -Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64 -Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86 -Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17 -Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37 -Other | | 0.002726 | | | 2.64 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 197 ave 197 max 197 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3094 ave 3094 max 3094 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3094 -Ave neighs/atom = 2.57833 -Ave special neighs/atom = 0.5 -Neighbor list builds = 52 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 - 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 - 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 - 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 - 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 - 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 - 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 - 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 - 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 - 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 -Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms - -Performance: 1208012.705 tau/day, 2796.326 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17 -Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38 -Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92 -Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45 -Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10 -Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34 -Other | | 0.00293 | | | 1.64 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 416 ave 416 max 416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8769 ave 8769 max 8769 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8769 -Ave neighs/atom = 7.3075 -Ave special neighs/atom = 0.5 -Neighbor list builds = 47 -Dangerous builds = 2 -unfix 2 -unfix 4 -unfix 5 -fix 5 solute rigid/small molecule - create bodies CPU = 0.00015378 secs -150 rigid bodies with 450 atoms - 1.30435 = max distance from body owner to body atom -fix 4 all enforce2d -run 500 -Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes -Step Temp E_pair E_mol TotEng Press - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 - 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 - 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 - 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 - 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 - 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 - 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 - 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 - 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 - 950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332 - 1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141 -Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms - -Performance: 1297278.008 tau/day, 3002.958 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51 -Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56 -Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83 -Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44 -Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11 -Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66 -Other | | 0.003141 | | | 1.89 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 415 ave 415 max 415 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8743 ave 8743 max 8743 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8743 -Ave neighs/atom = 7.28583 -Ave special neighs/atom = 0.5 -Neighbor list builds = 40 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 deleted file mode 100644 index e65f67a527..0000000000 --- a/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 +++ /dev/null @@ -1,260 +0,0 @@ -LAMMPS (29 Mar 2019) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000422001 secs - read_data CPU = 0.00473404 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000183344 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 - 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 - 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 - 200 0.45 1.01454 0.10663502 1.5708 4.7598476 - 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 - 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 - 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 - 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 - 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 - 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 -Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms - -Performance: 5066547.720 tau/day, 11728.120 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16 -Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95 -Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95 -Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78 -Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62 -Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28 -Other | | 0.002669 | | | 6.26 - -Nlocal: 300 ave 304 max 292 min -Histogram: 1 0 0 0 0 0 0 0 2 1 -Nghost: 103.5 ave 108 max 98 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Neighs: 773.5 ave 792 max 735 min -Histogram: 1 0 0 0 0 0 0 0 2 1 - -Total # of neighbors = 3094 -Ave neighs/atom = 2.57833 -Ave special neighs/atom = 0.5 -Neighbor list builds = 52 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 - 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 - 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 - 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 - 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 - 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 - 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 - 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 - 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 - 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 -Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms - -Performance: 2434100.210 tau/day, 5634.491 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74 -Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30 -Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32 -Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30 -Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29 -Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73 -Other | | 0.002938 | | | 3.31 - -Nlocal: 300 ave 309 max 291 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 218.75 ave 223 max 216 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Neighs: 2192.25 ave 2251 max 2113 min -Histogram: 1 0 0 1 0 0 0 0 0 2 - -Total # of neighbors = 8769 -Ave neighs/atom = 7.3075 -Ave special neighs/atom = 0.5 -Neighbor list builds = 47 -Dangerous builds = 2 -unfix 2 -unfix 4 -unfix 5 -fix 5 solute rigid/small molecule - create bodies CPU = 7.70092e-05 secs -150 rigid bodies with 450 atoms - 1.30435 = max distance from body owner to body atom -fix 4 all enforce2d -run 500 -Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes -Step Temp E_pair E_mol TotEng Press - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 - 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 - 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 - 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 - 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 - 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 - 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 - 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 - 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 - 950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332 - 1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141 -Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms - -Performance: 3671840.233 tau/day, 8499.630 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47 -Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93 -Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98 -Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29 -Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42 -Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11 -Other | | 0.00224 | | | 3.81 - -Nlocal: 300 ave 303 max 295 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 219 ave 224 max 215 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -Neighs: 2185.75 ave 2244 max 2143 min -Histogram: 1 1 0 0 0 1 0 0 0 1 - -Total # of neighbors = 8743 -Ave neighs/atom = 7.28583 -Ave special neighs/atom = 0.5 -Neighbor list builds = 40 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle.g++.1 b/examples/micelle/log.29Mar2019.micelle.g++.1 deleted file mode 100644 index d482d6c890..0000000000 --- a/examples/micelle/log.29Mar2019.micelle.g++.1 +++ /dev/null @@ -1,218 +0,0 @@ -LAMMPS (29 Mar 2019) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.00037837 secs - read_data CPU = 0.00206876 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000177383 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.208895 on 1 procs for 1000 steps with 1200 atoms - -Performance: 2068027.282 tau/day, 4787.100 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.14142 | 0.14142 | 0.14142 | 0.0 | 67.70 -Bond | 0.008441 | 0.008441 | 0.008441 | 0.0 | 4.04 -Neigh | 0.025716 | 0.025716 | 0.025716 | 0.0 | 12.31 -Comm | 0.0036864 | 0.0036864 | 0.0036864 | 0.0 | 1.76 -Output | 0.0003562 | 0.0003562 | 0.0003562 | 0.0 | 0.17 -Modify | 0.023699 | 0.023699 | 0.023699 | 0.0 | 11.35 -Other | | 0.00558 | | | 2.67 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 195 ave 195 max 195 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3136 ave 3136 max 3136 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3136 -Ave neighs/atom = 2.61333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 92 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -run 1000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 - 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 - 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 - 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 - 200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655 - 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 - 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 - 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 - 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 - 450 0.47220236 -1.9468502 0.065625624 -1.4094157 2.0984288 - 500 0.4684673 -1.9444333 0.076696283 -1.3996601 2.0528682 - 550 0.47683128 -1.958676 0.070589719 -1.4116523 2.0856022 - 600 0.46851243 -1.9338267 0.07060548 -1.3950992 2.26405 - 650 0.46874142 -1.9462493 0.069134685 -1.4087638 2.1070263 - 700 0.46437384 -1.9309953 0.071977522 -1.3950309 2.2256923 - 750 0.47326225 -1.9484255 0.075435845 -1.4001218 2.0880254 - 800 0.45 -1.9646005 0.064159585 -1.4508159 2.0612696 - 850 0.46748307 -1.970559 0.060384874 -1.4430806 1.9472879 - 900 0.46909484 -1.953723 0.062470295 -1.4225488 2.0222909 - 950 0.45631531 -1.9387753 0.067536568 -1.4153037 2.0638421 - 1000 0.45 -1.9727646 0.058607721 -1.4645318 1.9982315 -Loop time of 0.252254 on 1 procs for 1000 steps with 1200 atoms - -Performance: 1712557.882 tau/day, 3964.254 timesteps/s -99.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.17177 | 0.17177 | 0.17177 | 0.0 | 68.09 -Bond | 0.0084555 | 0.0084555 | 0.0084555 | 0.0 | 3.35 -Neigh | 0.03991 | 0.03991 | 0.03991 | 0.0 | 15.82 -Comm | 0.0049119 | 0.0049119 | 0.0049119 | 0.0 | 1.95 -Output | 0.00039077 | 0.00039077 | 0.00039077 | 0.0 | 0.15 -Modify | 0.021131 | 0.021131 | 0.021131 | 0.0 | 8.38 -Other | | 0.005685 | | | 2.25 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 415 ave 415 max 415 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8586 ave 8586 max 8586 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8586 -Ave neighs/atom = 7.155 -Ave special neighs/atom = 0.5 -Neighbor list builds = 86 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle.g++.4 b/examples/micelle/log.29Mar2019.micelle.g++.4 deleted file mode 100644 index f3a54970cf..0000000000 --- a/examples/micelle/log.29Mar2019.micelle.g++.4 +++ /dev/null @@ -1,218 +0,0 @@ -LAMMPS (29 Mar 2019) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000413656 secs - read_data CPU = 0.00487924 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000178576 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.0906248 on 4 procs for 1000 steps with 1200 atoms - -Performance: 4766906.584 tau/day, 11034.506 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.036572 | 0.039266 | 0.041216 | 1.0 | 43.33 -Bond | 0.0023205 | 0.0024512 | 0.0025697 | 0.2 | 2.70 -Neigh | 0.0088909 | 0.0089301 | 0.0089679 | 0.0 | 9.85 -Comm | 0.022308 | 0.024047 | 0.027175 | 1.3 | 26.53 -Output | 0.00057411 | 0.00061274 | 0.00071025 | 0.0 | 0.68 -Modify | 0.0083182 | 0.0092374 | 0.0098341 | 0.6 | 10.19 -Other | | 0.006081 | | | 6.71 - -Nlocal: 300 ave 305 max 292 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 100.25 ave 108 max 93 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Neighs: 784 ave 815 max 739 min -Histogram: 1 0 0 0 0 0 1 1 0 1 - -Total # of neighbors = 3136 -Ave neighs/atom = 2.61333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 92 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -run 1000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 - 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 - 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 - 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 - 200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655 - 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 - 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 - 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 - 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 - 450 0.47220236 -1.9468502 0.065625625 -1.4094157 2.0984288 - 500 0.4684673 -1.9444333 0.076696285 -1.3996601 2.0528682 - 550 0.47683128 -1.958676 0.070589721 -1.4116523 2.0856023 - 600 0.46851245 -1.9338267 0.070605469 -1.3950992 2.26405 - 650 0.46874143 -1.9462493 0.069134686 -1.4087638 2.1070262 - 700 0.4643739 -1.9309953 0.071977511 -1.3950309 2.225692 - 750 0.47326259 -1.9484258 0.075435808 -1.4001218 2.0880235 - 800 0.45 -1.9646003 0.06415956 -1.4508158 2.0612703 - 850 0.46748278 -1.9705588 0.06038513 -1.4430804 1.9472884 - 900 0.46909438 -1.9537221 0.062470305 -1.4225483 2.0223008 - 950 0.45631508 -1.9387742 0.067536066 -1.4153033 2.063854 - 1000 0.45 -1.9727651 0.058608085 -1.464532 1.9982447 -Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms - -Performance: 4917357.613 tau/day, 11382.772 timesteps/s -99.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.043517 | 0.044455 | 0.046903 | 0.7 | 50.60 -Bond | 0.0020199 | 0.0022303 | 0.0024347 | 0.4 | 2.54 -Neigh | 0.012207 | 0.012335 | 0.012512 | 0.1 | 14.04 -Comm | 0.014938 | 0.018265 | 0.020068 | 1.5 | 20.79 -Output | 0.00061369 | 0.00064814 | 0.00073504 | 0.0 | 0.74 -Modify | 0.0052264 | 0.0053691 | 0.0055039 | 0.2 | 6.11 -Other | | 0.00455 | | | 5.18 - -Nlocal: 300 ave 305 max 296 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Nghost: 219.5 ave 228 max 214 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 2146.5 ave 2201 max 2114 min -Histogram: 1 1 0 1 0 0 0 0 0 1 - -Total # of neighbors = 8586 -Ave neighs/atom = 7.155 -Ave special neighs/atom = 0.5 -Neighbor list builds = 86 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.infile.g++.1 b/examples/rigid/log.20Mar22.rigid.infile.g++.1 deleted file mode 100644 index 7c554d2778..0000000000 --- a/examples/rigid/log.20Mar22.rigid.infile.g++.1 +++ /dev/null @@ -1,312 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat - 9 rigid bodies with 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Reading rigid body data for 4 bodies from file bodyinfo.dat -Reading rigid body data for 4 bodies from file bodyinfo.dat -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722793e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06941 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532812 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652435 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156167 0 5269.5203 12.011611 - 9600 16738.549 -0.02681437 0 5269.5163 12.011415 - 9650 16738.765 -0.10191524 0 5269.5092 12.011013 - 9700 16735.041 1.0589895 0 5269.4979 12.062708 - 9750 16738.013 0.13550156 0 5269.5101 11.407246 - 9800 16738.512 -0.011620325 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270436 0 5269.5237 11.395099 - 9900 16738.489 -0.0002498452 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395077 - 10000 16738.49 0 0 5269.5246 11.395076 -Loop time of 0.0882903 on 1 procs for 10000 steps with 81 atoms - -Performance: 978589.581 tau/day, 113262.683 timesteps/s -97.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0064583 | 0.0064583 | 0.0064583 | 0.0 | 7.31 -Neigh | 0.027186 | 0.027186 | 0.027186 | 0.0 | 30.79 -Comm | 0.0057041 | 0.0057041 | 0.0057041 | 0.0 | 6.46 -Output | 0.0020628 | 0.0020628 | 0.0020628 | 0.0 | 2.34 -Modify | 0.042816 | 0.042816 | 0.042816 | 0.0 | 48.49 -Other | | 0.004063 | | | 4.60 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.infile.g++.4 b/examples/rigid/log.20Mar22.rigid.infile.g++.4 deleted file mode 100644 index 2e0535a69a..0000000000 --- a/examples/rigid/log.20Mar22.rigid.infile.g++.4 +++ /dev/null @@ -1,312 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat - 9 rigid bodies with 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Reading rigid body data for 4 bodies from file bodyinfo.dat -Reading rigid body data for 4 bodies from file bodyinfo.dat -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.972279e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706557 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06941 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.004530741 0 5269.5178 12.01162 - 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156168 0 5269.5203 12.011611 - 9600 16738.549 -0.026814371 0 5269.5163 12.011415 - 9650 16738.765 -0.10191524 0 5269.5092 12.011013 - 9700 16735.041 1.0589899 0 5269.4979 12.062708 - 9750 16738.013 0.13550149 0 5269.5101 11.407246 - 9800 16738.512 -0.011620325 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270428 0 5269.5237 11.395099 - 9900 16738.489 -0.0002498452 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395077 - 10000 16738.49 0 0 5269.5246 11.395076 -Loop time of 0.100422 on 4 procs for 10000 steps with 81 atoms - -Performance: 860368.209 tau/day, 99579.654 timesteps/s -99.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0014853 | 0.0020649 | 0.0026245 | 0.9 | 2.06 -Neigh | 0.0075956 | 0.0080256 | 0.0091971 | 0.8 | 7.99 -Comm | 0.037221 | 0.041059 | 0.043195 | 1.2 | 40.89 -Output | 0.0020995 | 0.0023594 | 0.003073 | 0.8 | 2.35 -Modify | 0.041318 | 0.042855 | 0.044215 | 0.5 | 42.67 -Other | | 0.004059 | | | 4.04 - -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.molecule.g++.1 b/examples/rigid/log.20Mar22.rigid.molecule.g++.1 deleted file mode 100644 index b4a4b28d92..0000000000 --- a/examples/rigid/log.20Mar22.rigid.molecule.g++.1 +++ /dev/null @@ -1,349 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid molecule - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.233 | 5.233 | 5.233 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.97228e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706557 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06941 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156166 0 5269.5203 12.011611 - 9600 16738.549 -0.026814371 0 5269.5163 12.011415 - 9650 16738.765 -0.10191524 0 5269.5092 12.011013 - 9700 16735.041 1.0589897 0 5269.4979 12.062708 - 9750 16738.013 0.1355014 0 5269.5101 11.407246 - 9800 16738.512 -0.011620325 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270449 0 5269.5237 11.395099 - 9900 16738.489 -0.00024984529 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395077 - 10000 16738.49 0 0 5269.5246 11.395076 -Loop time of 0.0974108 on 1 procs for 10000 steps with 81 atoms - -Performance: 886965.415 tau/day, 102658.034 timesteps/s -96.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0068054 | 0.0068054 | 0.0068054 | 0.0 | 6.99 -Bond | 0.00034618 | 0.00034618 | 0.00034618 | 0.0 | 0.36 -Neigh | 0.033076 | 0.033076 | 0.033076 | 0.0 | 33.96 -Comm | 0.0067938 | 0.0067938 | 0.0067938 | 0.0 | 6.97 -Output | 0.0022905 | 0.0022905 | 0.0022905 | 0.0 | 2.35 -Modify | 0.044027 | 0.044027 | 0.044027 | 0.0 | 45.20 -Other | | 0.004071 | | | 4.18 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.molecule.g++.4 b/examples/rigid/log.20Mar22.rigid.molecule.g++.4 deleted file mode 100644 index 63835843a0..0000000000 --- a/examples/rigid/log.20Mar22.rigid.molecule.g++.4 +++ /dev/null @@ -1,349 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid molecule - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.08 | 5.112 | 5.206 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722775e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934367 0 5269.4889 12.025288 - 3750 16737.731 0.20706556 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06941 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690662 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 - 8550 16738.483 -0.004530741 0 5269.5178 12.01162 - 8600 16738.474 -0.00076532815 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652439 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156171 0 5269.5203 12.011611 - 9600 16738.549 -0.026814373 0 5269.5163 12.011415 - 9650 16738.765 -0.10191525 0 5269.5092 12.011013 - 9700 16735.041 1.0589908 0 5269.4979 12.062708 - 9750 16738.013 0.13550139 0 5269.5101 11.407247 - 9800 16738.512 -0.011620323 0 5269.5201 11.394975 - 9850 16738.489 -0.00067270407 0 5269.5237 11.395099 - 9900 16738.489 -0.00024984518 0 5269.5242 11.395086 - 9950 16738.49 0 0 5269.5245 11.395077 - 10000 16738.49 0 0 5269.5246 11.395076 -Loop time of 0.102079 on 4 procs for 10000 steps with 81 atoms - -Performance: 846406.333 tau/day, 97963.696 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0015357 | 0.0020418 | 0.0024561 | 0.7 | 2.00 -Bond | 0.00030031 | 0.00031957 | 0.00034464 | 0.0 | 0.31 -Neigh | 0.0091719 | 0.0094934 | 0.010243 | 0.4 | 9.30 -Comm | 0.038015 | 0.041242 | 0.043481 | 1.1 | 40.40 -Output | 0.002223 | 0.0024412 | 0.0030738 | 0.7 | 2.39 -Modify | 0.040725 | 0.042557 | 0.043982 | 0.7 | 41.69 -Other | | 0.003983 | | | 3.90 - -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.poems.g++.1 b/examples/rigid/log.20Mar22.rigid.poems.g++.1 deleted file mode 100644 index 32edd0fd0c..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems.g++.1 +++ /dev/null @@ -1,328 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045742 - 850 17821.483 711.53827 0 3681.7854 7.438428 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19374 0 3681.3037 11.787982 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184716 - 1150 20849.582 206.01696 0 3680.9472 -0.86699118 - 1200 21815.003 45.317409 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064083 - 1300 20780.781 217.36511 0 3680.8286 6.0538604 - 1350 20558.971 254.36489 0 3680.8601 -3.6773868 - 1400 21485.029 99.812844 0 3680.6511 -16.185479 - 1450 21771.107 52.159653 0 3680.6775 -2.4756655 - 1500 21520.949 93.503876 0 3680.3286 2.1023573 - 1550 21351.419 121.6813 0 3680.2511 5.5159876 - 1600 20778.804 216.92191 0 3680.0559 15.089203 - 1650 21477.636 100.21873 0 3679.8247 -1.1045277 - 1700 18501.33 596.4807 0 3680.0357 -15.6798 - 1750 18563.64 587.34824 0 3681.2882 33.532308 - 1800 19110.175 494.82517 0 3679.8543 18.024074 - 1850 21364.178 119.23765 0 3679.9339 2.5290144 - 1900 20146.588 322.15509 0 3679.9197 5.7317299 - 1950 20692.676 231.25264 0 3680.0319 4.297803 - 2000 20943.902 189.11251 0 3679.7629 -22.643824 - 2050 19667.823 401.86882 0 3679.8394 3.6241915 - 2100 20280.125 299.81485 0 3679.8357 7.4804047 - 2150 19181.201 483.6306 0 3680.4975 22.63342 - 2200 21301.144 130.54014 0 3680.7308 4.7074288 - 2250 20484.876 266.98315 0 3681.1291 -8.6578278 - 2300 18648.161 573.07329 0 3681.1001 -5.2550954 - 2350 21515.748 95.243054 0 3681.201 -9.386512 - 2400 21462.551 104.18267 0 3681.2745 -29.46442 - 2450 20107.732 330.99437 0 3682.2831 35.38497 - 2500 20771.509 220.47713 0 3682.3953 -12.324858 - 2550 20499.887 265.58494 0 3682.2327 -22.713874 - 2600 21462.182 105.24427 0 3682.2747 -10.175788 - 2650 21004.949 181.51383 0 3682.3387 4.949195 - 2700 18673.552 570.45017 0 3682.7089 21.201437 - 2750 21257.562 139.198 0 3682.1249 -7.5793039 - 2800 21559.645 88.844759 0 3682.119 -6.2360467 - 2850 20865.227 204.46262 0 3682.0004 0.39575069 - 2900 19428.614 443.93293 0 3682.0352 12.796676 - 2950 19630.1 410.18487 0 3681.8681 -0.50572623 - 3000 19663.218 404.06316 0 3681.2661 6.0827093 - 3050 19087.572 500.8452 0 3682.1073 -6.3526476 - 3100 18229.94 643.77681 0 3682.1001 11.453637 - 3150 18927.492 527.51919 0 3682.1011 -1.662863 - 3200 18320.514 628.55895 0 3681.978 21.176126 - 3250 18204.677 647.96462 0 3682.0775 11.331521 - 3300 19231.978 477.02117 0 3682.3509 3.8381593 - 3350 18153.44 656.70376 0 3682.2772 15.135615 - 3400 17476.768 770.0598 0 3682.8545 -3.394312 - 3450 21097.531 166.17241 0 3682.4276 3.74301 - 3500 17605.784 747.54808 0 3681.8454 3.3420627 - 3550 19238.34 476.00608 0 3682.3961 1.1413836 - 3600 18155.288 656.57434 0 3682.4557 3.4360446 - 3650 18735.622 559.2377 0 3681.8413 28.760363 - 3700 15310.261 1134.4215 0 3686.1317 44.207018 - 3750 15377.116 1123.4786 0 3686.3313 7.6773215 - 3800 18798.895 549.05928 0 3682.2084 -12.905825 - 3850 18322.563 628.87744 0 3682.6379 -16.067793 - 3900 19963.049 355.65441 0 3682.8292 3.4694064 - 3950 19925.48 361.2507 0 3682.1641 5.0058567 - 4000 19141.423 492.41081 0 3682.648 -12.782769 - 4050 20022.241 345.61655 0 3682.6568 -3.0149905 - 4100 21348.635 124.95646 0 3683.0624 -4.85779 - 4150 21011.812 181.1132 0 3683.0819 -3.9526196 - 4200 20222.276 312.63945 0 3683.0187 -23.63437 - 4250 20957.757 189.77152 0 3682.731 -1.3712469 - 4300 20070.215 337.5751 0 3682.611 -6.8816517 - 4350 21322.437 129.09228 0 3682.8318 -6.9442178 - 4400 19440.445 442.77531 0 3682.8495 -0.11606236 - 4450 20964.516 188.67174 0 3682.7577 4.8533525 - 4500 13530.08 1428.5497 0 3683.563 12.333187 - 4550 20461.637 272.58882 0 3682.8616 4.5111943 - 4600 17072.994 836.58228 0 3682.0812 5.7611617 - 4650 18860.748 539.82027 0 3683.2782 -2.5558958 - 4700 18373.927 621.04093 0 3683.3621 5.4020702 - 4750 20321.437 296.63662 0 3683.5428 8.9571617 - 4800 21083.122 169.84086 0 3683.6946 10.566368 - 4850 20499.669 267.7012 0 3684.3128 4.2924237 - 4900 20308.781 300.38168 0 3685.1785 -12.396923 - 4950 21043.303 178.56295 0 3685.7801 3.8923762 - 5000 20718.383 232.52208 0 3685.5859 -12.43234 - 5050 21005.749 184.4363 0 3685.3945 -7.6463487 - 5100 20714.133 233.27745 0 3685.6329 -1.6944135 - 5150 19577.452 422.73035 0 3685.639 -21.831219 - 5200 14044.647 1343.9545 0 3684.729 -6.8407194 - 5250 19089.805 504.0893 0 3685.7235 4.05641 - 5300 21094.745 169.94699 0 3685.7378 -0.66593212 - 5350 19907.559 366.77598 0 3684.7024 1.5248525 - 5400 20382.81 289.13263 0 3686.2676 -11.919321 - 5450 19593.693 420.70548 0 3686.3209 -1.1568628 - 5500 20906.08 202.09801 0 3686.4447 -2.4284971 - 5550 16315.465 965.56973 0 3684.8138 -33.178221 - 5600 19714.57 400.39687 0 3686.1586 19.950231 - 5650 20561.724 259.54797 0 3686.502 8.2074524 - 5700 19349.502 460.7789 0 3685.6959 16.252649 - 5750 21006.818 185.56805 0 3686.7044 -11.96089 - 5800 20268.2 307.97547 0 3686.0089 17.322311 - 5850 21018.322 184.16179 0 3687.2154 -14.379909 - 5900 19695.647 404.57094 0 3687.1787 -20.718904 - 5950 21021.687 183.66311 0 3687.2776 -15.206081 - 6000 18947.535 529.30554 0 3687.2281 17.863927 - 6050 15272.373 1141.012 0 3686.4075 -0.43375666 - 6100 17766.197 721.75792 0 3682.7908 11.378913 - 6150 18612.573 584.06688 0 3686.1623 17.543241 - 6200 19005.155 518.97146 0 3686.4973 -16.223107 - 6250 20997.507 187.55499 0 3687.1394 -11.613546 - 6300 19639.901 413.58048 0 3686.8974 14.407136 - 6350 19580.399 423.02818 0 3686.428 -5.5801796 - 6400 14134.119 1332.0662 0 3687.7527 84.864425 - 6450 21598.824 87.419966 0 3687.224 -5.8358352 - 6500 18208.216 649.29108 0 3683.9938 -8.1510884 - 6550 19364.586 459.59813 0 3687.0291 -12.053563 - 6600 20710.927 235.11914 0 3686.9403 -1.0470193 - 6650 21132.334 165.08091 0 3687.1366 1.0785471 - 6700 20217.285 317.589 0 3687.1365 0.055447462 - 6750 21232.279 148.57412 0 3687.2873 -2.4551657 - 6800 20292.683 304.76539 0 3686.8793 -0.42311295 - 6850 19056.291 510.49927 0 3686.5478 6.9533826 - 6900 20429.82 282.23764 0 3687.2076 -4.2360112 - 6950 21281.278 140.27361 0 3687.1533 -0.07475261 - 7000 17173.388 824.54446 0 3686.7758 10.753828 - 7050 18079.7 674.56274 0 3687.846 12.975804 - 7100 16433.233 950.73904 0 3689.6112 -10.5102 - 7150 19033.335 515.59672 0 3687.8193 0.29109447 - 7200 17286.428 809.02352 0 3690.0948 2.3015698 - 7250 16811.962 886.6645 0 3688.6582 -7.4787512 - 7300 15992.461 1023.4849 0 3688.895 -5.2354222 - 7350 19211.451 487.63129 0 3689.5398 8.4351737 - 7400 19065.682 511.95629 0 3689.57 -12.47448 - 7450 21369.265 128.10098 0 3689.6451 2.2930546 - 7500 16807.109 888.64602 0 3689.8308 14.761969 - 7550 18063.046 679.21873 0 3689.7264 3.8950434 - 7600 17794.987 724.55404 0 3690.3851 14.379016 - 7650 17904.751 706.14354 0 3690.2688 23.813776 - 7700 19670.09 411.3021 0 3689.6504 14.099245 - 7750 18082.562 675.23975 0 3689.0001 15.788521 - 7800 17776.135 726.91445 0 3689.6037 6.9780735 - 7850 17062.575 846.33412 0 3690.0966 -8.9289256 - 7900 19059.2 513.07737 0 3689.6107 16.992843 - 7950 16269.685 978.48914 0 3690.1033 11.180179 - 8000 20115.278 336.91405 0 3689.4604 -6.4882518 - 8050 21173.72 161.15229 0 3690.1056 -2.2164491 - 8100 19238.235 484.42784 0 3690.8004 23.412709 - 8150 18438.4 617.58743 0 3690.6542 0.89156316 - 8200 21438.764 117.12721 0 3690.2546 -1.7193227 - 8250 21195.806 157.66607 0 3690.3003 3.820447 - 8300 21177.549 161.13702 0 3690.7286 0.94938203 - 8350 21060.267 181.06887 0 3691.1135 2.8179025 - 8400 20087.113 343.46206 0 3691.3142 8.1484473 - 8450 19298.478 474.87133 0 3691.2843 -16.239664 - 8500 21654.353 82.083485 0 3691.1423 -8.1464138 - 8550 19920.544 371.34795 0 3691.4386 20.765144 - 8600 21692.293 75.655154 0 3691.0373 -13.316763 - 8650 21231.322 151.8989 0 3690.4526 -11.388238 - 8700 19530.647 434.89585 0 3690.0037 2.7433786 - 8750 19720.63 403.07773 0 3689.8493 -6.416414 - 8800 21321.378 136.04091 0 3689.604 1.3661635 - 8850 19811.906 387.80489 0 3689.7893 3.704143 - 8900 19734.167 400.92444 0 3689.9523 2.5685155 - 8950 21076.459 177.18119 0 3689.9244 -11.939513 - 9000 20967.246 195.42966 0 3689.9707 2.0092705 - 9050 21122.023 169.62103 0 3689.9582 2.3791301 - 9100 20169.346 328.27229 0 3689.8299 -3.5017988 - 9150 21418.641 119.84513 0 3689.6187 2.486073 - 9200 20876.042 210.26452 0 3689.6048 -5.3839897 - 9250 21572.38 93.74407 0 3689.1407 -8.3676952 - 9300 20944.78 197.98577 0 3688.7824 1.3278314 - 9350 20706.52 237.48767 0 3688.5744 4.6944204 - 9400 16412.314 953.47251 0 3688.8581 26.134976 - 9450 20461.68 277.76243 0 3688.0424 17.647445 - 9500 20893.994 205.64261 0 3687.9749 -10.642418 - 9550 20503.447 270.63504 0 3687.8761 -17.769897 - 9600 19677.799 408.05887 0 3687.692 -2.7938604 - 9650 17480.971 774.1855 0 3687.6806 0.59827043 - 9700 17799.126 721.50817 0 3688.0292 44.387928 - 9750 20443.384 280.16837 0 3687.399 3.0619324 - 9800 20545.255 263.40108 0 3687.6102 3.6229381 - 9850 20722.819 233.57142 0 3687.3745 0.86462694 - 9900 21128.462 165.09767 0 3686.508 -6.9636843 - 9950 21343.307 130.46714 0 3687.685 -9.7382705 - 10000 20623.887 250.37866 0 3687.6932 2.7529835 -Loop time of 2.27157 on 1 procs for 10000 steps with 81 atoms - -Performance: 38035.351 tau/day, 4402.240 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.092926 | 0.092926 | 0.092926 | 0.0 | 4.09 -Neigh | 0.076362 | 0.076362 | 0.076362 | 0.0 | 3.36 -Comm | 0.0069691 | 0.0069691 | 0.0069691 | 0.0 | 0.31 -Output | 0.0037444 | 0.0037444 | 0.0037444 | 0.0 | 0.16 -Modify | 2.0832 | 2.0832 | 2.0832 | 0.0 | 91.71 -Other | | 0.00841 | | | 0.37 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 62 ave 62 max 62 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 905 ave 905 max 905 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 905 -Ave neighs/atom = 11.17284 -Neighbor list builds = 991 -Dangerous builds = 927 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems.g++.4 b/examples/rigid/log.20Mar22.rigid.poems.g++.4 deleted file mode 100644 index 7e651a7aaf..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems.g++.4 +++ /dev/null @@ -1,328 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045742 - 850 17821.483 711.53827 0 3681.7854 7.4384281 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19374 0 3681.3037 11.787982 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184716 - 1150 20849.582 206.01696 0 3680.9472 -0.86699115 - 1200 21815.003 45.317409 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064083 - 1300 20780.781 217.36511 0 3680.8286 6.0538606 - 1350 20558.971 254.36489 0 3680.8601 -3.6773868 - 1400 21485.03 99.812843 0 3680.6511 -16.185479 - 1450 21771.107 52.159652 0 3680.6775 -2.4756656 - 1500 21520.949 93.503872 0 3680.3286 2.1023574 - 1550 21351.419 121.68131 0 3680.2511 5.5159875 - 1600 20778.804 216.92191 0 3680.0559 15.089203 - 1650 21477.636 100.21877 0 3679.8247 -1.104524 - 1700 18501.329 596.48084 0 3680.0357 -15.679806 - 1750 18563.639 587.34841 0 3681.2882 33.532316 - 1800 19110.174 494.82524 0 3679.8543 18.024079 - 1850 21364.178 119.23767 0 3679.9339 2.5290075 - 1900 20146.588 322.15506 0 3679.9197 5.7317368 - 1950 20692.674 231.25288 0 3680.0319 4.2977982 - 2000 20943.904 189.11229 0 3679.7629 -22.643749 - 2050 19667.815 401.87016 0 3679.8394 3.6240972 - 2100 20280.109 299.81759 0 3679.8357 7.4803647 - 2150 19181.146 483.63975 0 3680.4974 22.634167 - 2200 21301.194 130.53171 0 3680.7308 4.7072523 - 2250 20484.79 266.99736 0 3681.1291 -8.6583002 - 2300 18648.002 573.09962 0 3681.1 -5.2548835 - 2350 21515.851 95.225745 0 3681.2009 -9.3875216 - 2400 21462.37 104.21272 0 3681.2744 -29.459857 - 2450 20108.034 330.94394 0 3682.2829 35.37058 - 2500 20771.818 220.42545 0 3682.3951 -12.318936 - 2550 20502.815 265.09577 0 3682.2316 -22.726822 - 2600 21462.006 105.2733 0 3682.2744 -10.180394 - 2650 21009.656 180.72738 0 3682.3367 4.9580828 - 2700 18680.012 569.37179 0 3682.7071 21.114114 - 2750 21256.19 139.42201 0 3682.1203 -7.4744399 - 2800 21552.267 90.071446 0 3682.1159 -6.2906304 - 2850 20879.958 202.00905 0 3682.0021 0.57990903 - 2900 19018.645 512.35214 0 3682.1262 13.883084 - 2950 19819.365 378.55747 0 3681.785 -0.7348943 - 3000 20269.229 303.35149 0 3681.5563 6.3088075 - 3050 19236.727 475.99457 0 3682.1158 -10.703575 - 3100 18391.55 616.96976 0 3682.2281 9.850079 - 3150 20258.563 305.82076 0 3682.248 7.1951283 - 3200 20716.384 229.15502 0 3681.8856 2.9042294 - 3250 18662.237 572.0784 0 3682.4512 9.2108597 - 3300 19162.278 488.60646 0 3682.3195 3.3306562 - 3350 21235.679 142.98279 0 3682.2626 0.29397483 - 3400 17677.053 736.09247 0 3682.2679 32.75269 - 3450 20852.392 206.65618 0 3682.0548 -4.8319056 - 3500 21182.918 151.46754 0 3681.9539 -5.6330382 - 3550 20589.85 250.40724 0 3682.049 12.582133 - 3600 20973.659 186.28043 0 3681.8903 10.935266 - 3650 17838.632 707.92145 0 3681.0268 -17.200926 - 3700 21538.002 92.744409 0 3682.4114 -0.72124229 - 3750 21390.294 117.90865 0 3682.9576 -7.8431786 - 3800 17921.046 696.50311 0 3683.344 -9.4641531 - 3850 20356.471 290.22624 0 3682.9715 2.4593463 - 3900 20374.077 287.10249 0 3682.782 -1.9519082 - 3950 20563.915 255.29993 0 3682.619 -6.124649 - 4000 20991.467 184.76183 0 3683.3397 1.8954961 - 4050 17805.623 716.24698 0 3683.8509 -20.454944 - 4100 19916.389 363.86301 0 3683.2611 -0.27912557 - 4150 19221.623 480.01232 0 3683.6161 -11.562492 - 4200 20526.82 261.78571 0 3682.9224 -3.9522917 - 4250 20922.813 196.1799 0 3683.3154 0.11947446 - 4300 19956.66 357.78133 0 3683.8914 19.156093 - 4350 19735.73 394.45981 0 3683.7482 14.865775 - 4400 21702.656 67.099805 0 3684.2092 -13.502538 - 4450 18163.055 656.97231 0 3684.1482 -0.6243111 - 4500 17477.718 771.25976 0 3684.2127 -0.4664004 - 4550 20676.507 238.19814 0 3684.2827 -19.444969 - 4600 17322.922 796.77058 0 3683.9242 27.003966 - 4650 11905.158 1704.9151 0 3689.1082 15.574169 - 4700 18689.079 569.80982 0 3684.6563 -14.67311 - 4750 19821.745 381.01914 0 3684.6433 5.0436795 - 4800 20621.335 247.96269 0 3684.8518 -16.407263 - 4850 21923.814 30.965964 0 3684.935 -13.418244 - 4900 18840.555 544.41538 0 3684.5079 11.005357 - 4950 15366.601 1124.2481 0 3685.3482 17.412375 - 5000 18274.314 639.01311 0 3684.732 5.3261109 - 5050 21173.687 155.83673 0 3684.7845 5.4056809 - 5100 21738.219 61.75201 0 3684.7885 -2.631945 - 5150 16597.949 918.84841 0 3685.1732 -10.124101 - 5200 20752.758 225.95919 0 3684.7522 -5.2441372 - 5250 17652.088 741.2645 0 3683.2793 2.0080739 - 5300 19907.523 366.53115 0 3684.4516 8.4266792 - 5350 20104.189 334.14522 0 3684.8433 17.21925 - 5400 21499.848 101.71631 0 3685.0243 -6.1103541 - 5450 21203.533 151.14574 0 3685.068 -5.9468503 - 5500 21076.513 172.45652 0 3685.2088 5.1418181 - 5550 20158.398 325.56609 0 3685.2992 -1.6486034 - 5600 20787.836 221.19563 0 3685.835 -10.66805 - 5650 19687.154 404.77204 0 3685.9644 -23.49128 - 5700 20419.311 282.58328 0 3685.8017 -0.52808211 - 5750 19738.522 395.95893 0 3685.7126 1.3889817 - 5800 18300.025 635.66905 0 3685.6732 23.490447 - 5850 20585.004 255.02032 0 3685.8543 -0.20699939 - 5900 20373.839 290.15881 0 3685.7987 -7.9712187 - 5950 18163.832 659.91192 0 3687.2173 5.4494586 - 6000 21049.247 177.43029 0 3685.6382 2.9138342 - 6050 21239.803 145.77613 0 3685.7433 -1.4927769 - 6100 20686.361 237.86454 0 3685.5913 -0.95516297 - 6150 20461.754 275.31546 0 3685.6079 -3.4166412 - 6200 19264.208 474.73017 0 3685.4316 11.750757 - 6250 21180.813 155.31746 0 3685.4529 2.8188219 - 6300 21047.543 177.4394 0 3685.3632 1.8641486 - 6350 20232.576 313.17716 0 3685.2731 2.8150209 - 6400 20185.616 321.33454 0 3685.6038 -3.8697311 - 6450 18969.632 523.95865 0 3685.5639 0.6725512 - 6500 17592.574 753.49959 0 3685.5952 -1.2557393 - 6550 21279.049 138.42524 0 3684.9335 -1.208945 - 6600 21408.457 116.4143 0 3684.4904 -1.5332953 - 6650 19758.218 391.17316 0 3684.2096 1.8511312 - 6700 20766.943 223.44631 0 3684.6036 -2.3672623 - 6750 20399.631 284.09914 0 3684.0377 -5.4089876 - 6800 21296.628 135.14662 0 3684.5847 -3.8442549 - 6850 20641.481 244.4451 0 3684.692 1.4020639 - 6900 20852.81 209.23009 0 3684.6984 1.8512104 - 6950 20940.555 194.66882 0 3684.7614 -6.554676 - 7000 19496.988 435.28199 0 3684.78 -15.120269 - 7050 19796.829 385.04227 0 3684.5138 -4.1068804 - 7100 19945.264 360.42431 0 3684.635 -4.0629042 - 7150 19431.123 446.12911 0 3684.6497 -6.8321751 - 7200 16864.851 873.80043 0 3684.6089 14.309069 - 7250 20438.75 277.85982 0 3684.3181 -11.41223 - 7300 17688.684 734.01576 0 3682.1298 35.938373 - 7350 21573.419 88.63421 0 3684.204 -3.9032749 - 7400 21198.486 150.72249 0 3683.8034 -7.1477117 - 7450 20586.708 252.93928 0 3684.0572 -7.6634645 - 7500 21815.377 48.180377 0 3684.0765 0.97457507 - 7550 17791.352 718.87564 0 3684.101 28.248235 - 7600 21828.874 45.928597 0 3684.0742 -0.25814944 - 7650 20827.961 212.35674 0 3683.6835 -3.4083384 - 7700 21319.176 130.43547 0 3683.6315 -12.434856 - 7750 20127.904 328.69643 0 3683.3471 -16.975711 - 7800 21741.772 59.679206 0 3683.3078 3.6261863 - 7850 19612.334 414.37418 0 3683.0964 1.3763274 - 7900 20071.318 337.74624 0 3682.9658 -0.40982763 - 7950 17925.664 695.29582 0 3682.9065 17.104439 - 8000 19125.978 492.76383 0 3680.4268 10.807662 - 8050 20233.848 310.42681 0 3682.7347 13.386237 - 8100 20551.619 257.86699 0 3683.1368 -13.97515 - 8150 21578.323 86.88362 0 3683.2708 -9.6811587 - 8200 21154.833 157.72897 0 3683.5344 0.62312375 - 8250 21321.143 129.83967 0 3683.3636 1.9536438 - 8300 21041.696 176.04177 0 3682.9911 4.7475567 - 8350 19883.39 369.32649 0 3683.2247 -7.0959328 - 8400 21626.067 79.062992 0 3683.4075 -14.919059 - 8450 21375.201 120.86836 0 3683.4019 -5.3461514 - 8500 20281.059 303.10304 0 3683.2796 3.7975093 - 8550 21170.533 154.48432 0 3682.9065 -1.1568561 - 8600 17754.931 724.00158 0 3683.1568 14.15254 - 8650 20685.478 235.65879 0 3683.2385 -5.2694179 - 8700 21489.165 101.90509 0 3683.4326 -4.2510612 - 8750 21106.682 165.41638 0 3683.1968 -3.9186708 - 8800 19149.516 491.5843 0 3683.1702 -11.419849 - 8850 21451.865 108.1814 0 3683.4923 -7.8256219 - 8900 19567.4 421.81206 0 3683.0454 -0.71997056 - 8950 20934.097 194.48033 0 3683.4965 -7.0106879 - 9000 18531.559 595.25957 0 3683.8528 3.7449399 - 9050 18868.821 537.22549 0 3682.029 9.9926092 - 9100 19972.527 354.73119 0 3683.4858 -0.30871263 - 9150 19641.651 409.18618 0 3682.7947 -1.3036238 - 9200 20019.08 346.19657 0 3682.7099 6.7425386 - 9250 19259.286 473.04973 0 3682.9308 -24.120659 - 9300 21597.757 82.971857 0 3682.598 -13.748483 - 9350 19348.379 457.23576 0 3681.9656 3.1571402 - 9400 19129.588 493.35235 0 3681.617 8.6293783 - 9450 20337.025 291.20959 0 3680.7138 6.8590795 - 9500 20581.788 249.65891 0 3679.9569 -18.892836 - 9550 19482.069 433.0077 0 3680.0192 23.029778 - 9600 19182.794 482.96871 0 3680.101 -11.081731 - 9650 20086.771 332.5311 0 3680.3263 -18.939681 - 9700 20274.046 300.98818 0 3679.9959 6.7538762 - 9750 18743.595 555.08045 0 3679.0129 8.2757138 - 9800 19464.311 435.66288 0 3679.7148 7.0528759 - 9850 21249.848 138.27382 0 3679.9152 -10.847402 - 9900 21156.214 153.84621 0 3679.8819 -7.8359674 - 9950 21643.134 72.547515 0 3679.7365 -10.507744 - 10000 19587.948 414.64942 0 3679.3075 6.1173553 -Loop time of 2.36879 on 4 procs for 10000 steps with 81 atoms - -Performance: 36474.344 tau/day, 4221.568 timesteps/s -99.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.005348 | 0.024925 | 0.056071 | 12.2 | 1.05 -Neigh | 0.0075012 | 0.022046 | 0.043933 | 9.3 | 0.93 -Comm | 0.13135 | 0.16461 | 0.1917 | 5.9 | 6.95 -Output | 0.0036298 | 0.004271 | 0.0056384 | 1.2 | 0.18 -Modify | 2.1147 | 2.1322 | 2.1418 | 0.7 | 90.01 -Other | | 0.02072 | | | 0.87 - -Nlocal: 20.25 ave 81 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 41 ave 78 max 11 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Neighs: 193.5 ave 774 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 774 -Ave neighs/atom = 9.5555556 -Neighbor list builds = 989 -Dangerous builds = 915 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems2.g++.1 b/examples/rigid/log.20Mar22.rigid.poems2.g++.1 deleted file mode 100644 index 57f2040a67..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems2.g++.1 +++ /dev/null @@ -1,330 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -2 clusters, 9 bodies, 7 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12774.759 1538.7382 0 3904.4344 18.086359 - 100 19803.641 237.21132 0 3904.5523 -3.1528278 - 150 20259.6 152.62072 0 3904.3985 -4.6173524 - 200 20705.978 69.977442 0 3904.4178 9.0928158 - 250 19552.211 283.50525 0 3904.285 15.670465 - 300 19266.324 333.5792 0 3901.4169 7.2119197 - 350 20738.325 63.738945 0 3904.1694 -23.03999 - 400 20616.682 86.082444 0 3903.9864 -13.783584 - 450 19831.326 230.13858 0 3902.6063 0.42074361 - 500 20365.825 131.47231 0 3902.9213 0.6921524 - 550 20794.102 52.163238 0 3902.9229 4.5895354 - 600 20853.873 40.899172 0 3902.7275 2.3593042 - 650 19255.802 336.29509 0 3902.1844 10.341742 - 700 18526.969 471.02462 0 3901.9448 -0.61898691 - 750 18960.662 391.26068 0 3902.4944 12.04731 - 800 20142.432 172.05177 0 3902.1317 4.6838621 - 850 19932.48 210.71175 0 3901.9118 3.4716043 - 900 20243.528 153.13972 0 3901.9411 3.6490762 - 950 20388.132 126.88722 0 3902.4671 -4.4518463 - 1000 20076.333 184.61915 0 3902.4586 -2.272315 - 1050 20859.506 39.696993 0 3902.5684 6.45166 - 1100 15284.661 1072.1908 0 3902.6836 21.194042 - 1150 19658.317 261.99809 0 3902.4272 -2.874422 - 1200 20767.681 56.717094 0 3902.5839 -34.817444 - 1250 20625.583 82.586399 0 3902.1388 11.697329 - 1300 20690.013 71.006478 0 3902.4903 -29.292777 - 1350 20936.019 26.022786 0 3903.0634 1.0316025 - 1400 19753.559 244.81785 0 3902.8844 6.7138514 - 1450 15690.149 998.342 0 3903.9252 48.124557 - 1500 20234.455 155.92516 0 3903.0465 13.17221 - 1550 20779.631 55.063009 0 3903.1428 -2.639045 - 1600 20642.753 80.233905 0 3902.9659 -2.4688467 - 1650 18785.696 423.90402 0 3902.7365 -5.6466663 - 1700 20965.076 20.760444 0 3903.182 -0.45364296 - 1750 18935.406 396.96067 0 3903.5173 25.913302 - 1800 20581.559 91.756972 0 3903.1567 3.8217234 - 1850 20616.946 85.184849 0 3903.1378 4.1907972 - 1900 16602.053 828.40949 0 3902.8637 -0.49505122 - 1950 20175.526 166.53362 0 3902.7421 5.603825 - 2000 20261.924 150.39322 0 3902.6014 -1.196958 - 2050 20170.339 167.40504 0 3902.6531 -0.80849882 - 2100 19820.132 231.26755 0 3901.6624 3.1476607 - 2150 20666.19 75.838461 0 3902.9106 0.53899287 - 2200 19873.51 222.53286 0 3902.8124 7.9310276 - 2250 18548.063 467.69698 0 3902.5235 16.905356 - 2300 20616.61 84.762399 0 3902.6531 -6.7872951 - 2350 18167.738 538.13635 0 3902.5322 -11.458285 - 2400 20120.227 177.01954 0 3902.9875 -1.2593018 - 2450 20436.599 118.32469 0 3902.8801 -6.5989174 - 2500 18919.923 400.26361 0 3903.9531 32.37476 - 2550 19675.809 259.77151 0 3903.4398 19.437327 - 2600 19739.842 247.86388 0 3903.3901 -7.519784 - 2650 20557.026 96.530313 0 3903.387 0.60211646 - 2700 20666.602 76.099892 0 3903.2484 0.16825503 - 2750 20924.585 28.453883 0 3903.3771 2.4227171 - 2800 20360.659 132.8596 0 3903.352 4.1440877 - 2850 20783.475 54.518625 0 3903.3102 -0.57312067 - 2900 20456.181 115.03745 0 3903.2191 -20.118887 - 2950 20779.493 55.321394 0 3903.3756 -0.26783079 - 3000 20011.867 197.30216 0 3903.2035 -1.4704201 - 3050 20741.875 62.208723 0 3903.2966 -7.5432815 - 3100 21001.754 14.148298 0 3903.362 2.9676438 - 3150 20244.086 154.44639 0 3903.3512 -1.9071213 - 3200 20639.615 81.136426 0 3903.2873 1.4826467 - 3250 20735.244 63.529571 0 3903.3895 2.1127055 - 3300 20142.891 173.22282 0 3903.3878 4.7739415 - 3350 19963.765 206.21899 0 3903.2126 5.5410771 - 3400 16628.667 824.13627 0 3903.519 36.087673 - 3450 19228.218 342.81569 0 3903.5968 3.1057274 - 3500 19759.293 244.57876 0 3903.707 2.2339557 - 3550 19853.21 227.06362 0 3903.584 -1.0882119 - 3600 19673.516 260.64854 0 3903.8923 -10.63775 - 3650 19619.238 270.5393 0 3903.7316 -6.3746003 - 3700 20756.865 59.790243 0 3903.6542 -8.3015766 - 3750 20265.025 150.47347 0 3903.2559 -5.7284695 - 3800 20944.683 24.669276 0 3903.3142 -0.070552298 - 3850 19344.831 320.59492 0 3902.971 13.040749 - 3900 19978.209 203.00247 0 3902.6708 0.15638133 - 3950 19864.118 224.19359 0 3902.734 0.453229 - 4000 17606.216 642.71493 0 3903.1252 -12.656002 - 4050 18017.895 566.54102 0 3903.1883 12.133906 - 4100 20092.963 182.17593 0 3903.095 7.7445947 - 4150 20555.337 96.395074 0 3902.939 -6.5429752 - 4200 20709.781 67.869199 0 3903.0138 -2.8653003 - 4250 18956.203 392.20748 0 3902.6155 -1.6249728 - 4300 17816.204 603.72704 0 3903.0241 23.089239 - 4350 18979.742 388.04678 0 3902.8138 3.2511108 - 4400 20272.085 148.82367 0 3902.9135 1.9518268 - 4450 18820.003 417.74789 0 3902.9337 6.3979299 - 4500 19991.936 200.50131 0 3902.7117 3.5118553 - 4550 20915.092 29.663898 0 3902.8291 -2.3174641 - 4600 20690.37 71.125087 0 3902.6752 -12.008575 - 4650 18893.76 404.50849 0 3903.3529 15.006184 - 4700 18611.123 456.1263 0 3902.6306 -5.3574892 - 4750 20497.821 106.5856 0 3902.4784 0.85039837 - 4800 20803.214 50.120522 0 3902.5675 3.8610873 - 4850 18849.598 411.72635 0 3902.3927 9.2029058 - 4900 18121.714 546.68042 0 3902.5533 9.4522272 - 4950 20377.499 128.99323 0 3902.6041 5.3825395 - 5000 20686.114 72.039749 0 3902.8016 -5.706271 - 5050 20180.449 165.51368 0 3902.634 -16.418461 - 5100 20274.947 148.36657 0 3902.9864 -5.6668309 - 5150 18042.324 560.74137 0 3901.9125 3.6791541 - 5200 20794.666 52.204446 0 3903.0685 -1.4517721 - 5250 19073.55 371.18834 0 3903.3272 -13.457439 - 5300 20821.412 47.364313 0 3903.1813 2.258098 - 5350 20583.073 91.271191 0 3902.9513 5.4323985 - 5400 20490.967 108.41184 0 3903.0353 4.122905 - 5450 18141.79 543.66874 0 3903.2594 -0.19951075 - 5500 20274.012 148.55528 0 3903.002 5.0489974 - 5550 17806.237 605.43454 0 3902.8858 43.80619 - 5600 20999.825 14.341937 0 3903.1983 1.0879933 - 5650 20930.929 27.025347 0 3903.1234 -7.0860209 - 5700 20677.725 73.853093 0 3903.0614 2.6864775 - 5750 20521.264 102.87509 0 3903.1092 2.6940548 - 5800 20792.571 52.596021 0 3903.0721 1.2910217 - 5850 20518.674 103.26595 0 3903.0204 -9.2547271 - 5900 18417.885 491.66696 0 3902.3865 -12.049357 - 5950 17243.837 709.37858 0 3902.6817 -6.2357188 - 6000 20262.525 149.56918 0 3901.8885 -0.28964823 - 6050 19883.554 219.14043 0 3901.2801 2.3071707 - 6100 16548.178 838.47869 0 3902.956 -11.715644 - 6150 19601.177 272.14674 0 3901.9944 -0.9008056 - 6200 20499.796 106.2363 0 3902.4949 0.79071424 - 6250 19601.106 272.50139 0 3902.3359 -1.9306693 - 6300 17210.685 712.70535 0 3899.8692 4.8890923 - 6350 19911.896 214.91041 0 3902.2985 12.691129 - 6400 18834.642 411.87123 0 3899.7678 -1.9447856 - 6450 20216.311 158.39781 0 3902.1591 2.6009109 - 6500 20452.025 114.97122 0 3902.3832 0.14644416 - 6550 19142.589 357.34097 0 3902.2649 2.8968485 - 6600 20412.915 122.08784 0 3902.2573 3.1343105 - 6650 17317.867 699.39994 0 3906.4123 42.25563 - 6700 20479.771 109.8036 0 3902.3537 1.3520625 - 6750 20306.902 142.12484 0 3902.6623 2.2032106 - 6800 20755.367 58.994834 0 3902.5814 -0.90518094 - 6850 20471.259 111.7197 0 3902.6936 1.5799331 - 6900 20702.025 69.15032 0 3902.8586 9.3910371 - 6950 20477.695 110.34414 0 3902.5099 1.8181164 - 7000 20560.727 95.057704 0 3902.5998 -15.686006 - 7050 20336.675 136.39386 0 3902.4448 1.3704327 - 7100 20757.399 58.950153 0 3902.913 -6.4250981 - 7150 20870.958 38.095649 0 3903.088 -4.1962169 - 7200 20706.869 68.489134 0 3903.0944 2.8322659 - 7250 20386.713 127.7432 0 3903.0604 6.0287391 - 7300 18391.773 497.21001 0 3903.0939 19.202343 - 7350 20178.898 166.4993 0 3903.3322 1.5682417 - 7400 16858.704 781.78682 0 3903.7691 21.317514 - 7450 17509.513 660.71963 0 3903.2221 -5.9456143 - 7500 19974.601 204.20412 0 3903.2043 -0.69202711 - 7550 20917.053 29.73415 0 3903.2626 -3.9962577 - 7600 20923.518 28.482703 0 3903.2083 -1.9016251 - 7650 20549.528 97.630612 0 3903.0987 3.5512257 - 7700 20861.441 39.903885 0 3903.1337 2.4426264 - 7750 18843.349 413.64461 0 3903.1537 2.677739 - 7800 20616.054 85.214364 0 3903.0021 3.9639004 - 7850 16478.851 851.93376 0 3903.5728 7.3763128 - 7900 20312.115 141.35103 0 3902.8539 4.6707271 - 7950 20389.623 127.16589 0 3903.0219 3.4414001 - 8000 20452.117 115.30715 0 3902.7362 -1.0162528 - 8050 20857.093 40.791886 0 3903.2164 -15.150068 - 8100 19817.543 233.4997 0 3903.415 0.89346046 - 8150 18649.521 449.9112 0 3903.5262 -0.40053588 - 8200 19619.276 270.37616 0 3903.5754 5.5161492 - 8250 20393.176 127.01336 0 3903.5275 2.122613 - 8300 19145.912 358.00424 0 3903.5435 3.863924 - 8350 19636.311 267.17226 0 3903.5262 -7.1496084 - 8400 19086.332 368.86693 0 3903.3729 7.0968952 - 8450 19494.416 292.89527 0 3902.9723 3.1750935 - 8500 20041.919 191.77756 0 3903.244 0.95215503 - 8550 20357.561 133.15478 0 3903.0736 -0.14020152 - 8600 16998.797 756.07003 0 3903.9954 -16.724408 - 8650 20853.26 41.386996 0 3903.1017 -3.2612965 - 8700 20767.768 57.360884 0 3903.2438 1.1157649 - 8750 20752.546 60.106518 0 3903.1705 0.39130547 - 8800 20574.407 92.99798 0 3903.0734 0.61728166 - 8850 20326.99 138.94203 0 3903.1995 -1.9434522 - 8900 17408.108 679.53222 0 3903.2559 21.935371 - 8950 20471.21 112.2721 0 3903.2368 1.8142747 - 9000 19129.591 360.35257 0 3902.8694 4.5786395 - 9050 20439.668 117.89541 0 3903.0191 2.5585685 - 9100 20780.375 54.788664 0 3903.0062 3.8312459 - 9150 19904.559 216.61504 0 3902.6445 12.150414 - 9200 20961.295 21.52065 0 3903.2419 -0.2120699 - 9250 19315.252 326.44175 0 3903.3402 -19.740867 - 9300 20653.002 78.77764 0 3903.4076 -7.8068233 - 9350 18961.572 391.20947 0 3902.6117 -12.660843 - 9400 16262.179 892.67633 0 3904.191 22.2435 - 9450 17064.394 743.33301 0 3903.406 36.139436 - 9500 18075.588 555.06436 0 3902.3954 24.598176 - 9550 20487.738 109.06287 0 3903.0884 2.6320759 - 9600 20358.609 133.36993 0 3903.4828 0.76449113 - 9650 19849.022 228.46312 0 3904.208 9.5547064 - 9700 20448.112 116.8757 0 3903.5632 -1.0845697 - 9750 20472.78 112.51661 0 3903.7722 -0.30676738 - 9800 19491.99 293.35361 0 3902.9814 -20.10857 - 9850 19895.603 218.42479 0 3902.7957 -0.18235641 - 9900 19704.336 254.55068 0 3903.5019 14.553184 - 9950 17689.462 627.9788 0 3903.805 4.9918088 - 10000 20184.205 165.29396 0 3903.1097 2.9472364 -Loop time of 2.2898 on 1 procs for 10000 steps with 81 atoms - -Performance: 37732.583 tau/day, 4367.197 timesteps/s -99.2% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.053341 | 0.053341 | 0.053341 | 0.0 | 2.33 -Neigh | 0.056174 | 0.056174 | 0.056174 | 0.0 | 2.45 -Comm | 0.0087028 | 0.0087028 | 0.0087028 | 0.0 | 0.38 -Output | 0.0036774 | 0.0036774 | 0.0036774 | 0.0 | 0.16 -Modify | 2.1598 | 2.1598 | 2.1598 | 0.0 | 94.32 -Other | | 0.008128 | | | 0.35 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 113 ave 113 max 113 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 582 ave 582 max 582 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 582 -Ave neighs/atom = 7.1851852 -Neighbor list builds = 993 -Dangerous builds = 950 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems2.g++.4 b/examples/rigid/log.20Mar22.rigid.poems2.g++.4 deleted file mode 100644 index 89585cd109..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems2.g++.4 +++ /dev/null @@ -1,330 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -2 clusters, 9 bodies, 7 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12774.759 1538.7382 0 3904.4344 18.086358 - 100 19803.641 237.21132 0 3904.5523 -3.1528278 - 150 20259.6 152.62072 0 3904.3985 -4.6173524 - 200 20705.978 69.977039 0 3904.4174 9.0928122 - 250 19552.211 283.50525 0 3904.285 15.670466 - 300 19266.324 333.5792 0 3901.4169 7.2119197 - 350 20738.325 63.738945 0 3904.1694 -23.03999 - 400 20616.682 86.082444 0 3903.9864 -13.783584 - 450 19831.326 230.13858 0 3902.6063 0.42074361 - 500 20365.825 131.47271 0 3902.9217 0.69215592 - 550 20794.102 52.163238 0 3902.9229 4.5895354 - 600 20853.873 40.899172 0 3902.7275 2.3593042 - 650 19255.802 336.29509 0 3902.1844 10.341742 - 700 18526.969 471.02462 0 3901.9448 -0.61898691 - 750 18960.662 391.26068 0 3902.4944 12.04731 - 800 20142.432 172.05197 0 3902.1319 4.6838632 - 850 19932.48 210.71175 0 3901.9118 3.4716031 - 900 20243.528 153.13972 0 3901.9411 3.6490762 - 950 20388.132 126.88722 0 3902.4671 -4.4518463 - 1000 20076.333 184.61915 0 3902.4586 -2.272315 - 1050 20859.506 39.696993 0 3902.5684 6.45166 - 1100 15284.661 1072.1908 0 3902.6836 21.194042 - 1150 19658.317 261.99809 0 3902.4272 -2.8744219 - 1200 20767.681 56.717095 0 3902.5839 -34.817444 - 1250 20625.583 82.586198 0 3902.1386 11.697328 - 1300 20690.013 71.006478 0 3902.4903 -29.29278 - 1350 20936.019 26.022786 0 3903.0634 1.0316025 - 1400 19753.56 244.81784 0 3902.8844 6.7138497 - 1450 15690.149 998.34213 0 3903.9252 48.124569 - 1500 20234.455 155.92516 0 3903.0465 13.172207 - 1550 20779.631 55.063019 0 3903.1428 -2.6390455 - 1600 20642.753 80.233821 0 3902.9659 -2.4688431 - 1650 18785.698 423.90364 0 3902.7365 -5.6466892 - 1700 20965.076 20.760451 0 3903.182 -0.45366172 - 1750 18935.412 396.95958 0 3903.5173 25.913174 - 1800 20581.554 91.757912 0 3903.1567 3.8218442 - 1850 20616.949 85.184789 0 3903.1382 4.1907933 - 1900 16601.896 828.43849 0 3902.8638 -0.49468175 - 1950 20175.564 166.52646 0 3902.7421 5.6035728 - 2000 20262.525 150.28224 0 3902.6017 -1.1967705 - 2050 20168.994 167.65314 0 3902.6521 -0.80723928 - 2100 19810.955 232.96524 0 3901.6605 3.1936531 - 2150 20667.232 75.645145 0 3902.9103 0.54812734 - 2200 19863.772 224.34646 0 3902.8228 7.9294465 - 2250 18808.943 419.2084 0 3902.3461 14.344526 - 2300 20573.665 92.761842 0 3902.6999 -6.7671703 - 2350 19075.104 369.95414 0 3902.3809 -9.5353568 - 2400 20273.873 148.53775 0 3902.9586 -1.93796 - 2450 20087.769 182.30216 0 3902.2593 2.131796 - 2500 20711.602 67.530554 0 3903.0124 2.6280244 - 2550 19971.224 204.75926 0 3903.134 3.1760522 - 2600 20620.084 85.027145 0 3903.5612 -0.92888063 - 2650 19737.546 248.65474 0 3903.7559 -3.3218688 - 2700 20650.724 79.522243 0 3903.7303 -7.5918025 - 2750 19863.245 225.2505 0 3903.6292 9.2140221 - 2800 18992.457 386.73547 0 3903.8572 2.6244537 - 2850 18703.899 440.48356 0 3904.1685 14.561348 - 2900 17939.805 581.74599 0 3903.932 -8.0863089 - 2950 20867.516 39.38186 0 3903.7367 3.0985423 - 3000 19767.994 242.8847 0 3903.6243 1.5943109 - 3050 20397.448 126.31591 0 3903.6212 -0.14982775 - 3100 20978.114 19.126395 0 3903.9623 -9.6797253 - 3150 18303.556 513.8514 0 3903.3989 4.5940322 - 3200 19156.505 356.46608 0 3903.9671 10.071308 - 3250 17484.205 666.52199 0 3904.3377 -4.1641768 - 3300 18069.94 557.75947 0 3904.0447 11.868707 - 3350 20855.645 41.964632 0 3904.1212 5.4186293 - 3400 18011.986 568.76255 0 3904.3155 25.262783 - 3450 18669.69 446.92755 0 3904.2776 -4.194499 - 3500 20248.799 154.22147 0 3903.9991 3.9211572 - 3550 20226.024 158.64726 0 3904.2072 1.5299114 - 3600 20267.02 151.25631 0 3904.4082 -8.9821729 - 3650 20522.946 103.65382 0 3904.1994 -14.433796 - 3700 20892.319 35.294614 0 3904.2426 -21.264596 - 3750 19942.202 211.02993 0 3904.0304 -1.6428817 - 3800 20421.678 122.08118 0 3903.8734 1.7137935 - 3850 17899.53 588.82593 0 3903.5536 -24.450276 - 3900 20721.119 66.486999 0 3903.7312 -7.1772088 - 3950 20946.484 24.799445 0 3903.778 -0.4028037 - 4000 20985.362 17.608355 0 3903.7865 4.7522266 - 4050 19969.779 205.46466 0 3903.5719 18.941639 - 4100 20479.578 110.56561 0 3903.08 2.3715952 - 4150 18110.701 549.53348 0 3903.367 1.133321 - 4200 19321.098 325.58216 0 3903.5634 -3.7574942 - 4250 20734.436 63.87616 0 3903.5865 0.48350623 - 4300 19446.823 302.1727 0 3903.4362 4.0462392 - 4350 20494.669 108.1918 0 3903.501 2.9789077 - 4400 20379.244 129.61413 0 3903.5482 4.0881089 - 4450 19710.564 253.4251 0 3903.5295 5.3334683 - 4500 20744.753 61.785082 0 3903.406 4.0015409 - 4550 19948.024 208.76984 0 3902.8484 2.705423 - 4600 18367.368 502.69569 0 3904.0602 21.476471 - 4650 20559.367 96.133242 0 3903.4234 2.2549454 - 4700 20940.135 25.547808 0 3903.3505 -8.9042666 - 4750 20128.703 175.82088 0 3903.3584 -8.1450176 - 4800 20632.27 82.543887 0 3903.3347 -0.55649542 - 4850 19864.539 224.63792 0 3903.2563 7.1553461 - 4900 19332.037 323.15561 0 3903.1625 17.020214 - 4950 19055.575 373.68069 0 3902.4908 10.149457 - 5000 20219.484 159.21383 0 3903.5627 3.1806346 - 5050 17557.761 652.32864 0 3903.7659 10.733736 - 5100 20615.337 85.795304 0 3903.4503 -3.6035636 - 5150 20759.853 59.155843 0 3903.573 2.0152286 - 5200 20082.007 184.39375 0 3903.2839 -5.3745109 - 5250 18689.521 442.59842 0 3903.6208 -9.8911164 - 5300 20038.496 192.34221 0 3903.1749 -2.1437039 - 5350 19897.455 218.70142 0 3903.4154 0.64582116 - 5400 18732.385 434.21543 0 3903.1755 12.98676 - 5450 19831.487 230.79099 0 3903.2886 11.439958 - 5500 20079.89 184.6953 0 3903.1935 4.0906279 - 5550 20453.497 115.47128 0 3903.1559 7.8844436 - 5600 16673.041 815.52661 0 3903.1267 -20.17797 - 5650 19691.378 256.6412 0 3903.1928 3.7103317 - 5700 20345.743 135.29997 0 3903.0302 5.6373816 - 5750 20769.613 56.906603 0 3903.1312 -17.564762 - 5800 20713.369 67.38314 0 3903.1922 -5.340631 - 5850 20799.947 51.348865 0 3903.1909 -2.7827653 - 5900 19581.933 273.51588 0 3899.7997 12.347375 - 5950 20444.438 116.909 0 3902.9161 -0.74896654 - 6000 18970.948 389.99664 0 3903.1352 26.642912 - 6050 19414.753 307.13217 0 3902.4568 25.86316 - 6100 20780.042 54.586474 0 3902.7424 1.5387425 - 6150 20885.872 35.091585 0 3902.8456 -8.251884 - 6200 19825.81 231.40943 0 3902.8558 6.7196589 - 6250 20578.278 92.255994 0 3903.0481 -5.9647091 - 6300 20093.43 181.8699 0 3902.8754 -9.9906069 - 6350 20605.294 87.180289 0 3902.9755 -3.5643876 - 6400 19737.257 247.84828 0 3902.8958 -4.2783347 - 6450 19884.717 220.81633 0 3903.1714 3.8758905 - 6500 18719.372 436.94802 0 3903.4984 1.7865904 - 6550 20096.883 181.63346 0 3903.2784 2.395512 - 6600 20888.673 35.003062 0 3903.2758 2.7728947 - 6650 20437.85 118.16373 0 3902.9507 8.1456757 - 6700 19241.051 339.73065 0 3902.8882 13.740454 - 6750 20407.542 123.94326 0 3903.1177 7.6285942 - 6800 20536.785 99.976706 0 3903.0851 8.3496632 - 6850 20625.328 83.579677 0 3903.0849 6.5074992 - 6900 20705.37 68.944625 0 3903.2724 3.1905177 - 6950 18872.424 408.67134 0 3903.5647 6.2638845 - 7000 20072.762 186.18051 0 3903.3586 -22.780407 - 7050 20461.879 114.07495 0 3903.3117 -11.495523 - 7100 19811.566 234.50237 0 3903.3108 1.1212695 - 7150 20742.918 61.884088 0 3903.1651 -3.7907508 - 7200 20911.192 30.599903 0 3903.0429 -7.0262304 - 7250 20879.755 36.30274 0 3902.9241 -5.8018787 - 7300 20682.32 72.703261 0 3902.7626 -3.3446789 - 7350 19401.046 309.70672 0 3902.493 3.4836528 - 7400 20220.542 157.83897 0 3902.3838 2.3400031 - 7450 17691.193 625.47764 0 3901.6244 25.239568 - 7500 19745.294 245.02566 0 3901.5615 5.3622843 - 7550 19685.719 256.70983 0 3902.2133 3.4560563 - 7600 18830.192 415.10021 0 3902.1727 -0.10282681 - 7650 19613.136 270.18979 0 3902.2521 8.2241536 - 7700 20989.015 15.636879 0 3902.4915 1.2955204 - 7750 20301.583 142.90625 0 3902.4586 0.12548373 - 7800 18360.147 502.50342 0 3902.5307 17.117272 - 7850 20796.478 51.032537 0 3902.2321 -3.0993883 - 7900 20284.267 145.64296 0 3901.9887 -1.2682383 - 7950 20280.983 146.13471 0 3901.8723 3.5999841 - 8000 20915.869 28.730821 0 3902.0399 2.4987291 - 8050 20745.162 60.19981 0 3901.8964 4.0643481 - 8100 20509.039 103.70462 0 3901.6748 1.0771863 - 8150 20212.97 158.64893 0 3901.7916 3.0000215 - 8200 20323.463 138.25912 0 3901.8634 -1.2802945 - 8250 19997.284 198.37183 0 3901.5727 -2.6431964 - 8300 20138.402 171.75824 0 3901.092 1.7669897 - 8350 20367.568 130.22531 0 3901.9972 -1.2153731 - 8400 19945.534 208.35675 0 3901.9741 1.6021151 - 8450 20112.534 177.18642 0 3901.7298 2.2413008 - 8500 20686.7 71.116816 0 3901.9873 2.2888545 - 8550 18081.94 553.83586 0 3902.3432 7.8257937 - 8600 18320.081 505.67086 0 3898.2784 16.554878 - 8650 20235.305 154.43021 0 3901.709 3.1740823 - 8700 20355.413 132.22512 0 3901.746 4.3436482 - 8750 20087.188 182.11349 0 3901.9631 10.422134 - 8800 20400.795 124.09819 0 3902.0232 2.1179177 - 8850 20678.731 72.825797 0 3902.2204 -3.4491441 - 8900 20372.643 129.5072 0 3902.2189 -8.2166415 - 8950 20851.731 40.899364 0 3902.331 -5.8382839 - 9000 20318.076 139.61775 0 3902.2243 -4.1960802 - 9050 16879.415 776.53739 0 3902.3549 -14.429475 - 9100 19135.149 358.68223 0 3902.2284 -15.50479 - 9150 20689.556 70.939656 0 3902.339 -2.9876179 - 9200 19949.801 207.54882 0 3901.9564 6.4259245 - 9250 20207.027 160.2813 0 3902.3233 1.7402195 - 9300 20030.005 192.99466 0 3902.2548 5.300728 - 9350 19795.291 236.24003 0 3902.0347 5.8677745 - 9400 18232.093 526.18752 0 3902.501 19.344893 - 9450 18789.641 422.30568 0 3901.8687 -7.5185247 - 9500 16332.599 874.10423 0 3898.6597 16.241378 - 9550 18572.572 462.19972 0 3901.5649 -10.777359 - 9600 19859.645 223.32209 0 3901.0341 0.89631957 - 9650 19092.741 365.35768 0 3901.0504 6.7830005 - 9700 18391.154 495.72792 0 3901.4972 6.0683847 - 9750 17790.092 608.60997 0 3903.0714 8.2090184 - 9800 17681.783 628.99951 0 3903.4038 14.231747 - 9850 17804.412 605.54067 0 3902.654 22.308453 - 9900 19134.472 359.37911 0 3902.7999 8.5633158 - 9950 20099.055 180.28604 0 3902.3332 4.7905855 - 10000 20035.447 192.30744 0 3902.5754 1.8299201 -Loop time of 2.31994 on 4 procs for 10000 steps with 81 atoms - -Performance: 37242.315 tau/day, 4310.453 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0052789 | 0.014781 | 0.038634 | 11.4 | 0.64 -Neigh | 0.0081228 | 0.016514 | 0.033404 | 7.7 | 0.71 -Comm | 0.12269 | 0.13668 | 0.14951 | 3.1 | 5.89 -Output | 0.0034489 | 0.0039413 | 0.0050811 | 1.1 | 0.17 -Modify | 2.1036 | 2.1312 | 2.1509 | 1.2 | 91.86 -Other | | 0.01685 | | | 0.73 - -Nlocal: 20.25 ave 36 max 0 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Nghost: 35.25 ave 47 max 24 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Neighs: 137.5 ave 252 max 0 min -Histogram: 1 0 0 1 0 0 0 0 1 1 - -Total # of neighbors = 550 -Ave neighs/atom = 6.7901235 -Neighbor list builds = 994 -Dangerous builds = 956 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems3.g++.1 b/examples/rigid/log.20Mar22.rigid.poems3.g++.1 deleted file mode 100644 index b565d9f79d..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems3.g++.1 +++ /dev/null @@ -1,329 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all poems file unconnected-bodies.dat -WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035) -9 clusters, 9 bodies, 0 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.686 571.71596 0 5265.8207 32.006226 - 100 16298.5 136.65142 0 5267.6607 16.443791 - 150 16682.639 17.488068 0 5269.43 14.900278 - 200 16733.955 1.3724268 0 5269.4692 14.569123 - 250 16738.877 -0.15250573 0 5269.4939 14.496287 - 300 16738.611 -0.05516662 0 5269.5077 14.495909 - 350 16738.515 -0.01744351 0 5269.5152 14.496329 - 400 16738.488 -0.0060096677 0 5269.5178 14.496497 - 450 16738.479 -0.0012712918 0 5269.5199 14.496575 - 500 16738.479 -0.00081070354 0 5269.5203 14.49658 - 550 16738.479 -0.00083205205 0 5269.5203 14.496577 - 600 16738.479 -0.0005835658 0 5269.5206 14.49658 - 650 16738.479 -0.00047227225 0 5269.5206 14.496583 - 700 16738.479 0 0 5269.521 14.496593 - 750 16738.479 0 0 5269.5211 14.496595 - 800 16738.479 0 0 5269.5211 14.496596 - 850 16738.479 0 0 5269.5211 14.496595 - 900 16738.479 0 0 5269.5212 14.496593 - 950 16738.485 -0.003532391 0 5269.5196 14.496546 - 1000 16738.609 -0.051135033 0 5269.5109 14.496098 - 1050 16737.381 0.32991002 0 5269.5055 14.525627 - 1100 16737.915 0.16210932 0 5269.5058 14.531848 - 1150 16738.726 -0.089235332 0 5269.5098 14.509768 - 1200 16738.49 -0.0075446298 0 5269.5169 14.510489 - 1250 16738.48 0 0 5269.5214 14.510585 - 1300 16738.48 0 0 5269.5214 14.510587 - 1350 16738.48 0 0 5269.5215 14.510588 - 1400 16738.48 -0.00044742303 0 5269.5211 14.510581 - 1450 16738.481 -0.0010975104 0 5269.5207 14.51057 - 1500 16738.481 -0.00057925965 0 5269.5211 14.510575 - 1550 16738.48 0 0 5269.5216 14.510582 - 1600 16738.48 0 0 5269.5216 14.510581 - 1650 16738.481 0 0 5269.5216 14.510581 - 1700 16738.481 0 0 5269.5217 14.510582 - 1750 16738.481 0 0 5269.5217 14.510583 - 1800 16738.481 0 0 5269.5217 14.510585 - 1850 16738.481 0 0 5269.5218 14.510585 - 1900 16738.481 0 0 5269.5218 14.510585 - 1950 16738.487 -0.0031700155 0 5269.5206 14.510534 - 2000 16738.514 -0.013238802 0 5269.5188 14.510401 - 2050 16738.578 -0.03654435 0 5269.5158 14.510155 - 2100 16738.656 -0.063182323 0 5269.5137 14.510082 - 2150 16738.63 -0.056004395 0 5269.5127 14.510096 - 2200 16738.579 -0.038415873 0 5269.5143 14.510273 - 2250 16738.538 -0.023709094 0 5269.516 14.510414 - 2300 16738.512 -0.013252539 0 5269.5182 14.510501 - 2350 16738.491 -0.0045593284 0 5269.5203 14.510598 - 2400 16738.482 -0.00052242487 0 5269.5217 14.510655 - 2450 16738.486 -0.0023245722 0 5269.5211 14.510627 - 2500 16738.491 -0.005189304 0 5269.5197 14.510606 - 2550 16738.604 -0.044988104 0 5269.5155 14.510185 - 2600 16738.446 0.00096754005 0 5269.5117 14.510521 - 2650 16732.887 1.753125 0 5269.5138 14.598792 - 2700 16738.784 -0.10629556 0 5269.5107 14.499176 - 2750 16734.136 1.359459 0 5269.5135 14.594678 - 2800 16738.608 -0.047184149 0 5269.5147 14.510254 - 2850 16738.509 -0.012527238 0 5269.5181 14.509344 - 2900 16738.487 -0.0026065529 0 5269.521 14.509512 - 2950 16738.498 -0.0082248532 0 5269.519 14.509457 - 3000 16738.683 -0.071294028 0 5269.514 14.509005 - 3050 16717.444 6.5874862 0 5269.4864 14.834144 - 3100 16657.654 25.431253 0 5269.5074 14.467824 - 3150 16739.322 -0.28964062 0 5269.497 13.658821 - 3200 16733.615 1.4969789 0 5269.487 11.998304 - 3250 16737.289 0.35071214 0 5269.4974 11.918931 - 3300 16732.493 1.8663821 0 5269.503 12.109003 - 3350 16738.717 -0.087719164 0 5269.5085 11.979747 - 3400 16738.586 -0.045267897 0 5269.5095 11.97972 - 3450 16738.662 -0.071274216 0 5269.5076 11.979564 - 3500 16738.853 -0.13644992 0 5269.5026 11.979658 - 3550 16729.612 2.7475277 0 5269.4774 12.195939 - 3600 16728.659 3.0596069 0 5269.4893 12.241248 - 3650 16738.923 -0.15949792 0 5269.5014 11.991857 - 3700 16738.76 -0.10695054 0 5269.5028 11.992932 - 3750 16738.751 -0.10105954 0 5269.5057 11.993137 - 3800 16738.597 -0.048627545 0 5269.5097 11.993456 - 3850 16738.507 -0.016053927 0 5269.5138 11.992973 - 3900 16738.485 -0.0060825487 0 5269.5169 11.993052 - 3950 16738.475 -0.0014953722 0 5269.5183 11.993119 - 4000 16738.472 -0.00054315391 0 5269.5184 11.99315 - 4050 16738.472 -0.00023792127 0 5269.5187 11.993172 - 4100 16738.472 0 0 5269.5189 11.993188 - 4150 16738.472 0 0 5269.5189 11.993188 - 4200 16738.472 0 0 5269.519 11.993178 - 4250 16738.472 0 0 5269.519 11.993164 - 4300 16738.472 0 0 5269.5191 11.993152 - 4350 16738.473 0 0 5269.5191 11.993147 - 4400 16738.473 0 0 5269.5192 11.993149 - 4450 16738.473 0 0 5269.5192 11.993158 - 4500 16738.473 0 0 5269.5193 11.99317 - 4550 16738.473 0 0 5269.5193 11.993176 - 4600 16738.473 0 0 5269.5194 11.993174 - 4650 16738.473 0 0 5269.5194 11.993167 - 4700 16738.474 0 0 5269.5195 11.993162 - 4750 16738.474 0 0 5269.5195 11.99316 - 4800 16738.474 0 0 5269.5196 11.99316 - 4850 16738.474 0 0 5269.5196 11.993163 - 4900 16738.474 0 0 5269.5197 11.99317 - 4950 16738.474 0 0 5269.5197 11.993176 - 5000 16738.475 0 0 5269.5198 11.993174 - 5050 16738.475 0 0 5269.5198 11.993165 - 5100 16738.475 0 0 5269.5199 11.993155 - 5150 16738.475 0 0 5269.5199 11.99315 - 5200 16738.475 0 0 5269.52 11.993153 - 5250 16738.475 0 0 5269.52 11.993161 - 5300 16738.476 0 0 5269.5201 11.993173 - 5350 16738.476 0 0 5269.5201 11.993185 - 5400 16738.476 0 0 5269.5202 11.993189 - 5450 16738.476 0 0 5269.5202 11.993181 - 5500 16738.476 0 0 5269.5203 11.993165 - 5550 16738.483 -0.0030091905 0 5269.5195 11.993097 - 5600 16738.534 -0.020777802 0 5269.5177 11.992799 - 5650 16738.649 -0.059321662 0 5269.5153 11.993266 - 5700 16409.08 103.75288 0 5269.5745 23.626238 - 5750 16738.578 -0.036776519 0 5269.5155 11.910545 - 5800 16738.484 -0.0047306177 0 5269.518 11.911008 - 5850 16738.477 -0.00022082692 0 5269.5202 11.911078 - 5900 16738.477 -0.00033136078 0 5269.5203 11.91107 - 5950 16738.478 -0.00036902212 0 5269.5203 11.911052 - 6000 16738.477 0 0 5269.5206 11.911044 - 6050 16738.477 0 0 5269.5207 11.911034 - 6100 16738.478 0 0 5269.5207 11.911032 - 6150 16738.478 0 0 5269.5208 11.911037 - 6200 16738.478 0 0 5269.5208 11.911049 - 6250 16738.478 0 0 5269.5209 11.911062 - 6300 16738.478 0 0 5269.5209 11.911068 - 6350 16738.478 0 0 5269.521 11.911065 - 6400 16738.478 0 0 5269.521 11.911058 - 6450 16738.479 0 0 5269.5211 11.911052 - 6500 16738.479 0 0 5269.5211 11.911047 - 6550 16738.479 0 0 5269.5212 11.911046 - 6600 16738.479 0 0 5269.5212 11.911049 - 6650 16738.479 0 0 5269.5213 11.911056 - 6700 16738.479 0 0 5269.5213 11.911062 - 6750 16738.48 0 0 5269.5214 11.91106 - 6800 16738.48 0 0 5269.5214 11.911051 - 6850 16738.48 0 0 5269.5215 11.911044 - 6900 16738.48 0 0 5269.5215 11.911041 - 6950 16738.48 0 0 5269.5216 11.911045 - 7000 16738.48 0 0 5269.5216 11.911053 - 7050 16738.481 0 0 5269.5217 11.911063 - 7100 16738.481 0 0 5269.5217 11.911071 - 7150 16738.481 0 0 5269.5218 11.911072 - 7200 16738.481 0 0 5269.5218 11.911063 - 7250 16738.481 0 0 5269.5219 11.911048 - 7300 16738.481 0 0 5269.5219 11.911036 - 7350 16738.482 0 0 5269.522 11.911031 - 7400 16738.482 0 0 5269.522 11.911035 - 7450 16738.482 0 0 5269.5221 11.911046 - 7500 16738.482 0 0 5269.5221 11.911062 - 7550 16738.482 0 0 5269.5222 11.911077 - 7600 16738.482 0 0 5269.5222 11.911081 - 7650 16738.483 0 0 5269.5223 11.911071 - 7700 16738.483 0 0 5269.5223 11.911054 - 7750 16738.483 0 0 5269.5224 11.911039 - 7800 16738.483 0 0 5269.5224 11.911031 - 7850 16738.483 0 0 5269.5225 11.911031 - 7900 16738.483 0 0 5269.5226 11.911039 - 7950 16738.484 0 0 5269.5226 11.911052 - 8000 16738.484 0 0 5269.5227 11.911065 - 8050 16738.484 0 0 5269.5227 11.91107 - 8100 16738.484 0 0 5269.5228 11.911065 - 8150 16738.484 0 0 5269.5228 11.911056 - 8200 16738.484 0 0 5269.5229 11.911047 - 8250 16738.485 0 0 5269.5229 11.911042 - 8300 16738.485 0 0 5269.523 11.911041 - 8350 16738.485 0 0 5269.523 11.911046 - 8400 16738.485 0 0 5269.5231 11.911055 - 8450 16738.485 0 0 5269.5231 11.911062 - 8500 16738.485 0 0 5269.5232 11.91106 - 8550 16738.486 0 0 5269.5232 11.911053 - 8600 16738.487 -0.00084974054 0 5269.5227 11.911032 - 8650 16738.486 0 0 5269.5233 11.911046 - 8700 16738.486 0 0 5269.5234 11.91105 - 8750 16738.486 0 0 5269.5235 11.911056 - 8800 16738.486 0 0 5269.5235 11.911063 - 8850 16738.487 -0.000227631 0 5269.5234 11.911065 - 8900 16738.487 0 0 5269.5236 11.911068 - 8950 16738.487 0 0 5269.5237 11.911058 - 9000 16738.487 0 0 5269.5237 11.911045 - 9050 16738.487 0 0 5269.5238 11.911036 - 9100 16738.487 0 0 5269.5238 11.911034 - 9150 16738.488 0 0 5269.5239 11.91104 - 9200 16738.488 0 0 5269.5239 11.911052 - 9250 16738.488 0 0 5269.524 11.911068 - 9300 16738.488 0 0 5269.524 11.911079 - 9350 16738.488 0 0 5269.5241 11.911078 - 9400 16738.492 -0.0016306436 0 5269.5235 11.911038 - 9450 16738.492 -0.0032567429 0 5269.522 11.911005 - 9500 16738.495 -0.0036645351 0 5269.5224 11.910982 - 9550 16738.49 -0.0010673912 0 5269.5237 11.911012 - 9600 16738.489 0 0 5269.5244 11.911032 - 9650 16738.489 0 0 5269.5244 11.911043 - 9700 16738.49 0 0 5269.5245 11.911058 - 9750 16738.49 0 0 5269.5245 11.911071 - 9800 16738.49 0 0 5269.5246 11.911073 - 9850 16738.49 0 0 5269.5246 11.911065 - 9900 16738.49 0 0 5269.5247 11.911053 - 9950 16738.491 -0.00058544643 0 5269.5243 11.911032 - 10000 16738.493 -0.0015244931 0 5269.5242 11.911015 -Loop time of 2.30195 on 1 procs for 10000 steps with 81 atoms - -Performance: 37533.440 tau/day, 4344.148 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0076839 | 0.0076839 | 0.0076839 | 0.0 | 0.33 -Neigh | 0.029562 | 0.029562 | 0.029562 | 0.0 | 1.28 -Comm | 0.0084877 | 0.0084877 | 0.0084877 | 0.0 | 0.37 -Output | 0.0037958 | 0.0037958 | 0.0037958 | 0.0 | 0.16 -Modify | 2.2446 | 2.2446 | 2.2446 | 0.0 | 97.51 -Other | | 0.00785 | | | 0.34 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 69 ave 69 max 69 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 4 ave 4 max 4 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4 -Ave neighs/atom = 0.049382716 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems3.g++.4 b/examples/rigid/log.20Mar22.rigid.poems3.g++.4 deleted file mode 100644 index 39fd6245e0..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems3.g++.4 +++ /dev/null @@ -1,329 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all poems file unconnected-bodies.dat -WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035) -9 clusters, 9 bodies, 0 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.686 571.71596 0 5265.8207 32.006226 - 100 16298.5 136.65142 0 5267.6607 16.443791 - 150 16682.639 17.488068 0 5269.43 14.900278 - 200 16733.955 1.3724268 0 5269.4692 14.569123 - 250 16738.877 -0.15250573 0 5269.4939 14.496287 - 300 16738.611 -0.05516662 0 5269.5077 14.495909 - 350 16738.515 -0.01744351 0 5269.5152 14.496329 - 400 16738.488 -0.0060096677 0 5269.5178 14.496497 - 450 16738.479 -0.0012712918 0 5269.5199 14.496575 - 500 16738.479 -0.00081070354 0 5269.5203 14.49658 - 550 16738.479 -0.00083205205 0 5269.5203 14.496577 - 600 16738.479 -0.0005835658 0 5269.5206 14.49658 - 650 16738.479 -0.00047227225 0 5269.5206 14.496583 - 700 16738.479 0 0 5269.521 14.496593 - 750 16738.479 0 0 5269.5211 14.496595 - 800 16738.479 0 0 5269.5211 14.496596 - 850 16738.479 0 0 5269.5211 14.496595 - 900 16738.479 0 0 5269.5212 14.496593 - 950 16738.485 -0.003532391 0 5269.5196 14.496546 - 1000 16738.609 -0.051135033 0 5269.5109 14.496098 - 1050 16737.381 0.32991002 0 5269.5055 14.525627 - 1100 16737.915 0.16210932 0 5269.5058 14.531848 - 1150 16738.726 -0.089235332 0 5269.5098 14.509768 - 1200 16738.49 -0.0075446298 0 5269.5169 14.510489 - 1250 16738.48 0 0 5269.5214 14.510585 - 1300 16738.48 0 0 5269.5214 14.510587 - 1350 16738.48 0 0 5269.5215 14.510588 - 1400 16738.48 -0.00044742303 0 5269.5211 14.510581 - 1450 16738.481 -0.0010975104 0 5269.5207 14.51057 - 1500 16738.481 -0.00057925965 0 5269.5211 14.510575 - 1550 16738.48 0 0 5269.5216 14.510582 - 1600 16738.48 0 0 5269.5216 14.510581 - 1650 16738.481 0 0 5269.5216 14.510581 - 1700 16738.481 0 0 5269.5217 14.510582 - 1750 16738.481 0 0 5269.5217 14.510583 - 1800 16738.481 0 0 5269.5217 14.510585 - 1850 16738.481 0 0 5269.5218 14.510585 - 1900 16738.481 0 0 5269.5218 14.510585 - 1950 16738.487 -0.0031700155 0 5269.5206 14.510534 - 2000 16738.514 -0.013238802 0 5269.5188 14.510401 - 2050 16738.578 -0.03654435 0 5269.5158 14.510155 - 2100 16738.656 -0.063182323 0 5269.5137 14.510082 - 2150 16738.63 -0.056004395 0 5269.5127 14.510096 - 2200 16738.579 -0.038415873 0 5269.5143 14.510273 - 2250 16738.538 -0.023709094 0 5269.516 14.510414 - 2300 16738.512 -0.013252539 0 5269.5182 14.510501 - 2350 16738.491 -0.0045593284 0 5269.5203 14.510598 - 2400 16738.482 -0.00052242487 0 5269.5217 14.510655 - 2450 16738.486 -0.0023245722 0 5269.5211 14.510627 - 2500 16738.491 -0.005189304 0 5269.5197 14.510606 - 2550 16738.604 -0.044988104 0 5269.5155 14.510185 - 2600 16738.446 0.0009675401 0 5269.5117 14.510521 - 2650 16732.887 1.753125 0 5269.5138 14.598792 - 2700 16738.784 -0.10629556 0 5269.5107 14.499176 - 2750 16734.136 1.359459 0 5269.5135 14.594678 - 2800 16738.608 -0.047184149 0 5269.5147 14.510254 - 2850 16738.509 -0.012527238 0 5269.5181 14.509344 - 2900 16738.487 -0.0026065529 0 5269.521 14.509512 - 2950 16738.498 -0.0082248532 0 5269.519 14.509457 - 3000 16738.683 -0.071294028 0 5269.514 14.509005 - 3050 16717.444 6.5874862 0 5269.4864 14.834144 - 3100 16657.654 25.431253 0 5269.5074 14.467824 - 3150 16739.322 -0.28964062 0 5269.497 13.658821 - 3200 16733.615 1.4969789 0 5269.487 11.998304 - 3250 16737.289 0.35071214 0 5269.4974 11.918931 - 3300 16732.493 1.8663821 0 5269.503 12.109003 - 3350 16738.717 -0.087719164 0 5269.5085 11.979747 - 3400 16738.586 -0.045267897 0 5269.5095 11.97972 - 3450 16738.662 -0.071274216 0 5269.5076 11.979564 - 3500 16738.853 -0.13644992 0 5269.5026 11.979658 - 3550 16729.612 2.7475277 0 5269.4774 12.195939 - 3600 16728.659 3.059607 0 5269.4893 12.241248 - 3650 16738.923 -0.15949792 0 5269.5014 11.991857 - 3700 16738.76 -0.10695054 0 5269.5028 11.992932 - 3750 16738.751 -0.10105954 0 5269.5057 11.993137 - 3800 16738.597 -0.048627545 0 5269.5097 11.993456 - 3850 16738.507 -0.016053927 0 5269.5138 11.992973 - 3900 16738.485 -0.0060825487 0 5269.5169 11.993052 - 3950 16738.475 -0.0014953722 0 5269.5183 11.993119 - 4000 16738.472 -0.00054315391 0 5269.5184 11.99315 - 4050 16738.472 -0.00023792126 0 5269.5187 11.993172 - 4100 16738.472 0 0 5269.5189 11.993188 - 4150 16738.472 0 0 5269.5189 11.993188 - 4200 16738.472 0 0 5269.519 11.993178 - 4250 16738.472 0 0 5269.519 11.993164 - 4300 16738.472 0 0 5269.5191 11.993152 - 4350 16738.473 0 0 5269.5191 11.993147 - 4400 16738.473 0 0 5269.5192 11.993149 - 4450 16738.473 0 0 5269.5192 11.993158 - 4500 16738.473 0 0 5269.5193 11.99317 - 4550 16738.473 0 0 5269.5193 11.993176 - 4600 16738.473 0 0 5269.5194 11.993174 - 4650 16738.473 0 0 5269.5194 11.993167 - 4700 16738.474 0 0 5269.5195 11.993162 - 4750 16738.474 0 0 5269.5195 11.99316 - 4800 16738.474 0 0 5269.5196 11.99316 - 4850 16738.474 0 0 5269.5196 11.993163 - 4900 16738.474 0 0 5269.5197 11.99317 - 4950 16738.474 0 0 5269.5197 11.993176 - 5000 16738.475 0 0 5269.5198 11.993174 - 5050 16738.475 0 0 5269.5198 11.993165 - 5100 16738.475 0 0 5269.5199 11.993155 - 5150 16738.475 0 0 5269.5199 11.99315 - 5200 16738.475 0 0 5269.52 11.993153 - 5250 16738.475 0 0 5269.52 11.993161 - 5300 16738.476 0 0 5269.5201 11.993173 - 5350 16738.476 0 0 5269.5201 11.993185 - 5400 16738.476 0 0 5269.5202 11.993189 - 5450 16738.476 0 0 5269.5202 11.993181 - 5500 16738.476 0 0 5269.5203 11.993165 - 5550 16738.483 -0.0030091905 0 5269.5195 11.993097 - 5600 16738.534 -0.020777802 0 5269.5177 11.992799 - 5650 16738.649 -0.059321662 0 5269.5153 11.993266 - 5700 16409.08 103.75288 0 5269.5745 23.626238 - 5750 16738.578 -0.036776519 0 5269.5155 11.910545 - 5800 16738.484 -0.0047306177 0 5269.518 11.911008 - 5850 16738.477 -0.00022082692 0 5269.5202 11.911078 - 5900 16738.477 -0.00033136078 0 5269.5203 11.91107 - 5950 16738.478 -0.00036902212 0 5269.5203 11.911052 - 6000 16738.477 0 0 5269.5206 11.911044 - 6050 16738.477 0 0 5269.5207 11.911034 - 6100 16738.478 0 0 5269.5207 11.911032 - 6150 16738.478 0 0 5269.5208 11.911037 - 6200 16738.478 0 0 5269.5208 11.911049 - 6250 16738.478 0 0 5269.5209 11.911062 - 6300 16738.478 0 0 5269.5209 11.911068 - 6350 16738.478 0 0 5269.521 11.911065 - 6400 16738.478 0 0 5269.521 11.911058 - 6450 16738.479 0 0 5269.5211 11.911052 - 6500 16738.479 0 0 5269.5211 11.911047 - 6550 16738.479 0 0 5269.5212 11.911046 - 6600 16738.479 0 0 5269.5212 11.911049 - 6650 16738.479 0 0 5269.5213 11.911056 - 6700 16738.479 0 0 5269.5213 11.911062 - 6750 16738.48 0 0 5269.5214 11.91106 - 6800 16738.48 0 0 5269.5214 11.911051 - 6850 16738.48 0 0 5269.5215 11.911044 - 6900 16738.48 0 0 5269.5215 11.911041 - 6950 16738.48 0 0 5269.5216 11.911045 - 7000 16738.48 0 0 5269.5216 11.911053 - 7050 16738.481 0 0 5269.5217 11.911063 - 7100 16738.481 0 0 5269.5217 11.911071 - 7150 16738.481 0 0 5269.5218 11.911072 - 7200 16738.481 0 0 5269.5218 11.911063 - 7250 16738.481 0 0 5269.5219 11.911048 - 7300 16738.481 0 0 5269.5219 11.911036 - 7350 16738.482 0 0 5269.522 11.911031 - 7400 16738.482 0 0 5269.522 11.911035 - 7450 16738.482 0 0 5269.5221 11.911046 - 7500 16738.482 0 0 5269.5221 11.911062 - 7550 16738.482 0 0 5269.5222 11.911077 - 7600 16738.482 0 0 5269.5222 11.911081 - 7650 16738.483 0 0 5269.5223 11.911071 - 7700 16738.483 0 0 5269.5223 11.911054 - 7750 16738.483 0 0 5269.5224 11.911039 - 7800 16738.483 0 0 5269.5224 11.911031 - 7850 16738.483 0 0 5269.5225 11.911031 - 7900 16738.483 0 0 5269.5226 11.911039 - 7950 16738.484 0 0 5269.5226 11.911052 - 8000 16738.484 0 0 5269.5227 11.911065 - 8050 16738.484 0 0 5269.5227 11.91107 - 8100 16738.484 0 0 5269.5228 11.911065 - 8150 16738.484 0 0 5269.5228 11.911056 - 8200 16738.484 0 0 5269.5229 11.911047 - 8250 16738.485 0 0 5269.5229 11.911042 - 8300 16738.485 0 0 5269.523 11.911041 - 8350 16738.485 0 0 5269.523 11.911046 - 8400 16738.485 0 0 5269.5231 11.911055 - 8450 16738.485 0 0 5269.5231 11.911062 - 8500 16738.485 0 0 5269.5232 11.91106 - 8550 16738.486 0 0 5269.5232 11.911053 - 8600 16738.487 -0.00084974055 0 5269.5227 11.911032 - 8650 16738.486 0 0 5269.5233 11.911046 - 8700 16738.486 0 0 5269.5234 11.91105 - 8750 16738.486 0 0 5269.5235 11.911056 - 8800 16738.486 0 0 5269.5235 11.911063 - 8850 16738.487 -0.000227631 0 5269.5234 11.911065 - 8900 16738.487 0 0 5269.5236 11.911068 - 8950 16738.487 0 0 5269.5237 11.911058 - 9000 16738.487 0 0 5269.5237 11.911045 - 9050 16738.487 0 0 5269.5238 11.911036 - 9100 16738.487 0 0 5269.5238 11.911034 - 9150 16738.488 0 0 5269.5239 11.91104 - 9200 16738.488 0 0 5269.5239 11.911052 - 9250 16738.488 0 0 5269.524 11.911068 - 9300 16738.488 0 0 5269.524 11.911079 - 9350 16738.488 0 0 5269.5241 11.911078 - 9400 16738.492 -0.0016306433 0 5269.5235 11.911038 - 9450 16738.492 -0.0032567425 0 5269.522 11.911005 - 9500 16738.495 -0.0036645345 0 5269.5224 11.910982 - 9550 16738.49 -0.001067391 0 5269.5237 11.911012 - 9600 16738.489 0 0 5269.5244 11.911032 - 9650 16738.489 0 0 5269.5244 11.911043 - 9700 16738.49 0 0 5269.5245 11.911058 - 9750 16738.49 0 0 5269.5245 11.911071 - 9800 16738.49 0 0 5269.5246 11.911073 - 9850 16738.49 0 0 5269.5246 11.911065 - 9900 16738.49 0 0 5269.5247 11.911053 - 9950 16738.491 -0.00058544648 0 5269.5243 11.911032 - 10000 16738.493 -0.0015244933 0 5269.5242 11.911015 -Loop time of 2.36483 on 4 procs for 10000 steps with 81 atoms - -Performance: 36535.358 tau/day, 4228.629 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0030635 | 0.0035263 | 0.0040903 | 0.7 | 0.15 -Neigh | 0.0093439 | 0.01002 | 0.010976 | 0.6 | 0.42 -Comm | 0.11912 | 0.12509 | 0.13346 | 1.5 | 5.29 -Output | 0.003411 | 0.0038449 | 0.0050123 | 1.1 | 0.16 -Modify | 2.1961 | 2.2052 | 2.2137 | 0.5 | 93.25 -Other | | 0.01717 | | | 0.73 - -Nlocal: 20.25 ave 27 max 9 min -Histogram: 1 0 0 0 0 1 0 0 0 2 -Nghost: 31.5 ave 51 max 15 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 1 ave 4 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 4 -Ave neighs/atom = 0.049382716 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems4.g++.1 b/examples/rigid/log.20Mar22.rigid.poems4.g++.1 deleted file mode 100644 index e2febc5ed9..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems4.g++.1 +++ /dev/null @@ -1,328 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems file connected-bodies.dat -1 clusters, 9 bodies, 8 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045742 - 850 17821.483 711.53827 0 3681.7854 7.438428 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19374 0 3681.3037 11.787982 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184716 - 1150 20849.582 206.01696 0 3680.9472 -0.86699118 - 1200 21815.003 45.317409 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064083 - 1300 20780.781 217.36511 0 3680.8286 6.0538604 - 1350 20558.971 254.36489 0 3680.8601 -3.6773868 - 1400 21485.029 99.812844 0 3680.6511 -16.185479 - 1450 21771.107 52.159653 0 3680.6775 -2.4756655 - 1500 21520.949 93.503876 0 3680.3286 2.1023573 - 1550 21351.419 121.6813 0 3680.2511 5.5159876 - 1600 20778.804 216.92191 0 3680.0559 15.089203 - 1650 21477.636 100.21873 0 3679.8247 -1.1045277 - 1700 18501.33 596.4807 0 3680.0357 -15.6798 - 1750 18563.64 587.34824 0 3681.2882 33.532308 - 1800 19110.175 494.82517 0 3679.8543 18.024074 - 1850 21364.178 119.23765 0 3679.9339 2.5290144 - 1900 20146.588 322.15509 0 3679.9197 5.7317299 - 1950 20692.676 231.25264 0 3680.0319 4.297803 - 2000 20943.902 189.11251 0 3679.7629 -22.643824 - 2050 19667.823 401.86882 0 3679.8394 3.6241915 - 2100 20280.125 299.81485 0 3679.8357 7.4804047 - 2150 19181.201 483.6306 0 3680.4975 22.63342 - 2200 21301.144 130.54014 0 3680.7308 4.7074288 - 2250 20484.876 266.98315 0 3681.1291 -8.6578278 - 2300 18648.161 573.07329 0 3681.1001 -5.2550954 - 2350 21515.748 95.243054 0 3681.201 -9.386512 - 2400 21462.551 104.18267 0 3681.2745 -29.46442 - 2450 20107.732 330.99437 0 3682.2831 35.38497 - 2500 20771.509 220.47713 0 3682.3953 -12.324858 - 2550 20499.887 265.58494 0 3682.2327 -22.713874 - 2600 21462.182 105.24427 0 3682.2747 -10.175788 - 2650 21004.949 181.51383 0 3682.3387 4.949195 - 2700 18673.552 570.45017 0 3682.7089 21.201437 - 2750 21257.562 139.198 0 3682.1249 -7.5793039 - 2800 21559.645 88.844759 0 3682.119 -6.2360467 - 2850 20865.227 204.46262 0 3682.0004 0.39575069 - 2900 19428.614 443.93293 0 3682.0352 12.796676 - 2950 19630.1 410.18487 0 3681.8681 -0.50572623 - 3000 19663.218 404.06316 0 3681.2661 6.0827093 - 3050 19087.572 500.8452 0 3682.1073 -6.3526476 - 3100 18229.94 643.77681 0 3682.1001 11.453637 - 3150 18927.492 527.51919 0 3682.1011 -1.662863 - 3200 18320.514 628.55895 0 3681.978 21.176126 - 3250 18204.677 647.96462 0 3682.0775 11.331521 - 3300 19231.978 477.02117 0 3682.3509 3.8381593 - 3350 18153.44 656.70376 0 3682.2772 15.135615 - 3400 17476.768 770.0598 0 3682.8545 -3.394312 - 3450 21097.531 166.17241 0 3682.4276 3.74301 - 3500 17605.784 747.54808 0 3681.8454 3.3420627 - 3550 19238.34 476.00608 0 3682.3961 1.1413836 - 3600 18155.288 656.57434 0 3682.4557 3.4360446 - 3650 18735.622 559.2377 0 3681.8413 28.760363 - 3700 15310.261 1134.4215 0 3686.1317 44.207018 - 3750 15377.116 1123.4786 0 3686.3313 7.6773215 - 3800 18798.895 549.05928 0 3682.2084 -12.905825 - 3850 18322.563 628.87744 0 3682.6379 -16.067793 - 3900 19963.049 355.65441 0 3682.8292 3.4694064 - 3950 19925.48 361.2507 0 3682.1641 5.0058567 - 4000 19141.423 492.41081 0 3682.648 -12.782769 - 4050 20022.241 345.61655 0 3682.6568 -3.0149905 - 4100 21348.635 124.95646 0 3683.0624 -4.85779 - 4150 21011.812 181.1132 0 3683.0819 -3.9526196 - 4200 20222.276 312.63945 0 3683.0187 -23.63437 - 4250 20957.757 189.77152 0 3682.731 -1.3712469 - 4300 20070.215 337.5751 0 3682.611 -6.8816517 - 4350 21322.437 129.09228 0 3682.8318 -6.9442178 - 4400 19440.445 442.77531 0 3682.8495 -0.11606236 - 4450 20964.516 188.67174 0 3682.7577 4.8533525 - 4500 13530.08 1428.5497 0 3683.563 12.333187 - 4550 20461.637 272.58882 0 3682.8616 4.5111943 - 4600 17072.994 836.58228 0 3682.0812 5.7611617 - 4650 18860.748 539.82027 0 3683.2782 -2.5558958 - 4700 18373.927 621.04093 0 3683.3621 5.4020702 - 4750 20321.437 296.63662 0 3683.5428 8.9571617 - 4800 21083.122 169.84086 0 3683.6946 10.566368 - 4850 20499.669 267.7012 0 3684.3128 4.2924237 - 4900 20308.781 300.38168 0 3685.1785 -12.396923 - 4950 21043.303 178.56295 0 3685.7801 3.8923762 - 5000 20718.383 232.52208 0 3685.5859 -12.43234 - 5050 21005.749 184.4363 0 3685.3945 -7.6463487 - 5100 20714.133 233.27745 0 3685.6329 -1.6944135 - 5150 19577.452 422.73035 0 3685.639 -21.831219 - 5200 14044.647 1343.9545 0 3684.729 -6.8407194 - 5250 19089.805 504.0893 0 3685.7235 4.05641 - 5300 21094.745 169.94699 0 3685.7378 -0.66593212 - 5350 19907.559 366.77598 0 3684.7024 1.5248525 - 5400 20382.81 289.13263 0 3686.2676 -11.919321 - 5450 19593.693 420.70548 0 3686.3209 -1.1568628 - 5500 20906.08 202.09801 0 3686.4447 -2.4284971 - 5550 16315.465 965.56973 0 3684.8138 -33.178221 - 5600 19714.57 400.39687 0 3686.1586 19.950231 - 5650 20561.724 259.54797 0 3686.502 8.2074524 - 5700 19349.502 460.7789 0 3685.6959 16.252649 - 5750 21006.818 185.56805 0 3686.7044 -11.96089 - 5800 20268.2 307.97547 0 3686.0089 17.322311 - 5850 21018.322 184.16179 0 3687.2154 -14.379909 - 5900 19695.647 404.57094 0 3687.1787 -20.718904 - 5950 21021.687 183.66311 0 3687.2776 -15.206081 - 6000 18947.535 529.30554 0 3687.2281 17.863927 - 6050 15272.373 1141.012 0 3686.4075 -0.43375666 - 6100 17766.197 721.75792 0 3682.7908 11.378913 - 6150 18612.573 584.06688 0 3686.1623 17.543241 - 6200 19005.155 518.97146 0 3686.4973 -16.223107 - 6250 20997.507 187.55499 0 3687.1394 -11.613546 - 6300 19639.901 413.58048 0 3686.8974 14.407136 - 6350 19580.399 423.02818 0 3686.428 -5.5801796 - 6400 14134.119 1332.0662 0 3687.7527 84.864425 - 6450 21598.824 87.419966 0 3687.224 -5.8358352 - 6500 18208.216 649.29108 0 3683.9938 -8.1510884 - 6550 19364.586 459.59813 0 3687.0291 -12.053563 - 6600 20710.927 235.11914 0 3686.9403 -1.0470193 - 6650 21132.334 165.08091 0 3687.1366 1.0785471 - 6700 20217.285 317.589 0 3687.1365 0.055447462 - 6750 21232.279 148.57412 0 3687.2873 -2.4551657 - 6800 20292.683 304.76539 0 3686.8793 -0.42311295 - 6850 19056.291 510.49927 0 3686.5478 6.9533826 - 6900 20429.82 282.23764 0 3687.2076 -4.2360112 - 6950 21281.278 140.27361 0 3687.1533 -0.07475261 - 7000 17173.388 824.54446 0 3686.7758 10.753828 - 7050 18079.7 674.56274 0 3687.846 12.975804 - 7100 16433.233 950.73904 0 3689.6112 -10.5102 - 7150 19033.335 515.59672 0 3687.8193 0.29109447 - 7200 17286.428 809.02352 0 3690.0948 2.3015698 - 7250 16811.962 886.6645 0 3688.6582 -7.4787512 - 7300 15992.461 1023.4849 0 3688.895 -5.2354222 - 7350 19211.451 487.63129 0 3689.5398 8.4351737 - 7400 19065.682 511.95629 0 3689.57 -12.47448 - 7450 21369.265 128.10098 0 3689.6451 2.2930546 - 7500 16807.109 888.64602 0 3689.8308 14.761969 - 7550 18063.046 679.21873 0 3689.7264 3.8950434 - 7600 17794.987 724.55404 0 3690.3851 14.379016 - 7650 17904.751 706.14354 0 3690.2688 23.813776 - 7700 19670.09 411.3021 0 3689.6504 14.099245 - 7750 18082.562 675.23975 0 3689.0001 15.788521 - 7800 17776.135 726.91445 0 3689.6037 6.9780735 - 7850 17062.575 846.33412 0 3690.0966 -8.9289256 - 7900 19059.2 513.07737 0 3689.6107 16.992843 - 7950 16269.685 978.48914 0 3690.1033 11.180179 - 8000 20115.278 336.91405 0 3689.4604 -6.4882518 - 8050 21173.72 161.15229 0 3690.1056 -2.2164491 - 8100 19238.235 484.42784 0 3690.8004 23.412709 - 8150 18438.4 617.58743 0 3690.6542 0.89156316 - 8200 21438.764 117.12721 0 3690.2546 -1.7193227 - 8250 21195.806 157.66607 0 3690.3003 3.820447 - 8300 21177.549 161.13702 0 3690.7286 0.94938203 - 8350 21060.267 181.06887 0 3691.1135 2.8179025 - 8400 20087.113 343.46206 0 3691.3142 8.1484473 - 8450 19298.478 474.87133 0 3691.2843 -16.239664 - 8500 21654.353 82.083485 0 3691.1423 -8.1464138 - 8550 19920.544 371.34795 0 3691.4386 20.765144 - 8600 21692.293 75.655154 0 3691.0373 -13.316763 - 8650 21231.322 151.8989 0 3690.4526 -11.388238 - 8700 19530.647 434.89585 0 3690.0037 2.7433786 - 8750 19720.63 403.07773 0 3689.8493 -6.416414 - 8800 21321.378 136.04091 0 3689.604 1.3661635 - 8850 19811.906 387.80489 0 3689.7893 3.704143 - 8900 19734.167 400.92444 0 3689.9523 2.5685155 - 8950 21076.459 177.18119 0 3689.9244 -11.939513 - 9000 20967.246 195.42966 0 3689.9707 2.0092705 - 9050 21122.023 169.62103 0 3689.9582 2.3791301 - 9100 20169.346 328.27229 0 3689.8299 -3.5017988 - 9150 21418.641 119.84513 0 3689.6187 2.486073 - 9200 20876.042 210.26452 0 3689.6048 -5.3839897 - 9250 21572.38 93.74407 0 3689.1407 -8.3676952 - 9300 20944.78 197.98577 0 3688.7824 1.3278314 - 9350 20706.52 237.48767 0 3688.5744 4.6944204 - 9400 16412.314 953.47251 0 3688.8581 26.134976 - 9450 20461.68 277.76243 0 3688.0424 17.647445 - 9500 20893.994 205.64261 0 3687.9749 -10.642418 - 9550 20503.447 270.63504 0 3687.8761 -17.769897 - 9600 19677.799 408.05887 0 3687.692 -2.7938604 - 9650 17480.971 774.1855 0 3687.6806 0.59827043 - 9700 17799.126 721.50817 0 3688.0292 44.387928 - 9750 20443.384 280.16837 0 3687.399 3.0619324 - 9800 20545.255 263.40108 0 3687.6102 3.6229381 - 9850 20722.819 233.57142 0 3687.3745 0.86462694 - 9900 21128.462 165.09767 0 3686.508 -6.9636843 - 9950 21343.307 130.46714 0 3687.685 -9.7382705 - 10000 20623.887 250.37866 0 3687.6932 2.7529835 -Loop time of 2.28812 on 1 procs for 10000 steps with 81 atoms - -Performance: 37760.318 tau/day, 4370.407 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.094122 | 0.094122 | 0.094122 | 0.0 | 4.11 -Neigh | 0.076427 | 0.076427 | 0.076427 | 0.0 | 3.34 -Comm | 0.0066867 | 0.0066867 | 0.0066867 | 0.0 | 0.29 -Output | 0.003606 | 0.003606 | 0.003606 | 0.0 | 0.16 -Modify | 2.0986 | 2.0986 | 2.0986 | 0.0 | 91.72 -Other | | 0.008698 | | | 0.38 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 62 ave 62 max 62 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 905 ave 905 max 905 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 905 -Ave neighs/atom = 11.17284 -Neighbor list builds = 991 -Dangerous builds = 927 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems4.g++.4 b/examples/rigid/log.20Mar22.rigid.poems4.g++.4 deleted file mode 100644 index 6240237758..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems4.g++.4 +++ /dev/null @@ -1,328 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems file connected-bodies.dat -1 clusters, 9 bodies, 8 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045742 - 850 17821.483 711.53827 0 3681.7854 7.4384281 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19374 0 3681.3037 11.787982 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184716 - 1150 20849.582 206.01696 0 3680.9472 -0.86699115 - 1200 21815.003 45.317409 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064083 - 1300 20780.781 217.36511 0 3680.8286 6.0538606 - 1350 20558.971 254.36489 0 3680.8601 -3.6773868 - 1400 21485.03 99.812843 0 3680.6511 -16.185479 - 1450 21771.107 52.159652 0 3680.6775 -2.4756656 - 1500 21520.949 93.503872 0 3680.3286 2.1023574 - 1550 21351.419 121.68131 0 3680.2511 5.5159875 - 1600 20778.804 216.92191 0 3680.0559 15.089203 - 1650 21477.636 100.21877 0 3679.8247 -1.104524 - 1700 18501.329 596.48084 0 3680.0357 -15.679806 - 1750 18563.639 587.34841 0 3681.2882 33.532316 - 1800 19110.174 494.82524 0 3679.8543 18.024079 - 1850 21364.178 119.23767 0 3679.9339 2.5290075 - 1900 20146.588 322.15506 0 3679.9197 5.7317368 - 1950 20692.674 231.25288 0 3680.0319 4.2977982 - 2000 20943.904 189.11229 0 3679.7629 -22.643749 - 2050 19667.815 401.87016 0 3679.8394 3.6240972 - 2100 20280.109 299.81759 0 3679.8357 7.4803647 - 2150 19181.146 483.63975 0 3680.4974 22.634167 - 2200 21301.194 130.53171 0 3680.7308 4.7072523 - 2250 20484.79 266.99736 0 3681.1291 -8.6583002 - 2300 18648.002 573.09962 0 3681.1 -5.2548835 - 2350 21515.851 95.225745 0 3681.2009 -9.3875216 - 2400 21462.37 104.21272 0 3681.2744 -29.459857 - 2450 20108.034 330.94394 0 3682.2829 35.37058 - 2500 20771.818 220.42545 0 3682.3951 -12.318936 - 2550 20502.815 265.09577 0 3682.2316 -22.726822 - 2600 21462.006 105.2733 0 3682.2744 -10.180394 - 2650 21009.656 180.72738 0 3682.3367 4.9580828 - 2700 18680.012 569.37179 0 3682.7071 21.114114 - 2750 21256.19 139.42201 0 3682.1203 -7.4744399 - 2800 21552.267 90.071446 0 3682.1159 -6.2906304 - 2850 20879.958 202.00905 0 3682.0021 0.57990903 - 2900 19018.645 512.35214 0 3682.1262 13.883084 - 2950 19819.365 378.55747 0 3681.785 -0.7348943 - 3000 20269.229 303.35149 0 3681.5563 6.3088075 - 3050 19236.727 475.99457 0 3682.1158 -10.703575 - 3100 18391.55 616.96976 0 3682.2281 9.850079 - 3150 20258.563 305.82076 0 3682.248 7.1951283 - 3200 20716.384 229.15502 0 3681.8856 2.9042294 - 3250 18662.237 572.0784 0 3682.4512 9.2108597 - 3300 19162.278 488.60646 0 3682.3195 3.3306562 - 3350 21235.679 142.98279 0 3682.2626 0.29397483 - 3400 17677.053 736.09247 0 3682.2679 32.75269 - 3450 20852.392 206.65618 0 3682.0548 -4.8319056 - 3500 21182.918 151.46754 0 3681.9539 -5.6330382 - 3550 20589.85 250.40724 0 3682.049 12.582133 - 3600 20973.659 186.28043 0 3681.8903 10.935266 - 3650 17838.632 707.92145 0 3681.0268 -17.200926 - 3700 21538.002 92.744409 0 3682.4114 -0.72124229 - 3750 21390.294 117.90865 0 3682.9576 -7.8431786 - 3800 17921.046 696.50311 0 3683.344 -9.4641531 - 3850 20356.471 290.22624 0 3682.9715 2.4593463 - 3900 20374.077 287.10249 0 3682.782 -1.9519082 - 3950 20563.915 255.29993 0 3682.619 -6.124649 - 4000 20991.467 184.76183 0 3683.3397 1.8954961 - 4050 17805.623 716.24698 0 3683.8509 -20.454944 - 4100 19916.389 363.86301 0 3683.2611 -0.27912557 - 4150 19221.623 480.01232 0 3683.6161 -11.562492 - 4200 20526.82 261.78571 0 3682.9224 -3.9522917 - 4250 20922.813 196.1799 0 3683.3154 0.11947446 - 4300 19956.66 357.78133 0 3683.8914 19.156093 - 4350 19735.73 394.45981 0 3683.7482 14.865775 - 4400 21702.656 67.099805 0 3684.2092 -13.502538 - 4450 18163.055 656.97231 0 3684.1482 -0.6243111 - 4500 17477.718 771.25976 0 3684.2127 -0.4664004 - 4550 20676.507 238.19814 0 3684.2827 -19.444969 - 4600 17322.922 796.77058 0 3683.9242 27.003966 - 4650 11905.158 1704.9151 0 3689.1082 15.574169 - 4700 18689.079 569.80982 0 3684.6563 -14.67311 - 4750 19821.745 381.01914 0 3684.6433 5.0436795 - 4800 20621.335 247.96269 0 3684.8518 -16.407263 - 4850 21923.814 30.965964 0 3684.935 -13.418244 - 4900 18840.555 544.41538 0 3684.5079 11.005357 - 4950 15366.601 1124.2481 0 3685.3482 17.412375 - 5000 18274.314 639.01311 0 3684.732 5.3261109 - 5050 21173.687 155.83673 0 3684.7845 5.4056809 - 5100 21738.219 61.75201 0 3684.7885 -2.631945 - 5150 16597.949 918.84841 0 3685.1732 -10.124101 - 5200 20752.758 225.95919 0 3684.7522 -5.2441372 - 5250 17652.088 741.2645 0 3683.2793 2.0080739 - 5300 19907.523 366.53115 0 3684.4516 8.4266792 - 5350 20104.189 334.14522 0 3684.8433 17.21925 - 5400 21499.848 101.71631 0 3685.0243 -6.1103541 - 5450 21203.533 151.14574 0 3685.068 -5.9468503 - 5500 21076.513 172.45652 0 3685.2088 5.1418181 - 5550 20158.398 325.56609 0 3685.2992 -1.6486034 - 5600 20787.836 221.19563 0 3685.835 -10.66805 - 5650 19687.154 404.77204 0 3685.9644 -23.49128 - 5700 20419.311 282.58328 0 3685.8017 -0.52808211 - 5750 19738.522 395.95893 0 3685.7126 1.3889817 - 5800 18300.025 635.66905 0 3685.6732 23.490447 - 5850 20585.004 255.02032 0 3685.8543 -0.20699939 - 5900 20373.839 290.15881 0 3685.7987 -7.9712187 - 5950 18163.832 659.91192 0 3687.2173 5.4494586 - 6000 21049.247 177.43029 0 3685.6382 2.9138342 - 6050 21239.803 145.77613 0 3685.7433 -1.4927769 - 6100 20686.361 237.86454 0 3685.5913 -0.95516297 - 6150 20461.754 275.31546 0 3685.6079 -3.4166412 - 6200 19264.208 474.73017 0 3685.4316 11.750757 - 6250 21180.813 155.31746 0 3685.4529 2.8188219 - 6300 21047.543 177.4394 0 3685.3632 1.8641486 - 6350 20232.576 313.17716 0 3685.2731 2.8150209 - 6400 20185.616 321.33454 0 3685.6038 -3.8697311 - 6450 18969.632 523.95865 0 3685.5639 0.6725512 - 6500 17592.574 753.49959 0 3685.5952 -1.2557393 - 6550 21279.049 138.42524 0 3684.9335 -1.208945 - 6600 21408.457 116.4143 0 3684.4904 -1.5332953 - 6650 19758.218 391.17316 0 3684.2096 1.8511312 - 6700 20766.943 223.44631 0 3684.6036 -2.3672623 - 6750 20399.631 284.09914 0 3684.0377 -5.4089876 - 6800 21296.628 135.14662 0 3684.5847 -3.8442549 - 6850 20641.481 244.4451 0 3684.692 1.4020639 - 6900 20852.81 209.23009 0 3684.6984 1.8512104 - 6950 20940.555 194.66882 0 3684.7614 -6.554676 - 7000 19496.988 435.28199 0 3684.78 -15.120269 - 7050 19796.829 385.04227 0 3684.5138 -4.1068804 - 7100 19945.264 360.42431 0 3684.635 -4.0629042 - 7150 19431.123 446.12911 0 3684.6497 -6.8321751 - 7200 16864.851 873.80043 0 3684.6089 14.309069 - 7250 20438.75 277.85982 0 3684.3181 -11.41223 - 7300 17688.684 734.01576 0 3682.1298 35.938373 - 7350 21573.419 88.63421 0 3684.204 -3.9032749 - 7400 21198.486 150.72249 0 3683.8034 -7.1477117 - 7450 20586.708 252.93928 0 3684.0572 -7.6634645 - 7500 21815.377 48.180377 0 3684.0765 0.97457507 - 7550 17791.352 718.87564 0 3684.101 28.248235 - 7600 21828.874 45.928597 0 3684.0742 -0.25814944 - 7650 20827.961 212.35674 0 3683.6835 -3.4083384 - 7700 21319.176 130.43547 0 3683.6315 -12.434856 - 7750 20127.904 328.69643 0 3683.3471 -16.975711 - 7800 21741.772 59.679206 0 3683.3078 3.6261863 - 7850 19612.334 414.37418 0 3683.0964 1.3763274 - 7900 20071.318 337.74624 0 3682.9658 -0.40982763 - 7950 17925.664 695.29582 0 3682.9065 17.104439 - 8000 19125.978 492.76383 0 3680.4268 10.807662 - 8050 20233.848 310.42681 0 3682.7347 13.386237 - 8100 20551.619 257.86699 0 3683.1368 -13.97515 - 8150 21578.323 86.88362 0 3683.2708 -9.6811587 - 8200 21154.833 157.72897 0 3683.5344 0.62312375 - 8250 21321.143 129.83967 0 3683.3636 1.9536438 - 8300 21041.696 176.04177 0 3682.9911 4.7475567 - 8350 19883.39 369.32649 0 3683.2247 -7.0959328 - 8400 21626.067 79.062992 0 3683.4075 -14.919059 - 8450 21375.201 120.86836 0 3683.4019 -5.3461514 - 8500 20281.059 303.10304 0 3683.2796 3.7975093 - 8550 21170.533 154.48432 0 3682.9065 -1.1568561 - 8600 17754.931 724.00158 0 3683.1568 14.15254 - 8650 20685.478 235.65879 0 3683.2385 -5.2694179 - 8700 21489.165 101.90509 0 3683.4326 -4.2510612 - 8750 21106.682 165.41638 0 3683.1968 -3.9186708 - 8800 19149.516 491.5843 0 3683.1702 -11.419849 - 8850 21451.865 108.1814 0 3683.4923 -7.8256219 - 8900 19567.4 421.81206 0 3683.0454 -0.71997056 - 8950 20934.097 194.48033 0 3683.4965 -7.0106879 - 9000 18531.559 595.25957 0 3683.8528 3.7449399 - 9050 18868.821 537.22549 0 3682.029 9.9926092 - 9100 19972.527 354.73119 0 3683.4858 -0.30871263 - 9150 19641.651 409.18618 0 3682.7947 -1.3036238 - 9200 20019.08 346.19657 0 3682.7099 6.7425386 - 9250 19259.286 473.04973 0 3682.9308 -24.120659 - 9300 21597.757 82.971857 0 3682.598 -13.748483 - 9350 19348.379 457.23576 0 3681.9656 3.1571402 - 9400 19129.588 493.35235 0 3681.617 8.6293783 - 9450 20337.025 291.20959 0 3680.7138 6.8590795 - 9500 20581.788 249.65891 0 3679.9569 -18.892836 - 9550 19482.069 433.0077 0 3680.0192 23.029778 - 9600 19182.794 482.96871 0 3680.101 -11.081731 - 9650 20086.771 332.5311 0 3680.3263 -18.939681 - 9700 20274.046 300.98818 0 3679.9959 6.7538762 - 9750 18743.595 555.08045 0 3679.0129 8.2757138 - 9800 19464.311 435.66288 0 3679.7148 7.0528759 - 9850 21249.848 138.27382 0 3679.9152 -10.847402 - 9900 21156.214 153.84621 0 3679.8819 -7.8359674 - 9950 21643.134 72.547515 0 3679.7365 -10.507744 - 10000 19587.948 414.64942 0 3679.3075 6.1173553 -Loop time of 2.35562 on 4 procs for 10000 steps with 81 atoms - -Performance: 36678.236 tau/day, 4245.166 timesteps/s -99.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0055581 | 0.024882 | 0.055326 | 12.0 | 1.06 -Neigh | 0.0073809 | 0.022107 | 0.043683 | 9.2 | 0.94 -Comm | 0.12484 | 0.14528 | 0.1833 | 6.2 | 6.17 -Output | 0.0035526 | 0.0041048 | 0.0055462 | 1.3 | 0.17 -Modify | 2.1078 | 2.1414 | 2.162 | 1.5 | 90.91 -Other | | 0.0178 | | | 0.76 - -Nlocal: 20.25 ave 81 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 41 ave 78 max 11 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Neighs: 193.5 ave 774 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 774 -Ave neighs/atom = 9.5555556 -Neighbor list builds = 989 -Dangerous builds = 915 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems5.g++.1 b/examples/rigid/log.20Mar22.rigid.poems5.g++.1 deleted file mode 100644 index 5a18042516..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems5.g++.1 +++ /dev/null @@ -1,329 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems file connected-bodies2.dat -2 clusters, 9 bodies, 7 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12774.759 1538.7382 0 3904.4344 18.086359 - 100 19803.641 237.21132 0 3904.5523 -3.1528278 - 150 20259.6 152.62072 0 3904.3985 -4.6173524 - 200 20705.978 69.977442 0 3904.4178 9.0928158 - 250 19552.211 283.50525 0 3904.285 15.670465 - 300 19266.324 333.5792 0 3901.4169 7.2119197 - 350 20738.325 63.738945 0 3904.1694 -23.03999 - 400 20616.682 86.082444 0 3903.9864 -13.783584 - 450 19831.326 230.13858 0 3902.6063 0.42074361 - 500 20365.825 131.47231 0 3902.9213 0.6921524 - 550 20794.102 52.163238 0 3902.9229 4.5895354 - 600 20853.873 40.899172 0 3902.7275 2.3593042 - 650 19255.802 336.29509 0 3902.1844 10.341742 - 700 18526.969 471.02462 0 3901.9448 -0.61898691 - 750 18960.662 391.26068 0 3902.4944 12.04731 - 800 20142.432 172.05177 0 3902.1317 4.6838621 - 850 19932.48 210.71175 0 3901.9118 3.4716043 - 900 20243.528 153.13972 0 3901.9411 3.6490762 - 950 20388.132 126.88722 0 3902.4671 -4.4518463 - 1000 20076.333 184.61915 0 3902.4586 -2.272315 - 1050 20859.506 39.696993 0 3902.5684 6.45166 - 1100 15284.661 1072.1908 0 3902.6836 21.194042 - 1150 19658.317 261.99809 0 3902.4272 -2.874422 - 1200 20767.681 56.717094 0 3902.5839 -34.817444 - 1250 20625.583 82.586399 0 3902.1388 11.697329 - 1300 20690.013 71.006478 0 3902.4903 -29.292777 - 1350 20936.019 26.022786 0 3903.0634 1.0316025 - 1400 19753.559 244.81785 0 3902.8844 6.7138514 - 1450 15690.149 998.342 0 3903.9252 48.124557 - 1500 20234.455 155.92516 0 3903.0465 13.17221 - 1550 20779.631 55.063009 0 3903.1428 -2.639045 - 1600 20642.753 80.233905 0 3902.9659 -2.4688467 - 1650 18785.696 423.90402 0 3902.7365 -5.6466663 - 1700 20965.076 20.760444 0 3903.182 -0.45364296 - 1750 18935.406 396.96067 0 3903.5173 25.913302 - 1800 20581.559 91.756972 0 3903.1567 3.8217234 - 1850 20616.946 85.184849 0 3903.1378 4.1907972 - 1900 16602.053 828.40949 0 3902.8637 -0.49505122 - 1950 20175.526 166.53362 0 3902.7421 5.603825 - 2000 20261.924 150.39322 0 3902.6014 -1.196958 - 2050 20170.339 167.40504 0 3902.6531 -0.80849882 - 2100 19820.132 231.26755 0 3901.6624 3.1476607 - 2150 20666.19 75.838461 0 3902.9106 0.53899287 - 2200 19873.51 222.53286 0 3902.8124 7.9310276 - 2250 18548.063 467.69698 0 3902.5235 16.905356 - 2300 20616.61 84.762399 0 3902.6531 -6.7872951 - 2350 18167.738 538.13635 0 3902.5322 -11.458285 - 2400 20120.227 177.01954 0 3902.9875 -1.2593018 - 2450 20436.599 118.32469 0 3902.8801 -6.5989174 - 2500 18919.923 400.26361 0 3903.9531 32.37476 - 2550 19675.809 259.77151 0 3903.4398 19.437327 - 2600 19739.842 247.86388 0 3903.3901 -7.519784 - 2650 20557.026 96.530313 0 3903.387 0.60211646 - 2700 20666.602 76.099892 0 3903.2484 0.16825503 - 2750 20924.585 28.453883 0 3903.3771 2.4227171 - 2800 20360.659 132.8596 0 3903.352 4.1440877 - 2850 20783.475 54.518625 0 3903.3102 -0.57312067 - 2900 20456.181 115.03745 0 3903.2191 -20.118887 - 2950 20779.493 55.321394 0 3903.3756 -0.26783079 - 3000 20011.867 197.30216 0 3903.2035 -1.4704201 - 3050 20741.875 62.208723 0 3903.2966 -7.5432815 - 3100 21001.754 14.148298 0 3903.362 2.9676438 - 3150 20244.086 154.44639 0 3903.3512 -1.9071213 - 3200 20639.615 81.136426 0 3903.2873 1.4826467 - 3250 20735.244 63.529571 0 3903.3895 2.1127055 - 3300 20142.891 173.22282 0 3903.3878 4.7739415 - 3350 19963.765 206.21899 0 3903.2126 5.5410771 - 3400 16628.667 824.13627 0 3903.519 36.087673 - 3450 19228.218 342.81569 0 3903.5968 3.1057274 - 3500 19759.293 244.57876 0 3903.707 2.2339557 - 3550 19853.21 227.06362 0 3903.584 -1.0882119 - 3600 19673.516 260.64854 0 3903.8923 -10.63775 - 3650 19619.238 270.5393 0 3903.7316 -6.3746003 - 3700 20756.865 59.790243 0 3903.6542 -8.3015766 - 3750 20265.025 150.47347 0 3903.2559 -5.7284695 - 3800 20944.683 24.669276 0 3903.3142 -0.070552298 - 3850 19344.831 320.59492 0 3902.971 13.040749 - 3900 19978.209 203.00247 0 3902.6708 0.15638133 - 3950 19864.118 224.19359 0 3902.734 0.453229 - 4000 17606.216 642.71493 0 3903.1252 -12.656002 - 4050 18017.895 566.54102 0 3903.1883 12.133906 - 4100 20092.963 182.17593 0 3903.095 7.7445947 - 4150 20555.337 96.395074 0 3902.939 -6.5429752 - 4200 20709.781 67.869199 0 3903.0138 -2.8653003 - 4250 18956.203 392.20748 0 3902.6155 -1.6249728 - 4300 17816.204 603.72704 0 3903.0241 23.089239 - 4350 18979.742 388.04678 0 3902.8138 3.2511108 - 4400 20272.085 148.82367 0 3902.9135 1.9518268 - 4450 18820.003 417.74789 0 3902.9337 6.3979299 - 4500 19991.936 200.50131 0 3902.7117 3.5118553 - 4550 20915.092 29.663898 0 3902.8291 -2.3174641 - 4600 20690.37 71.125087 0 3902.6752 -12.008575 - 4650 18893.76 404.50849 0 3903.3529 15.006184 - 4700 18611.123 456.1263 0 3902.6306 -5.3574892 - 4750 20497.821 106.5856 0 3902.4784 0.85039837 - 4800 20803.214 50.120522 0 3902.5675 3.8610873 - 4850 18849.598 411.72635 0 3902.3927 9.2029058 - 4900 18121.714 546.68042 0 3902.5533 9.4522272 - 4950 20377.499 128.99323 0 3902.6041 5.3825395 - 5000 20686.114 72.039749 0 3902.8016 -5.706271 - 5050 20180.449 165.51368 0 3902.634 -16.418461 - 5100 20274.947 148.36657 0 3902.9864 -5.6668309 - 5150 18042.324 560.74137 0 3901.9125 3.6791541 - 5200 20794.666 52.204446 0 3903.0685 -1.4517721 - 5250 19073.55 371.18834 0 3903.3272 -13.457439 - 5300 20821.412 47.364313 0 3903.1813 2.258098 - 5350 20583.073 91.271191 0 3902.9513 5.4323985 - 5400 20490.967 108.41184 0 3903.0353 4.122905 - 5450 18141.79 543.66874 0 3903.2594 -0.19951075 - 5500 20274.012 148.55528 0 3903.002 5.0489974 - 5550 17806.237 605.43454 0 3902.8858 43.80619 - 5600 20999.825 14.341937 0 3903.1983 1.0879933 - 5650 20930.929 27.025347 0 3903.1234 -7.0860209 - 5700 20677.725 73.853093 0 3903.0614 2.6864775 - 5750 20521.264 102.87509 0 3903.1092 2.6940548 - 5800 20792.571 52.596021 0 3903.0721 1.2910217 - 5850 20518.674 103.26595 0 3903.0204 -9.2547271 - 5900 18417.885 491.66696 0 3902.3865 -12.049357 - 5950 17243.837 709.37858 0 3902.6817 -6.2357188 - 6000 20262.525 149.56918 0 3901.8885 -0.28964823 - 6050 19883.554 219.14043 0 3901.2801 2.3071707 - 6100 16548.178 838.47869 0 3902.956 -11.715644 - 6150 19601.177 272.14674 0 3901.9944 -0.9008056 - 6200 20499.796 106.2363 0 3902.4949 0.79071424 - 6250 19601.106 272.50139 0 3902.3359 -1.9306693 - 6300 17210.685 712.70535 0 3899.8692 4.8890923 - 6350 19911.896 214.91041 0 3902.2985 12.691129 - 6400 18834.642 411.87123 0 3899.7678 -1.9447856 - 6450 20216.311 158.39781 0 3902.1591 2.6009109 - 6500 20452.025 114.97122 0 3902.3832 0.14644416 - 6550 19142.589 357.34097 0 3902.2649 2.8968485 - 6600 20412.915 122.08784 0 3902.2573 3.1343105 - 6650 17317.867 699.39994 0 3906.4123 42.25563 - 6700 20479.771 109.8036 0 3902.3537 1.3520625 - 6750 20306.902 142.12484 0 3902.6623 2.2032106 - 6800 20755.367 58.994834 0 3902.5814 -0.90518094 - 6850 20471.259 111.7197 0 3902.6936 1.5799331 - 6900 20702.025 69.15032 0 3902.8586 9.3910371 - 6950 20477.695 110.34414 0 3902.5099 1.8181164 - 7000 20560.727 95.057704 0 3902.5998 -15.686006 - 7050 20336.675 136.39386 0 3902.4448 1.3704327 - 7100 20757.399 58.950153 0 3902.913 -6.4250981 - 7150 20870.958 38.095649 0 3903.088 -4.1962169 - 7200 20706.869 68.489134 0 3903.0944 2.8322659 - 7250 20386.713 127.7432 0 3903.0604 6.0287391 - 7300 18391.773 497.21001 0 3903.0939 19.202343 - 7350 20178.898 166.4993 0 3903.3322 1.5682417 - 7400 16858.704 781.78682 0 3903.7691 21.317514 - 7450 17509.513 660.71963 0 3903.2221 -5.9456143 - 7500 19974.601 204.20412 0 3903.2043 -0.69202711 - 7550 20917.053 29.73415 0 3903.2626 -3.9962577 - 7600 20923.518 28.482703 0 3903.2083 -1.9016251 - 7650 20549.528 97.630612 0 3903.0987 3.5512257 - 7700 20861.441 39.903885 0 3903.1337 2.4426264 - 7750 18843.349 413.64461 0 3903.1537 2.677739 - 7800 20616.054 85.214364 0 3903.0021 3.9639004 - 7850 16478.851 851.93376 0 3903.5728 7.3763128 - 7900 20312.115 141.35103 0 3902.8539 4.6707271 - 7950 20389.623 127.16589 0 3903.0219 3.4414001 - 8000 20452.117 115.30715 0 3902.7362 -1.0162528 - 8050 20857.093 40.791886 0 3903.2164 -15.150068 - 8100 19817.543 233.4997 0 3903.415 0.89346046 - 8150 18649.521 449.9112 0 3903.5262 -0.40053588 - 8200 19619.276 270.37616 0 3903.5754 5.5161492 - 8250 20393.176 127.01336 0 3903.5275 2.122613 - 8300 19145.912 358.00424 0 3903.5435 3.863924 - 8350 19636.311 267.17226 0 3903.5262 -7.1496084 - 8400 19086.332 368.86693 0 3903.3729 7.0968952 - 8450 19494.416 292.89527 0 3902.9723 3.1750935 - 8500 20041.919 191.77756 0 3903.244 0.95215503 - 8550 20357.561 133.15478 0 3903.0736 -0.14020152 - 8600 16998.797 756.07003 0 3903.9954 -16.724408 - 8650 20853.26 41.386996 0 3903.1017 -3.2612965 - 8700 20767.768 57.360884 0 3903.2438 1.1157649 - 8750 20752.546 60.106518 0 3903.1705 0.39130547 - 8800 20574.407 92.99798 0 3903.0734 0.61728166 - 8850 20326.99 138.94203 0 3903.1995 -1.9434522 - 8900 17408.108 679.53222 0 3903.2559 21.935371 - 8950 20471.21 112.2721 0 3903.2368 1.8142747 - 9000 19129.591 360.35257 0 3902.8694 4.5786395 - 9050 20439.668 117.89541 0 3903.0191 2.5585685 - 9100 20780.375 54.788664 0 3903.0062 3.8312459 - 9150 19904.559 216.61504 0 3902.6445 12.150414 - 9200 20961.295 21.52065 0 3903.2419 -0.2120699 - 9250 19315.252 326.44175 0 3903.3402 -19.740867 - 9300 20653.002 78.77764 0 3903.4076 -7.8068233 - 9350 18961.572 391.20947 0 3902.6117 -12.660843 - 9400 16262.179 892.67633 0 3904.191 22.2435 - 9450 17064.394 743.33301 0 3903.406 36.139436 - 9500 18075.588 555.06436 0 3902.3954 24.598176 - 9550 20487.738 109.06287 0 3903.0884 2.6320759 - 9600 20358.609 133.36993 0 3903.4828 0.76449113 - 9650 19849.022 228.46312 0 3904.208 9.5547064 - 9700 20448.112 116.8757 0 3903.5632 -1.0845697 - 9750 20472.78 112.51661 0 3903.7722 -0.30676738 - 9800 19491.99 293.35361 0 3902.9814 -20.10857 - 9850 19895.603 218.42479 0 3902.7957 -0.18235641 - 9900 19704.336 254.55068 0 3903.5019 14.553184 - 9950 17689.462 627.9788 0 3903.805 4.9918088 - 10000 20184.205 165.29396 0 3903.1097 2.9472364 -Loop time of 2.28393 on 1 procs for 10000 steps with 81 atoms - -Performance: 37829.498 tau/day, 4378.414 timesteps/s -99.3% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.052911 | 0.052911 | 0.052911 | 0.0 | 2.32 -Neigh | 0.056658 | 0.056658 | 0.056658 | 0.0 | 2.48 -Comm | 0.0087389 | 0.0087389 | 0.0087389 | 0.0 | 0.38 -Output | 0.0037996 | 0.0037996 | 0.0037996 | 0.0 | 0.17 -Modify | 2.1537 | 2.1537 | 2.1537 | 0.0 | 94.30 -Other | | 0.008147 | | | 0.36 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 113 ave 113 max 113 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 582 ave 582 max 582 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 582 -Ave neighs/atom = 7.1851852 -Neighbor list builds = 993 -Dangerous builds = 950 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems5.g++.4 b/examples/rigid/log.20Mar22.rigid.poems5.g++.4 deleted file mode 100644 index cbf8b05490..0000000000 --- a/examples/rigid/log.20Mar22.rigid.poems5.g++.4 +++ /dev/null @@ -1,329 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems file connected-bodies2.dat -2 clusters, 9 bodies, 7 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: - -@Article{Mukherjee08, - author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, - title = {Substructured molecular dynamics using multibody dynamics algorithms}, - journal = {Intl.~J.~Non-linear Mechanics}, - year = 2008, - volume = 43, - pages = {1045--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12774.759 1538.7382 0 3904.4344 18.086358 - 100 19803.641 237.21132 0 3904.5523 -3.1528278 - 150 20259.6 152.62072 0 3904.3985 -4.6173524 - 200 20705.978 69.977039 0 3904.4174 9.0928122 - 250 19552.211 283.50525 0 3904.285 15.670466 - 300 19266.324 333.5792 0 3901.4169 7.2119197 - 350 20738.325 63.738945 0 3904.1694 -23.03999 - 400 20616.682 86.082444 0 3903.9864 -13.783584 - 450 19831.326 230.13858 0 3902.6063 0.42074361 - 500 20365.825 131.47271 0 3902.9217 0.69215592 - 550 20794.102 52.163238 0 3902.9229 4.5895354 - 600 20853.873 40.899172 0 3902.7275 2.3593042 - 650 19255.802 336.29509 0 3902.1844 10.341742 - 700 18526.969 471.02462 0 3901.9448 -0.61898691 - 750 18960.662 391.26068 0 3902.4944 12.04731 - 800 20142.432 172.05197 0 3902.1319 4.6838632 - 850 19932.48 210.71175 0 3901.9118 3.4716031 - 900 20243.528 153.13972 0 3901.9411 3.6490762 - 950 20388.132 126.88722 0 3902.4671 -4.4518463 - 1000 20076.333 184.61915 0 3902.4586 -2.272315 - 1050 20859.506 39.696993 0 3902.5684 6.45166 - 1100 15284.661 1072.1908 0 3902.6836 21.194042 - 1150 19658.317 261.99809 0 3902.4272 -2.8744219 - 1200 20767.681 56.717095 0 3902.5839 -34.817444 - 1250 20625.583 82.586198 0 3902.1386 11.697328 - 1300 20690.013 71.006478 0 3902.4903 -29.29278 - 1350 20936.019 26.022786 0 3903.0634 1.0316025 - 1400 19753.56 244.81784 0 3902.8844 6.7138497 - 1450 15690.149 998.34213 0 3903.9252 48.124569 - 1500 20234.455 155.92516 0 3903.0465 13.172207 - 1550 20779.631 55.063019 0 3903.1428 -2.6390455 - 1600 20642.753 80.233821 0 3902.9659 -2.4688431 - 1650 18785.698 423.90364 0 3902.7365 -5.6466892 - 1700 20965.076 20.760451 0 3903.182 -0.45366172 - 1750 18935.412 396.95958 0 3903.5173 25.913174 - 1800 20581.554 91.757912 0 3903.1567 3.8218442 - 1850 20616.949 85.184789 0 3903.1382 4.1907933 - 1900 16601.896 828.43849 0 3902.8638 -0.49468175 - 1950 20175.564 166.52646 0 3902.7421 5.6035728 - 2000 20262.525 150.28224 0 3902.6017 -1.1967705 - 2050 20168.994 167.65314 0 3902.6521 -0.80723928 - 2100 19810.955 232.96524 0 3901.6605 3.1936531 - 2150 20667.232 75.645145 0 3902.9103 0.54812734 - 2200 19863.772 224.34646 0 3902.8228 7.9294465 - 2250 18808.943 419.2084 0 3902.3461 14.344526 - 2300 20573.665 92.761842 0 3902.6999 -6.7671703 - 2350 19075.104 369.95414 0 3902.3809 -9.5353568 - 2400 20273.873 148.53775 0 3902.9586 -1.93796 - 2450 20087.769 182.30216 0 3902.2593 2.131796 - 2500 20711.602 67.530554 0 3903.0124 2.6280244 - 2550 19971.224 204.75926 0 3903.134 3.1760522 - 2600 20620.084 85.027145 0 3903.5612 -0.92888063 - 2650 19737.546 248.65474 0 3903.7559 -3.3218688 - 2700 20650.724 79.522243 0 3903.7303 -7.5918025 - 2750 19863.245 225.2505 0 3903.6292 9.2140221 - 2800 18992.457 386.73547 0 3903.8572 2.6244537 - 2850 18703.899 440.48356 0 3904.1685 14.561348 - 2900 17939.805 581.74599 0 3903.932 -8.0863089 - 2950 20867.516 39.38186 0 3903.7367 3.0985423 - 3000 19767.994 242.8847 0 3903.6243 1.5943109 - 3050 20397.448 126.31591 0 3903.6212 -0.14982775 - 3100 20978.114 19.126395 0 3903.9623 -9.6797253 - 3150 18303.556 513.8514 0 3903.3989 4.5940322 - 3200 19156.505 356.46608 0 3903.9671 10.071308 - 3250 17484.205 666.52199 0 3904.3377 -4.1641768 - 3300 18069.94 557.75947 0 3904.0447 11.868707 - 3350 20855.645 41.964632 0 3904.1212 5.4186293 - 3400 18011.986 568.76255 0 3904.3155 25.262783 - 3450 18669.69 446.92755 0 3904.2776 -4.194499 - 3500 20248.799 154.22147 0 3903.9991 3.9211572 - 3550 20226.024 158.64726 0 3904.2072 1.5299114 - 3600 20267.02 151.25631 0 3904.4082 -8.9821729 - 3650 20522.946 103.65382 0 3904.1994 -14.433796 - 3700 20892.319 35.294614 0 3904.2426 -21.264596 - 3750 19942.202 211.02993 0 3904.0304 -1.6428817 - 3800 20421.678 122.08118 0 3903.8734 1.7137935 - 3850 17899.53 588.82593 0 3903.5536 -24.450276 - 3900 20721.119 66.486999 0 3903.7312 -7.1772088 - 3950 20946.484 24.799445 0 3903.778 -0.4028037 - 4000 20985.362 17.608355 0 3903.7865 4.7522266 - 4050 19969.779 205.46466 0 3903.5719 18.941639 - 4100 20479.578 110.56561 0 3903.08 2.3715952 - 4150 18110.701 549.53348 0 3903.367 1.133321 - 4200 19321.098 325.58216 0 3903.5634 -3.7574942 - 4250 20734.436 63.87616 0 3903.5865 0.48350623 - 4300 19446.823 302.1727 0 3903.4362 4.0462392 - 4350 20494.669 108.1918 0 3903.501 2.9789077 - 4400 20379.244 129.61413 0 3903.5482 4.0881089 - 4450 19710.564 253.4251 0 3903.5295 5.3334683 - 4500 20744.753 61.785082 0 3903.406 4.0015409 - 4550 19948.024 208.76984 0 3902.8484 2.705423 - 4600 18367.368 502.69569 0 3904.0602 21.476471 - 4650 20559.367 96.133242 0 3903.4234 2.2549454 - 4700 20940.135 25.547808 0 3903.3505 -8.9042666 - 4750 20128.703 175.82088 0 3903.3584 -8.1450176 - 4800 20632.27 82.543887 0 3903.3347 -0.55649542 - 4850 19864.539 224.63792 0 3903.2563 7.1553461 - 4900 19332.037 323.15561 0 3903.1625 17.020214 - 4950 19055.575 373.68069 0 3902.4908 10.149457 - 5000 20219.484 159.21383 0 3903.5627 3.1806346 - 5050 17557.761 652.32864 0 3903.7659 10.733736 - 5100 20615.337 85.795304 0 3903.4503 -3.6035636 - 5150 20759.853 59.155843 0 3903.573 2.0152286 - 5200 20082.007 184.39375 0 3903.2839 -5.3745109 - 5250 18689.521 442.59842 0 3903.6208 -9.8911164 - 5300 20038.496 192.34221 0 3903.1749 -2.1437039 - 5350 19897.455 218.70142 0 3903.4154 0.64582116 - 5400 18732.385 434.21543 0 3903.1755 12.98676 - 5450 19831.487 230.79099 0 3903.2886 11.439958 - 5500 20079.89 184.6953 0 3903.1935 4.0906279 - 5550 20453.497 115.47128 0 3903.1559 7.8844436 - 5600 16673.041 815.52661 0 3903.1267 -20.17797 - 5650 19691.378 256.6412 0 3903.1928 3.7103317 - 5700 20345.743 135.29997 0 3903.0302 5.6373816 - 5750 20769.613 56.906603 0 3903.1312 -17.564762 - 5800 20713.369 67.38314 0 3903.1922 -5.340631 - 5850 20799.947 51.348865 0 3903.1909 -2.7827653 - 5900 19581.933 273.51588 0 3899.7997 12.347375 - 5950 20444.438 116.909 0 3902.9161 -0.74896654 - 6000 18970.948 389.99664 0 3903.1352 26.642912 - 6050 19414.753 307.13217 0 3902.4568 25.86316 - 6100 20780.042 54.586474 0 3902.7424 1.5387425 - 6150 20885.872 35.091585 0 3902.8456 -8.251884 - 6200 19825.81 231.40943 0 3902.8558 6.7196589 - 6250 20578.278 92.255994 0 3903.0481 -5.9647091 - 6300 20093.43 181.8699 0 3902.8754 -9.9906069 - 6350 20605.294 87.180289 0 3902.9755 -3.5643876 - 6400 19737.257 247.84828 0 3902.8958 -4.2783347 - 6450 19884.717 220.81633 0 3903.1714 3.8758905 - 6500 18719.372 436.94802 0 3903.4984 1.7865904 - 6550 20096.883 181.63346 0 3903.2784 2.395512 - 6600 20888.673 35.003062 0 3903.2758 2.7728947 - 6650 20437.85 118.16373 0 3902.9507 8.1456757 - 6700 19241.051 339.73065 0 3902.8882 13.740454 - 6750 20407.542 123.94326 0 3903.1177 7.6285942 - 6800 20536.785 99.976706 0 3903.0851 8.3496632 - 6850 20625.328 83.579677 0 3903.0849 6.5074992 - 6900 20705.37 68.944625 0 3903.2724 3.1905177 - 6950 18872.424 408.67134 0 3903.5647 6.2638845 - 7000 20072.762 186.18051 0 3903.3586 -22.780407 - 7050 20461.879 114.07495 0 3903.3117 -11.495523 - 7100 19811.566 234.50237 0 3903.3108 1.1212695 - 7150 20742.918 61.884088 0 3903.1651 -3.7907508 - 7200 20911.192 30.599903 0 3903.0429 -7.0262304 - 7250 20879.755 36.30274 0 3902.9241 -5.8018787 - 7300 20682.32 72.703261 0 3902.7626 -3.3446789 - 7350 19401.046 309.70672 0 3902.493 3.4836528 - 7400 20220.542 157.83897 0 3902.3838 2.3400031 - 7450 17691.193 625.47764 0 3901.6244 25.239568 - 7500 19745.294 245.02566 0 3901.5615 5.3622843 - 7550 19685.719 256.70983 0 3902.2133 3.4560563 - 7600 18830.192 415.10021 0 3902.1727 -0.10282681 - 7650 19613.136 270.18979 0 3902.2521 8.2241536 - 7700 20989.015 15.636879 0 3902.4915 1.2955204 - 7750 20301.583 142.90625 0 3902.4586 0.12548373 - 7800 18360.147 502.50342 0 3902.5307 17.117272 - 7850 20796.478 51.032537 0 3902.2321 -3.0993883 - 7900 20284.267 145.64296 0 3901.9887 -1.2682383 - 7950 20280.983 146.13471 0 3901.8723 3.5999841 - 8000 20915.869 28.730821 0 3902.0399 2.4987291 - 8050 20745.162 60.19981 0 3901.8964 4.0643481 - 8100 20509.039 103.70462 0 3901.6748 1.0771863 - 8150 20212.97 158.64893 0 3901.7916 3.0000215 - 8200 20323.463 138.25912 0 3901.8634 -1.2802945 - 8250 19997.284 198.37183 0 3901.5727 -2.6431964 - 8300 20138.402 171.75824 0 3901.092 1.7669897 - 8350 20367.568 130.22531 0 3901.9972 -1.2153731 - 8400 19945.534 208.35675 0 3901.9741 1.6021151 - 8450 20112.534 177.18642 0 3901.7298 2.2413008 - 8500 20686.7 71.116816 0 3901.9873 2.2888545 - 8550 18081.94 553.83586 0 3902.3432 7.8257937 - 8600 18320.081 505.67086 0 3898.2784 16.554878 - 8650 20235.305 154.43021 0 3901.709 3.1740823 - 8700 20355.413 132.22512 0 3901.746 4.3436482 - 8750 20087.188 182.11349 0 3901.9631 10.422134 - 8800 20400.795 124.09819 0 3902.0232 2.1179177 - 8850 20678.731 72.825797 0 3902.2204 -3.4491441 - 8900 20372.643 129.5072 0 3902.2189 -8.2166415 - 8950 20851.731 40.899364 0 3902.331 -5.8382839 - 9000 20318.076 139.61775 0 3902.2243 -4.1960802 - 9050 16879.415 776.53739 0 3902.3549 -14.429475 - 9100 19135.149 358.68223 0 3902.2284 -15.50479 - 9150 20689.556 70.939656 0 3902.339 -2.9876179 - 9200 19949.801 207.54882 0 3901.9564 6.4259245 - 9250 20207.027 160.2813 0 3902.3233 1.7402195 - 9300 20030.005 192.99466 0 3902.2548 5.300728 - 9350 19795.291 236.24003 0 3902.0347 5.8677745 - 9400 18232.093 526.18752 0 3902.501 19.344893 - 9450 18789.641 422.30568 0 3901.8687 -7.5185247 - 9500 16332.599 874.10423 0 3898.6597 16.241378 - 9550 18572.572 462.19972 0 3901.5649 -10.777359 - 9600 19859.645 223.32209 0 3901.0341 0.89631957 - 9650 19092.741 365.35768 0 3901.0504 6.7830005 - 9700 18391.154 495.72792 0 3901.4972 6.0683847 - 9750 17790.092 608.60997 0 3903.0714 8.2090184 - 9800 17681.783 628.99951 0 3903.4038 14.231747 - 9850 17804.412 605.54067 0 3902.654 22.308453 - 9900 19134.472 359.37911 0 3902.7999 8.5633158 - 9950 20099.055 180.28604 0 3902.3332 4.7905855 - 10000 20035.447 192.30744 0 3902.5754 1.8299201 -Loop time of 2.34062 on 4 procs for 10000 steps with 81 atoms - -Performance: 36913.309 tau/day, 4272.374 timesteps/s -99.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0052865 | 0.014915 | 0.039366 | 11.6 | 0.64 -Neigh | 0.0080708 | 0.016504 | 0.03345 | 7.7 | 0.71 -Comm | 0.1357 | 0.14237 | 0.15111 | 1.5 | 6.08 -Output | 0.0033429 | 0.0037922 | 0.0050931 | 1.2 | 0.16 -Modify | 2.1033 | 2.1433 | 2.1609 | 1.6 | 91.57 -Other | | 0.01973 | | | 0.84 - -Nlocal: 20.25 ave 36 max 0 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Nghost: 35.25 ave 47 max 24 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Neighs: 137.5 ave 252 max 0 min -Histogram: 1 0 0 1 0 0 0 0 1 1 - -Total # of neighbors = 550 -Ave neighs/atom = 6.7901235 -Neighbor list builds = 994 -Dangerous builds = 956 -Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.1 b/examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.1 deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.4 b/examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.4 deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/examples/rigid/log.20Mar22.rigid.small.g++.1 b/examples/rigid/log.20Mar22.rigid.small.g++.1 deleted file mode 100644 index e34bdad80d..0000000000 --- a/examples/rigid/log.20Mar22.rigid.small.g++.1 +++ /dev/null @@ -1,322 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/small molecule - create bodies CPU = 0.000 seconds - 9 rigid bodies with 81 atoms - 1.2247449 = max distance from body owner to body atom - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722826e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.255443 0 5269.4841 11.963561 - 3300 16732.156 1.9585966 0 5269.4893 12.234024 - 3350 16738.655 -0.079693235 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.05932751 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.092031 - 3550 16713.405 7.8460623 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663192 0 5269.4882 12.027009 - 3700 16738.602 -0.070934371 0 5269.4889 12.025288 - 3750 16737.731 0.20706562 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690678 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646809 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307407 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532803 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.0003765242 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156153 0 5269.5203 12.011611 - 9600 16738.549 -0.026814361 0 5269.5163 12.011415 - 9650 16738.765 -0.1019152 0 5269.5092 12.011013 - 9700 16735.041 1.0589855 0 5269.4979 12.062708 - 9750 16738.013 0.13550223 0 5269.5101 11.407246 - 9800 16738.512 -0.01162033 0 5269.5201 11.394974 - 9850 16738.489 -0.000672705 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984511 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395077 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.097001 on 1 procs for 10000 steps with 81 atoms - -Performance: 890712.494 tau/day, 103091.724 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0064264 | 0.0064264 | 0.0064264 | 0.0 | 6.63 -Bond | 0.0003385 | 0.0003385 | 0.0003385 | 0.0 | 0.35 -Neigh | 0.030894 | 0.030894 | 0.030894 | 0.0 | 31.85 -Comm | 0.0065732 | 0.0065732 | 0.0065732 | 0.0 | 6.78 -Output | 0.0021773 | 0.0021773 | 0.0021773 | 0.0 | 2.24 -Modify | 0.046477 | 0.046477 | 0.046477 | 0.0 | 47.91 -Other | | 0.004115 | | | 4.24 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.small.g++.4 b/examples/rigid/log.20Mar22.rigid.small.g++.4 deleted file mode 100644 index 03bb7a39c0..0000000000 --- a/examples/rigid/log.20Mar22.rigid.small.g++.4 +++ /dev/null @@ -1,322 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/small molecule - create bodies CPU = 0.000 seconds - 9 rigid bodies with 81 atoms - 1.2247449 = max distance from body owner to body atom - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.972281e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532812 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652435 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156165 0 5269.5203 12.011611 - 9600 16738.549 -0.02681437 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589893 0 5269.4979 12.062708 - 9750 16738.013 0.1355014 0 5269.5101 11.407246 - 9800 16738.512 -0.011620326 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270465 0 5269.5237 11.395099 - 9900 16738.489 -0.00024984533 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395077 - 10000 16738.49 0 0 5269.5246 11.395076 -Loop time of 0.115632 on 4 procs for 10000 steps with 81 atoms - -Performance: 747196.558 tau/day, 86481.083 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0014528 | 0.0020376 | 0.0024938 | 0.9 | 1.76 -Bond | 0.00030255 | 0.00030731 | 0.00031718 | 0.0 | 0.27 -Neigh | 0.0089963 | 0.0094964 | 0.010494 | 0.6 | 8.21 -Comm | 0.035947 | 0.038848 | 0.040951 | 1.0 | 33.60 -Output | 0.0022924 | 0.002542 | 0.0032643 | 0.8 | 2.20 -Modify | 0.056743 | 0.058255 | 0.059447 | 0.4 | 50.38 -Other | | 0.004146 | | | 3.59 - -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.small.infile.g++.1 b/examples/rigid/log.20Mar22.rigid.small.infile.g++.1 deleted file mode 100644 index 7c5f672309..0000000000 --- a/examples/rigid/log.20Mar22.rigid.small.infile.g++.1 +++ /dev/null @@ -1,323 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/small molecule infile bodyinfo.dat - create bodies CPU = 0.000 seconds - 9 rigid bodies with 81 atoms - 1.2247449 = max distance from body owner to body atom - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Reading rigid body data for 4 bodies from file bodyinfo.dat -Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722817e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.05932751 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934369 0 5269.4889 12.025288 - 3750 16737.731 0.20706559 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690668 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646805 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652432 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589884 0 5269.4979 12.062708 - 9750 16738.013 0.13550153 0 5269.5101 11.407246 - 9800 16738.512 -0.011620327 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270481 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984532 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395077 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.0973982 on 1 procs for 10000 steps with 81 atoms - -Performance: 887079.894 tau/day, 102671.284 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0065928 | 0.0065928 | 0.0065928 | 0.0 | 6.77 -Bond | 0.00033457 | 0.00033457 | 0.00033457 | 0.0 | 0.34 -Neigh | 0.031245 | 0.031245 | 0.031245 | 0.0 | 32.08 -Comm | 0.0065444 | 0.0065444 | 0.0065444 | 0.0 | 6.72 -Output | 0.0024004 | 0.0024004 | 0.0024004 | 0.0 | 2.46 -Modify | 0.045966 | 0.045966 | 0.045966 | 0.0 | 47.19 -Other | | 0.004315 | | | 4.43 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.small.infile.g++.4 b/examples/rigid/log.20Mar22.rigid.small.infile.g++.4 deleted file mode 100644 index aad4e878dc..0000000000 --- a/examples/rigid/log.20Mar22.rigid.small.infile.g++.4 +++ /dev/null @@ -1,323 +0,0 @@ -LAMMPS (17 Feb 2022) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/small molecule infile bodyinfo.dat - create bodies CPU = 0.000 seconds - 9 rigid bodies with 81 atoms - 1.2247449 = max distance from body owner to body atom - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Reading rigid body data for 4 bodies from file bodyinfo.dat -Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722791e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585966 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.05932751 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460622 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663193 0 5269.4882 12.027009 - 3700 16738.602 -0.070934369 0 5269.4889 12.025288 - 3750 16737.731 0.20706559 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690669 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646806 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532809 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.0003765243 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156164 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589884 0 5269.4979 12.062708 - 9750 16738.013 0.13550185 0 5269.5101 11.407246 - 9800 16738.512 -0.011620326 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270434 0 5269.5237 11.395099 - 9900 16738.489 -0.00024984508 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395077 - 10000 16738.49 0 0 5269.5246 11.395076 -Loop time of 0.135757 on 4 procs for 10000 steps with 81 atoms - -Performance: 636433.251 tau/day, 73661.256 timesteps/s -98.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0020781 | 0.0024716 | 0.0032187 | 0.9 | 1.82 -Bond | 0.00029013 | 0.000332 | 0.00037076 | 0.0 | 0.24 -Neigh | 0.0087772 | 0.011705 | 0.014134 | 2.3 | 8.62 -Comm | 0.042702 | 0.045012 | 0.048023 | 1.1 | 33.16 -Output | 0.0027373 | 0.0030292 | 0.0036178 | 0.6 | 2.23 -Modify | 0.067437 | 0.068617 | 0.069634 | 0.3 | 50.54 -Other | | 0.004589 | | | 3.38 - -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.atomfile.g++.1 b/examples/rigid/log.25Mar24.rigid.atomfile.g++.1 new file mode 100644 index 0000000000..4f76779be7 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.atomfile.g++.1 @@ -0,0 +1,341 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atomfile bodies.txt +fix 1 all rigid custom v_bodies + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.483 | 4.483 | 4.483 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 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5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191522 0 5269.5092 12.011013 + 9700 16735.041 1.0589881 0 5269.4979 12.062708 + 9750 16738.013 0.13550093 0 5269.5101 11.407245 + 9800 16738.512 -0.01162033 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 + 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.119912 on 1 procs for 10000 steps with 81 atoms + +Performance: 720528.892 tau/day, 83394.548 timesteps/s, 6.755 Matom-step/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.007138 | 0.007138 | 0.007138 | 0.0 | 5.95 +Neigh | 0.04331 | 0.04331 | 0.04331 | 0.0 | 36.12 +Comm | 0.0080707 | 0.0080707 | 0.0080707 | 0.0 | 6.73 +Output | 0.001757 | 0.001757 | 0.001757 | 0.0 | 1.47 +Modify | 0.052965 | 0.052965 | 0.052965 | 0.0 | 44.17 +Other | | 0.006671 | | | 5.56 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.atomfile.g++.4 b/examples/rigid/log.25Mar24.rigid.atomfile.g++.4 new file mode 100644 index 0000000000..071a4de5d0 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.atomfile.g++.4 @@ -0,0 +1,341 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atomfile bodies.txt +fix 1 all rigid custom v_bodies + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.33 | 4.362 | 4.456 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 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2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 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0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589886 0 5269.4979 12.062708 + 9750 16738.013 0.13550089 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.135195 on 4 procs for 10000 steps with 81 atoms + +Performance: 639077.466 tau/day, 73967.299 timesteps/s, 5.991 Matom-step/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0016842 | 0.0023498 | 0.0027328 | 0.8 | 1.74 +Neigh | 0.012614 | 0.013371 | 0.014361 | 0.5 | 9.89 +Comm | 0.062345 | 0.06407 | 0.065902 | 0.6 | 47.39 +Output | 0.0018312 | 0.0019801 | 0.0024023 | 0.5 | 1.46 +Modify | 0.038532 | 0.039713 | 0.041474 | 0.6 | 29.37 +Other | | 0.01371 | | | 10.14 + +Nlocal: 20.25 ave 37 max 3 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.atomvar.g++.1 b/examples/rigid/log.25Mar24.rigid.atomvar.g++.1 new file mode 100644 index 0000000000..7510d35ec1 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.atomvar.g++.1 @@ -0,0 +1,341 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) +fix 1 all rigid custom v_bodies + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.358 | 4.358 | 4.358 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 + 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191522 0 5269.5092 12.011013 + 9700 16735.041 1.0589881 0 5269.4979 12.062708 + 9750 16738.013 0.13550093 0 5269.5101 11.407245 + 9800 16738.512 -0.01162033 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 + 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.131374 on 1 procs for 10000 steps with 81 atoms + +Performance: 657662.971 tau/day, 76118.399 timesteps/s, 6.166 Matom-step/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0075531 | 0.0075531 | 0.0075531 | 0.0 | 5.75 +Neigh | 0.047177 | 0.047177 | 0.047177 | 0.0 | 35.91 +Comm | 0.0090961 | 0.0090961 | 0.0090961 | 0.0 | 6.92 +Output | 0.0018917 | 0.0018917 | 0.0018917 | 0.0 | 1.44 +Modify | 0.058064 | 0.058064 | 0.058064 | 0.0 | 44.20 +Other | | 0.007593 | | | 5.78 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.atomvar.g++.4 b/examples/rigid/log.25Mar24.rigid.atomvar.g++.4 new file mode 100644 index 0000000000..b7adcacb14 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.atomvar.g++.4 @@ -0,0 +1,341 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) +fix 1 all rigid custom v_bodies + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.205 | 4.237 | 4.331 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589886 0 5269.4979 12.062708 + 9750 16738.013 0.13550089 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.135534 on 4 procs for 10000 steps with 81 atoms + +Performance: 637479.927 tau/day, 73782.399 timesteps/s, 5.976 Matom-step/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0016589 | 0.0022805 | 0.0027973 | 0.9 | 1.68 +Neigh | 0.012838 | 0.013347 | 0.014456 | 0.6 | 9.85 +Comm | 0.062667 | 0.064428 | 0.066142 | 0.6 | 47.54 +Output | 0.0018075 | 0.001966 | 0.0024125 | 0.6 | 1.45 +Modify | 0.038219 | 0.039639 | 0.041101 | 0.6 | 29.25 +Other | | 0.01387 | | | 10.24 + +Nlocal: 20.25 ave 37 max 3 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.early.g++.1 b/examples/rigid/log.25Mar24.rigid.early.g++.1 new file mode 100644 index 0000000000..9f5d86312e --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.early.g++.1 @@ -0,0 +1,340 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 + 9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 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5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 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11.395075 +Loop time of 0.127115 on 1 procs for 10000 steps with 81 atoms + +Performance: 679698.303 tau/day, 78668.785 timesteps/s, 6.372 Matom-step/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0074904 | 0.0074904 | 0.0074904 | 0.0 | 5.89 +Neigh | 0.044675 | 0.044675 | 0.044675 | 0.0 | 35.15 +Comm | 0.0079194 | 0.0079194 | 0.0079194 | 0.0 | 6.23 +Output | 0.0018129 | 0.0018129 | 0.0018129 | 0.0 | 1.43 +Modify | 0.057845 | 0.057845 | 0.057845 | 0.0 | 45.51 +Other | | 0.007372 | | | 5.80 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.early.g++.4 b/examples/rigid/log.25Mar24.rigid.early.g++.4 new file mode 100644 index 0000000000..e0b182d9fc --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.early.g++.4 @@ -0,0 +1,340 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 + 9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 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16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 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5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589886 0 5269.4979 12.062708 + 9750 16738.013 0.13550089 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.133679 on 4 procs for 10000 steps with 81 atoms + +Performance: 646325.439 tau/day, 74806.185 timesteps/s, 6.059 Matom-step/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0016629 | 0.0023406 | 0.0028762 | 0.9 | 1.75 +Neigh | 0.012558 | 0.013331 | 0.015279 | 1.0 | 9.97 +Comm | 0.060677 | 0.062779 | 0.0646 | 0.7 | 46.96 +Output | 0.0017495 | 0.001914 | 0.0023526 | 0.6 | 1.43 +Modify | 0.037566 | 0.039361 | 0.040514 | 0.6 | 29.44 +Other | | 0.01395 | | | 10.44 + +Nlocal: 20.25 ave 37 max 3 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.g++.1 b/examples/rigid/log.25Mar24.rigid.g++.1 new file mode 100644 index 0000000000..6b27146c6b --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.g++.1 @@ -0,0 +1,338 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.002 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 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5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 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-0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 + 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191522 0 5269.5092 12.011013 + 9700 16735.041 1.0589881 0 5269.4979 12.062708 + 9750 16738.013 0.13550093 0 5269.5101 11.407245 + 9800 16738.512 -0.01162033 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 + 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.136528 on 1 procs for 10000 steps with 81 atoms + +Performance: 632835.120 tau/day, 73244.806 timesteps/s, 5.933 Matom-step/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0091674 | 0.0091674 | 0.0091674 | 0.0 | 6.71 +Neigh | 0.046854 | 0.046854 | 0.046854 | 0.0 | 34.32 +Comm | 0.0076933 | 0.0076933 | 0.0076933 | 0.0 | 5.63 +Output | 0.001779 | 0.001779 | 0.001779 | 0.0 | 1.30 +Modify | 0.063842 | 0.063842 | 0.063842 | 0.0 | 46.76 +Other | | 0.007193 | | | 5.27 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.g++.4 b/examples/rigid/log.25Mar24.rigid.g++.4 new file mode 100644 index 0000000000..c2f691b7ec --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.g++.4 @@ -0,0 +1,338 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589886 0 5269.4979 12.062708 + 9750 16738.013 0.13550089 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.134503 on 4 procs for 10000 steps with 81 atoms + +Performance: 642365.322 tau/day, 74347.838 timesteps/s, 6.022 Matom-step/s +96.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0016076 | 0.0023247 | 0.002836 | 0.9 | 1.73 +Neigh | 0.012491 | 0.013229 | 0.0145 | 0.7 | 9.84 +Comm | 0.062105 | 0.063666 | 0.06514 | 0.5 | 47.33 +Output | 0.0017602 | 0.0019318 | 0.0024227 | 0.6 | 1.44 +Modify | 0.038132 | 0.039518 | 0.040852 | 0.5 | 29.38 +Other | | 0.01383 | | | 10.29 + +Nlocal: 20.25 ave 37 max 3 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.gravity.g++.1 b/examples/rigid/log.25Mar24.rigid.gravity.g++.1 new file mode 100644 index 0000000000..87b814dfab --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.gravity.g++.1 @@ -0,0 +1,228 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +#Pour composite granular particles on flat wall + +newton on +atom_style sphere +atom_modify map array sort 0 0 + +thermo_modify flush yes +units si + +variable minrad equal 0.5 +variable maxrad equal 1.4 + +variable skin equal 0.3*${maxrad} +variable skin equal 0.3*1.4 + +boundary p p f +region reg block 0 20 0 20 0 200 units box +create_box 1 reg +Created orthogonal box = (0 0 0) to (20 20 200) + 1 by 1 by 1 MPI processor grid + +fix prop all property/atom mol ghost yes + +variable dumpfreq equal 1000 +variable logfreq equal 1000 + +pair_style gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0 +pair_coeff * * + +timestep 0.0001 + +group particles type 1 +0 atoms in group particles +atom_modify first particles + +neighbor ${skin} bin +neighbor 0.42 bin +group rigid type 1 +0 atoms in group rigid +neigh_modify every 1 delay 0 check yes exclude molecule/intra all + +thermo ${logfreq} +thermo 1000 +thermo_style custom step cpu atoms ke +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904) +thermo_modify flush yes lost warn + +comm_modify vel yes cutoff 3 + +molecule mymol molecule.data +Read molecule template mymol: +LAMMPS data file created for rigid body molecule template + 1 molecules + 0 fragments + 5 atoms with max type 1 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region pourreg block 5 15 5 15 80 100 side in units box + +#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity +# and the 'gravity' keyword to fix rigid/small were not available. +# These settings produce undesirable behavior, where gravity can induce +# torque on rigid bodies. +#fix gravfix all gravity 9.8 vector 0 0 -1 #disable +#fix rigidfix all rigid/small molecule mol mymol #gravity gravfix + +#The correct behavior is recovered with the following settings: +fix gravfix all gravity 9.8 vector 0 0 -1 disable +fix rigidfix all rigid/small molecule mol mymol gravity gravfix + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.2 = max distance from body owner to body atom + +fix pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix +Particle insertion: 15 every 20203 steps, 5 by step 1 + +fix zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL + +#dump 1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz + +run 100000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62 + ghost atom cutoff = 3 + binsize = 0.81, bins = 25 25 247 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hooke/history, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.893 | 6.893 | 6.893 Mbytes + Step CPU Atoms KinEng + 0 0 0 -0 + 1000 0.005385611 25 -0 + 2000 0.01106897 25 -0 + 3000 0.01569532 25 -0 + 4000 0.020782538 25 -0 + 5000 0.02656256 25 -0 + 6000 0.03132421 25 -0 + 7000 0.035996621 25 -0 + 8000 0.040816339 25 -0 + 9000 0.045911912 25 -0 + 10000 0.051486339 25 -0 + 11000 0.058049641 25 -0 + 12000 0.063206805 25 -0 + 13000 0.068374138 25 -0 + 14000 0.073423818 25 -0 + 15000 0.078890587 25 -0 + 16000 0.086372246 25 -0 + 17000 0.091912312 25 -0 + 18000 0.097317178 25 -0 + 19000 0.10284163 25 -0 + 20000 0.10836857 25 -0 + 21000 0.11476057 25 -0 + 22000 0.12201322 25 -0 + 23000 0.127963 25 -0 + 24000 0.13386968 25 -0 + 25000 0.1397396 25 -0 + 26000 0.14672759 25 -0 + 27000 0.15447534 25 -0 + 28000 0.16103509 25 -0 + 29000 0.16703686 25 -0 + 30000 0.17306375 25 -0 + 31000 0.18150464 25 -0 + 32000 0.1874536 25 -0 + 33000 0.19372953 25 -0 + 34000 0.19997087 25 -0 + 35000 0.20643521 25 -0 + 36000 0.21499446 25 -0 + 37000 0.22129475 25 -0 + 38000 0.2278159 25 -0 + 39000 0.23262556 25 -0 + 40000 0.23679 25 -0 + 41000 0.2428383 25 -0 + 42000 0.24757287 25 -0 + 43000 0.25190701 25 -0 + 44000 0.25617771 25 -0 + 45000 0.26057242 25 -0 + 46000 0.26469065 25 -0 + 47000 0.26921214 25 -0 + 48000 0.27502337 25 -0 + 49000 0.27911905 25 -0 + 50000 0.28338379 25 -0 + 51000 0.28736617 25 -0 + 52000 0.29127304 25 -0 + 53000 0.29504445 25 -0 + 54000 0.29898933 25 -0 + 55000 0.30479176 25 -0 + 56000 0.30893347 25 -0 + 57000 0.31277358 25 -0 + 58000 0.31658797 25 -0 + 59000 0.32024112 25 -0 + 60000 0.32373109 25 -0 + 61000 0.32753442 25 -0 + 62000 0.33123815 25 -0 + 63000 0.33643285 25 -0 + 64000 0.34036569 25 -0 + 65000 0.34399532 25 -0 + 66000 0.3475875 25 -0 + 67000 0.35124833 25 -0 + 68000 0.35503825 25 -0 + 69000 0.35870471 25 -0 + 70000 0.3624294 25 -0 + 71000 0.36714884 25 -0 + 72000 0.37082887 25 -0 + 73000 0.37459885 25 -0 + 74000 0.37835449 25 -0 + 75000 0.38245549 25 -0 + 76000 0.38681838 25 -0 + 77000 0.39069919 25 -0 + 78000 0.39460729 25 -0 + 79000 0.39908672 25 -0 + 80000 0.40266481 25 -0 + 81000 0.40645032 25 -0 + 82000 0.41005038 25 -0 + 83000 0.41355864 25 -0 + 84000 0.41741638 25 -0 + 85000 0.42182475 25 -0 + 86000 0.42614449 25 -0 + 87000 0.43024819 25 -0 + 88000 0.43389722 25 -0 + 89000 0.4372946 25 -0 + 90000 0.44097963 25 -0 + 91000 0.44451596 25 -0 + 92000 0.44800886 25 -0 + 93000 0.45171482 25 -0 + 94000 0.45568312 25 -0 + 95000 0.46068385 25 -0 + 96000 0.46423783 25 -0 + 97000 0.46783791 25 -0 + 98000 0.47132532 25 -0 + 99000 0.47462675 25 -0 + 100000 0.47811781 25 -0 +Loop time of 0.478128 on 1 procs for 100000 steps with 25 atoms + +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.016638 | 0.016638 | 0.016638 | 0.0 | 3.48 +Neigh | 0.12338 | 0.12338 | 0.12338 | 0.0 | 25.81 +Comm | 0.026212 | 0.026212 | 0.026212 | 0.0 | 5.48 +Output | 0.0015672 | 0.0015672 | 0.0015672 | 0.0 | 0.33 +Modify | 0.28303 | 0.28303 | 0.28303 | 0.0 | 59.20 +Other | | 0.0273 | | | 5.71 + +Nlocal: 25 ave 25 max 25 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1 ave 1 max 1 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 703 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.gravity.g++.4 b/examples/rigid/log.25Mar24.rigid.gravity.g++.4 new file mode 100644 index 0000000000..ddf76fb4d6 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.gravity.g++.4 @@ -0,0 +1,228 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +#Pour composite granular particles on flat wall + +newton on +atom_style sphere +atom_modify map array sort 0 0 + +thermo_modify flush yes +units si + +variable minrad equal 0.5 +variable maxrad equal 1.4 + +variable skin equal 0.3*${maxrad} +variable skin equal 0.3*1.4 + +boundary p p f +region reg block 0 20 0 20 0 200 units box +create_box 1 reg +Created orthogonal box = (0 0 0) to (20 20 200) + 1 by 1 by 4 MPI processor grid + +fix prop all property/atom mol ghost yes + +variable dumpfreq equal 1000 +variable logfreq equal 1000 + +pair_style gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0 +pair_coeff * * + +timestep 0.0001 + +group particles type 1 +0 atoms in group particles +atom_modify first particles + +neighbor ${skin} bin +neighbor 0.42 bin +group rigid type 1 +0 atoms in group rigid +neigh_modify every 1 delay 0 check yes exclude molecule/intra all + +thermo ${logfreq} +thermo 1000 +thermo_style custom step cpu atoms ke +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904) +thermo_modify flush yes lost warn + +comm_modify vel yes cutoff 3 + +molecule mymol molecule.data +Read molecule template mymol: +LAMMPS data file created for rigid body molecule template + 1 molecules + 0 fragments + 5 atoms with max type 1 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +region pourreg block 5 15 5 15 80 100 side in units box + +#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity +# and the 'gravity' keyword to fix rigid/small were not available. +# These settings produce undesirable behavior, where gravity can induce +# torque on rigid bodies. +#fix gravfix all gravity 9.8 vector 0 0 -1 #disable +#fix rigidfix all rigid/small molecule mol mymol #gravity gravfix + +#The correct behavior is recovered with the following settings: +fix gravfix all gravity 9.8 vector 0 0 -1 disable +fix rigidfix all rigid/small molecule mol mymol gravity gravfix + create bodies CPU = 0.000 seconds + 0 rigid bodies with 0 atoms + 1.2 = max distance from body owner to body atom + +fix pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix +Particle insertion: 15 every 20203 steps, 5 by step 1 + +fix zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL + +#dump 1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz + +run 100000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62 + ghost atom cutoff = 3 + binsize = 0.81, bins = 25 25 247 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hooke/history, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.09 | 6.09 | 6.09 Mbytes + Step CPU Atoms KinEng + 0 0 0 -0 + 1000 0.007155423 25 -0 + 2000 0.013621411 25 -0 + 3000 0.018069993 25 -0 + 4000 0.022375597 25 -0 + 5000 0.027610001 25 -0 + 6000 0.032700728 25 -0 + 7000 0.036781214 25 -0 + 8000 0.041026343 25 -0 + 9000 0.045133974 25 -0 + 10000 0.049302504 25 -0 + 11000 0.053475155 25 -0 + 12000 0.058101552 25 -0 + 13000 0.063617332 25 -0 + 14000 0.070220865 25 -0 + 15000 0.079467476 25 -0 + 16000 0.085128592 25 -0 + 17000 0.088670803 25 -0 + 18000 0.093576466 25 -0 + 19000 0.096967506 25 -0 + 20000 0.10032704 25 -0 + 21000 0.1037381 25 -0 + 22000 0.10714647 25 -0 + 23000 0.11062389 25 -0 + 24000 0.11408744 25 -0 + 25000 0.12017243 25 -0 + 26000 0.12858759 25 -0 + 27000 0.13356253 25 -0 + 28000 0.13819667 25 -0 + 29000 0.14299332 25 -0 + 30000 0.14766723 25 -0 + 31000 0.15258071 25 -0 + 32000 0.15836989 25 -0 + 33000 0.16306841 25 -0 + 34000 0.16769723 25 -0 + 35000 0.172317 25 -0 + 36000 0.17698336 25 -0 + 37000 0.18173594 25 -0 + 38000 0.1879449 25 -0 + 39000 0.19236501 25 -0 + 40000 0.1964458 25 -0 + 41000 0.20045733 25 -0 + 42000 0.20454794 25 -0 + 43000 0.20872097 25 -0 + 44000 0.21291348 25 -0 + 45000 0.21780319 25 -0 + 46000 0.22260816 25 -0 + 47000 0.22686931 25 -0 + 48000 0.23117793 25 -0 + 49000 0.23535185 25 -0 + 50000 0.24054306 25 -0 + 51000 0.24463963 25 -0 + 52000 0.24938311 25 -0 + 53000 0.25348209 25 -0 + 54000 0.25745703 25 -0 + 55000 0.26145377 25 -0 + 56000 0.26534485 25 -0 + 57000 0.26928518 25 -0 + 58000 0.27321574 25 -0 + 59000 0.27791991 25 -0 + 60000 0.28284558 25 -0 + 61000 0.28673327 25 -0 + 62000 0.29055931 25 -0 + 63000 0.2945131 25 -0 + 64000 0.29846467 25 -0 + 65000 0.30238139 25 -0 + 66000 0.3062491 25 -0 + 67000 0.31026454 25 -0 + 68000 0.31498685 25 -0 + 69000 0.31887771 25 -0 + 70000 0.32278066 25 -0 + 71000 0.32658541 25 -0 + 72000 0.33047871 25 -0 + 73000 0.33441507 25 -0 + 74000 0.33830186 25 -0 + 75000 0.34298503 25 -0 + 76000 0.3470502 25 -0 + 77000 0.35093166 25 -0 + 78000 0.35472767 25 -0 + 79000 0.35858626 25 -0 + 80000 0.36236101 25 -0 + 81000 0.36621078 25 -0 + 82000 0.36998141 25 -0 + 83000 0.37417451 25 -0 + 84000 0.37850331 25 -0 + 85000 0.38230344 25 -0 + 86000 0.38621429 25 -0 + 87000 0.38998154 25 -0 + 88000 0.39378687 25 -0 + 89000 0.397529 25 -0 + 90000 0.40133202 25 -0 + 91000 0.40575097 25 -0 + 92000 0.41012392 25 -0 + 93000 0.41397633 25 -0 + 94000 0.41791732 25 -0 + 95000 0.42174915 25 -0 + 96000 0.42570384 25 -0 + 97000 0.4295687 25 -0 + 98000 0.43339555 25 -0 + 99000 0.43810319 25 -0 + 100000 0.44205356 25 -0 +Loop time of 0.442071 on 4 procs for 100000 steps with 25 atoms + +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0043596 | 0.0077919 | 0.015026 | 4.9 | 1.76 +Neigh | 0.03639 | 0.037869 | 0.038842 | 0.5 | 8.57 +Comm | 0.029189 | 0.034805 | 0.038937 | 2.3 | 7.87 +Output | 0.00094691 | 0.0012173 | 0.0019545 | 1.2 | 0.28 +Modify | 0.031085 | 0.10076 | 0.24754 | 27.5 | 22.79 +Other | | 0.2596 | | | 58.73 + +Nlocal: 6.25 ave 25 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 0.25 ave 1 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 703 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.infile.g++.1 b/examples/rigid/log.25Mar24.rigid.infile.g++.1 new file mode 100644 index 0000000000..a8d6f550aa --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.infile.g++.1 @@ -0,0 +1,310 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat + 9 rigid bodies with 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Reading rigid body data for 4 bodies from file bodyinfo.dat +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722859e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.05932751 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663193 0 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12.011692 + 9550 16738.493 -0.0053156155 0 5269.5203 12.011611 + 9600 16738.549 -0.026814365 0 5269.5163 12.011415 + 9650 16738.765 -0.10191521 0 5269.5092 12.011013 + 9700 16735.041 1.0589871 0 5269.4979 12.062708 + 9750 16738.013 0.13550136 0 5269.5101 11.407245 + 9800 16738.512 -0.01162033 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270559 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984558 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.134486 on 1 procs for 10000 steps with 81 atoms + +Performance: 642445.705 tau/day, 74357.142 timesteps/s, 6.023 Matom-step/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0076798 | 0.0076798 | 0.0076798 | 0.0 | 5.71 +Neigh | 0.048776 | 0.048776 | 0.048776 | 0.0 | 36.27 +Comm | 0.0085249 | 0.0085249 | 0.0085249 | 0.0 | 6.34 +Output | 0.0021846 | 0.0021846 | 0.0021846 | 0.0 | 1.62 +Modify | 0.059372 | 0.059372 | 0.059372 | 0.0 | 44.15 +Other | | 0.007949 | | | 5.91 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.infile.g++.4 b/examples/rigid/log.25Mar24.rigid.infile.g++.4 new file mode 100644 index 0000000000..0e4f37b698 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.infile.g++.4 @@ -0,0 +1,310 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat + 9 rigid bodies with 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Reading rigid body data for 4 bodies from file bodyinfo.dat +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 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16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722861e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 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16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690667 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532809 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652433 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 + 9600 16738.549 -0.026814367 0 5269.5163 12.011415 + 9650 16738.765 -0.10191522 0 5269.5092 12.011013 + 9700 16735.041 1.0589878 0 5269.4979 12.062708 + 9750 16738.013 0.13550114 0 5269.5101 11.407245 + 9800 16738.512 -0.01162033 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270564 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984568 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.135118 on 4 procs for 10000 steps with 81 atoms + +Performance: 639441.862 tau/day, 74009.475 timesteps/s, 5.995 Matom-step/s +97.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0015919 | 0.0022753 | 0.0028384 | 0.9 | 1.68 +Neigh | 0.012494 | 0.013468 | 0.015484 | 1.0 | 9.97 +Comm | 0.061357 | 0.0636 | 0.06555 | 0.7 | 47.07 +Output | 0.0017441 | 0.0018894 | 0.0023095 | 0.6 | 1.40 +Modify | 0.037856 | 0.039816 | 0.041217 | 0.6 | 29.47 +Other | | 0.01407 | | | 10.41 + +Nlocal: 20.25 ave 37 max 3 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.molecule.g++.1 b/examples/rigid/log.25Mar24.rigid.molecule.g++.1 new file mode 100644 index 0000000000..75d05c3d07 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.molecule.g++.1 @@ -0,0 +1,319 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid molecule + 9 rigid bodies with 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.233 | 5.233 | 5.233 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 + 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191522 0 5269.5092 12.011013 + 9700 16735.041 1.0589881 0 5269.4979 12.062708 + 9750 16738.013 0.13550093 0 5269.5101 11.407245 + 9800 16738.512 -0.01162033 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 + 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.130618 on 1 procs for 10000 steps with 81 atoms + +Performance: 661470.393 tau/day, 76559.073 timesteps/s, 6.201 Matom-step/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0069622 | 0.0069622 | 0.0069622 | 0.0 | 5.33 +Bond | 0.00033246 | 0.00033246 | 0.00033246 | 0.0 | 0.25 +Neigh | 0.053402 | 0.053402 | 0.053402 | 0.0 | 40.88 +Comm | 0.008192 | 0.008192 | 0.008192 | 0.0 | 6.27 +Output | 0.0015884 | 0.0015884 | 0.0015884 | 0.0 | 1.22 +Modify | 0.053219 | 0.053219 | 0.053219 | 0.0 | 40.74 +Other | | 0.006922 | | | 5.30 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.molecule.g++.4 b/examples/rigid/log.25Mar24.rigid.molecule.g++.4 new file mode 100644 index 0000000000..6cbb88d471 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.molecule.g++.4 @@ -0,0 +1,319 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid molecule + 9 rigid bodies with 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.08 | 5.112 | 5.206 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589886 0 5269.4979 12.062708 + 9750 16738.013 0.13550089 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.139893 on 4 procs for 10000 steps with 81 atoms + +Performance: 617616.025 tau/day, 71483.336 timesteps/s, 5.790 Matom-step/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0015795 | 0.0022375 | 0.0027109 | 0.9 | 1.60 +Bond | 0.00031772 | 0.00032314 | 0.00032894 | 0.0 | 0.23 +Neigh | 0.015169 | 0.016101 | 0.017803 | 0.8 | 11.51 +Comm | 0.063065 | 0.06514 | 0.06737 | 0.7 | 46.56 +Output | 0.001945 | 0.0020985 | 0.0025044 | 0.5 | 1.50 +Modify | 0.03865 | 0.039853 | 0.041246 | 0.6 | 28.49 +Other | | 0.01414 | | | 10.11 + +Nlocal: 20.25 ave 37 max 3 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.nve.early.g++.1 b/examples/rigid/log.25Mar24.rigid.nve.early.g++.1 new file mode 100644 index 0000000000..d9fbe7ee28 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.nve.early.g++.1 @@ -0,0 +1,340 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 + 9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.688 571.72044 0 5265.826 32.006558 + 100 16298.426 136.669 0 5267.6551 16.445373 + 150 16682.627 17.489692 0 5269.4277 14.900277 + 200 16733.935 1.3740602 0 5269.4647 14.569704 + 250 16738.854 -0.15258528 0 5269.4868 14.496759 + 300 16738.584 -0.055187603 0 5269.4992 14.496371 + 350 16738.492 -0.017449036 0 5269.5078 14.496801 + 400 16738.472 -0.006012316 0 5269.513 14.496991 + 450 16738.469 -0.0012715314 0 5269.5169 14.497085 + 500 16738.471 -0.00081065611 0 5269.5177 14.497095 + 550 16738.47 -0.00083201064 0 5269.5175 14.497091 + 600 16738.469 -0.00058353965 0 5269.5174 14.497091 + 650 16738.467 -0.0004722653 0 5269.5169 14.497088 + 700 16738.462 0 0 5269.5158 14.497085 + 750 16738.454 0 0 5269.5134 14.497066 + 800 16738.449 0 0 5269.5116 14.497052 + 850 16738.451 0 0 5269.5123 14.497057 + 900 16738.46 0 0 5269.5151 14.497079 + 950 16738.475 -0.0035324469 0 5269.5163 14.497056 + 1000 16738.603 -0.05113463 0 5269.509 14.496621 + 1050 16737.376 0.32970882 0 5269.5037 14.526144 + 1100 16737.909 0.16215423 0 5269.5038 14.53237 + 1150 16738.719 -0.089236594 0 5269.5074 14.510282 + 1200 16738.477 -0.0075446521 0 5269.513 14.51099 + 1250 16738.458 0 0 5269.5146 14.511061 + 1300 16738.448 0 0 5269.5114 14.511036 + 1350 16738.444 0 0 5269.5102 14.511026 + 1400 16738.449 -0.00044714105 0 5269.5113 14.511031 + 1450 16738.458 -0.0010956657 0 5269.5136 14.511043 + 1500 16738.464 -0.00057735083 0 5269.516 14.511066 + 1550 16738.467 0 0 5269.5173 14.511083 + 1600 16738.469 0 0 5269.5179 14.511087 + 1650 16738.47 0 0 5269.5183 14.511091 + 1700 16738.469 0 0 5269.5181 14.511089 + 1750 16738.464 0 0 5269.5164 14.511076 + 1800 16738.455 0 0 5269.5137 14.511055 + 1850 16738.45 0 0 5269.5121 14.511042 + 1900 16738.453 0 0 5269.513 14.511049 + 1950 16738.468 -0.0031854173 0 5269.5144 14.51102 + 2000 16738.501 -0.01331726 0 5269.5148 14.510906 + 2050 16738.568 -0.036719673 0 5269.5126 14.510668 + 2100 16738.646 -0.063312431 0 5269.5103 14.510597 + 2150 16738.619 -0.05606591 0 5269.5091 14.510608 + 2200 16738.566 -0.038448437 0 5269.5101 14.510779 + 2250 16738.52 -0.023712465 0 5269.5103 14.510906 + 2300 16738.485 -0.01323561 0 5269.5099 14.510971 + 2350 16738.457 -0.0045452995 0 5269.5097 14.511049 + 2400 16738.449 -0.00052013007 0 5269.5113 14.511107 + 2450 16738.461 -0.002321933 0 5269.5132 14.511099 + 2500 16738.474 -0.0051804641 0 5269.5145 14.511103 + 2550 16738.592 -0.04492566 0 5269.5117 14.510696 + 2600 16738.45 -0.0038193536 0 5269.5082 14.510939 + 2650 16733.621 1.5177478 0 5269.5097 14.586333 + 2700 16738.772 -0.1064304 0 5269.5069 14.500913 + 2750 16733.165 1.6598389 0 5269.5082 14.616957 + 2800 16738.577 -0.04523598 0 5269.5068 14.51458 + 2850 16738.475 -0.01269037 0 5269.5073 14.513396 + 2900 16738.449 -0.002688737 0 5269.5089 14.513555 + 2950 16738.465 -0.0082345477 0 5269.5084 14.513515 + 3000 16738.657 -0.071197475 0 5269.5061 14.513024 + 3050 16706.71 9.9435728 0 5269.4634 15.021496 + 3100 16643.257 29.968327 0 5269.5123 14.548247 + 3150 16739.45 -0.33134743 0 5269.4956 13.595814 + 3200 16731.445 2.1723572 0 5269.4792 12.100834 + 3250 16612.686 39.57457 0 5269.4942 13.879807 + 3300 16738.601 -0.059713795 0 5269.4997 12.666612 + 3350 16738.587 -0.044640809 0 5269.5106 12.663574 + 3400 16737.995 0.14468663 0 5269.5136 12.680161 + 3450 16738.607 -0.050706049 0 5269.5107 12.665118 + 3500 16738.819 -0.12122411 0 5269.5069 12.665394 + 3550 16738.498 -0.021940182 0 5269.5052 12.676141 + 3600 16673.205 20.482364 0 5269.4544 13.525704 + 3650 16738.648 -0.074052044 0 5269.5003 12.817014 + 3700 16738.632 -0.07184695 0 5269.4975 12.810978 + 3750 16738.621 -0.07013081 0 5269.4958 12.811663 + 3800 16738.552 -0.044378799 0 5269.4998 12.811871 + 3850 16738.492 -0.015384402 0 5269.5099 12.811397 + 3900 16738.487 -0.0058199162 0 5269.518 12.811514 + 3950 16738.482 -0.0012032457 0 5269.521 12.811589 + 4000 16738.478 -0.00020707654 0 5269.5208 12.811606 + 4050 16738.477 0 0 5269.5207 12.811608 + 4100 16738.477 0 0 5269.5206 12.811607 + 4150 16738.475 0 0 5269.5199 12.811602 + 4200 16738.464 0 0 5269.5165 12.811576 + 4250 16738.446 0 0 5269.5109 12.811532 + 4300 16738.44 0 0 5269.5089 12.811516 + 4350 16738.454 0 0 5269.5131 12.811549 + 4400 16738.468 0 0 5269.5177 12.811585 + 4450 16738.47 0 0 5269.5184 12.811591 + 4500 16738.466 0 0 5269.517 12.811579 + 4550 16738.463 0 0 5269.5162 12.811573 + 4600 16738.466 0 0 5269.517 12.81158 + 4650 16738.471 0 0 5269.5186 12.811592 + 4700 16738.47 0 0 5269.5182 12.811589 + 4750 16738.456 0 0 5269.5139 12.811556 + 4800 16738.441 0 0 5269.5091 12.811518 + 4850 16738.444 0 0 5269.5102 12.811526 + 4900 16738.462 0 0 5269.5159 12.81157 + 4950 16738.475 0 0 5269.5201 12.811603 + 5000 16738.479 0 0 5269.5212 12.811612 + 5050 16738.479 0 0 5269.5212 12.811612 + 5100 16738.479 0 0 5269.5212 12.811612 + 5150 16738.478 0 0 5269.5209 12.81161 + 5200 16738.472 0 0 5269.519 12.811595 + 5250 16738.456 0 0 5269.5138 12.811555 + 5300 16738.432 0 0 5269.5064 12.811497 + 5350 16738.422 0 0 5269.5033 12.811472 + 5400 16738.438 0 0 5269.5082 12.81151 + 5450 16738.46 0 0 5269.515 12.811564 + 5500 16738.471 -0.0002100851 0 5269.5183 12.811588 + 5550 16738.481 -0.003484166 0 5269.5185 12.811534 + 5600 16738.542 -0.024500002 0 5269.5164 12.81122 + 5650 16738.641 -0.058023282 0 5269.5142 12.812225 + 5700 16384.935 111.24508 0 5269.4653 26.09278 + 5750 16738.555 -0.030778873 0 5269.5142 13.052328 + 5800 16738.462 -0.0034050629 0 5269.5125 13.052653 + 5850 16738.441 -0.00034406845 0 5269.5089 13.052656 + 5900 16738.443 0 0 5269.5098 13.052667 + 5950 16738.459 0 0 5269.5149 13.052707 + 6000 16738.468 0 0 5269.5177 13.052729 + 6050 16738.466 0 0 5269.5172 13.052725 + 6100 16738.462 0 0 5269.516 13.052715 + 6150 16738.463 0 0 5269.5162 13.052717 + 6200 16738.468 0 0 5269.5178 13.052729 + 6250 16738.472 0 0 5269.5189 13.052738 + 6300 16738.465 0 0 5269.5169 13.052723 + 6350 16738.448 0 0 5269.5115 13.052681 + 6400 16738.439 0 0 5269.5086 13.052658 + 6450 16738.451 0 0 5269.5124 13.052687 + 6500 16738.469 0 0 5269.5181 13.052732 + 6550 16738.478 0 0 5269.5209 13.052754 + 6600 16738.48 0 0 5269.5214 13.052758 + 6650 16738.479 0 0 5269.5213 13.052757 + 6700 16738.48 -0.00057913194 0 5269.521 13.052744 + 6750 16738.483 -0.0025329373 0 5269.5198 13.0527 + 6800 16738.482 -0.0065110045 0 5269.5156 13.052612 + 6850 16738.465 -0.0072245165 0 5269.5095 13.052574 + 6900 16738.436 -0.0036561206 0 5269.5039 13.052609 + 6950 16738.433 -0.0010530752 0 5269.5056 13.052661 + 7000 16738.455 -0.00056878712 0 5269.5132 13.052723 + 7050 16738.475 -0.0011717775 0 5269.5187 13.052755 + 7100 16738.48 -0.00047531448 0 5269.5209 13.052781 + 7150 16738.479 0 0 5269.5211 13.052788 + 7200 16738.478 0 0 5269.5207 13.052785 + 7250 16738.477 0 0 5269.5207 13.052785 + 7300 16738.476 0 0 5269.5201 13.052781 + 7350 16738.466 0 0 5269.5172 13.052758 + 7400 16738.448 0 0 5269.5115 13.052714 + 7450 16738.438 0 0 5269.5083 13.052688 + 7500 16738.448 0 0 5269.5115 13.052713 + 7550 16738.464 -0.00053504438 0 5269.5158 13.052742 + 7600 16738.483 -0.010043243 0 5269.5123 13.052657 + 7650 16738.674 -0.077543712 0 5269.5051 13.052041 + 7700 16736.839 0.49724664 0 5269.502 13.085872 + 7750 16731.931 2.0427463 0 5269.5024 13.190769 + 7800 16738.762 -0.10404434 0 5269.5061 13.082626 + 7850 16738.525 -0.024994384 0 5269.5108 13.082681 + 7900 16738.479 -0.008372534 0 5269.5129 13.082885 + 7950 16738.449 -0.0038549468 0 5269.5079 13.082917 + 8000 16738.441 -0.0016367618 0 5269.5074 13.082937 + 8050 16738.455 -0.0014865651 0 5269.5123 13.082971 + 8100 16738.47 -0.00072796093 0 5269.5175 13.083021 + 8150 16738.476 0 0 5269.5202 13.08305 + 8200 16738.477 0 0 5269.5204 13.083051 + 8250 16738.476 0 0 5269.5201 13.083049 + 8300 16738.474 0 0 5269.5197 13.083046 + 8350 16738.47 0 0 5269.5185 13.083036 + 8400 16738.462 -0.0017116105 0 5269.5142 13.082984 + 8450 16738.447 -0.003289664 0 5269.5078 13.082915 + 8500 16738.429 -0.00098100125 0 5269.5043 13.082918 + 8550 16738.435 0 0 5269.5075 13.082953 + 8600 16738.458 0 0 5269.5146 13.083009 + 8650 16738.474 0 0 5269.5195 13.083048 + 8700 16738.478 0 0 5269.5208 13.083058 + 8750 16738.477 0 0 5269.5206 13.083056 + 8800 16738.476 0 0 5269.5203 13.083054 + 8850 16738.477 0 0 5269.5206 13.083056 + 8900 16738.476 0 0 5269.5203 13.083054 + 8950 16738.468 0 0 5269.5177 13.083034 + 9000 16738.451 0 0 5269.5122 13.082991 + 9050 16738.44 0 0 5269.5089 13.082965 + 9100 16738.448 0 0 5269.5113 13.082984 + 9150 16738.46 0 0 5269.5153 13.083014 + 9200 16738.464 0 0 5269.5163 13.083023 + 9250 16738.462 0 0 5269.5158 13.083019 + 9300 16738.462 0 0 5269.5159 13.08302 + 9350 16738.467 0 0 5269.5174 13.083031 + 9400 16738.472 -0.00023657901 0 5269.5188 13.083039 + 9450 16738.472 0 0 5269.519 13.083044 + 9500 16738.46 0 0 5269.5153 13.083016 + 9550 16738.443 0 0 5269.5099 13.082974 + 9600 16738.441 0 0 5269.5092 13.082967 + 9650 16738.458 -0.00038368065 0 5269.5142 13.083 + 9700 16738.475 -0.00099963025 0 5269.519 13.083029 + 9750 16738.492 -0.0049852397 0 5269.5203 13.082953 + 9800 16738.483 -0.0018715252 0 5269.5204 13.083034 + 9850 16738.477 0 0 5269.5205 13.083063 + 9900 16738.477 -0.0018402419 0 5269.5186 13.083025 + 9950 16738.482 -0.005648013 0 5269.5164 13.082936 + 10000 16738.467 -0.0045058746 0 5269.5129 13.082944 +Loop time of 0.13715 on 1 procs for 10000 steps with 81 atoms + +Performance: 629968.103 tau/day, 72912.975 timesteps/s, 5.906 Matom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0074777 | 0.0074777 | 0.0074777 | 0.0 | 5.45 +Neigh | 0.043608 | 0.043608 | 0.043608 | 0.0 | 31.80 +Comm | 0.0078838 | 0.0078838 | 0.0078838 | 0.0 | 5.75 +Output | 0.002002 | 0.002002 | 0.002002 | 0.0 | 1.46 +Modify | 0.06884 | 0.06884 | 0.06884 | 0.0 | 50.19 +Other | | 0.007339 | | | 5.35 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 63 ave 63 max 63 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19 ave 19 max 19 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19 +Ave neighs/atom = 0.2345679 +Neighbor list builds = 1481 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.nve.early.g++.4 b/examples/rigid/log.25Mar24.rigid.nve.early.g++.4 new file mode 100644 index 0000000000..077e7976b9 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.nve.early.g++.4 @@ -0,0 +1,340 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 + 9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.688 571.72044 0 5265.826 32.006558 + 100 16298.426 136.669 0 5267.6551 16.445373 + 150 16682.627 17.489692 0 5269.4277 14.900277 + 200 16733.935 1.3740602 0 5269.4647 14.569704 + 250 16738.854 -0.15258528 0 5269.4868 14.496759 + 300 16738.584 -0.055187603 0 5269.4992 14.496371 + 350 16738.492 -0.017449036 0 5269.5078 14.496801 + 400 16738.472 -0.006012316 0 5269.513 14.496991 + 450 16738.469 -0.0012715314 0 5269.5169 14.497085 + 500 16738.471 -0.00081065611 0 5269.5177 14.497095 + 550 16738.47 -0.00083201064 0 5269.5175 14.497091 + 600 16738.469 -0.00058353965 0 5269.5174 14.497091 + 650 16738.467 -0.0004722653 0 5269.5169 14.497088 + 700 16738.462 0 0 5269.5158 14.497085 + 750 16738.454 0 0 5269.5134 14.497066 + 800 16738.449 0 0 5269.5116 14.497052 + 850 16738.451 0 0 5269.5123 14.497057 + 900 16738.46 0 0 5269.5151 14.497079 + 950 16738.475 -0.0035324469 0 5269.5163 14.497056 + 1000 16738.603 -0.05113463 0 5269.509 14.496621 + 1050 16737.376 0.32970882 0 5269.5037 14.526144 + 1100 16737.909 0.16215423 0 5269.5038 14.53237 + 1150 16738.719 -0.089236594 0 5269.5074 14.510282 + 1200 16738.477 -0.0075446521 0 5269.513 14.51099 + 1250 16738.458 0 0 5269.5146 14.511061 + 1300 16738.448 0 0 5269.5114 14.511036 + 1350 16738.444 0 0 5269.5102 14.511026 + 1400 16738.449 -0.00044714105 0 5269.5113 14.511031 + 1450 16738.458 -0.0010956657 0 5269.5136 14.511043 + 1500 16738.464 -0.00057735083 0 5269.516 14.511066 + 1550 16738.467 0 0 5269.5173 14.511083 + 1600 16738.469 0 0 5269.5179 14.511087 + 1650 16738.47 0 0 5269.5183 14.511091 + 1700 16738.469 0 0 5269.5181 14.511089 + 1750 16738.464 0 0 5269.5164 14.511076 + 1800 16738.455 0 0 5269.5137 14.511055 + 1850 16738.45 0 0 5269.5121 14.511042 + 1900 16738.453 0 0 5269.513 14.511049 + 1950 16738.468 -0.0031854173 0 5269.5144 14.51102 + 2000 16738.501 -0.01331726 0 5269.5148 14.510906 + 2050 16738.568 -0.036719673 0 5269.5126 14.510668 + 2100 16738.646 -0.063312431 0 5269.5103 14.510597 + 2150 16738.619 -0.05606591 0 5269.5091 14.510608 + 2200 16738.566 -0.038448437 0 5269.5101 14.510779 + 2250 16738.52 -0.023712465 0 5269.5103 14.510906 + 2300 16738.485 -0.01323561 0 5269.5099 14.510971 + 2350 16738.457 -0.0045452995 0 5269.5097 14.511049 + 2400 16738.449 -0.00052013007 0 5269.5113 14.511107 + 2450 16738.461 -0.002321933 0 5269.5132 14.511099 + 2500 16738.474 -0.0051804641 0 5269.5145 14.511103 + 2550 16738.592 -0.04492566 0 5269.5117 14.510696 + 2600 16738.45 -0.0038193536 0 5269.5082 14.510939 + 2650 16733.621 1.5177478 0 5269.5097 14.586333 + 2700 16738.772 -0.1064304 0 5269.5069 14.500913 + 2750 16733.165 1.6598389 0 5269.5082 14.616957 + 2800 16738.577 -0.04523598 0 5269.5068 14.51458 + 2850 16738.475 -0.01269037 0 5269.5073 14.513396 + 2900 16738.449 -0.002688737 0 5269.5089 14.513555 + 2950 16738.465 -0.0082345477 0 5269.5084 14.513515 + 3000 16738.657 -0.071197475 0 5269.5061 14.513024 + 3050 16706.71 9.9435728 0 5269.4634 15.021496 + 3100 16643.257 29.968327 0 5269.5123 14.548247 + 3150 16739.45 -0.33134743 0 5269.4956 13.595814 + 3200 16731.445 2.1723572 0 5269.4792 12.100834 + 3250 16612.686 39.57457 0 5269.4942 13.879807 + 3300 16738.601 -0.059713795 0 5269.4997 12.666612 + 3350 16738.587 -0.044640809 0 5269.5106 12.663574 + 3400 16737.995 0.14468663 0 5269.5136 12.680161 + 3450 16738.607 -0.050706049 0 5269.5107 12.665118 + 3500 16738.819 -0.12122411 0 5269.5069 12.665394 + 3550 16738.498 -0.021940181 0 5269.5052 12.676141 + 3600 16673.205 20.482364 0 5269.4544 13.525704 + 3650 16738.648 -0.074052045 0 5269.5003 12.817014 + 3700 16738.632 -0.07184695 0 5269.4975 12.810978 + 3750 16738.621 -0.07013081 0 5269.4958 12.811663 + 3800 16738.552 -0.044378799 0 5269.4998 12.811871 + 3850 16738.492 -0.015384402 0 5269.5099 12.811397 + 3900 16738.487 -0.0058199162 0 5269.518 12.811514 + 3950 16738.482 -0.0012032457 0 5269.521 12.811589 + 4000 16738.478 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13.052723 + 6350 16738.448 0 0 5269.5115 13.052681 + 6400 16738.439 0 0 5269.5086 13.052658 + 6450 16738.451 0 0 5269.5124 13.052687 + 6500 16738.469 0 0 5269.5181 13.052732 + 6550 16738.478 0 0 5269.5209 13.052754 + 6600 16738.48 0 0 5269.5214 13.052758 + 6650 16738.479 0 0 5269.5213 13.052757 + 6700 16738.48 -0.00057913195 0 5269.521 13.052744 + 6750 16738.483 -0.0025329373 0 5269.5198 13.0527 + 6800 16738.482 -0.0065110047 0 5269.5156 13.052612 + 6850 16738.465 -0.0072245166 0 5269.5095 13.052574 + 6900 16738.436 -0.0036561206 0 5269.5039 13.052609 + 6950 16738.433 -0.0010530752 0 5269.5056 13.052661 + 7000 16738.455 -0.00056878712 0 5269.5132 13.052723 + 7050 16738.475 -0.0011717775 0 5269.5187 13.052755 + 7100 16738.48 -0.00047531448 0 5269.5209 13.052781 + 7150 16738.479 0 0 5269.5211 13.052788 + 7200 16738.478 0 0 5269.5207 13.052785 + 7250 16738.477 0 0 5269.5207 13.052785 + 7300 16738.476 0 0 5269.5201 13.052781 + 7350 16738.466 0 0 5269.5172 13.052758 + 7400 16738.448 0 0 5269.5115 13.052714 + 7450 16738.438 0 0 5269.5083 13.052688 + 7500 16738.448 0 0 5269.5115 13.052713 + 7550 16738.464 -0.00053504439 0 5269.5158 13.052742 + 7600 16738.483 -0.010043243 0 5269.5123 13.052657 + 7650 16738.674 -0.077543714 0 5269.5051 13.052041 + 7700 16736.839 0.49724671 0 5269.502 13.085872 + 7750 16731.931 2.0427465 0 5269.5024 13.190769 + 7800 16738.762 -0.10404434 0 5269.5061 13.082626 + 7850 16738.525 -0.024994385 0 5269.5108 13.082681 + 7900 16738.479 -0.008372534 0 5269.5129 13.082885 + 7950 16738.449 -0.0038549468 0 5269.5079 13.082917 + 8000 16738.441 -0.0016367617 0 5269.5074 13.082937 + 8050 16738.455 -0.0014865651 0 5269.5123 13.082971 + 8100 16738.47 -0.00072796092 0 5269.5175 13.083021 + 8150 16738.476 0 0 5269.5202 13.08305 + 8200 16738.477 0 0 5269.5204 13.083051 + 8250 16738.476 0 0 5269.5201 13.083049 + 8300 16738.474 0 0 5269.5197 13.083046 + 8350 16738.47 0 0 5269.5185 13.083036 + 8400 16738.462 -0.0017116105 0 5269.5142 13.082984 + 8450 16738.447 -0.003289664 0 5269.5078 13.082915 + 8500 16738.429 -0.00098100125 0 5269.5043 13.082918 + 8550 16738.435 0 0 5269.5075 13.082953 + 8600 16738.458 0 0 5269.5146 13.083009 + 8650 16738.474 0 0 5269.5195 13.083048 + 8700 16738.478 0 0 5269.5208 13.083058 + 8750 16738.477 0 0 5269.5206 13.083056 + 8800 16738.476 0 0 5269.5203 13.083054 + 8850 16738.477 0 0 5269.5206 13.083056 + 8900 16738.476 0 0 5269.5203 13.083054 + 8950 16738.468 0 0 5269.5177 13.083034 + 9000 16738.451 0 0 5269.5122 13.082991 + 9050 16738.44 0 0 5269.5089 13.082965 + 9100 16738.448 0 0 5269.5113 13.082984 + 9150 16738.46 0 0 5269.5153 13.083014 + 9200 16738.464 0 0 5269.5163 13.083023 + 9250 16738.462 0 0 5269.5158 13.083019 + 9300 16738.462 0 0 5269.5159 13.08302 + 9350 16738.467 0 0 5269.5174 13.083031 + 9400 16738.472 -0.00023657902 0 5269.5188 13.083039 + 9450 16738.472 0 0 5269.519 13.083044 + 9500 16738.46 0 0 5269.5153 13.083016 + 9550 16738.443 0 0 5269.5099 13.082974 + 9600 16738.441 0 0 5269.5092 13.082967 + 9650 16738.458 -0.00038368067 0 5269.5142 13.083 + 9700 16738.475 -0.00099963027 0 5269.519 13.083029 + 9750 16738.492 -0.00498524 0 5269.5203 13.082953 + 9800 16738.483 -0.0018715253 0 5269.5204 13.083034 + 9850 16738.477 0 0 5269.5205 13.083063 + 9900 16738.477 -0.0018402419 0 5269.5186 13.083025 + 9950 16738.482 -0.0056480132 0 5269.5164 13.082936 + 10000 16738.467 -0.0045058747 0 5269.5129 13.082944 +Loop time of 0.14818 on 4 procs for 10000 steps with 81 atoms + +Performance: 583075.499 tau/day, 67485.590 timesteps/s, 5.466 Matom-step/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0018099 | 0.0023754 | 0.0030445 | 1.0 | 1.60 +Neigh | 0.011989 | 0.012986 | 0.01555 | 1.3 | 8.76 +Comm | 0.062426 | 0.065066 | 0.066364 | 0.6 | 43.91 +Output | 0.0017674 | 0.0019257 | 0.002368 | 0.6 | 1.30 +Modify | 0.050371 | 0.051161 | 0.052809 | 0.4 | 34.53 +Other | | 0.01467 | | | 9.90 + +Nlocal: 20.25 ave 35 max 0 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 41 ave 52 max 30 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 4.75 ave 19 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 19 +Ave neighs/atom = 0.2345679 +Neighbor list builds = 1481 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.nve.g++.1 b/examples/rigid/log.25Mar24.rigid.nve.g++.1 new file mode 100644 index 0000000000..45bfc9f8d4 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.nve.g++.1 @@ -0,0 +1,338 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.688 571.72044 0 5265.826 32.006558 + 100 16298.426 136.669 0 5267.6551 16.445373 + 150 16682.627 17.489692 0 5269.4277 14.900277 + 200 16733.935 1.3740602 0 5269.4647 14.569704 + 250 16738.854 -0.15258528 0 5269.4868 14.496759 + 300 16738.584 -0.055187603 0 5269.4992 14.496371 + 350 16738.492 -0.017449036 0 5269.5078 14.496801 + 400 16738.472 -0.006012316 0 5269.513 14.496991 + 450 16738.469 -0.0012715314 0 5269.5169 14.497085 + 500 16738.471 -0.00081065611 0 5269.5177 14.497095 + 550 16738.47 -0.00083201064 0 5269.5175 14.497091 + 600 16738.469 -0.00058353965 0 5269.5174 14.497091 + 650 16738.467 -0.0004722653 0 5269.5169 14.497088 + 700 16738.462 0 0 5269.5158 14.497085 + 750 16738.454 0 0 5269.5134 14.497066 + 800 16738.449 0 0 5269.5116 14.497052 + 850 16738.451 0 0 5269.5123 14.497057 + 900 16738.46 0 0 5269.5151 14.497079 + 950 16738.475 -0.0035324469 0 5269.5163 14.497056 + 1000 16738.603 -0.05113463 0 5269.509 14.496621 + 1050 16737.376 0.32970882 0 5269.5037 14.526144 + 1100 16737.909 0.16215423 0 5269.5038 14.53237 + 1150 16738.719 -0.089236594 0 5269.5074 14.510282 + 1200 16738.477 -0.0075446521 0 5269.513 14.51099 + 1250 16738.458 0 0 5269.5146 14.511061 + 1300 16738.448 0 0 5269.5114 14.511036 + 1350 16738.444 0 0 5269.5102 14.511026 + 1400 16738.449 -0.00044714105 0 5269.5113 14.511031 + 1450 16738.458 -0.0010956657 0 5269.5136 14.511043 + 1500 16738.464 -0.00057735083 0 5269.516 14.511066 + 1550 16738.467 0 0 5269.5173 14.511083 + 1600 16738.469 0 0 5269.5179 14.511087 + 1650 16738.47 0 0 5269.5183 14.511091 + 1700 16738.469 0 0 5269.5181 14.511089 + 1750 16738.464 0 0 5269.5164 14.511076 + 1800 16738.455 0 0 5269.5137 14.511055 + 1850 16738.45 0 0 5269.5121 14.511042 + 1900 16738.453 0 0 5269.513 14.511049 + 1950 16738.468 -0.0031854173 0 5269.5144 14.51102 + 2000 16738.501 -0.01331726 0 5269.5148 14.510906 + 2050 16738.568 -0.036719673 0 5269.5126 14.510668 + 2100 16738.646 -0.063312431 0 5269.5103 14.510597 + 2150 16738.619 -0.05606591 0 5269.5091 14.510608 + 2200 16738.566 -0.038448437 0 5269.5101 14.510779 + 2250 16738.52 -0.023712465 0 5269.5103 14.510906 + 2300 16738.485 -0.01323561 0 5269.5099 14.510971 + 2350 16738.457 -0.0045452995 0 5269.5097 14.511049 + 2400 16738.449 -0.00052013007 0 5269.5113 14.511107 + 2450 16738.461 -0.002321933 0 5269.5132 14.511099 + 2500 16738.474 -0.0051804641 0 5269.5145 14.511103 + 2550 16738.592 -0.04492566 0 5269.5117 14.510696 + 2600 16738.45 -0.0038193536 0 5269.5082 14.510939 + 2650 16733.621 1.5177478 0 5269.5097 14.586333 + 2700 16738.772 -0.1064304 0 5269.5069 14.500913 + 2750 16733.165 1.6598389 0 5269.5082 14.616957 + 2800 16738.577 -0.04523598 0 5269.5068 14.51458 + 2850 16738.475 -0.01269037 0 5269.5073 14.513396 + 2900 16738.449 -0.002688737 0 5269.5089 14.513555 + 2950 16738.465 -0.0082345477 0 5269.5084 14.513515 + 3000 16738.657 -0.071197475 0 5269.5061 14.513024 + 3050 16706.71 9.9435728 0 5269.4634 15.021496 + 3100 16643.257 29.968327 0 5269.5123 14.548247 + 3150 16739.45 -0.33134743 0 5269.4956 13.595814 + 3200 16731.445 2.1723572 0 5269.4792 12.100834 + 3250 16612.686 39.57457 0 5269.4942 13.879807 + 3300 16738.601 -0.059713795 0 5269.4997 12.666612 + 3350 16738.587 -0.044640809 0 5269.5106 12.663574 + 3400 16737.995 0.14468663 0 5269.5136 12.680161 + 3450 16738.607 -0.050706049 0 5269.5107 12.665118 + 3500 16738.819 -0.12122411 0 5269.5069 12.665394 + 3550 16738.498 -0.021940182 0 5269.5052 12.676141 + 3600 16673.205 20.482364 0 5269.4544 13.525704 + 3650 16738.648 -0.074052044 0 5269.5003 12.817014 + 3700 16738.632 -0.07184695 0 5269.4975 12.810978 + 3750 16738.621 -0.07013081 0 5269.4958 12.811663 + 3800 16738.552 -0.044378799 0 5269.4998 12.811871 + 3850 16738.492 -0.015384402 0 5269.5099 12.811397 + 3900 16738.487 -0.0058199162 0 5269.518 12.811514 + 3950 16738.482 -0.0012032457 0 5269.521 12.811589 + 4000 16738.478 -0.00020707654 0 5269.5208 12.811606 + 4050 16738.477 0 0 5269.5207 12.811608 + 4100 16738.477 0 0 5269.5206 12.811607 + 4150 16738.475 0 0 5269.5199 12.811602 + 4200 16738.464 0 0 5269.5165 12.811576 + 4250 16738.446 0 0 5269.5109 12.811532 + 4300 16738.44 0 0 5269.5089 12.811516 + 4350 16738.454 0 0 5269.5131 12.811549 + 4400 16738.468 0 0 5269.5177 12.811585 + 4450 16738.47 0 0 5269.5184 12.811591 + 4500 16738.466 0 0 5269.517 12.811579 + 4550 16738.463 0 0 5269.5162 12.811573 + 4600 16738.466 0 0 5269.517 12.81158 + 4650 16738.471 0 0 5269.5186 12.811592 + 4700 16738.47 0 0 5269.5182 12.811589 + 4750 16738.456 0 0 5269.5139 12.811556 + 4800 16738.441 0 0 5269.5091 12.811518 + 4850 16738.444 0 0 5269.5102 12.811526 + 4900 16738.462 0 0 5269.5159 12.81157 + 4950 16738.475 0 0 5269.5201 12.811603 + 5000 16738.479 0 0 5269.5212 12.811612 + 5050 16738.479 0 0 5269.5212 12.811612 + 5100 16738.479 0 0 5269.5212 12.811612 + 5150 16738.478 0 0 5269.5209 12.81161 + 5200 16738.472 0 0 5269.519 12.811595 + 5250 16738.456 0 0 5269.5138 12.811555 + 5300 16738.432 0 0 5269.5064 12.811497 + 5350 16738.422 0 0 5269.5033 12.811472 + 5400 16738.438 0 0 5269.5082 12.81151 + 5450 16738.46 0 0 5269.515 12.811564 + 5500 16738.471 -0.0002100851 0 5269.5183 12.811588 + 5550 16738.481 -0.003484166 0 5269.5185 12.811534 + 5600 16738.542 -0.024500002 0 5269.5164 12.81122 + 5650 16738.641 -0.058023282 0 5269.5142 12.812225 + 5700 16384.935 111.24508 0 5269.4653 26.09278 + 5750 16738.555 -0.030778873 0 5269.5142 13.052328 + 5800 16738.462 -0.0034050629 0 5269.5125 13.052653 + 5850 16738.441 -0.00034406845 0 5269.5089 13.052656 + 5900 16738.443 0 0 5269.5098 13.052667 + 5950 16738.459 0 0 5269.5149 13.052707 + 6000 16738.468 0 0 5269.5177 13.052729 + 6050 16738.466 0 0 5269.5172 13.052725 + 6100 16738.462 0 0 5269.516 13.052715 + 6150 16738.463 0 0 5269.5162 13.052717 + 6200 16738.468 0 0 5269.5178 13.052729 + 6250 16738.472 0 0 5269.5189 13.052738 + 6300 16738.465 0 0 5269.5169 13.052723 + 6350 16738.448 0 0 5269.5115 13.052681 + 6400 16738.439 0 0 5269.5086 13.052658 + 6450 16738.451 0 0 5269.5124 13.052687 + 6500 16738.469 0 0 5269.5181 13.052732 + 6550 16738.478 0 0 5269.5209 13.052754 + 6600 16738.48 0 0 5269.5214 13.052758 + 6650 16738.479 0 0 5269.5213 13.052757 + 6700 16738.48 -0.00057913194 0 5269.521 13.052744 + 6750 16738.483 -0.0025329373 0 5269.5198 13.0527 + 6800 16738.482 -0.0065110045 0 5269.5156 13.052612 + 6850 16738.465 -0.0072245165 0 5269.5095 13.052574 + 6900 16738.436 -0.0036561206 0 5269.5039 13.052609 + 6950 16738.433 -0.0010530752 0 5269.5056 13.052661 + 7000 16738.455 -0.00056878712 0 5269.5132 13.052723 + 7050 16738.475 -0.0011717775 0 5269.5187 13.052755 + 7100 16738.48 -0.00047531448 0 5269.5209 13.052781 + 7150 16738.479 0 0 5269.5211 13.052788 + 7200 16738.478 0 0 5269.5207 13.052785 + 7250 16738.477 0 0 5269.5207 13.052785 + 7300 16738.476 0 0 5269.5201 13.052781 + 7350 16738.466 0 0 5269.5172 13.052758 + 7400 16738.448 0 0 5269.5115 13.052714 + 7450 16738.438 0 0 5269.5083 13.052688 + 7500 16738.448 0 0 5269.5115 13.052713 + 7550 16738.464 -0.00053504438 0 5269.5158 13.052742 + 7600 16738.483 -0.010043243 0 5269.5123 13.052657 + 7650 16738.674 -0.077543712 0 5269.5051 13.052041 + 7700 16736.839 0.49724664 0 5269.502 13.085872 + 7750 16731.931 2.0427463 0 5269.5024 13.190769 + 7800 16738.762 -0.10404434 0 5269.5061 13.082626 + 7850 16738.525 -0.024994384 0 5269.5108 13.082681 + 7900 16738.479 -0.008372534 0 5269.5129 13.082885 + 7950 16738.449 -0.0038549468 0 5269.5079 13.082917 + 8000 16738.441 -0.0016367618 0 5269.5074 13.082937 + 8050 16738.455 -0.0014865651 0 5269.5123 13.082971 + 8100 16738.47 -0.00072796093 0 5269.5175 13.083021 + 8150 16738.476 0 0 5269.5202 13.08305 + 8200 16738.477 0 0 5269.5204 13.083051 + 8250 16738.476 0 0 5269.5201 13.083049 + 8300 16738.474 0 0 5269.5197 13.083046 + 8350 16738.47 0 0 5269.5185 13.083036 + 8400 16738.462 -0.0017116105 0 5269.5142 13.082984 + 8450 16738.447 -0.003289664 0 5269.5078 13.082915 + 8500 16738.429 -0.00098100125 0 5269.5043 13.082918 + 8550 16738.435 0 0 5269.5075 13.082953 + 8600 16738.458 0 0 5269.5146 13.083009 + 8650 16738.474 0 0 5269.5195 13.083048 + 8700 16738.478 0 0 5269.5208 13.083058 + 8750 16738.477 0 0 5269.5206 13.083056 + 8800 16738.476 0 0 5269.5203 13.083054 + 8850 16738.477 0 0 5269.5206 13.083056 + 8900 16738.476 0 0 5269.5203 13.083054 + 8950 16738.468 0 0 5269.5177 13.083034 + 9000 16738.451 0 0 5269.5122 13.082991 + 9050 16738.44 0 0 5269.5089 13.082965 + 9100 16738.448 0 0 5269.5113 13.082984 + 9150 16738.46 0 0 5269.5153 13.083014 + 9200 16738.464 0 0 5269.5163 13.083023 + 9250 16738.462 0 0 5269.5158 13.083019 + 9300 16738.462 0 0 5269.5159 13.08302 + 9350 16738.467 0 0 5269.5174 13.083031 + 9400 16738.472 -0.00023657901 0 5269.5188 13.083039 + 9450 16738.472 0 0 5269.519 13.083044 + 9500 16738.46 0 0 5269.5153 13.083016 + 9550 16738.443 0 0 5269.5099 13.082974 + 9600 16738.441 0 0 5269.5092 13.082967 + 9650 16738.458 -0.00038368065 0 5269.5142 13.083 + 9700 16738.475 -0.00099963025 0 5269.519 13.083029 + 9750 16738.492 -0.0049852397 0 5269.5203 13.082953 + 9800 16738.483 -0.0018715252 0 5269.5204 13.083034 + 9850 16738.477 0 0 5269.5205 13.083063 + 9900 16738.477 -0.0018402419 0 5269.5186 13.083025 + 9950 16738.482 -0.005648013 0 5269.5164 13.082936 + 10000 16738.467 -0.0045058746 0 5269.5129 13.082944 +Loop time of 0.139287 on 1 procs for 10000 steps with 81 atoms + +Performance: 620300.751 tau/day, 71794.068 timesteps/s, 5.815 Matom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0074128 | 0.0074128 | 0.0074128 | 0.0 | 5.32 +Neigh | 0.045566 | 0.045566 | 0.045566 | 0.0 | 32.71 +Comm | 0.007912 | 0.007912 | 0.007912 | 0.0 | 5.68 +Output | 0.0015912 | 0.0015912 | 0.0015912 | 0.0 | 1.14 +Modify | 0.06951 | 0.06951 | 0.06951 | 0.0 | 49.90 +Other | | 0.007295 | | | 5.24 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 63 ave 63 max 63 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19 ave 19 max 19 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 19 +Ave neighs/atom = 0.2345679 +Neighbor list builds = 1481 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.nve.g++.4 b/examples/rigid/log.25Mar24.rigid.nve.g++.4 new file mode 100644 index 0000000000..af3c1c6489 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.nve.g++.4 @@ -0,0 +1,338 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.688 571.72044 0 5265.826 32.006558 + 100 16298.426 136.669 0 5267.6551 16.445373 + 150 16682.627 17.489692 0 5269.4277 14.900277 + 200 16733.935 1.3740602 0 5269.4647 14.569704 + 250 16738.854 -0.15258528 0 5269.4868 14.496759 + 300 16738.584 -0.055187603 0 5269.4992 14.496371 + 350 16738.492 -0.017449036 0 5269.5078 14.496801 + 400 16738.472 -0.006012316 0 5269.513 14.496991 + 450 16738.469 -0.0012715314 0 5269.5169 14.497085 + 500 16738.471 -0.00081065611 0 5269.5177 14.497095 + 550 16738.47 -0.00083201064 0 5269.5175 14.497091 + 600 16738.469 -0.00058353965 0 5269.5174 14.497091 + 650 16738.467 -0.0004722653 0 5269.5169 14.497088 + 700 16738.462 0 0 5269.5158 14.497085 + 750 16738.454 0 0 5269.5134 14.497066 + 800 16738.449 0 0 5269.5116 14.497052 + 850 16738.451 0 0 5269.5123 14.497057 + 900 16738.46 0 0 5269.5151 14.497079 + 950 16738.475 -0.0035324469 0 5269.5163 14.497056 + 1000 16738.603 -0.05113463 0 5269.509 14.496621 + 1050 16737.376 0.32970882 0 5269.5037 14.526144 + 1100 16737.909 0.16215423 0 5269.5038 14.53237 + 1150 16738.719 -0.089236594 0 5269.5074 14.510282 + 1200 16738.477 -0.0075446521 0 5269.513 14.51099 + 1250 16738.458 0 0 5269.5146 14.511061 + 1300 16738.448 0 0 5269.5114 14.511036 + 1350 16738.444 0 0 5269.5102 14.511026 + 1400 16738.449 -0.00044714105 0 5269.5113 14.511031 + 1450 16738.458 -0.0010956657 0 5269.5136 14.511043 + 1500 16738.464 -0.00057735083 0 5269.516 14.511066 + 1550 16738.467 0 0 5269.5173 14.511083 + 1600 16738.469 0 0 5269.5179 14.511087 + 1650 16738.47 0 0 5269.5183 14.511091 + 1700 16738.469 0 0 5269.5181 14.511089 + 1750 16738.464 0 0 5269.5164 14.511076 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2800 16738.577 -0.04523598 0 5269.5068 14.51458 + 2850 16738.475 -0.01269037 0 5269.5073 14.513396 + 2900 16738.449 -0.002688737 0 5269.5089 14.513555 + 2950 16738.465 -0.0082345477 0 5269.5084 14.513515 + 3000 16738.657 -0.071197475 0 5269.5061 14.513024 + 3050 16706.71 9.9435728 0 5269.4634 15.021496 + 3100 16643.257 29.968327 0 5269.5123 14.548247 + 3150 16739.45 -0.33134743 0 5269.4956 13.595814 + 3200 16731.445 2.1723572 0 5269.4792 12.100834 + 3250 16612.686 39.57457 0 5269.4942 13.879807 + 3300 16738.601 -0.059713795 0 5269.4997 12.666612 + 3350 16738.587 -0.044640809 0 5269.5106 12.663574 + 3400 16737.995 0.14468663 0 5269.5136 12.680161 + 3450 16738.607 -0.050706049 0 5269.5107 12.665118 + 3500 16738.819 -0.12122411 0 5269.5069 12.665394 + 3550 16738.498 -0.021940181 0 5269.5052 12.676141 + 3600 16673.205 20.482364 0 5269.4544 13.525704 + 3650 16738.648 -0.074052045 0 5269.5003 12.817014 + 3700 16738.632 -0.07184695 0 5269.4975 12.810978 + 3750 16738.621 -0.07013081 0 5269.4958 12.811663 + 3800 16738.552 -0.044378799 0 5269.4998 12.811871 + 3850 16738.492 -0.015384402 0 5269.5099 12.811397 + 3900 16738.487 -0.0058199162 0 5269.518 12.811514 + 3950 16738.482 -0.0012032457 0 5269.521 12.811589 + 4000 16738.478 -0.00020707654 0 5269.5208 12.811606 + 4050 16738.477 0 0 5269.5207 12.811608 + 4100 16738.477 0 0 5269.5206 12.811607 + 4150 16738.475 0 0 5269.5199 12.811602 + 4200 16738.464 0 0 5269.5165 12.811576 + 4250 16738.446 0 0 5269.5109 12.811532 + 4300 16738.44 0 0 5269.5089 12.811516 + 4350 16738.454 0 0 5269.5131 12.811549 + 4400 16738.468 0 0 5269.5177 12.811585 + 4450 16738.47 0 0 5269.5184 12.811591 + 4500 16738.466 0 0 5269.517 12.811579 + 4550 16738.463 0 0 5269.5162 12.811573 + 4600 16738.466 0 0 5269.517 12.81158 + 4650 16738.471 0 0 5269.5186 12.811592 + 4700 16738.47 0 0 5269.5182 12.811589 + 4750 16738.456 0 0 5269.5139 12.811556 + 4800 16738.441 0 0 5269.5091 12.811518 + 4850 16738.444 0 0 5269.5102 12.811526 + 4900 16738.462 0 0 5269.5159 12.81157 + 4950 16738.475 0 0 5269.5201 12.811603 + 5000 16738.479 0 0 5269.5212 12.811612 + 5050 16738.479 0 0 5269.5212 12.811612 + 5100 16738.479 0 0 5269.5212 12.811612 + 5150 16738.478 0 0 5269.5209 12.81161 + 5200 16738.472 0 0 5269.519 12.811595 + 5250 16738.456 0 0 5269.5138 12.811555 + 5300 16738.432 0 0 5269.5064 12.811497 + 5350 16738.422 0 0 5269.5033 12.811472 + 5400 16738.438 0 0 5269.5082 12.81151 + 5450 16738.46 0 0 5269.515 12.811564 + 5500 16738.471 -0.0002100851 0 5269.5183 12.811588 + 5550 16738.481 -0.003484166 0 5269.5185 12.811534 + 5600 16738.542 -0.024500002 0 5269.5164 12.81122 + 5650 16738.641 -0.058023282 0 5269.5142 12.812225 + 5700 16384.935 111.24508 0 5269.4653 26.09278 + 5750 16738.555 -0.030778873 0 5269.5142 13.052328 + 5800 16738.462 -0.0034050628 0 5269.5125 13.052653 + 5850 16738.441 -0.00034406845 0 5269.5089 13.052656 + 5900 16738.443 0 0 5269.5098 13.052667 + 5950 16738.459 0 0 5269.5149 13.052707 + 6000 16738.468 0 0 5269.5177 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5269.5209 13.052781 + 7150 16738.479 0 0 5269.5211 13.052788 + 7200 16738.478 0 0 5269.5207 13.052785 + 7250 16738.477 0 0 5269.5207 13.052785 + 7300 16738.476 0 0 5269.5201 13.052781 + 7350 16738.466 0 0 5269.5172 13.052758 + 7400 16738.448 0 0 5269.5115 13.052714 + 7450 16738.438 0 0 5269.5083 13.052688 + 7500 16738.448 0 0 5269.5115 13.052713 + 7550 16738.464 -0.00053504439 0 5269.5158 13.052742 + 7600 16738.483 -0.010043243 0 5269.5123 13.052657 + 7650 16738.674 -0.077543714 0 5269.5051 13.052041 + 7700 16736.839 0.49724671 0 5269.502 13.085872 + 7750 16731.931 2.0427465 0 5269.5024 13.190769 + 7800 16738.762 -0.10404434 0 5269.5061 13.082626 + 7850 16738.525 -0.024994385 0 5269.5108 13.082681 + 7900 16738.479 -0.008372534 0 5269.5129 13.082885 + 7950 16738.449 -0.0038549468 0 5269.5079 13.082917 + 8000 16738.441 -0.0016367617 0 5269.5074 13.082937 + 8050 16738.455 -0.0014865651 0 5269.5123 13.082971 + 8100 16738.47 -0.00072796092 0 5269.5175 13.083021 + 8150 16738.476 0 0 5269.5202 13.08305 + 8200 16738.477 0 0 5269.5204 13.083051 + 8250 16738.476 0 0 5269.5201 13.083049 + 8300 16738.474 0 0 5269.5197 13.083046 + 8350 16738.47 0 0 5269.5185 13.083036 + 8400 16738.462 -0.0017116105 0 5269.5142 13.082984 + 8450 16738.447 -0.003289664 0 5269.5078 13.082915 + 8500 16738.429 -0.00098100125 0 5269.5043 13.082918 + 8550 16738.435 0 0 5269.5075 13.082953 + 8600 16738.458 0 0 5269.5146 13.083009 + 8650 16738.474 0 0 5269.5195 13.083048 + 8700 16738.478 0 0 5269.5208 13.083058 + 8750 16738.477 0 0 5269.5206 13.083056 + 8800 16738.476 0 0 5269.5203 13.083054 + 8850 16738.477 0 0 5269.5206 13.083056 + 8900 16738.476 0 0 5269.5203 13.083054 + 8950 16738.468 0 0 5269.5177 13.083034 + 9000 16738.451 0 0 5269.5122 13.082991 + 9050 16738.44 0 0 5269.5089 13.082965 + 9100 16738.448 0 0 5269.5113 13.082984 + 9150 16738.46 0 0 5269.5153 13.083014 + 9200 16738.464 0 0 5269.5163 13.083023 + 9250 16738.462 0 0 5269.5158 13.083019 + 9300 16738.462 0 0 5269.5159 13.08302 + 9350 16738.467 0 0 5269.5174 13.083031 + 9400 16738.472 -0.00023657902 0 5269.5188 13.083039 + 9450 16738.472 0 0 5269.519 13.083044 + 9500 16738.46 0 0 5269.5153 13.083016 + 9550 16738.443 0 0 5269.5099 13.082974 + 9600 16738.441 0 0 5269.5092 13.082967 + 9650 16738.458 -0.00038368067 0 5269.5142 13.083 + 9700 16738.475 -0.00099963027 0 5269.519 13.083029 + 9750 16738.492 -0.00498524 0 5269.5203 13.082953 + 9800 16738.483 -0.0018715253 0 5269.5204 13.083034 + 9850 16738.477 0 0 5269.5205 13.083063 + 9900 16738.477 -0.0018402419 0 5269.5186 13.083025 + 9950 16738.482 -0.0056480132 0 5269.5164 13.082936 + 10000 16738.467 -0.0045058747 0 5269.5129 13.082944 +Loop time of 0.147071 on 4 procs for 10000 steps with 81 atoms + +Performance: 587469.667 tau/day, 67994.174 timesteps/s, 5.508 Matom-step/s +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0016588 | 0.0023518 | 0.0030017 | 1.0 | 1.60 +Neigh | 0.011581 | 0.012949 | 0.014883 | 1.1 | 8.80 +Comm | 0.063654 | 0.065097 | 0.066501 | 0.4 | 44.26 +Output | 0.0017378 | 0.0018782 | 0.0022756 | 0.5 | 1.28 +Modify | 0.049872 | 0.050432 | 0.051195 | 0.2 | 34.29 +Other | | 0.01436 | | | 9.77 + +Nlocal: 20.25 ave 35 max 0 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 41 ave 52 max 30 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 4.75 ave 19 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 19 +Ave neighs/atom = 0.2345679 +Neighbor list builds = 1481 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.poems.g++.1 b/examples/rigid/log.25Mar24.rigid.poems.g++.1 new file mode 100644 index 0000000000..0e69724dda --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems.g++.1 @@ -0,0 +1,328 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384279 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184717 + 1150 20849.582 206.01695 0 3680.9472 -0.86699135 + 1200 21815.003 45.317412 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.06408 + 1300 20780.781 217.36509 0 3680.8286 6.0538614 + 1350 20558.971 254.36485 0 3680.8601 -3.6773923 + 1400 21485.029 99.812891 0 3680.6511 -16.185475 + 1450 21771.107 52.159624 0 3680.6775 -2.4756668 + 1500 21520.948 93.503905 0 3680.3286 2.1023577 + 1550 21351.418 121.68136 0 3680.2511 5.5159922 + 1600 20778.805 216.92182 0 3680.0559 15.089193 + 1650 21477.637 100.21853 0 3679.8247 -1.1045536 + 1700 18501.335 596.47986 0 3680.0357 -15.679729 + 1750 18563.64 587.34819 0 3681.2882 33.532254 + 1800 19110.181 494.82407 0 3679.8543 18.02406 + 1850 21364.186 119.23625 0 3679.9339 2.5290683 + 1900 20146.613 322.15086 0 3679.9197 5.7314718 + 1950 20692.671 231.25334 0 3680.0319 4.2977791 + 2000 20943.905 189.11211 0 3679.7629 -22.644575 + 2050 19667.965 401.84519 0 3679.8394 3.6247265 + 2100 20280.309 299.78396 0 3679.8355 7.4806221 + 2150 19181.565 483.57073 0 3680.4982 22.62593 + 2200 21300.569 130.63684 0 3680.7316 4.7090558 + 2250 20486.112 266.77753 0 3681.1296 -8.6505201 + 2300 18651.193 572.56862 0 3681.1008 -5.2604682 + 2350 21514.435 95.462414 0 3681.2016 -9.3718933 + 2400 21464.75 103.81741 0 3681.2757 -29.521964 + 2450 20103.185 331.7557 0 3682.2865 35.600257 + 2500 20767.309 221.18002 0 3682.3981 -12.41075 + 2550 20461.88 271.93545 0 3682.2488 -22.542329 + 2600 21463.807 104.97703 0 3682.2782 -10.118749 + 2650 20902.135 198.66716 0 3682.3564 5.0103958 + 2700 18582.384 585.6465 0 3682.7106 22.212808 + 2750 21079.961 168.86261 0 3682.1894 -8.8401109 + 2800 21425.876 111.18035 0 3682.1598 -6.7933883 + 2850 17414.605 780.0645 0 3682.4987 28.180022 + 2900 19978.961 352.1845 0 3682.0113 8.4280816 + 2950 21189.046 150.47808 0 3681.9858 2.8898793 + 3000 19271.367 469.54947 0 3681.4439 -7.1530396 + 3050 21470.889 103.45294 0 3681.9344 -1.4975516 + 3100 21574.513 85.87604 0 3681.6282 7.0301554 + 3150 21649.42 73.506656 0 3681.7434 1.6649326 + 3200 20857.44 205.3704 0 3681.6104 2.9318184 + 3250 18573.575 585.73328 0 3681.3292 5.9394399 + 3300 17938.353 691.67199 0 3681.3975 9.7205454 + 3350 18668.795 570.23722 0 3681.7031 3.6442733 + 3400 16834.721 876.36804 0 3682.1548 21.869594 + 3450 20148.848 323.06988 0 3681.2112 3.8120475 + 3500 21039.942 175.06064 0 3681.7177 1.4965105 + 3550 21439.472 108.66655 0 3681.9119 4.192594 + 3600 21457.784 105.54883 0 3681.8461 -2.932673 + 3650 21409.999 113.49591 0 3681.829 -15.09817 + 3700 21380.023 118.56895 0 3681.9061 -15.461367 + 3750 20422.085 277.28852 0 3680.9694 19.331799 + 3800 18275.038 635.75951 0 3681.5992 22.413362 + 3850 20906.341 197.06897 0 3681.4592 2.5691289 + 3900 20041.032 341.11847 0 3681.2905 1.8089245 + 3950 18917.084 528.44677 0 3681.2941 -10.656627 + 4000 20425.89 276.98688 0 3681.3018 7.5960674 + 4050 18289.157 633.13575 0 3681.3286 6.5695895 + 4100 19601.884 414.64621 0 3681.6269 8.6144847 + 4150 20790.308 216.9575 0 3682.0088 1.6300255 + 4200 21043.169 174.98738 0 3682.1822 3.8942459 + 4250 19073.45 503.63057 0 3682.5389 -10.975988 + 4300 21251.971 140.63454 0 3682.6298 -7.7937426 + 4350 20844.867 208.08653 0 3682.2311 -10.295096 + 4400 20869.781 203.57469 0 3681.8716 -8.7176985 + 4450 20384.41 284.19751 0 3681.5992 3.9044821 + 4500 20002.241 346.95848 0 3680.6654 12.100678 + 4550 21410.259 112.40994 0 3680.7864 -6.6653767 + 4600 18230.418 641.88921 0 3680.2922 22.502391 + 4650 21319.778 127.76737 0 3681.0638 -0.50309316 + 4700 19429.05 441.85455 0 3680.0296 20.851722 + 4750 20395.967 281.13332 0 3680.4611 12.635024 + 4800 19405.371 446.47714 0 3680.7056 -3.0340076 + 4850 19935.979 358.4478 0 3681.1109 -7.9390554 + 4900 18822.801 543.80607 0 3680.9396 -3.1086099 + 4950 20569.881 252.87963 0 3681.1932 11.807076 + 5000 20311.182 296.63458 0 3681.8315 -4.2409472 + 5050 20187.672 316.83663 0 3681.4486 1.8723981 + 5100 17439.679 775.35516 0 3681.9684 -5.7037267 + 5150 20394.4 282.56755 0 3681.6342 4.3399253 + 5200 20294.84 299.10095 0 3681.5742 -9.9868412 + 5250 20396.122 282.31614 0 3681.6698 -4.9932521 + 5300 20617.465 245.11679 0 3681.3609 0.97429493 + 5350 21651.191 72.878802 0 3681.4106 2.0913693 + 5400 19097.721 498.69617 0 3681.6496 21.808511 + 5450 21856.73 38.930299 0 3681.7186 -4.0225451 + 5500 20087.477 334.09405 0 3682.0069 5.7109498 + 5550 17734.477 726.10594 0 3681.8522 16.277738 + 5600 21183.231 151.714 0 3682.2525 -2.1080998 + 5650 20832.185 210.14251 0 3682.1733 -8.0602581 + 5700 18879.226 535.50935 0 3682.0471 -14.351666 + 5750 18931.81 529.67506 0 3684.9768 4.8675164 + 5800 21674.979 70.259619 0 3682.7561 -14.990544 + 5850 21395.905 116.47471 0 3682.4588 -0.94334402 + 5900 18532.955 593.27143 0 3682.0973 26.072477 + 5950 20767.534 220.78554 0 3682.0413 -1.6468662 + 6000 21546.127 91.167146 0 3682.1882 -5.4664857 + 6050 20085.534 334.40872 0 3681.9977 -0.34825498 + 6100 21218.156 145.88926 0 3682.2486 2.2871905 + 6150 20902.857 198.59424 0 3682.4038 6.0082154 + 6200 21726.547 61.195607 0 3682.2868 -2.2981656 + 6250 17507.589 764.20763 0 3682.1392 9.4977327 + 6300 21687.283 67.283821 0 3681.831 -8.694756 + 6350 19806.474 380.24632 0 3681.3254 -0.94067379 + 6400 21128.461 160.65399 0 3682.0641 -4.8435757 + 6450 19747.214 390.89694 0 3682.0992 1.9108969 + 6500 20460.408 272.79545 0 3682.8634 -4.1094877 + 6550 16740.095 892.11547 0 3682.1313 13.20551 + 6600 18326.164 628.80415 0 3683.1648 -19.884336 + 6650 18469.284 605.36384 0 3683.5778 10.345658 + 6700 21086.876 168.61821 0 3683.0976 -0.036118094 + 6750 19924.801 361.46485 0 3682.2649 -2.1144953 + 6800 19812.028 380.5919 0 3682.5966 11.119936 + 6850 19118.501 496.38857 0 3682.8054 0.53906703 + 6900 19221.04 478.31879 0 3681.8255 11.13851 + 6950 20482.79 269.03445 0 3682.8328 2.6705981 + 7000 16350.403 957.96283 0 3683.03 -2.9783385 + 7050 20789.906 218.36242 0 3683.3467 4.2465754 + 7100 17718.126 730.09011 0 3683.111 15.271811 + 7150 19020.414 513.34591 0 3683.4149 -8.3035633 + 7200 21165.007 156.24494 0 3683.7461 -7.3085107 + 7250 20520.422 264.35574 0 3684.4261 -6.7803072 + 7300 19078.795 505.10953 0 3684.9087 -11.147107 + 7350 20529.173 263.85389 0 3685.3827 0.59881989 + 7400 20548.068 261.27337 0 3685.9513 -5.0067382 + 7450 20849.172 211.46852 0 3686.3306 -0.80175538 + 7500 20869.894 207.95335 0 3686.2689 0.44541197 + 7550 18490.583 605.63557 0 3687.3993 -11.744631 + 7600 19185.381 488.52218 0 3686.0857 3.0881652 + 7650 20520.848 265.65037 0 3685.7917 -0.28165722 + 7700 20599.631 251.69265 0 3684.9645 0.19835423 + 7750 18428.55 614.11446 0 3685.5395 5.8092563 + 7800 19660.337 408.61674 0 3685.3396 4.9902979 + 7850 19409.663 450.30454 0 3685.2483 8.8641567 + 7900 21307.628 133.95865 0 3685.23 -1.8297128 + 7950 17828.245 713.05722 0 3684.4314 5.9673166 + 8000 15894.788 1036.4896 0 3685.621 57.567209 + 8050 18588.022 587.45738 0 3685.4611 1.5643233 + 8100 20664.194 241.59965 0 3685.632 -4.9298687 + 8150 17745.538 728.43249 0 3686.0221 6.121885 + 8200 18433.239 612.84747 0 3685.0539 17.078623 + 8250 19162.628 492.52511 0 3686.2965 12.204945 + 8300 18507.768 602.21188 0 3686.8399 -14.003487 + 8350 21010.715 184.80032 0 3686.5861 -0.93351338 + 8400 20888.233 205.24214 0 3686.6143 -5.3433619 + 8450 20920.621 199.6941 0 3686.4643 -30.437742 + 8500 17085.22 840.80474 0 3688.3414 3.9123878 + 8550 20900.377 203.87077 0 3687.267 -6.7525851 + 8600 19771.517 392.67499 0 3687.9278 13.762684 + 8650 19541.099 431.09497 0 3687.9448 2.0785077 + 8700 21056.327 178.88314 0 3688.2709 -13.663758 + 8750 20109.075 336.93228 0 3688.4447 -1.0445182 + 8800 21821.77 51.337654 0 3688.2993 -10.263971 + 8850 17653.401 740.45074 0 3682.6842 49.147758 + 8900 20311.01 302.92663 0 3688.095 -8.1910583 + 8950 19745.488 396.38557 0 3687.3003 -16.948557 + 9000 20248.989 311.52221 0 3686.3537 -2.4158415 + 9050 17850.649 710.17969 0 3685.2878 25.692377 + 9100 19370.284 456.73812 0 3685.1187 -21.201413 + 9150 20452.896 276.95741 0 3685.7735 2.0316457 + 9200 19174.266 488.9925 0 3684.7035 10.317202 + 9250 20174.171 323.4614 0 3685.8232 -2.1072552 + 9300 21442.761 111.68542 0 3685.479 -12.303658 + 9350 19697.287 402.21503 0 3685.0963 8.4697153 + 9400 21553.763 93.03581 0 3685.3297 -6.7286485 + 9450 18946.935 527.04498 0 3684.8674 -6.6174191 + 9500 21162.915 158.64321 0 3685.7957 -3.2085936 + 9550 20704.844 235.41227 0 3686.2196 10.847095 + 9600 20664.074 242.09733 0 3686.1096 3.7301969 + 9650 20829.655 214.20146 0 3685.8107 7.2197609 + 9700 17336.625 797.22781 0 3686.6654 14.775351 + 9750 19978.15 356.51126 0 3686.2029 -1.1978838 + 9800 21150.487 162.1616 0 3687.2427 -15.596643 + 9850 20849.962 213.10316 0 3688.0968 -5.5443282 + 9900 18407.158 620.93592 0 3688.7956 10.177471 + 9950 20459.637 278.24203 0 3688.1815 0.0020687238 + 10000 21667.112 78.10938 0 3689.2948 -12.660594 +Loop time of 3.06048 on 1 procs for 10000 steps with 81 atoms + +Performance: 28230.843 tau/day, 3267.459 timesteps/s, 264.664 katom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.11571 | 0.11571 | 0.11571 | 0.0 | 3.78 +Neigh | 0.094982 | 0.094982 | 0.094982 | 0.0 | 3.10 +Comm | 0.0098585 | 0.0098585 | 0.0098585 | 0.0 | 0.32 +Output | 0.003355 | 0.003355 | 0.003355 | 0.0 | 0.11 +Modify | 2.8226 | 2.8226 | 2.8226 | 0.0 | 92.23 +Other | | 0.01395 | | | 0.46 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 115 ave 115 max 115 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 808 ave 808 max 808 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 808 +Ave neighs/atom = 9.9753086 +Neighbor list builds = 1162 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems.g++.4 b/examples/rigid/log.25Mar24.rigid.poems.g++.4 new file mode 100644 index 0000000000..b75701792d --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems.g++.4 @@ -0,0 +1,328 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384277 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184718 + 1150 20849.582 206.01695 0 3680.9472 -0.86699156 + 1200 21815.003 45.317416 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064076 + 1300 20780.781 217.36505 0 3680.8286 6.0538619 + 1350 20558.972 254.36481 0 3680.8601 -3.6773978 + 1400 21485.029 99.812941 0 3680.6511 -16.185471 + 1450 21771.108 52.159596 0 3680.6775 -2.4756679 + 1500 21520.948 93.503942 0 3680.3286 2.1023578 + 1550 21351.418 121.6814 0 3680.2511 5.5159969 + 1600 20778.805 216.92173 0 3680.0559 15.089183 + 1650 21477.639 100.21825 0 3679.8247 -1.1045878 + 1700 18501.342 596.47873 0 3680.0357 -15.679646 + 1750 18563.643 587.34777 0 3681.2882 33.532181 + 1800 19110.189 494.82286 0 3679.8543 18.024038 + 1850 21364.195 119.2348 0 3679.9339 2.5291365 + 1900 20146.638 322.1467 0 3679.9197 5.7312008 + 1950 20692.67 231.25355 0 3680.0319 4.297766 + 2000 20943.904 189.1122 0 3679.7629 -22.645478 + 2050 19668.123 401.81885 0 3679.8394 3.6254541 + 2100 20280.531 299.74669 0 3679.8352 7.4808896 + 2150 19182.034 483.49332 0 3680.4991 22.616956 + 2200 21299.885 130.75166 0 3680.7326 4.7110487 + 2250 20487.525 266.54254 0 3681.1301 -8.6422018 + 2300 18654.522 572.01515 0 3681.1021 -5.2661499 + 2350 21512.897 95.719565 0 3681.2024 -9.3553511 + 2400 21467.306 103.39279 0 3681.2771 -29.588234 + 2450 20097.914 332.63812 0 3682.2904 35.845886 + 2500 20762.362 222.00787 0 3682.4016 -12.509872 + 2550 20417.692 279.31982 0 3682.2685 -22.320693 + 2600 21468.738 104.15905 0 3682.2821 -10.050868 + 2650 20742.305 225.31121 0 3682.362 5.2887043 + 2700 18575.367 586.68141 0 3682.5759 21.990986 + 2750 20577.766 252.52411 0 3682.1518 -5.8697894 + 2800 20683.69 234.89244 0 3682.1741 -6.7464964 + 2850 16088.831 1001.1454 0 3682.6172 27.686908 + 2900 20715.565 229.46407 0 3682.0583 6.5207552 + 2950 19969.143 353.98595 0 3682.1765 5.3891903 + 3000 20429.639 277.11063 0 3682.0505 -10.302229 + 3050 19840.965 375.78339 0 3682.611 -6.1970263 + 3100 19149.859 490.69976 0 3682.3429 22.372557 + 3150 20421.772 278.3256 0 3681.9543 8.7381033 + 3200 19492.899 433.22833 0 3682.0448 4.3431162 + 3250 20231.034 310.12852 0 3681.9675 -3.2734265 + 3300 19420.155 445.8855 0 3682.578 14.157316 + 3350 21386.445 117.85565 0 3682.2631 1.9590216 + 3400 20372.28 286.91596 0 3682.296 8.2472357 + 3450 20870.351 203.91619 0 3682.308 7.9601676 + 3500 21469.401 104.14434 0 3682.3778 2.5067348 + 3550 21630.799 77.317219 0 3682.4504 -6.5148709 + 3600 21291.513 133.97558 0 3682.5611 -8.8761801 + 3650 19138.211 493.09199 0 3682.7937 25.075733 + 3700 21282.953 135.36631 0 3682.5252 -8.1163312 + 3750 20660.876 239.15863 0 3682.638 -24.806983 + 3800 20161.169 322.26065 0 3682.4555 13.204808 + 3850 19477.477 435.56421 0 3681.8105 31.065794 + 3900 21108.425 164.35492 0 3682.4258 0.37839399 + 3950 21195.124 150.68497 0 3683.2056 -10.098889 + 4000 21477.025 103.95273 0 3683.4568 -4.139886 + 4050 20603.58 249.35497 0 3683.2849 1.3114756 + 4100 19724.656 396.37166 0 3683.8144 -6.6159163 + 4150 20768.839 221.21034 0 3682.6835 -3.4649381 + 4200 19675.942 404.01538 0 3683.339 17.586922 + 4250 21022.927 179.12036 0 3682.9415 0.59436606 + 4300 20511.134 264.68208 0 3683.2044 8.8380269 + 4350 21038.204 177.05256 0 3683.42 -1.3698914 + 4400 18866.857 539.5082 0 3683.9844 10.461602 + 4450 21607.322 83.184316 0 3684.4046 -1.5071605 + 4500 20895.628 201.9445 0 3684.5492 5.7578991 + 4550 20210.744 316.5044 0 3684.9617 5.6678493 + 4600 20416.269 282.24539 0 3684.9569 -3.0067543 + 4650 18811.283 549.46791 0 3684.6817 7.5182454 + 4700 20899.462 201.92249 0 3685.1661 2.6998262 + 4750 20771.285 223.44307 0 3685.3239 12.165622 + 4800 21834.653 46.231798 0 3685.3407 2.021615 + 4850 21282.348 138.2858 0 3685.3437 4.2174481 + 4900 21892.433 36.607993 0 3685.3468 -10.208769 + 4950 21731.003 63.442124 0 3685.2759 -26.918841 + 5000 21476.967 105.69026 0 3685.1848 -10.007088 + 5050 20485.84 270.81814 0 3685.1248 0.65119013 + 5100 21485.763 104.28837 0 3685.2488 -5.3826149 + 5150 21485.096 104.44183 0 3685.2912 -1.274141 + 5200 21388.175 120.61165 0 3685.3074 -7.7953815 + 5250 20656.672 242.51472 0 3685.2934 -4.4067447 + 5300 20132.262 330.10916 0 3685.4862 -11.466755 + 5350 19080.054 505.63228 0 3685.6413 4.6356684 + 5400 21683.337 71.886529 0 3685.7761 -8.4520633 + 5450 20632.669 246.77173 0 3685.5499 5.5429152 + 5500 20896.92 202.76984 0 3685.5898 3.9762924 + 5550 21172.409 156.92085 0 3685.6557 2.6573146 + 5600 20695.91 236.255 0 3685.5733 -18.109158 + 5650 21741.679 61.956471 0 3685.5697 -3.7520994 + 5700 21164.94 157.60813 0 3685.098 2.4020734 + 5750 21075.393 172.84386 0 3685.4093 7.646915 + 5800 20638.831 245.82076 0 3685.6259 8.3009859 + 5850 20262.966 308.37489 0 3685.5359 7.5861941 + 5900 21730.418 63.97074 0 3685.7071 -6.2813552 + 5950 21820.659 48.990687 0 3685.7673 -5.6400713 + 6000 21027.051 181.2853 0 3685.7937 1.213872 + 6050 14422.66 1284.4174 0 3688.194 57.908667 + 6100 19852.685 377.0743 0 3685.8552 -5.1418207 + 6150 20678.783 239.10987 0 3685.5737 -11.982018 + 6200 19788.097 387.62127 0 3685.6375 -2.684571 + 6250 21611.523 83.575418 0 3685.496 1.7544019 + 6300 19214.109 482.45067 0 3684.8021 24.711965 + 6350 18800.074 553.07966 0 3686.4254 11.125791 + 6400 19771.53 390.40388 0 3685.659 -6.1254643 + 6450 20192.282 319.53713 0 3684.9175 13.959536 + 6500 20360.332 292.28682 0 3685.6755 4.4265274 + 6550 21778.739 56.056362 0 3685.8462 -4.6705452 + 6600 16612.689 917.96646 0 3686.748 -32.617733 + 6650 21068.368 174.38501 0 3685.7797 -0.84207954 + 6700 20749.675 227.41249 0 3685.6916 2.9235268 + 6750 20594.96 253.47665 0 3685.9699 -12.440843 + 6800 19974.133 357.05242 0 3686.0745 34.064247 + 6850 21802.523 52.05173 0 3685.8055 -1.4073818 + 6900 18644.747 577.97031 0 3685.4282 19.759245 + 6950 20463.441 274.90799 0 3685.4815 1.2230553 + 7000 20213.292 316.50714 0 3685.3892 23.9288 + 7050 21571.525 90.089593 0 3685.3437 -26.539261 + 7100 20480.036 271.77541 0 3685.1147 -0.13969301 + 7150 21064.842 174.4144 0 3685.2214 3.5451037 + 7200 21179.296 154.8514 0 3684.7341 -5.007319 + 7250 20714.182 232.84783 0 3685.2115 10.601943 + 7300 19341.561 461.91524 0 3685.5087 18.89547 + 7350 21011.016 183.55321 0 3685.3893 1.6481821 + 7400 21206.598 151.07364 0 3685.5066 1.5040526 + 7450 19999.404 352.83129 0 3686.0652 -18.58587 + 7500 21581.952 88.519362 0 3685.5114 -4.0009441 + 7550 21652.618 76.962392 0 3685.7321 -5.758242 + 7600 21207.411 150.86712 0 3685.4355 -0.023727123 + 7650 21756.168 59.804311 0 3685.8323 0.76768563 + 7700 21825.037 48.380795 0 3685.8869 -0.11098207 + 7750 21581.665 89.078228 0 3686.0223 -0.50220667 + 7800 21714.856 66.946216 0 3686.0889 4.637364 + 7850 21319.774 132.905 0 3686.2007 3.4663558 + 7900 21730.647 64.263898 0 3686.0384 1.0898763 + 7950 21597.663 86.255996 0 3685.8664 3.2847476 + 8000 21724.118 65.137632 0 3685.8239 3.7318614 + 8050 19672.702 406.56191 0 3685.3456 -0.37960768 + 8100 21696.026 69.71367 0 3685.7179 -6.2273451 + 8150 18869.648 540.09908 0 3685.0403 22.915669 + 8200 21717.002 66.01922 0 3685.5196 -4.8553801 + 8250 20292.502 303.3445 0 3685.4282 -13.203008 + 8300 21314.341 133.18215 0 3685.5724 -10.023288 + 8350 20992.272 186.87998 0 3685.592 -4.5538872 + 8400 21726.088 64.55825 0 3685.573 -5.1228188 + 8450 21188.98 153.93449 0 3685.4311 -6.8622554 + 8500 21113.87 166.54678 0 3685.5251 2.6009221 + 8550 20620.735 248.66776 0 3685.4569 -8.0047984 + 8600 19715.276 399.79648 0 3685.6758 -10.980391 + 8650 18898.94 535.95488 0 3685.7782 22.513752 + 8700 21692.841 70.067726 0 3685.5413 -3.3917479 + 8750 20242.909 311.87115 0 3685.6893 17.996012 + 8800 19253.702 476.69077 0 3685.6411 3.7170165 + 8850 17625.913 748.07802 0 3685.7302 11.095548 + 8900 21554.709 92.817998 0 3685.2696 0.30720376 + 8950 21585.337 87.685891 0 3685.2421 -0.22047593 + 9000 17454.847 776.14227 0 3685.2834 22.631913 + 9050 20023.106 347.35041 0 3684.5348 4.0008899 + 9100 21100.691 168.07199 0 3684.8539 2.9016681 + 9150 20307.206 299.45669 0 3683.991 2.1630277 + 9200 21747.579 60.245542 0 3684.8421 -15.419887 + 9250 21525.571 97.26157 0 3684.8567 -7.0449498 + 9300 15084.149 1170.5925 0 3684.6173 43.259279 + 9350 21198.648 151.70957 0 3684.8176 3.0716881 + 9400 17771.533 724.65805 0 3686.5802 -18.320033 + 9450 20029.819 346.23988 0 3684.543 -4.0976705 + 9500 19913.342 365.57743 0 3684.4677 2.4909741 + 9550 20594.619 252.35578 0 3684.7923 -4.4263632 + 9600 21013.668 182.33425 0 3684.6122 -1.9371919 + 9650 16915.052 865.78051 0 3684.9559 1.8697619 + 9700 18789.78 553.48818 0 3685.1181 15.642074 + 9750 21236.716 145.75801 0 3685.2107 -3.6730702 + 9800 20972.957 189.72849 0 3685.2214 0.85691231 + 9850 19658.721 408.29826 0 3684.7517 14.8446 + 9900 21624.401 81.484234 0 3685.5511 3.4507557 + 9950 21883.535 38.474607 0 3685.7304 0.3038348 + 10000 21355.31 126.72088 0 3685.9392 -5.5872974 +Loop time of 3.32742 on 4 procs for 10000 steps with 81 atoms + +Performance: 25966.084 tau/day, 3005.334 timesteps/s, 243.432 katom-step/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0073125 | 0.031081 | 0.067049 | 13.5 | 0.93 +Neigh | 0.010912 | 0.030444 | 0.058202 | 10.8 | 0.91 +Comm | 0.084952 | 0.12347 | 0.18323 | 10.9 | 3.71 +Output | 0.0033463 | 0.0038996 | 0.0047508 | 0.9 | 0.12 +Modify | 2.8501 | 2.9361 | 3.0072 | 3.5 | 88.24 +Other | | 0.2024 | | | 6.08 + +Nlocal: 20.25 ave 81 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 33.5 ave 66 max 2 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 212.5 ave 850 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 850 +Ave neighs/atom = 10.493827 +Neighbor list builds = 1246 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems2.g++.1 b/examples/rigid/log.25Mar24.rigid.poems2.g++.1 new file mode 100644 index 0000000000..4a8cb1298a --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems2.g++.1 @@ -0,0 +1,330 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7378 0 3904.434 18.086356 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173512 + 200 20705.978 69.977442 0 3904.4178 9.0928146 + 250 19552.211 283.50505 0 3904.2848 15.670464 + 300 19266.324 333.5788 0 3901.4165 7.2119173 + 350 20738.325 63.738945 0 3904.1694 -23.039989 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13818 0 3902.6059 0.42074126 + 500 20365.825 131.47231 0 3902.9213 0.69215475 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26028 0 3902.494 12.047308 + 800 20142.432 172.05197 0 3902.1319 4.6838632 + 850 19932.48 210.71155 0 3901.9116 3.471602 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61916 0 3902.4586 -2.2723139 + 1050 20859.506 39.696992 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.8744219 + 1200 20767.681 56.717093 0 3902.5839 -34.817443 + 1250 20625.583 82.586395 0 3902.1388 11.697328 + 1300 20690.013 71.006479 0 3902.4903 -29.292783 + 1350 20936.019 26.022787 0 3903.0634 1.0316033 + 1400 19753.56 244.81774 0 3902.8844 6.7138457 + 1450 15690.143 998.34271 0 3903.9248 48.124667 + 1500 20234.455 155.92517 0 3903.0465 13.172173 + 1550 20779.63 55.062895 0 3903.1426 -2.6390424 + 1600 20642.757 80.232879 0 3902.9657 -2.4687934 + 1650 18785.716 423.90031 0 3902.7365 -5.6468747 + 1700 20965.076 20.760295 0 3903.1818 -0.45382233 + 1750 18935.466 396.94949 0 3903.5173 25.912008 + 1800 20581.509 91.766145 0 3903.1567 3.8229018 + 1850 20616.968 85.18122 0 3903.1382 4.1907646 + 1900 16600.676 828.66496 0 3902.8643 -0.49197745 + 1950 20175.677 166.50513 0 3902.7416 5.6027746 + 2000 20268.078 149.2566 0 3902.6044 -1.1951453 + 2050 20155.388 170.16328 0 3902.6425 -0.79473147 + 2100 19715.497 250.63403 0 3901.652 3.6719022 + 2150 20677.205 73.792009 0 3902.9041 0.64246071 + 2200 20041.156 191.58407 0 3902.9093 7.4438342 + 2250 19924.453 213.0259 0 3902.7394 2.3652069 + 2300 20432.764 119.13103 0 3902.9763 -11.527566 + 2350 18265.828 520.75569 0 3903.3165 -8.9634198 + 2400 19574.981 277.7963 0 3902.7927 1.8085002 + 2450 20655.975 77.958119 0 3903.1387 3.4001031 + 2500 19783.143 239.3546 0 3902.8995 24.872182 + 2550 16660.113 818.36907 0 3903.5752 -11.766765 + 2600 19789.524 238.61817 0 3903.3448 3.3910931 + 2650 18532.96 471.8684 0 3903.898 -4.812577 + 2700 19081.457 369.81185 0 3903.4151 -0.49159968 + 2750 20370.042 131.6764 0 3903.9064 -3.3818893 + 2800 20727.087 65.499688 0 3903.8491 4.3537941 + 2850 18252.657 523.061 0 3903.1827 11.774986 + 2900 20780.391 55.586541 0 3903.8071 5.4415831 + 2950 20361.047 132.98647 0 3903.5508 -2.4847656 + 3000 19528.633 284.87405 0 3901.2876 14.23453 + 3050 20385.56 127.80448 0 3902.9081 -0.51079949 + 3100 19040.7 376.96613 0 3903.0216 -8.9425331 + 3150 20053.417 189.7312 0 3903.327 4.6695643 + 3200 20862.681 40.219985 0 3903.6795 1.2220199 + 3250 20692.32 71.660474 0 3903.5716 2.118694 + 3300 20560.104 95.905282 0 3903.332 5.9856809 + 3350 20693.236 71.35789 0 3903.4387 3.9315564 + 3400 19045.135 376.64379 0 3903.5206 3.9692419 + 3450 20354.826 134.28157 0 3903.6938 7.6208552 + 3500 20528.053 102.12643 0 3903.6178 7.2863414 + 3550 20525.13 103.01612 0 3903.9661 8.4807852 + 3600 19782.42 240.28031 0 3903.6914 1.0181878 + 3650 20519.52 104.05243 0 3903.9636 -2.36641 + 3700 20024.307 195.68587 0 3903.8908 -6.261818 + 3750 20239.643 155.72722 0 3903.8092 -20.781566 + 3800 20601.2 88.794605 0 3903.8317 -11.491217 + 3850 20973.346 19.675436 0 3903.6283 -9.0554155 + 3900 16212.846 902.10241 0 3904.4813 -19.773976 + 3950 19645.576 264.59477 0 3902.6643 16.065663 + 4000 17439.655 673.47397 0 3903.0398 -3.7357722 + 4050 19305.077 328.50056 0 3903.5148 10.43441 + 4100 18634.36 451.24343 0 3902.0508 3.4327844 + 4150 20249.11 153.64108 0 3903.4763 -2.5190604 + 4200 19177.928 351.81896 0 3903.2871 -5.5110274 + 4250 20754.898 60.189732 0 3903.6893 -3.3019026 + 4300 19693.307 256.31591 0 3903.2245 5.8795929 + 4350 18411.713 494.6957 0 3904.2722 4.2513782 + 4400 18499.707 474.35141 0 3900.2231 10.120914 + 4450 18620.543 449.98137 0 3898.2301 0.74648702 + 4500 18930.676 398.47668 0 3904.1573 -3.3953153 + 4550 18708.382 438.70363 0 3903.2188 8.478793 + 4600 19937.049 211.7655 0 3903.8117 4.8300368 + 4650 19919.169 214.98435 0 3903.7194 -1.0166319 + 4700 19345.329 321.18127 0 3903.6496 -23.032019 + 4750 18391.67 498.629 0 3904.4939 -15.40779 + 4800 18597.103 459.20983 0 3903.1179 9.3900723 + 4850 19857.892 226.27908 0 3903.6665 4.1998427 + 4900 20428.515 120.59483 0 3903.6532 -1.8636046 + 4950 18457.127 485.79992 0 3903.7864 -7.2380409 + 5000 20543.123 99.480661 0 3903.7627 -0.39555479 + 5050 18716.671 436.46735 0 3902.5175 29.395654 + 5100 20048.411 191.03727 0 3903.706 -0.91178091 + 5150 19647.675 265.24989 0 3903.7083 3.8658742 + 5200 20787.465 54.078505 0 3903.6091 -3.3582221 + 5250 20630.096 83.165593 0 3903.5538 -11.86045 + 5300 16598.926 830.02918 0 3903.9043 -1.8793568 + 5350 19114.667 363.424 0 3903.1772 11.894383 + 5400 19563.654 280.22257 0 3903.1215 8.8285523 + 5450 20012.628 197.27325 0 3903.3154 2.1981092 + 5500 17845.428 599.4114 0 3904.1202 20.091131 + 5550 20630.423 82.857857 0 3903.3065 0.93827014 + 5600 19675.125 259.89939 0 3903.4411 -2.4034875 + 5650 19932.349 212.22024 0 3903.3961 2.0064698 + 5700 20499.192 107.17918 0 3903.3259 2.5440649 + 5750 19522.335 287.94941 0 3903.1966 -0.7615272 + 5800 18010.242 568.31554 0 3903.5455 -6.3433889 + 5850 20177.497 166.64243 0 3903.2159 -0.95012013 + 5900 17919.358 584.40694 0 3902.8065 10.49282 + 5950 18390.453 498.29164 0 3903.9311 10.026285 + 6000 18040.232 562.71939 0 3903.5032 0.22172862 + 6050 19777.355 240.88597 0 3903.3592 -3.1899015 + 6100 19132.014 360.58765 0 3903.5531 1.6644736 + 6150 19780.214 240.31985 0 3903.3224 4.2403325 + 6200 18883.45 406.45503 0 3903.3902 -3.5422327 + 6250 19875.924 222.49729 0 3903.2239 3.0535292 + 6300 19882.454 221.4928 0 3903.4287 5.7371152 + 6350 19040.565 377.18193 0 3903.2124 -0.26454332 + 6400 19137.008 359.7025 0 3903.5929 9.5375531 + 6450 19655.205 263.59789 0 3903.4507 -1.8592763 + 6500 18385.045 499.5436 0 3904.1816 -7.8549266 + 6550 18823.423 417.69964 0 3903.5187 -2.8268518 + 6600 19414.118 308.11966 0 3903.3268 4.6627243 + 6650 20533.065 100.75047 0 3903.1698 3.3716972 + 6700 20206.283 161.18079 0 3903.085 5.6368472 + 6750 19517.622 288.72511 0 3903.0995 0.3337076 + 6800 18152.278 541.45525 0 3902.9883 -7.2734044 + 6850 18910.032 401.19322 0 3903.0511 6.2653128 + 6900 18580.612 462.26403 0 3903.1182 15.681586 + 6950 20459.012 114.44928 0 3903.1552 -0.82985388 + 7000 20866.868 38.822988 0 3903.0578 -6.2182429 + 7050 20460.074 114.11492 0 3903.0175 -2.1465384 + 7100 20553.533 96.636153 0 3902.846 -5.105486 + 7150 20447.915 116.30898 0 3902.9599 8.2035464 + 7200 20703.396 69.030336 0 3902.9926 9.1221166 + 7250 19652.215 263.63438 0 3902.9335 17.675447 + 7300 20691.205 71.094727 0 3902.7994 -1.7423404 + 7350 18845.785 412.74313 0 3902.7033 -2.0276584 + 7400 18462.131 483.73088 0 3902.6441 -0.22424322 + 7450 20458.641 113.96173 0 3902.599 -4.9286236 + 7500 17681.258 628.1576 0 3902.4647 -16.803813 + 7550 19149.34 356.35773 0 3902.5318 -5.3481685 + 7600 19723.907 249.45462 0 3902.03 7.2597963 + 7650 19317.18 325.01536 0 3902.271 -0.16642424 + 7700 19620.248 269.22043 0 3902.5996 -4.6771277 + 7750 17751.083 615.46827 0 3902.7058 7.3637076 + 7800 20724.904 64.633157 0 3902.5784 5.2079592 + 7850 19966.924 204.60327 0 3902.1817 6.4943932 + 7900 19730.339 248.88701 0 3902.6536 8.4392109 + 7950 19907.748 216.06587 0 3902.6859 -5.1989259 + 8000 18217.971 528.46486 0 3902.1632 -15.394144 + 8050 17868.898 592.98294 0 3902.0381 9.1139508 + 8100 19370.601 315.22753 0 3902.3759 7.9651368 + 8150 18199.01 532.43818 0 3902.6252 10.07163 + 8200 20646.337 79.222148 0 3902.6179 0.17396159 + 8250 20811.938 48.374613 0 3902.4372 -14.594973 + 8300 20906.571 30.626024 0 3902.2132 -12.34909 + 8350 19873.431 221.86861 0 3902.1335 7.1435615 + 8400 20374.979 127.96219 0 3901.1064 10.527044 + 8450 20701.502 68.073078 0 3901.6846 2.5071154 + 8500 20452.423 113.98399 0 3901.4698 4.2164058 + 8550 19695.059 253.87834 0 3901.1115 8.0656507 + 8600 19447.531 299.45597 0 3900.8505 -0.71982287 + 8650 17202.668 714.55842 0 3900.2378 -16.743518 + 8700 18579.153 459.20676 0 3899.7906 3.4494692 + 8750 20247.204 150.39086 0 3899.8731 -0.1022032 + 8800 18520.797 469.57224 0 3899.3494 5.7412252 + 8850 16011.411 934.80107 0 3899.8772 34.500452 + 8900 19045.914 372.92529 0 3899.9464 10.001612 + 8950 19798.369 233.70991 0 3900.0746 9.3270865 + 9000 17141.02 725.70858 0 3899.9716 -6.7470927 + 9050 17722.847 617.81927 0 3899.828 -10.909071 + 9100 20811.604 45.701413 0 3899.7021 -12.300065 + 9150 18066.034 554.62654 0 3900.1884 -5.7606837 + 9200 19259.884 332.49612 0 3899.1412 -40.231609 + 9250 19116.782 359.42396 0 3899.5689 0.68271469 + 9300 18785.022 421.1178 0 3899.8256 -20.433345 + 9350 19018.32 377.90289 0 3899.814 3.2963902 + 9400 17321.798 691.93839 0 3899.6788 24.552549 + 9450 18318.437 507.12661 0 3899.4297 6.1367468 + 9500 16431.681 857.32722 0 3900.2311 25.431389 + 9550 17920.939 581.45381 0 3900.1462 9.1734747 + 9600 16603.394 825.79291 0 3900.4954 -5.9643183 + 9650 17753.931 607.15019 0 3894.9151 2.2302338 + 9700 17452.305 668.30613 0 3900.2145 2.4635322 + 9750 15955.164 945.80159 0 3900.4617 20.290857 + 9800 17958.495 574.7055 0 3900.3526 12.218625 + 9850 18759.766 423.66965 0 3897.7005 -4.8999337 + 9900 19798.529 232.2507 0 3898.6449 0.10312101 + 9950 18260.87 517.50071 0 3899.1432 5.7261992 + 10000 19116.279 359.58291 0 3899.6345 3.2110764 +Loop time of 3.11933 on 1 procs for 10000 steps with 81 atoms + +Performance: 27698.233 tau/day, 3205.814 timesteps/s, 259.671 katom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.063297 | 0.063297 | 0.063297 | 0.0 | 2.03 +Neigh | 0.072119 | 0.072119 | 0.072119 | 0.0 | 2.31 +Comm | 0.012058 | 0.012058 | 0.012058 | 0.0 | 0.39 +Output | 0.0036722 | 0.0036722 | 0.0036722 | 0.0 | 0.12 +Modify | 2.953 | 2.953 | 2.953 | 0.0 | 94.67 +Other | | 0.01515 | | | 0.49 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 105 ave 105 max 105 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 498 ave 498 max 498 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 498 +Ave neighs/atom = 6.1481481 +Neighbor list builds = 1202 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems2.g++.4 b/examples/rigid/log.25Mar24.rigid.poems2.g++.4 new file mode 100644 index 0000000000..bc26f32538 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems2.g++.4 @@ -0,0 +1,330 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7378 0 3904.434 18.086356 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62032 0 3904.3981 -4.6173548 + 200 20705.978 69.977442 0 3904.4178 9.0928146 + 250 19552.211 283.50525 0 3904.285 15.670465 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47271 0 3902.9217 0.69215592 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05197 0 3902.1319 4.6838632 + 850 19932.48 210.71175 0 3901.9118 3.4716031 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61916 0 3902.4586 -2.272315 + 1050 20859.506 39.696992 0 3902.5684 6.45166 + 1100 15284.661 1072.1906 0 3902.6833 21.194041 + 1150 19658.317 261.99809 0 3902.4272 -2.8744196 + 1200 20767.681 56.717093 0 3902.5839 -34.817444 + 1250 20625.583 82.586396 0 3902.1388 11.697328 + 1300 20690.013 71.006479 0 3902.4903 -29.292783 + 1350 20936.019 26.022787 0 3903.0634 1.0316031 + 1400 19753.56 244.81777 0 3902.8844 6.713847 + 1450 15690.145 998.34279 0 3903.9252 48.124638 + 1500 20234.455 155.92476 0 3903.0461 13.17218 + 1550 20779.631 55.063072 0 3903.1428 -2.6390427 + 1600 20642.756 80.233303 0 3902.9659 -2.4688077 + 1650 18785.71 423.90132 0 3902.7365 -5.6468182 + 1700 20965.076 20.760481 0 3903.182 -0.45377448 + 1750 18935.45 396.95247 0 3903.5173 25.912353 + 1800 20581.523 91.763662 0 3903.1567 3.8225817 + 1850 20616.962 85.182351 0 3903.1382 4.1907744 + 1900 16601.061 828.59343 0 3902.8639 -0.49284971 + 1950 20175.618 166.51633 0 3902.7419 5.6031735 + 2000 20266.439 149.55931 0 3902.6036 -1.1956447 + 2050 20159.308 169.44017 0 3902.6453 -0.7983344 + 2100 19743.72 245.40822 0 3901.6527 3.5301052 + 2150 20674.556 74.284034 0 3902.9055 0.61532081 + 2200 19950.784 208.30189 0 3902.8915 7.6523945 + 2250 19817.161 232.7485 0 3902.5932 3.4492756 + 2300 20459.058 114.2307 0 3902.9451 -11.066393 + 2350 18359.21 503.25787 0 3903.1115 -9.0741539 + 2400 19952.914 207.84881 0 3902.8328 -0.53972874 + 2450 19661.352 259.78979 0 3900.781 7.8669927 + 2500 20917.293 29.699201 0 3903.2719 1.1433085 + 2550 20763.955 57.990256 0 3903.1671 -1.1088372 + 2600 20640.005 80.556339 0 3902.7795 9.6127007 + 2650 20823.227 47.292746 0 3903.446 2.2923503 + 2700 20401.43 125.53141 0 3903.5739 -8.0683618 + 2750 20689.918 72.242212 0 3903.7084 0.22078527 + 2800 20783.922 54.87309 0 3903.7476 2.0668249 + 2850 19258.563 336.84835 0 3903.2488 4.2704683 + 2900 20565.694 95.184831 0 3903.6468 -0.24799068 + 2950 20915.041 30.344751 0 3903.5004 -2.9900907 + 3000 19571.964 278.74004 0 3903.1778 12.195325 + 3050 20356.693 133.43974 0 3903.1976 0.11608195 + 3100 20047.888 190.69627 0 3903.268 -4.5895546 + 3150 19834.363 230.59072 0 3903.6209 -1.4352632 + 3200 20213.412 160.25129 0 3903.4757 3.7488266 + 3250 19286.774 332.04497 0 3903.6699 -5.0835358 + 3300 20952.226 23.774103 0 3903.816 0.10019546 + 3350 20407.952 124.62932 0 3903.8798 0.4403531 + 3400 19401.716 311.03567 0 3903.9461 1.8034568 + 3450 20880.78 37.20558 0 3904.0167 6.3948533 + 3500 19529.313 287.50301 0 3904.0425 12.311168 + 3550 20943.604 25.677677 0 3904.1228 5.1786098 + 3600 20272.725 149.91697 0 3904.1254 1.196909 + 3650 19781.047 240.95421 0 3904.1111 -8.5091671 + 3700 20613.433 86.53896 0 3903.8414 -9.1622102 + 3750 20567.605 95.294456 0 3904.1101 -0.11887825 + 3800 19891.98 220.32932 0 3904.0292 6.8801146 + 3850 20669.735 76.407858 0 3904.1365 -7.4310509 + 3900 20908.711 32.197181 0 3904.1807 -4.6573356 + 3950 20822.78 48.03134 0 3904.1018 0.086779759 + 4000 20199.055 163.66262 0 3904.2283 2.0027771 + 4050 20072.638 187.07041 0 3904.2256 4.4103784 + 4100 17724.651 619.7903 0 3902.1331 11.210006 + 4150 20760.201 60.001382 0 3904.4831 -3.8510009 + 4200 19159.102 356.30472 0 3904.2865 -2.3503308 + 4250 19403.974 311.3497 0 3904.6783 -1.2458384 + 4300 20858.687 42.000734 0 3904.7206 2.1750528 + 4350 20486.989 110.94383 0 3904.8306 5.017245 + 4400 20231.073 158.28825 0 3904.7832 7.4295979 + 4450 16369.689 873.39361 0 3904.8175 14.371454 + 4500 20745.196 63.11427 0 3904.8172 -7.855609 + 4550 18688.003 443.85636 0 3904.5977 9.8067426 + 4600 17755.672 616.68475 0 3904.7721 -3.9654703 + 4650 19843.131 230.34486 0 3904.9988 -0.13553926 + 4700 18873.202 409.99341 0 3905.0308 15.912724 + 4750 20605.355 89.223116 0 3905.0295 2.0847611 + 4800 20136.483 176.1278 0 3905.1062 -1.7091113 + 4850 19808.073 236.83278 0 3904.9945 5.0982271 + 4900 19142.083 359.55764 0 3904.3878 8.2072008 + 4950 20539.687 101.08198 0 3904.7277 8.0469319 + 5000 20840.809 45.759021 0 3905.168 4.771755 + 5050 20009.696 199.45528 0 3904.9546 6.1191423 + 5100 20882.034 38.247578 0 3905.2909 -6.3068822 + 5150 20329.869 140.47458 0 3905.2651 -21.720979 + 5200 17334.411 695.67098 0 3905.7471 -9.8243617 + 5250 19602.025 275.17282 0 3905.1775 -3.2371379 + 5300 20858.74 42.630642 0 3905.3603 0.38011789 + 5350 20828.619 48.188698 0 3905.3403 5.7187945 + 5400 20978.428 20.447148 0 3905.3413 6.1168011 + 5450 20115.374 179.9294 0 3904.9987 8.6440563 + 5500 20522.744 104.7733 0 3905.2815 -2.6561664 + 5550 20625.724 85.600795 0 3905.1792 -1.327206 + 5600 19559.638 282.68742 0 3904.8426 17.893028 + 5650 20552.224 98.978098 0 3904.9455 2.4489071 + 5700 19982.142 204.09989 0 3904.4966 9.9034011 + 5750 20408.825 125.30875 0 3904.7209 1.2515548 + 5800 19773.143 243.02134 0 3904.7144 -2.6729948 + 5850 20781.934 56.310486 0 3904.8168 -1.659054 + 5900 19807.668 236.54392 0 3904.6306 0.49776361 + 5950 20741.237 63.921667 0 3904.8916 4.2800039 + 6000 20322.7 140.98125 0 3904.4442 7.4978024 + 6050 20858.439 42.383629 0 3905.0575 -4.6872323 + 6100 20212.538 162.022 0 3905.0847 -7.0796165 + 6150 18513.957 476.7087 0 3905.2193 7.107138 + 6200 20802.734 52.621638 0 3904.9797 3.7242428 + 6250 20818.044 49.717458 0 3904.9109 -0.91041774 + 6300 19987.245 203.4635 0 3904.8052 -0.86714551 + 6350 20806.906 51.449749 0 3904.5806 -4.0699629 + 6400 20530.3 103.09809 0 3905.0055 1.660177 + 6450 20667.085 77.715553 0 3904.9535 0.99217521 + 6500 20515.816 105.81762 0 3905.0428 3.0994091 + 6550 20548.348 99.627131 0 3904.8769 -0.77417688 + 6600 19827.378 232.99889 0 3904.7355 3.295082 + 6650 19237.199 342.94808 0 3905.3923 -6.2226637 + 6700 19611.621 273.139 0 3904.9206 -3.5465535 + 6750 20874.805 39.1893 0 3904.8939 -0.051336814 + 6800 19433.717 305.99952 0 3904.8361 -19.858865 + 6850 20119.223 179.19987 0 3904.9818 4.6466283 + 6900 20467.389 114.77871 0 3905.0359 10.290214 + 6950 20334.202 139.43289 0 3905.0259 7.5448433 + 7000 20504.591 107.86929 0 3905.0158 -0.10092084 + 7050 17969.214 576.83722 0 3904.4694 10.852897 + 7100 19186.398 351.80467 0 3904.8414 0.24779979 + 7150 20261.23 152.54684 0 3904.6265 -7.0175844 + 7200 20696.821 71.985154 0 3904.7298 3.9649146 + 7250 18456.212 487.1819 0 3904.9989 5.8280225 + 7300 17705.1 625.95928 0 3904.6816 6.8298215 + 7350 17032.039 750.96958 0 3905.051 11.833303 + 7400 20557.431 97.599213 0 3904.5308 0.43747863 + 7450 20466.847 114.5693 0 3904.7261 1.9786538 + 7500 20416.862 123.31643 0 3904.2168 -2.9094738 + 7550 18433.95 487.50767 0 3901.2022 4.0921479 + 7600 19950.107 209.92208 0 3904.3863 3.9114888 + 7650 16037.844 934.94785 0 3904.9189 -1.2183461 + 7700 20145.239 173.99945 0 3904.5993 3.1185554 + 7750 18672.579 446.35236 0 3904.2373 4.1086445 + 7800 19740.616 249.10395 0 3904.7737 4.6048428 + 7850 20801.917 52.742096 0 3904.9489 1.5978265 + 7900 20305.348 144.57749 0 3904.8272 2.7348725 + 7950 20221.086 159.31958 0 3903.9652 7.1592496 + 8000 20826.907 47.953835 0 3904.7884 6.2728901 + 8050 18646.418 452.02126 0 3905.0617 5.9716218 + 8100 20653.653 80.183024 0 3904.9336 -1.8274783 + 8150 20843.275 45.172279 0 3905.0379 -6.9445524 + 8200 20364.78 133.45082 0 3904.7064 -12.094533 + 8250 18163.745 541.08818 0 3904.7447 -2.6103997 + 8300 20889.664 36.793018 0 3905.2494 -9.2650749 + 8350 20307.367 144.33088 0 3904.9543 -0.65999546 + 8400 20485.202 111.41317 0 3904.9691 -0.42802224 + 8450 20864.395 41.146879 0 3904.9238 7.7084978 + 8500 20901.899 34.291267 0 3905.0132 -5.2070823 + 8550 20211.78 162.02611 0 3904.9484 -5.8363409 + 8600 19639.538 268.05291 0 3905.0044 3.8180903 + 8650 19919.356 216.24885 0 3905.0185 0.17130921 + 8700 19499.449 293.97522 0 3904.9843 -4.897872 + 8750 20270.687 151.1571 0 3904.9879 0.28558082 + 8800 18804.137 422.61651 0 3904.864 15.351015 + 8850 20654.443 80.110976 0 3905.0078 4.1368065 + 8900 19953.725 209.81046 0 3904.9447 10.71743 + 8950 18195.013 536.67764 0 3906.1245 21.497802 + 9000 20478.531 112.78923 0 3905.1098 -13.053056 + 9050 20866.484 40.901611 0 3905.0653 -3.6134066 + 9100 20322.595 141.61419 0 3905.0577 15.459697 + 9150 20855.456 42.94311 0 3905.0646 4.9123213 + 9200 20208.201 162.79363 0 3905.0531 2.5454472 + 9250 18394.203 498.63686 0 3904.9707 0.041811692 + 9300 18776.997 427.7118 0 3904.9335 -7.652483 + 9350 18330.751 510.07857 0 3904.6621 8.3424059 + 9400 17538.366 657.08623 0 3904.9319 8.5478668 + 9450 20309.605 143.77142 0 3904.8093 6.6831447 + 9500 19982.331 203.81545 0 3904.2471 -7.6711411 + 9550 19410.612 310.1139 0 3904.6717 5.3983286 + 9600 19198.225 349.06634 0 3904.2932 -4.107658 + 9650 19388.043 314.31566 0 3904.6939 6.1198194 + 9700 18849.37 414.1045 0 3904.7286 5.4468861 + 9750 18263.312 523.38716 0 3905.4819 -0.56480349 + 9800 20421.858 122.53973 0 3904.3653 -15.641399 + 9850 17678.959 631.15683 0 3905.0381 -1.805446 + 9900 19421.046 306.67446 0 3903.1644 7.0287747 + 9950 18460.64 483.18902 0 3901.8261 3.658774 + 10000 19781.151 239.38136 0 3902.5575 6.3312911 +Loop time of 3.44431 on 4 procs for 10000 steps with 81 atoms + +Performance: 25084.833 tau/day, 2903.337 timesteps/s, 235.170 katom-step/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.007256 | 0.017426 | 0.044845 | 12.0 | 0.51 +Neigh | 0.010951 | 0.023139 | 0.043878 | 8.2 | 0.67 +Comm | 0.070404 | 0.096764 | 0.1104 | 5.0 | 2.81 +Output | 0.0039809 | 0.0074043 | 0.010167 | 2.6 | 0.21 +Modify | 3.0537 | 3.0735 | 3.1272 | 1.8 | 89.23 +Other | | 0.226 | | | 6.56 + +Nlocal: 20.25 ave 36 max 0 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 38.25 ave 50 max 28 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 126.5 ave 213 max 0 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 506 +Ave neighs/atom = 6.2469136 +Neighbor list builds = 1207 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems3.g++.1 b/examples/rigid/log.25Mar24.rigid.poems3.g++.1 new file mode 100644 index 0000000000..2554c0f610 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems3.g++.1 @@ -0,0 +1,329 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all poems file unconnected-bodies.dat +WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1038) +9 clusters, 9 bodies, 0 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.686 571.71596 0 5265.8207 32.006226 + 100 16298.5 136.65142 0 5267.6607 16.443791 + 150 16682.639 17.488068 0 5269.43 14.900278 + 200 16733.955 1.3724268 0 5269.4692 14.569123 + 250 16738.877 -0.15250573 0 5269.4939 14.496287 + 300 16738.611 -0.05516662 0 5269.5077 14.495909 + 350 16738.515 -0.01744351 0 5269.5152 14.496329 + 400 16738.488 -0.0060096677 0 5269.5178 14.496497 + 450 16738.479 -0.0012712918 0 5269.5199 14.496575 + 500 16738.479 -0.00081070354 0 5269.5203 14.49658 + 550 16738.479 -0.00083205205 0 5269.5203 14.496577 + 600 16738.479 -0.0005835658 0 5269.5206 14.49658 + 650 16738.479 -0.00047227225 0 5269.5206 14.496583 + 700 16738.479 0 0 5269.521 14.496593 + 750 16738.479 0 0 5269.5211 14.496595 + 800 16738.479 0 0 5269.5211 14.496596 + 850 16738.479 0 0 5269.5211 14.496595 + 900 16738.479 0 0 5269.5212 14.496593 + 950 16738.485 -0.003532391 0 5269.5196 14.496546 + 1000 16738.609 -0.051135033 0 5269.5109 14.496098 + 1050 16737.381 0.32991002 0 5269.5055 14.525627 + 1100 16737.915 0.16210932 0 5269.5058 14.531848 + 1150 16738.726 -0.089235332 0 5269.5098 14.509768 + 1200 16738.49 -0.0075446298 0 5269.5169 14.510489 + 1250 16738.48 0 0 5269.5214 14.510585 + 1300 16738.48 0 0 5269.5214 14.510587 + 1350 16738.48 0 0 5269.5215 14.510588 + 1400 16738.48 -0.00044742303 0 5269.5211 14.510581 + 1450 16738.481 -0.0010975104 0 5269.5207 14.51057 + 1500 16738.481 -0.00057925965 0 5269.5211 14.510575 + 1550 16738.48 0 0 5269.5216 14.510582 + 1600 16738.48 0 0 5269.5216 14.510581 + 1650 16738.481 0 0 5269.5216 14.510581 + 1700 16738.481 0 0 5269.5217 14.510582 + 1750 16738.481 0 0 5269.5217 14.510583 + 1800 16738.481 0 0 5269.5217 14.510585 + 1850 16738.481 0 0 5269.5218 14.510585 + 1900 16738.481 0 0 5269.5218 14.510585 + 1950 16738.487 -0.0031700155 0 5269.5206 14.510534 + 2000 16738.514 -0.013238802 0 5269.5188 14.510401 + 2050 16738.578 -0.03654435 0 5269.5158 14.510155 + 2100 16738.656 -0.063182323 0 5269.5137 14.510082 + 2150 16738.63 -0.056004395 0 5269.5127 14.510096 + 2200 16738.579 -0.038415873 0 5269.5143 14.510273 + 2250 16738.538 -0.023709094 0 5269.516 14.510414 + 2300 16738.512 -0.013252539 0 5269.5182 14.510501 + 2350 16738.491 -0.0045593284 0 5269.5203 14.510598 + 2400 16738.482 -0.00052242487 0 5269.5217 14.510655 + 2450 16738.486 -0.0023245722 0 5269.5211 14.510627 + 2500 16738.491 -0.005189304 0 5269.5197 14.510606 + 2550 16738.604 -0.044988104 0 5269.5155 14.510185 + 2600 16738.446 0.00096754004 0 5269.5117 14.510521 + 2650 16732.887 1.753125 0 5269.5138 14.598792 + 2700 16738.784 -0.10629556 0 5269.5107 14.499176 + 2750 16734.136 1.359459 0 5269.5135 14.594678 + 2800 16738.608 -0.047184149 0 5269.5147 14.510254 + 2850 16738.509 -0.012527238 0 5269.5181 14.509344 + 2900 16738.487 -0.0026065529 0 5269.521 14.509512 + 2950 16738.498 -0.0082248532 0 5269.519 14.509457 + 3000 16738.683 -0.071294028 0 5269.514 14.509005 + 3050 16717.444 6.5874862 0 5269.4864 14.834144 + 3100 16657.654 25.431253 0 5269.5074 14.467824 + 3150 16739.322 -0.28964062 0 5269.497 13.658821 + 3200 16733.615 1.4969789 0 5269.487 11.998304 + 3250 16737.289 0.35071213 0 5269.4974 11.918931 + 3300 16732.493 1.8663821 0 5269.503 12.109003 + 3350 16738.717 -0.087719164 0 5269.5085 11.979747 + 3400 16738.586 -0.045267897 0 5269.5095 11.97972 + 3450 16738.662 -0.071274216 0 5269.5076 11.979564 + 3500 16738.853 -0.13644992 0 5269.5026 11.979658 + 3550 16729.612 2.7475276 0 5269.4774 12.195939 + 3600 16728.659 3.059607 0 5269.4893 12.241248 + 3650 16738.923 -0.15949792 0 5269.5014 11.991857 + 3700 16738.76 -0.10695054 0 5269.5028 11.992932 + 3750 16738.751 -0.10105954 0 5269.5057 11.993137 + 3800 16738.597 -0.048627545 0 5269.5097 11.993456 + 3850 16738.507 -0.016053927 0 5269.5138 11.992973 + 3900 16738.485 -0.0060825487 0 5269.5169 11.993052 + 3950 16738.475 -0.0014953722 0 5269.5183 11.993119 + 4000 16738.472 -0.00054315391 0 5269.5184 11.99315 + 4050 16738.472 -0.00023792127 0 5269.5187 11.993172 + 4100 16738.472 0 0 5269.5189 11.993188 + 4150 16738.472 0 0 5269.5189 11.993188 + 4200 16738.472 0 0 5269.519 11.993178 + 4250 16738.472 0 0 5269.519 11.993164 + 4300 16738.472 0 0 5269.5191 11.993152 + 4350 16738.473 0 0 5269.5191 11.993147 + 4400 16738.473 0 0 5269.5192 11.993149 + 4450 16738.473 0 0 5269.5192 11.993158 + 4500 16738.473 0 0 5269.5193 11.99317 + 4550 16738.473 0 0 5269.5193 11.993176 + 4600 16738.473 0 0 5269.5194 11.993174 + 4650 16738.473 0 0 5269.5194 11.993167 + 4700 16738.474 0 0 5269.5195 11.993162 + 4750 16738.474 0 0 5269.5195 11.99316 + 4800 16738.474 0 0 5269.5196 11.99316 + 4850 16738.474 0 0 5269.5196 11.993163 + 4900 16738.474 0 0 5269.5197 11.99317 + 4950 16738.474 0 0 5269.5197 11.993176 + 5000 16738.475 0 0 5269.5198 11.993174 + 5050 16738.475 0 0 5269.5198 11.993165 + 5100 16738.475 0 0 5269.5199 11.993155 + 5150 16738.475 0 0 5269.5199 11.99315 + 5200 16738.475 0 0 5269.52 11.993153 + 5250 16738.475 0 0 5269.52 11.993161 + 5300 16738.476 0 0 5269.5201 11.993173 + 5350 16738.476 0 0 5269.5201 11.993185 + 5400 16738.476 0 0 5269.5202 11.993189 + 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5269.5224 11.911039 + 7800 16738.483 0 0 5269.5224 11.911031 + 7850 16738.483 0 0 5269.5225 11.911031 + 7900 16738.483 0 0 5269.5226 11.911039 + 7950 16738.484 0 0 5269.5226 11.911052 + 8000 16738.484 0 0 5269.5227 11.911065 + 8050 16738.484 0 0 5269.5227 11.91107 + 8100 16738.484 0 0 5269.5228 11.911065 + 8150 16738.484 0 0 5269.5228 11.911056 + 8200 16738.484 0 0 5269.5229 11.911047 + 8250 16738.485 0 0 5269.5229 11.911042 + 8300 16738.485 0 0 5269.523 11.911041 + 8350 16738.485 0 0 5269.523 11.911046 + 8400 16738.485 0 0 5269.5231 11.911055 + 8450 16738.485 0 0 5269.5231 11.911062 + 8500 16738.485 0 0 5269.5232 11.91106 + 8550 16738.486 0 0 5269.5232 11.911053 + 8600 16738.487 -0.00084974053 0 5269.5227 11.911032 + 8650 16738.486 0 0 5269.5233 11.911046 + 8700 16738.486 0 0 5269.5234 11.91105 + 8750 16738.486 0 0 5269.5235 11.911056 + 8800 16738.486 0 0 5269.5235 11.911063 + 8850 16738.487 -0.00022763101 0 5269.5234 11.911065 + 8900 16738.487 0 0 5269.5236 11.911068 + 8950 16738.487 0 0 5269.5237 11.911058 + 9000 16738.487 0 0 5269.5237 11.911045 + 9050 16738.487 0 0 5269.5238 11.911036 + 9100 16738.487 0 0 5269.5238 11.911034 + 9150 16738.488 0 0 5269.5239 11.91104 + 9200 16738.488 0 0 5269.5239 11.911052 + 9250 16738.488 0 0 5269.524 11.911068 + 9300 16738.488 0 0 5269.524 11.911079 + 9350 16738.488 0 0 5269.5241 11.911078 + 9400 16738.492 -0.0016306436 0 5269.5235 11.911038 + 9450 16738.492 -0.0032567427 0 5269.522 11.911005 + 9500 16738.495 -0.0036645346 0 5269.5224 11.910982 + 9550 16738.49 -0.001067391 0 5269.5237 11.911012 + 9600 16738.489 0 0 5269.5244 11.911032 + 9650 16738.489 0 0 5269.5244 11.911043 + 9700 16738.49 0 0 5269.5245 11.911058 + 9750 16738.49 0 0 5269.5245 11.911071 + 9800 16738.49 0 0 5269.5246 11.911073 + 9850 16738.49 0 0 5269.5246 11.911065 + 9900 16738.49 0 0 5269.5247 11.911053 + 9950 16738.491 -0.00058544655 0 5269.5243 11.911032 + 10000 16738.493 -0.0015244935 0 5269.5242 11.911015 +Loop time of 3.15773 on 1 procs for 10000 steps with 81 atoms + +Performance: 27361.390 tau/day, 3166.828 timesteps/s, 256.513 katom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0090105 | 0.0090105 | 0.0090105 | 0.0 | 0.29 +Neigh | 0.047552 | 0.047552 | 0.047552 | 0.0 | 1.51 +Comm | 0.012213 | 0.012213 | 0.012213 | 0.0 | 0.39 +Output | 0.0028666 | 0.0028666 | 0.0028666 | 0.0 | 0.09 +Modify | 3.0714 | 3.0714 | 3.0714 | 0.0 | 97.27 +Other | | 0.01471 | | | 0.47 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 66 ave 66 max 66 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4 +Ave neighs/atom = 0.049382716 +Neighbor list builds = 1576 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems3.g++.4 b/examples/rigid/log.25Mar24.rigid.poems3.g++.4 new file mode 100644 index 0000000000..142b81ad80 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems3.g++.4 @@ -0,0 +1,329 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all poems file unconnected-bodies.dat +WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1038) +9 clusters, 9 bodies, 0 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.686 571.71596 0 5265.8207 32.006226 + 100 16298.5 136.65142 0 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6550 16738.479 0 0 5269.5212 11.911046 + 6600 16738.479 0 0 5269.5212 11.911049 + 6650 16738.479 0 0 5269.5213 11.911056 + 6700 16738.479 0 0 5269.5213 11.911062 + 6750 16738.48 0 0 5269.5214 11.91106 + 6800 16738.48 0 0 5269.5214 11.911051 + 6850 16738.48 0 0 5269.5215 11.911044 + 6900 16738.48 0 0 5269.5215 11.911041 + 6950 16738.48 0 0 5269.5216 11.911045 + 7000 16738.48 0 0 5269.5216 11.911053 + 7050 16738.481 0 0 5269.5217 11.911063 + 7100 16738.481 0 0 5269.5217 11.911071 + 7150 16738.481 0 0 5269.5218 11.911072 + 7200 16738.481 0 0 5269.5218 11.911063 + 7250 16738.481 0 0 5269.5219 11.911048 + 7300 16738.481 0 0 5269.5219 11.911036 + 7350 16738.482 0 0 5269.522 11.911031 + 7400 16738.482 0 0 5269.522 11.911035 + 7450 16738.482 0 0 5269.5221 11.911046 + 7500 16738.482 0 0 5269.5221 11.911062 + 7550 16738.482 0 0 5269.5222 11.911077 + 7600 16738.482 0 0 5269.5222 11.911081 + 7650 16738.483 0 0 5269.5223 11.911071 + 7700 16738.483 0 0 5269.5223 11.911054 + 7750 16738.483 0 0 5269.5224 11.911039 + 7800 16738.483 0 0 5269.5224 11.911031 + 7850 16738.483 0 0 5269.5225 11.911031 + 7900 16738.483 0 0 5269.5226 11.911039 + 7950 16738.484 0 0 5269.5226 11.911052 + 8000 16738.484 0 0 5269.5227 11.911065 + 8050 16738.484 0 0 5269.5227 11.91107 + 8100 16738.484 0 0 5269.5228 11.911065 + 8150 16738.484 0 0 5269.5228 11.911056 + 8200 16738.484 0 0 5269.5229 11.911047 + 8250 16738.485 0 0 5269.5229 11.911042 + 8300 16738.485 0 0 5269.523 11.911041 + 8350 16738.485 0 0 5269.523 11.911046 + 8400 16738.485 0 0 5269.5231 11.911055 + 8450 16738.485 0 0 5269.5231 11.911062 + 8500 16738.485 0 0 5269.5232 11.91106 + 8550 16738.486 0 0 5269.5232 11.911053 + 8600 16738.487 -0.00084974054 0 5269.5227 11.911032 + 8650 16738.486 0 0 5269.5233 11.911046 + 8700 16738.486 0 0 5269.5234 11.91105 + 8750 16738.486 0 0 5269.5235 11.911056 + 8800 16738.486 0 0 5269.5235 11.911063 + 8850 16738.487 -0.00022763102 0 5269.5234 11.911065 + 8900 16738.487 0 0 5269.5236 11.911068 + 8950 16738.487 0 0 5269.5237 11.911058 + 9000 16738.487 0 0 5269.5237 11.911045 + 9050 16738.487 0 0 5269.5238 11.911036 + 9100 16738.487 0 0 5269.5238 11.911034 + 9150 16738.488 0 0 5269.5239 11.91104 + 9200 16738.488 0 0 5269.5239 11.911052 + 9250 16738.488 0 0 5269.524 11.911068 + 9300 16738.488 0 0 5269.524 11.911079 + 9350 16738.488 0 0 5269.5241 11.911078 + 9400 16738.492 -0.0016306434 0 5269.5235 11.911038 + 9450 16738.492 -0.0032567424 0 5269.522 11.911005 + 9500 16738.495 -0.0036645342 0 5269.5224 11.910982 + 9550 16738.49 -0.0010673909 0 5269.5237 11.911012 + 9600 16738.489 0 0 5269.5244 11.911032 + 9650 16738.489 0 0 5269.5244 11.911043 + 9700 16738.49 0 0 5269.5245 11.911058 + 9750 16738.49 0 0 5269.5245 11.911071 + 9800 16738.49 0 0 5269.5246 11.911073 + 9850 16738.49 0 0 5269.5246 11.911065 + 9900 16738.49 0 0 5269.5247 11.911053 + 9950 16738.491 -0.0005854466 0 5269.5243 11.911032 + 10000 16738.493 -0.0015244937 0 5269.5242 11.911015 +Loop time of 3.27386 on 4 procs for 10000 steps with 81 atoms + +Performance: 26390.874 tau/day, 3054.499 timesteps/s, 247.414 katom-step/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.003643 | 0.0042095 | 0.0048106 | 0.7 | 0.13 +Neigh | 0.015047 | 0.01644 | 0.018121 | 0.9 | 0.50 +Comm | 0.08923 | 0.091442 | 0.093047 | 0.5 | 2.79 +Output | 0.0033998 | 0.0040485 | 0.0051625 | 1.0 | 0.12 +Modify | 2.9783 | 2.9943 | 3.0343 | 1.3 | 91.46 +Other | | 0.1635 | | | 4.99 + +Nlocal: 20.25 ave 27 max 9 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 30.5 ave 50 max 14 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 1 ave 4 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 4 +Ave neighs/atom = 0.049382716 +Neighbor list builds = 1576 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems4.g++.1 b/examples/rigid/log.25Mar24.rigid.poems4.g++.1 new file mode 100644 index 0000000000..f754fba3b4 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems4.g++.1 @@ -0,0 +1,328 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies.dat +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384279 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184717 + 1150 20849.582 206.01695 0 3680.9472 -0.86699135 + 1200 21815.003 45.317412 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.06408 + 1300 20780.781 217.36509 0 3680.8286 6.0538614 + 1350 20558.971 254.36485 0 3680.8601 -3.6773923 + 1400 21485.029 99.812891 0 3680.6511 -16.185475 + 1450 21771.107 52.159624 0 3680.6775 -2.4756668 + 1500 21520.948 93.503905 0 3680.3286 2.1023577 + 1550 21351.418 121.68136 0 3680.2511 5.5159922 + 1600 20778.805 216.92182 0 3680.0559 15.089193 + 1650 21477.637 100.21853 0 3679.8247 -1.1045536 + 1700 18501.335 596.47986 0 3680.0357 -15.679729 + 1750 18563.64 587.34819 0 3681.2882 33.532254 + 1800 19110.181 494.82407 0 3679.8543 18.02406 + 1850 21364.186 119.23625 0 3679.9339 2.5290683 + 1900 20146.613 322.15086 0 3679.9197 5.7314718 + 1950 20692.671 231.25334 0 3680.0319 4.2977791 + 2000 20943.905 189.11211 0 3679.7629 -22.644575 + 2050 19667.965 401.84519 0 3679.8394 3.6247265 + 2100 20280.309 299.78396 0 3679.8355 7.4806221 + 2150 19181.565 483.57073 0 3680.4982 22.62593 + 2200 21300.569 130.63684 0 3680.7316 4.7090558 + 2250 20486.112 266.77753 0 3681.1296 -8.6505201 + 2300 18651.193 572.56862 0 3681.1008 -5.2604682 + 2350 21514.435 95.462414 0 3681.2016 -9.3718933 + 2400 21464.75 103.81741 0 3681.2757 -29.521964 + 2450 20103.185 331.7557 0 3682.2865 35.600257 + 2500 20767.309 221.18002 0 3682.3981 -12.41075 + 2550 20461.88 271.93545 0 3682.2488 -22.542329 + 2600 21463.807 104.97703 0 3682.2782 -10.118749 + 2650 20902.135 198.66716 0 3682.3564 5.0103958 + 2700 18582.384 585.6465 0 3682.7106 22.212808 + 2750 21079.961 168.86261 0 3682.1894 -8.8401109 + 2800 21425.876 111.18035 0 3682.1598 -6.7933883 + 2850 17414.605 780.0645 0 3682.4987 28.180022 + 2900 19978.961 352.1845 0 3682.0113 8.4280816 + 2950 21189.046 150.47808 0 3681.9858 2.8898793 + 3000 19271.367 469.54947 0 3681.4439 -7.1530396 + 3050 21470.889 103.45294 0 3681.9344 -1.4975516 + 3100 21574.513 85.87604 0 3681.6282 7.0301554 + 3150 21649.42 73.506656 0 3681.7434 1.6649326 + 3200 20857.44 205.3704 0 3681.6104 2.9318184 + 3250 18573.575 585.73328 0 3681.3292 5.9394399 + 3300 17938.353 691.67199 0 3681.3975 9.7205454 + 3350 18668.795 570.23722 0 3681.7031 3.6442733 + 3400 16834.721 876.36804 0 3682.1548 21.869594 + 3450 20148.848 323.06988 0 3681.2112 3.8120475 + 3500 21039.942 175.06064 0 3681.7177 1.4965105 + 3550 21439.472 108.66655 0 3681.9119 4.192594 + 3600 21457.784 105.54883 0 3681.8461 -2.932673 + 3650 21409.999 113.49591 0 3681.829 -15.09817 + 3700 21380.023 118.56895 0 3681.9061 -15.461367 + 3750 20422.085 277.28852 0 3680.9694 19.331799 + 3800 18275.038 635.75951 0 3681.5992 22.413362 + 3850 20906.341 197.06897 0 3681.4592 2.5691289 + 3900 20041.032 341.11847 0 3681.2905 1.8089245 + 3950 18917.084 528.44677 0 3681.2941 -10.656627 + 4000 20425.89 276.98688 0 3681.3018 7.5960674 + 4050 18289.157 633.13575 0 3681.3286 6.5695895 + 4100 19601.884 414.64621 0 3681.6269 8.6144847 + 4150 20790.308 216.9575 0 3682.0088 1.6300255 + 4200 21043.169 174.98738 0 3682.1822 3.8942459 + 4250 19073.45 503.63057 0 3682.5389 -10.975988 + 4300 21251.971 140.63454 0 3682.6298 -7.7937426 + 4350 20844.867 208.08653 0 3682.2311 -10.295096 + 4400 20869.781 203.57469 0 3681.8716 -8.7176985 + 4450 20384.41 284.19751 0 3681.5992 3.9044821 + 4500 20002.241 346.95848 0 3680.6654 12.100678 + 4550 21410.259 112.40994 0 3680.7864 -6.6653767 + 4600 18230.418 641.88921 0 3680.2922 22.502391 + 4650 21319.778 127.76737 0 3681.0638 -0.50309316 + 4700 19429.05 441.85455 0 3680.0296 20.851722 + 4750 20395.967 281.13332 0 3680.4611 12.635024 + 4800 19405.371 446.47714 0 3680.7056 -3.0340076 + 4850 19935.979 358.4478 0 3681.1109 -7.9390554 + 4900 18822.801 543.80607 0 3680.9396 -3.1086099 + 4950 20569.881 252.87963 0 3681.1932 11.807076 + 5000 20311.182 296.63458 0 3681.8315 -4.2409472 + 5050 20187.672 316.83663 0 3681.4486 1.8723981 + 5100 17439.679 775.35516 0 3681.9684 -5.7037267 + 5150 20394.4 282.56755 0 3681.6342 4.3399253 + 5200 20294.84 299.10095 0 3681.5742 -9.9868412 + 5250 20396.122 282.31614 0 3681.6698 -4.9932521 + 5300 20617.465 245.11679 0 3681.3609 0.97429493 + 5350 21651.191 72.878802 0 3681.4106 2.0913693 + 5400 19097.721 498.69617 0 3681.6496 21.808511 + 5450 21856.73 38.930299 0 3681.7186 -4.0225451 + 5500 20087.477 334.09405 0 3682.0069 5.7109498 + 5550 17734.477 726.10594 0 3681.8522 16.277738 + 5600 21183.231 151.714 0 3682.2525 -2.1080998 + 5650 20832.185 210.14251 0 3682.1733 -8.0602581 + 5700 18879.226 535.50935 0 3682.0471 -14.351666 + 5750 18931.81 529.67506 0 3684.9768 4.8675164 + 5800 21674.979 70.259619 0 3682.7561 -14.990544 + 5850 21395.905 116.47471 0 3682.4588 -0.94334402 + 5900 18532.955 593.27143 0 3682.0973 26.072477 + 5950 20767.534 220.78554 0 3682.0413 -1.6468662 + 6000 21546.127 91.167146 0 3682.1882 -5.4664857 + 6050 20085.534 334.40872 0 3681.9977 -0.34825498 + 6100 21218.156 145.88926 0 3682.2486 2.2871905 + 6150 20902.857 198.59424 0 3682.4038 6.0082154 + 6200 21726.547 61.195607 0 3682.2868 -2.2981656 + 6250 17507.589 764.20763 0 3682.1392 9.4977327 + 6300 21687.283 67.283821 0 3681.831 -8.694756 + 6350 19806.474 380.24632 0 3681.3254 -0.94067379 + 6400 21128.461 160.65399 0 3682.0641 -4.8435757 + 6450 19747.214 390.89694 0 3682.0992 1.9108969 + 6500 20460.408 272.79545 0 3682.8634 -4.1094877 + 6550 16740.095 892.11547 0 3682.1313 13.20551 + 6600 18326.164 628.80415 0 3683.1648 -19.884336 + 6650 18469.284 605.36384 0 3683.5778 10.345658 + 6700 21086.876 168.61821 0 3683.0976 -0.036118094 + 6750 19924.801 361.46485 0 3682.2649 -2.1144953 + 6800 19812.028 380.5919 0 3682.5966 11.119936 + 6850 19118.501 496.38857 0 3682.8054 0.53906703 + 6900 19221.04 478.31879 0 3681.8255 11.13851 + 6950 20482.79 269.03445 0 3682.8328 2.6705981 + 7000 16350.403 957.96283 0 3683.03 -2.9783385 + 7050 20789.906 218.36242 0 3683.3467 4.2465754 + 7100 17718.126 730.09011 0 3683.111 15.271811 + 7150 19020.414 513.34591 0 3683.4149 -8.3035633 + 7200 21165.007 156.24494 0 3683.7461 -7.3085107 + 7250 20520.422 264.35574 0 3684.4261 -6.7803072 + 7300 19078.795 505.10953 0 3684.9087 -11.147107 + 7350 20529.173 263.85389 0 3685.3827 0.59881989 + 7400 20548.068 261.27337 0 3685.9513 -5.0067382 + 7450 20849.172 211.46852 0 3686.3306 -0.80175538 + 7500 20869.894 207.95335 0 3686.2689 0.44541197 + 7550 18490.583 605.63557 0 3687.3993 -11.744631 + 7600 19185.381 488.52218 0 3686.0857 3.0881652 + 7650 20520.848 265.65037 0 3685.7917 -0.28165722 + 7700 20599.631 251.69265 0 3684.9645 0.19835423 + 7750 18428.55 614.11446 0 3685.5395 5.8092563 + 7800 19660.337 408.61674 0 3685.3396 4.9902979 + 7850 19409.663 450.30454 0 3685.2483 8.8641567 + 7900 21307.628 133.95865 0 3685.23 -1.8297128 + 7950 17828.245 713.05722 0 3684.4314 5.9673166 + 8000 15894.788 1036.4896 0 3685.621 57.567209 + 8050 18588.022 587.45738 0 3685.4611 1.5643233 + 8100 20664.194 241.59965 0 3685.632 -4.9298687 + 8150 17745.538 728.43249 0 3686.0221 6.121885 + 8200 18433.239 612.84747 0 3685.0539 17.078623 + 8250 19162.628 492.52511 0 3686.2965 12.204945 + 8300 18507.768 602.21188 0 3686.8399 -14.003487 + 8350 21010.715 184.80032 0 3686.5861 -0.93351338 + 8400 20888.233 205.24214 0 3686.6143 -5.3433619 + 8450 20920.621 199.6941 0 3686.4643 -30.437742 + 8500 17085.22 840.80474 0 3688.3414 3.9123878 + 8550 20900.377 203.87077 0 3687.267 -6.7525851 + 8600 19771.517 392.67499 0 3687.9278 13.762684 + 8650 19541.099 431.09497 0 3687.9448 2.0785077 + 8700 21056.327 178.88314 0 3688.2709 -13.663758 + 8750 20109.075 336.93228 0 3688.4447 -1.0445182 + 8800 21821.77 51.337654 0 3688.2993 -10.263971 + 8850 17653.401 740.45074 0 3682.6842 49.147758 + 8900 20311.01 302.92663 0 3688.095 -8.1910583 + 8950 19745.488 396.38557 0 3687.3003 -16.948557 + 9000 20248.989 311.52221 0 3686.3537 -2.4158415 + 9050 17850.649 710.17969 0 3685.2878 25.692377 + 9100 19370.284 456.73812 0 3685.1187 -21.201413 + 9150 20452.896 276.95741 0 3685.7735 2.0316457 + 9200 19174.266 488.9925 0 3684.7035 10.317202 + 9250 20174.171 323.4614 0 3685.8232 -2.1072552 + 9300 21442.761 111.68542 0 3685.479 -12.303658 + 9350 19697.287 402.21503 0 3685.0963 8.4697153 + 9400 21553.763 93.03581 0 3685.3297 -6.7286485 + 9450 18946.935 527.04498 0 3684.8674 -6.6174191 + 9500 21162.915 158.64321 0 3685.7957 -3.2085936 + 9550 20704.844 235.41227 0 3686.2196 10.847095 + 9600 20664.074 242.09733 0 3686.1096 3.7301969 + 9650 20829.655 214.20146 0 3685.8107 7.2197609 + 9700 17336.625 797.22781 0 3686.6654 14.775351 + 9750 19978.15 356.51126 0 3686.2029 -1.1978838 + 9800 21150.487 162.1616 0 3687.2427 -15.596643 + 9850 20849.962 213.10316 0 3688.0968 -5.5443282 + 9900 18407.158 620.93592 0 3688.7956 10.177471 + 9950 20459.637 278.24203 0 3688.1815 0.0020687238 + 10000 21667.112 78.10938 0 3689.2948 -12.660594 +Loop time of 3.40889 on 1 procs for 10000 steps with 81 atoms + +Performance: 25345.463 tau/day, 2933.503 timesteps/s, 237.614 katom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12904 | 0.12904 | 0.12904 | 0.0 | 3.79 +Neigh | 0.10613 | 0.10613 | 0.10613 | 0.0 | 3.11 +Comm | 0.011135 | 0.011135 | 0.011135 | 0.0 | 0.33 +Output | 0.0042137 | 0.0042137 | 0.0042137 | 0.0 | 0.12 +Modify | 3.142 | 3.142 | 3.142 | 0.0 | 92.17 +Other | | 0.01636 | | | 0.48 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 115 ave 115 max 115 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 808 ave 808 max 808 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 808 +Ave neighs/atom = 9.9753086 +Neighbor list builds = 1162 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems4.g++.4 b/examples/rigid/log.25Mar24.rigid.poems4.g++.4 new file mode 100644 index 0000000000..e78a2e0f05 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems4.g++.4 @@ -0,0 +1,328 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies.dat +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384277 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184718 + 1150 20849.582 206.01695 0 3680.9472 -0.86699156 + 1200 21815.003 45.317416 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064076 + 1300 20780.781 217.36505 0 3680.8286 6.0538619 + 1350 20558.972 254.36481 0 3680.8601 -3.6773978 + 1400 21485.029 99.812941 0 3680.6511 -16.185471 + 1450 21771.108 52.159596 0 3680.6775 -2.4756679 + 1500 21520.948 93.503942 0 3680.3286 2.1023578 + 1550 21351.418 121.6814 0 3680.2511 5.5159969 + 1600 20778.805 216.92173 0 3680.0559 15.089183 + 1650 21477.639 100.21825 0 3679.8247 -1.1045878 + 1700 18501.342 596.47873 0 3680.0357 -15.679646 + 1750 18563.643 587.34777 0 3681.2882 33.532181 + 1800 19110.189 494.82286 0 3679.8543 18.024038 + 1850 21364.195 119.2348 0 3679.9339 2.5291365 + 1900 20146.638 322.1467 0 3679.9197 5.7312008 + 1950 20692.67 231.25355 0 3680.0319 4.297766 + 2000 20943.904 189.1122 0 3679.7629 -22.645478 + 2050 19668.123 401.81885 0 3679.8394 3.6254541 + 2100 20280.531 299.74669 0 3679.8352 7.4808896 + 2150 19182.034 483.49332 0 3680.4991 22.616956 + 2200 21299.885 130.75166 0 3680.7326 4.7110487 + 2250 20487.525 266.54254 0 3681.1301 -8.6422018 + 2300 18654.522 572.01515 0 3681.1021 -5.2661499 + 2350 21512.897 95.719565 0 3681.2024 -9.3553511 + 2400 21467.306 103.39279 0 3681.2771 -29.588234 + 2450 20097.914 332.63812 0 3682.2904 35.845886 + 2500 20762.362 222.00787 0 3682.4016 -12.509872 + 2550 20417.692 279.31982 0 3682.2685 -22.320693 + 2600 21468.738 104.15905 0 3682.2821 -10.050868 + 2650 20742.305 225.31121 0 3682.362 5.2887043 + 2700 18575.367 586.68141 0 3682.5759 21.990986 + 2750 20577.766 252.52411 0 3682.1518 -5.8697894 + 2800 20683.69 234.89244 0 3682.1741 -6.7464964 + 2850 16088.831 1001.1454 0 3682.6172 27.686908 + 2900 20715.565 229.46407 0 3682.0583 6.5207552 + 2950 19969.143 353.98595 0 3682.1765 5.3891903 + 3000 20429.639 277.11063 0 3682.0505 -10.302229 + 3050 19840.965 375.78339 0 3682.611 -6.1970263 + 3100 19149.859 490.69976 0 3682.3429 22.372557 + 3150 20421.772 278.3256 0 3681.9543 8.7381033 + 3200 19492.899 433.22833 0 3682.0448 4.3431162 + 3250 20231.034 310.12852 0 3681.9675 -3.2734265 + 3300 19420.155 445.8855 0 3682.578 14.157316 + 3350 21386.445 117.85565 0 3682.2631 1.9590216 + 3400 20372.28 286.91596 0 3682.296 8.2472357 + 3450 20870.351 203.91619 0 3682.308 7.9601676 + 3500 21469.401 104.14434 0 3682.3778 2.5067348 + 3550 21630.799 77.317219 0 3682.4504 -6.5148709 + 3600 21291.513 133.97558 0 3682.5611 -8.8761801 + 3650 19138.211 493.09199 0 3682.7937 25.075733 + 3700 21282.953 135.36631 0 3682.5252 -8.1163312 + 3750 20660.876 239.15863 0 3682.638 -24.806983 + 3800 20161.169 322.26065 0 3682.4555 13.204808 + 3850 19477.477 435.56421 0 3681.8105 31.065794 + 3900 21108.425 164.35492 0 3682.4258 0.37839399 + 3950 21195.124 150.68497 0 3683.2056 -10.098889 + 4000 21477.025 103.95273 0 3683.4568 -4.139886 + 4050 20603.58 249.35497 0 3683.2849 1.3114756 + 4100 19724.656 396.37166 0 3683.8144 -6.6159163 + 4150 20768.839 221.21034 0 3682.6835 -3.4649381 + 4200 19675.942 404.01538 0 3683.339 17.586922 + 4250 21022.927 179.12036 0 3682.9415 0.59436606 + 4300 20511.134 264.68208 0 3683.2044 8.8380269 + 4350 21038.204 177.05256 0 3683.42 -1.3698914 + 4400 18866.857 539.5082 0 3683.9844 10.461602 + 4450 21607.322 83.184316 0 3684.4046 -1.5071605 + 4500 20895.628 201.9445 0 3684.5492 5.7578991 + 4550 20210.744 316.5044 0 3684.9617 5.6678493 + 4600 20416.269 282.24539 0 3684.9569 -3.0067543 + 4650 18811.283 549.46791 0 3684.6817 7.5182454 + 4700 20899.462 201.92249 0 3685.1661 2.6998262 + 4750 20771.285 223.44307 0 3685.3239 12.165622 + 4800 21834.653 46.231798 0 3685.3407 2.021615 + 4850 21282.348 138.2858 0 3685.3437 4.2174481 + 4900 21892.433 36.607993 0 3685.3468 -10.208769 + 4950 21731.003 63.442124 0 3685.2759 -26.918841 + 5000 21476.967 105.69026 0 3685.1848 -10.007088 + 5050 20485.84 270.81814 0 3685.1248 0.65119013 + 5100 21485.763 104.28837 0 3685.2488 -5.3826149 + 5150 21485.096 104.44183 0 3685.2912 -1.274141 + 5200 21388.175 120.61165 0 3685.3074 -7.7953815 + 5250 20656.672 242.51472 0 3685.2934 -4.4067447 + 5300 20132.262 330.10916 0 3685.4862 -11.466755 + 5350 19080.054 505.63228 0 3685.6413 4.6356684 + 5400 21683.337 71.886529 0 3685.7761 -8.4520633 + 5450 20632.669 246.77173 0 3685.5499 5.5429152 + 5500 20896.92 202.76984 0 3685.5898 3.9762924 + 5550 21172.409 156.92085 0 3685.6557 2.6573146 + 5600 20695.91 236.255 0 3685.5733 -18.109158 + 5650 21741.679 61.956471 0 3685.5697 -3.7520994 + 5700 21164.94 157.60813 0 3685.098 2.4020734 + 5750 21075.393 172.84386 0 3685.4093 7.646915 + 5800 20638.831 245.82076 0 3685.6259 8.3009859 + 5850 20262.966 308.37489 0 3685.5359 7.5861941 + 5900 21730.418 63.97074 0 3685.7071 -6.2813552 + 5950 21820.659 48.990687 0 3685.7673 -5.6400713 + 6000 21027.051 181.2853 0 3685.7937 1.213872 + 6050 14422.66 1284.4174 0 3688.194 57.908667 + 6100 19852.685 377.0743 0 3685.8552 -5.1418207 + 6150 20678.783 239.10987 0 3685.5737 -11.982018 + 6200 19788.097 387.62127 0 3685.6375 -2.684571 + 6250 21611.523 83.575418 0 3685.496 1.7544019 + 6300 19214.109 482.45067 0 3684.8021 24.711965 + 6350 18800.074 553.07966 0 3686.4254 11.125791 + 6400 19771.53 390.40388 0 3685.659 -6.1254643 + 6450 20192.282 319.53713 0 3684.9175 13.959536 + 6500 20360.332 292.28682 0 3685.6755 4.4265274 + 6550 21778.739 56.056362 0 3685.8462 -4.6705452 + 6600 16612.689 917.96646 0 3686.748 -32.617733 + 6650 21068.368 174.38501 0 3685.7797 -0.84207954 + 6700 20749.675 227.41249 0 3685.6916 2.9235268 + 6750 20594.96 253.47665 0 3685.9699 -12.440843 + 6800 19974.133 357.05242 0 3686.0745 34.064247 + 6850 21802.523 52.05173 0 3685.8055 -1.4073818 + 6900 18644.747 577.97031 0 3685.4282 19.759245 + 6950 20463.441 274.90799 0 3685.4815 1.2230553 + 7000 20213.292 316.50714 0 3685.3892 23.9288 + 7050 21571.525 90.089593 0 3685.3437 -26.539261 + 7100 20480.036 271.77541 0 3685.1147 -0.13969301 + 7150 21064.842 174.4144 0 3685.2214 3.5451037 + 7200 21179.296 154.8514 0 3684.7341 -5.007319 + 7250 20714.182 232.84783 0 3685.2115 10.601943 + 7300 19341.561 461.91524 0 3685.5087 18.89547 + 7350 21011.016 183.55321 0 3685.3893 1.6481821 + 7400 21206.598 151.07364 0 3685.5066 1.5040526 + 7450 19999.404 352.83129 0 3686.0652 -18.58587 + 7500 21581.952 88.519362 0 3685.5114 -4.0009441 + 7550 21652.618 76.962392 0 3685.7321 -5.758242 + 7600 21207.411 150.86712 0 3685.4355 -0.023727123 + 7650 21756.168 59.804311 0 3685.8323 0.76768563 + 7700 21825.037 48.380795 0 3685.8869 -0.11098207 + 7750 21581.665 89.078228 0 3686.0223 -0.50220667 + 7800 21714.856 66.946216 0 3686.0889 4.637364 + 7850 21319.774 132.905 0 3686.2007 3.4663558 + 7900 21730.647 64.263898 0 3686.0384 1.0898763 + 7950 21597.663 86.255996 0 3685.8664 3.2847476 + 8000 21724.118 65.137632 0 3685.8239 3.7318614 + 8050 19672.702 406.56191 0 3685.3456 -0.37960768 + 8100 21696.026 69.71367 0 3685.7179 -6.2273451 + 8150 18869.648 540.09908 0 3685.0403 22.915669 + 8200 21717.002 66.01922 0 3685.5196 -4.8553801 + 8250 20292.502 303.3445 0 3685.4282 -13.203008 + 8300 21314.341 133.18215 0 3685.5724 -10.023288 + 8350 20992.272 186.87998 0 3685.592 -4.5538872 + 8400 21726.088 64.55825 0 3685.573 -5.1228188 + 8450 21188.98 153.93449 0 3685.4311 -6.8622554 + 8500 21113.87 166.54678 0 3685.5251 2.6009221 + 8550 20620.735 248.66776 0 3685.4569 -8.0047984 + 8600 19715.276 399.79648 0 3685.6758 -10.980391 + 8650 18898.94 535.95488 0 3685.7782 22.513752 + 8700 21692.841 70.067726 0 3685.5413 -3.3917479 + 8750 20242.909 311.87115 0 3685.6893 17.996012 + 8800 19253.702 476.69077 0 3685.6411 3.7170165 + 8850 17625.913 748.07802 0 3685.7302 11.095548 + 8900 21554.709 92.817998 0 3685.2696 0.30720376 + 8950 21585.337 87.685891 0 3685.2421 -0.22047593 + 9000 17454.847 776.14227 0 3685.2834 22.631913 + 9050 20023.106 347.35041 0 3684.5348 4.0008899 + 9100 21100.691 168.07199 0 3684.8539 2.9016681 + 9150 20307.206 299.45669 0 3683.991 2.1630277 + 9200 21747.579 60.245542 0 3684.8421 -15.419887 + 9250 21525.571 97.26157 0 3684.8567 -7.0449498 + 9300 15084.149 1170.5925 0 3684.6173 43.259279 + 9350 21198.648 151.70957 0 3684.8176 3.0716881 + 9400 17771.533 724.65805 0 3686.5802 -18.320033 + 9450 20029.819 346.23988 0 3684.543 -4.0976705 + 9500 19913.342 365.57743 0 3684.4677 2.4909741 + 9550 20594.619 252.35578 0 3684.7923 -4.4263632 + 9600 21013.668 182.33425 0 3684.6122 -1.9371919 + 9650 16915.052 865.78051 0 3684.9559 1.8697619 + 9700 18789.78 553.48818 0 3685.1181 15.642074 + 9750 21236.716 145.75801 0 3685.2107 -3.6730702 + 9800 20972.957 189.72849 0 3685.2214 0.85691231 + 9850 19658.721 408.29826 0 3684.7517 14.8446 + 9900 21624.401 81.484234 0 3685.5511 3.4507557 + 9950 21883.535 38.474607 0 3685.7304 0.3038348 + 10000 21355.31 126.72088 0 3685.9392 -5.5872974 +Loop time of 3.23589 on 4 procs for 10000 steps with 81 atoms + +Performance: 26700.576 tau/day, 3090.344 timesteps/s, 250.318 katom-step/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0072165 | 0.030554 | 0.065382 | 13.2 | 0.94 +Neigh | 0.010707 | 0.029677 | 0.056594 | 10.6 | 0.92 +Comm | 0.083225 | 0.12075 | 0.17828 | 10.6 | 3.73 +Output | 0.0034779 | 0.0040163 | 0.0050814 | 1.0 | 0.12 +Modify | 2.8247 | 2.8749 | 2.9245 | 2.6 | 88.85 +Other | | 0.176 | | | 5.44 + +Nlocal: 20.25 ave 81 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 33.5 ave 66 max 2 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 212.5 ave 850 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 850 +Ave neighs/atom = 10.493827 +Neighbor list builds = 1246 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems5.g++.1 b/examples/rigid/log.25Mar24.rigid.poems5.g++.1 new file mode 100644 index 0000000000..03ca091c13 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems5.g++.1 @@ -0,0 +1,329 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies2.dat +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7378 0 3904.434 18.086356 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173512 + 200 20705.978 69.977442 0 3904.4178 9.0928146 + 250 19552.211 283.50505 0 3904.2848 15.670464 + 300 19266.324 333.5788 0 3901.4165 7.2119173 + 350 20738.325 63.738945 0 3904.1694 -23.039989 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13818 0 3902.6059 0.42074126 + 500 20365.825 131.47231 0 3902.9213 0.69215475 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26028 0 3902.494 12.047308 + 800 20142.432 172.05197 0 3902.1319 4.6838632 + 850 19932.48 210.71155 0 3901.9116 3.471602 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61916 0 3902.4586 -2.2723139 + 1050 20859.506 39.696992 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.8744219 + 1200 20767.681 56.717093 0 3902.5839 -34.817443 + 1250 20625.583 82.586395 0 3902.1388 11.697328 + 1300 20690.013 71.006479 0 3902.4903 -29.292783 + 1350 20936.019 26.022787 0 3903.0634 1.0316033 + 1400 19753.56 244.81774 0 3902.8844 6.7138457 + 1450 15690.143 998.34271 0 3903.9248 48.124667 + 1500 20234.455 155.92517 0 3903.0465 13.172173 + 1550 20779.63 55.062895 0 3903.1426 -2.6390424 + 1600 20642.757 80.232879 0 3902.9657 -2.4687934 + 1650 18785.716 423.90031 0 3902.7365 -5.6468747 + 1700 20965.076 20.760295 0 3903.1818 -0.45382233 + 1750 18935.466 396.94949 0 3903.5173 25.912008 + 1800 20581.509 91.766145 0 3903.1567 3.8229018 + 1850 20616.968 85.18122 0 3903.1382 4.1907646 + 1900 16600.676 828.66496 0 3902.8643 -0.49197745 + 1950 20175.677 166.50513 0 3902.7416 5.6027746 + 2000 20268.078 149.2566 0 3902.6044 -1.1951453 + 2050 20155.388 170.16328 0 3902.6425 -0.79473147 + 2100 19715.497 250.63403 0 3901.652 3.6719022 + 2150 20677.205 73.792009 0 3902.9041 0.64246071 + 2200 20041.156 191.58407 0 3902.9093 7.4438342 + 2250 19924.453 213.0259 0 3902.7394 2.3652069 + 2300 20432.764 119.13103 0 3902.9763 -11.527566 + 2350 18265.828 520.75569 0 3903.3165 -8.9634198 + 2400 19574.981 277.7963 0 3902.7927 1.8085002 + 2450 20655.975 77.958119 0 3903.1387 3.4001031 + 2500 19783.143 239.3546 0 3902.8995 24.872182 + 2550 16660.113 818.36907 0 3903.5752 -11.766765 + 2600 19789.524 238.61817 0 3903.3448 3.3910931 + 2650 18532.96 471.8684 0 3903.898 -4.812577 + 2700 19081.457 369.81185 0 3903.4151 -0.49159968 + 2750 20370.042 131.6764 0 3903.9064 -3.3818893 + 2800 20727.087 65.499688 0 3903.8491 4.3537941 + 2850 18252.657 523.061 0 3903.1827 11.774986 + 2900 20780.391 55.586541 0 3903.8071 5.4415831 + 2950 20361.047 132.98647 0 3903.5508 -2.4847656 + 3000 19528.633 284.87405 0 3901.2876 14.23453 + 3050 20385.56 127.80448 0 3902.9081 -0.51079949 + 3100 19040.7 376.96613 0 3903.0216 -8.9425331 + 3150 20053.417 189.7312 0 3903.327 4.6695643 + 3200 20862.681 40.219985 0 3903.6795 1.2220199 + 3250 20692.32 71.660474 0 3903.5716 2.118694 + 3300 20560.104 95.905282 0 3903.332 5.9856809 + 3350 20693.236 71.35789 0 3903.4387 3.9315564 + 3400 19045.135 376.64379 0 3903.5206 3.9692419 + 3450 20354.826 134.28157 0 3903.6938 7.6208552 + 3500 20528.053 102.12643 0 3903.6178 7.2863414 + 3550 20525.13 103.01612 0 3903.9661 8.4807852 + 3600 19782.42 240.28031 0 3903.6914 1.0181878 + 3650 20519.52 104.05243 0 3903.9636 -2.36641 + 3700 20024.307 195.68587 0 3903.8908 -6.261818 + 3750 20239.643 155.72722 0 3903.8092 -20.781566 + 3800 20601.2 88.794605 0 3903.8317 -11.491217 + 3850 20973.346 19.675436 0 3903.6283 -9.0554155 + 3900 16212.846 902.10241 0 3904.4813 -19.773976 + 3950 19645.576 264.59477 0 3902.6643 16.065663 + 4000 17439.655 673.47397 0 3903.0398 -3.7357722 + 4050 19305.077 328.50056 0 3903.5148 10.43441 + 4100 18634.36 451.24343 0 3902.0508 3.4327844 + 4150 20249.11 153.64108 0 3903.4763 -2.5190604 + 4200 19177.928 351.81896 0 3903.2871 -5.5110274 + 4250 20754.898 60.189732 0 3903.6893 -3.3019026 + 4300 19693.307 256.31591 0 3903.2245 5.8795929 + 4350 18411.713 494.6957 0 3904.2722 4.2513782 + 4400 18499.707 474.35141 0 3900.2231 10.120914 + 4450 18620.543 449.98137 0 3898.2301 0.74648702 + 4500 18930.676 398.47668 0 3904.1573 -3.3953153 + 4550 18708.382 438.70363 0 3903.2188 8.478793 + 4600 19937.049 211.7655 0 3903.8117 4.8300368 + 4650 19919.169 214.98435 0 3903.7194 -1.0166319 + 4700 19345.329 321.18127 0 3903.6496 -23.032019 + 4750 18391.67 498.629 0 3904.4939 -15.40779 + 4800 18597.103 459.20983 0 3903.1179 9.3900723 + 4850 19857.892 226.27908 0 3903.6665 4.1998427 + 4900 20428.515 120.59483 0 3903.6532 -1.8636046 + 4950 18457.127 485.79992 0 3903.7864 -7.2380409 + 5000 20543.123 99.480661 0 3903.7627 -0.39555479 + 5050 18716.671 436.46735 0 3902.5175 29.395654 + 5100 20048.411 191.03727 0 3903.706 -0.91178091 + 5150 19647.675 265.24989 0 3903.7083 3.8658742 + 5200 20787.465 54.078505 0 3903.6091 -3.3582221 + 5250 20630.096 83.165593 0 3903.5538 -11.86045 + 5300 16598.926 830.02918 0 3903.9043 -1.8793568 + 5350 19114.667 363.424 0 3903.1772 11.894383 + 5400 19563.654 280.22257 0 3903.1215 8.8285523 + 5450 20012.628 197.27325 0 3903.3154 2.1981092 + 5500 17845.428 599.4114 0 3904.1202 20.091131 + 5550 20630.423 82.857857 0 3903.3065 0.93827014 + 5600 19675.125 259.89939 0 3903.4411 -2.4034875 + 5650 19932.349 212.22024 0 3903.3961 2.0064698 + 5700 20499.192 107.17918 0 3903.3259 2.5440649 + 5750 19522.335 287.94941 0 3903.1966 -0.7615272 + 5800 18010.242 568.31554 0 3903.5455 -6.3433889 + 5850 20177.497 166.64243 0 3903.2159 -0.95012013 + 5900 17919.358 584.40694 0 3902.8065 10.49282 + 5950 18390.453 498.29164 0 3903.9311 10.026285 + 6000 18040.232 562.71939 0 3903.5032 0.22172862 + 6050 19777.355 240.88597 0 3903.3592 -3.1899015 + 6100 19132.014 360.58765 0 3903.5531 1.6644736 + 6150 19780.214 240.31985 0 3903.3224 4.2403325 + 6200 18883.45 406.45503 0 3903.3902 -3.5422327 + 6250 19875.924 222.49729 0 3903.2239 3.0535292 + 6300 19882.454 221.4928 0 3903.4287 5.7371152 + 6350 19040.565 377.18193 0 3903.2124 -0.26454332 + 6400 19137.008 359.7025 0 3903.5929 9.5375531 + 6450 19655.205 263.59789 0 3903.4507 -1.8592763 + 6500 18385.045 499.5436 0 3904.1816 -7.8549266 + 6550 18823.423 417.69964 0 3903.5187 -2.8268518 + 6600 19414.118 308.11966 0 3903.3268 4.6627243 + 6650 20533.065 100.75047 0 3903.1698 3.3716972 + 6700 20206.283 161.18079 0 3903.085 5.6368472 + 6750 19517.622 288.72511 0 3903.0995 0.3337076 + 6800 18152.278 541.45525 0 3902.9883 -7.2734044 + 6850 18910.032 401.19322 0 3903.0511 6.2653128 + 6900 18580.612 462.26403 0 3903.1182 15.681586 + 6950 20459.012 114.44928 0 3903.1552 -0.82985388 + 7000 20866.868 38.822988 0 3903.0578 -6.2182429 + 7050 20460.074 114.11492 0 3903.0175 -2.1465384 + 7100 20553.533 96.636153 0 3902.846 -5.105486 + 7150 20447.915 116.30898 0 3902.9599 8.2035464 + 7200 20703.396 69.030336 0 3902.9926 9.1221166 + 7250 19652.215 263.63438 0 3902.9335 17.675447 + 7300 20691.205 71.094727 0 3902.7994 -1.7423404 + 7350 18845.785 412.74313 0 3902.7033 -2.0276584 + 7400 18462.131 483.73088 0 3902.6441 -0.22424322 + 7450 20458.641 113.96173 0 3902.599 -4.9286236 + 7500 17681.258 628.1576 0 3902.4647 -16.803813 + 7550 19149.34 356.35773 0 3902.5318 -5.3481685 + 7600 19723.907 249.45462 0 3902.03 7.2597963 + 7650 19317.18 325.01536 0 3902.271 -0.16642424 + 7700 19620.248 269.22043 0 3902.5996 -4.6771277 + 7750 17751.083 615.46827 0 3902.7058 7.3637076 + 7800 20724.904 64.633157 0 3902.5784 5.2079592 + 7850 19966.924 204.60327 0 3902.1817 6.4943932 + 7900 19730.339 248.88701 0 3902.6536 8.4392109 + 7950 19907.748 216.06587 0 3902.6859 -5.1989259 + 8000 18217.971 528.46486 0 3902.1632 -15.394144 + 8050 17868.898 592.98294 0 3902.0381 9.1139508 + 8100 19370.601 315.22753 0 3902.3759 7.9651368 + 8150 18199.01 532.43818 0 3902.6252 10.07163 + 8200 20646.337 79.222148 0 3902.6179 0.17396159 + 8250 20811.938 48.374613 0 3902.4372 -14.594973 + 8300 20906.571 30.626024 0 3902.2132 -12.34909 + 8350 19873.431 221.86861 0 3902.1335 7.1435615 + 8400 20374.979 127.96219 0 3901.1064 10.527044 + 8450 20701.502 68.073078 0 3901.6846 2.5071154 + 8500 20452.423 113.98399 0 3901.4698 4.2164058 + 8550 19695.059 253.87834 0 3901.1115 8.0656507 + 8600 19447.531 299.45597 0 3900.8505 -0.71982287 + 8650 17202.668 714.55842 0 3900.2378 -16.743518 + 8700 18579.153 459.20676 0 3899.7906 3.4494692 + 8750 20247.204 150.39086 0 3899.8731 -0.1022032 + 8800 18520.797 469.57224 0 3899.3494 5.7412252 + 8850 16011.411 934.80107 0 3899.8772 34.500452 + 8900 19045.914 372.92529 0 3899.9464 10.001612 + 8950 19798.369 233.70991 0 3900.0746 9.3270865 + 9000 17141.02 725.70858 0 3899.9716 -6.7470927 + 9050 17722.847 617.81927 0 3899.828 -10.909071 + 9100 20811.604 45.701413 0 3899.7021 -12.300065 + 9150 18066.034 554.62654 0 3900.1884 -5.7606837 + 9200 19259.884 332.49612 0 3899.1412 -40.231609 + 9250 19116.782 359.42396 0 3899.5689 0.68271469 + 9300 18785.022 421.1178 0 3899.8256 -20.433345 + 9350 19018.32 377.90289 0 3899.814 3.2963902 + 9400 17321.798 691.93839 0 3899.6788 24.552549 + 9450 18318.437 507.12661 0 3899.4297 6.1367468 + 9500 16431.681 857.32722 0 3900.2311 25.431389 + 9550 17920.939 581.45381 0 3900.1462 9.1734747 + 9600 16603.394 825.79291 0 3900.4954 -5.9643183 + 9650 17753.931 607.15019 0 3894.9151 2.2302338 + 9700 17452.305 668.30613 0 3900.2145 2.4635322 + 9750 15955.164 945.80159 0 3900.4617 20.290857 + 9800 17958.495 574.7055 0 3900.3526 12.218625 + 9850 18759.766 423.66965 0 3897.7005 -4.8999337 + 9900 19798.529 232.2507 0 3898.6449 0.10312101 + 9950 18260.87 517.50071 0 3899.1432 5.7261992 + 10000 19116.279 359.58291 0 3899.6345 3.2110764 +Loop time of 3.40298 on 1 procs for 10000 steps with 81 atoms + +Performance: 25389.516 tau/day, 2938.601 timesteps/s, 238.027 katom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.068835 | 0.068835 | 0.068835 | 0.0 | 2.02 +Neigh | 0.078603 | 0.078603 | 0.078603 | 0.0 | 2.31 +Comm | 0.013957 | 0.013957 | 0.013957 | 0.0 | 0.41 +Output | 0.0034786 | 0.0034786 | 0.0034786 | 0.0 | 0.10 +Modify | 3.2212 | 3.2212 | 3.2212 | 0.0 | 94.66 +Other | | 0.01692 | | | 0.50 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 105 ave 105 max 105 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 498 ave 498 max 498 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 498 +Ave neighs/atom = 6.1481481 +Neighbor list builds = 1202 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems5.g++.4 b/examples/rigid/log.25Mar24.rigid.poems5.g++.4 new file mode 100644 index 0000000000..78f4d4417b --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.poems5.g++.4 @@ -0,0 +1,329 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies2.dat +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 + +@Article{Mukherjee08, + author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, + title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, + journal = {Intl.\ J.\ Non-Linear Mechanics}, + year = 2008, + volume = 43, + number = 10, + pages = {1040--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7378 0 3904.434 18.086356 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62032 0 3904.3981 -4.6173548 + 200 20705.978 69.977442 0 3904.4178 9.0928146 + 250 19552.211 283.50525 0 3904.285 15.670465 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47271 0 3902.9217 0.69215592 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05197 0 3902.1319 4.6838632 + 850 19932.48 210.71175 0 3901.9118 3.4716031 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61916 0 3902.4586 -2.272315 + 1050 20859.506 39.696992 0 3902.5684 6.45166 + 1100 15284.661 1072.1906 0 3902.6833 21.194041 + 1150 19658.317 261.99809 0 3902.4272 -2.8744196 + 1200 20767.681 56.717093 0 3902.5839 -34.817444 + 1250 20625.583 82.586396 0 3902.1388 11.697328 + 1300 20690.013 71.006479 0 3902.4903 -29.292783 + 1350 20936.019 26.022787 0 3903.0634 1.0316031 + 1400 19753.56 244.81777 0 3902.8844 6.713847 + 1450 15690.145 998.34279 0 3903.9252 48.124638 + 1500 20234.455 155.92476 0 3903.0461 13.17218 + 1550 20779.631 55.063072 0 3903.1428 -2.6390427 + 1600 20642.756 80.233303 0 3902.9659 -2.4688077 + 1650 18785.71 423.90132 0 3902.7365 -5.6468182 + 1700 20965.076 20.760481 0 3903.182 -0.45377448 + 1750 18935.45 396.95247 0 3903.5173 25.912353 + 1800 20581.523 91.763662 0 3903.1567 3.8225817 + 1850 20616.962 85.182351 0 3903.1382 4.1907744 + 1900 16601.061 828.59343 0 3902.8639 -0.49284971 + 1950 20175.618 166.51633 0 3902.7419 5.6031735 + 2000 20266.439 149.55931 0 3902.6036 -1.1956447 + 2050 20159.308 169.44017 0 3902.6453 -0.7983344 + 2100 19743.72 245.40822 0 3901.6527 3.5301052 + 2150 20674.556 74.284034 0 3902.9055 0.61532081 + 2200 19950.784 208.30189 0 3902.8915 7.6523945 + 2250 19817.161 232.7485 0 3902.5932 3.4492756 + 2300 20459.058 114.2307 0 3902.9451 -11.066393 + 2350 18359.21 503.25787 0 3903.1115 -9.0741539 + 2400 19952.914 207.84881 0 3902.8328 -0.53972874 + 2450 19661.352 259.78979 0 3900.781 7.8669927 + 2500 20917.293 29.699201 0 3903.2719 1.1433085 + 2550 20763.955 57.990256 0 3903.1671 -1.1088372 + 2600 20640.005 80.556339 0 3902.7795 9.6127007 + 2650 20823.227 47.292746 0 3903.446 2.2923503 + 2700 20401.43 125.53141 0 3903.5739 -8.0683618 + 2750 20689.918 72.242212 0 3903.7084 0.22078527 + 2800 20783.922 54.87309 0 3903.7476 2.0668249 + 2850 19258.563 336.84835 0 3903.2488 4.2704683 + 2900 20565.694 95.184831 0 3903.6468 -0.24799068 + 2950 20915.041 30.344751 0 3903.5004 -2.9900907 + 3000 19571.964 278.74004 0 3903.1778 12.195325 + 3050 20356.693 133.43974 0 3903.1976 0.11608195 + 3100 20047.888 190.69627 0 3903.268 -4.5895546 + 3150 19834.363 230.59072 0 3903.6209 -1.4352632 + 3200 20213.412 160.25129 0 3903.4757 3.7488266 + 3250 19286.774 332.04497 0 3903.6699 -5.0835358 + 3300 20952.226 23.774103 0 3903.816 0.10019546 + 3350 20407.952 124.62932 0 3903.8798 0.4403531 + 3400 19401.716 311.03567 0 3903.9461 1.8034568 + 3450 20880.78 37.20558 0 3904.0167 6.3948533 + 3500 19529.313 287.50301 0 3904.0425 12.311168 + 3550 20943.604 25.677677 0 3904.1228 5.1786098 + 3600 20272.725 149.91697 0 3904.1254 1.196909 + 3650 19781.047 240.95421 0 3904.1111 -8.5091671 + 3700 20613.433 86.53896 0 3903.8414 -9.1622102 + 3750 20567.605 95.294456 0 3904.1101 -0.11887825 + 3800 19891.98 220.32932 0 3904.0292 6.8801146 + 3850 20669.735 76.407858 0 3904.1365 -7.4310509 + 3900 20908.711 32.197181 0 3904.1807 -4.6573356 + 3950 20822.78 48.03134 0 3904.1018 0.086779759 + 4000 20199.055 163.66262 0 3904.2283 2.0027771 + 4050 20072.638 187.07041 0 3904.2256 4.4103784 + 4100 17724.651 619.7903 0 3902.1331 11.210006 + 4150 20760.201 60.001382 0 3904.4831 -3.8510009 + 4200 19159.102 356.30472 0 3904.2865 -2.3503308 + 4250 19403.974 311.3497 0 3904.6783 -1.2458384 + 4300 20858.687 42.000734 0 3904.7206 2.1750528 + 4350 20486.989 110.94383 0 3904.8306 5.017245 + 4400 20231.073 158.28825 0 3904.7832 7.4295979 + 4450 16369.689 873.39361 0 3904.8175 14.371454 + 4500 20745.196 63.11427 0 3904.8172 -7.855609 + 4550 18688.003 443.85636 0 3904.5977 9.8067426 + 4600 17755.672 616.68475 0 3904.7721 -3.9654703 + 4650 19843.131 230.34486 0 3904.9988 -0.13553926 + 4700 18873.202 409.99341 0 3905.0308 15.912724 + 4750 20605.355 89.223116 0 3905.0295 2.0847611 + 4800 20136.483 176.1278 0 3905.1062 -1.7091113 + 4850 19808.073 236.83278 0 3904.9945 5.0982271 + 4900 19142.083 359.55764 0 3904.3878 8.2072008 + 4950 20539.687 101.08198 0 3904.7277 8.0469319 + 5000 20840.809 45.759021 0 3905.168 4.771755 + 5050 20009.696 199.45528 0 3904.9546 6.1191423 + 5100 20882.034 38.247578 0 3905.2909 -6.3068822 + 5150 20329.869 140.47458 0 3905.2651 -21.720979 + 5200 17334.411 695.67098 0 3905.7471 -9.8243617 + 5250 19602.025 275.17282 0 3905.1775 -3.2371379 + 5300 20858.74 42.630642 0 3905.3603 0.38011789 + 5350 20828.619 48.188698 0 3905.3403 5.7187945 + 5400 20978.428 20.447148 0 3905.3413 6.1168011 + 5450 20115.374 179.9294 0 3904.9987 8.6440563 + 5500 20522.744 104.7733 0 3905.2815 -2.6561664 + 5550 20625.724 85.600795 0 3905.1792 -1.327206 + 5600 19559.638 282.68742 0 3904.8426 17.893028 + 5650 20552.224 98.978098 0 3904.9455 2.4489071 + 5700 19982.142 204.09989 0 3904.4966 9.9034011 + 5750 20408.825 125.30875 0 3904.7209 1.2515548 + 5800 19773.143 243.02134 0 3904.7144 -2.6729948 + 5850 20781.934 56.310486 0 3904.8168 -1.659054 + 5900 19807.668 236.54392 0 3904.6306 0.49776361 + 5950 20741.237 63.921667 0 3904.8916 4.2800039 + 6000 20322.7 140.98125 0 3904.4442 7.4978024 + 6050 20858.439 42.383629 0 3905.0575 -4.6872323 + 6100 20212.538 162.022 0 3905.0847 -7.0796165 + 6150 18513.957 476.7087 0 3905.2193 7.107138 + 6200 20802.734 52.621638 0 3904.9797 3.7242428 + 6250 20818.044 49.717458 0 3904.9109 -0.91041774 + 6300 19987.245 203.4635 0 3904.8052 -0.86714551 + 6350 20806.906 51.449749 0 3904.5806 -4.0699629 + 6400 20530.3 103.09809 0 3905.0055 1.660177 + 6450 20667.085 77.715553 0 3904.9535 0.99217521 + 6500 20515.816 105.81762 0 3905.0428 3.0994091 + 6550 20548.348 99.627131 0 3904.8769 -0.77417688 + 6600 19827.378 232.99889 0 3904.7355 3.295082 + 6650 19237.199 342.94808 0 3905.3923 -6.2226637 + 6700 19611.621 273.139 0 3904.9206 -3.5465535 + 6750 20874.805 39.1893 0 3904.8939 -0.051336814 + 6800 19433.717 305.99952 0 3904.8361 -19.858865 + 6850 20119.223 179.19987 0 3904.9818 4.6466283 + 6900 20467.389 114.77871 0 3905.0359 10.290214 + 6950 20334.202 139.43289 0 3905.0259 7.5448433 + 7000 20504.591 107.86929 0 3905.0158 -0.10092084 + 7050 17969.214 576.83722 0 3904.4694 10.852897 + 7100 19186.398 351.80467 0 3904.8414 0.24779979 + 7150 20261.23 152.54684 0 3904.6265 -7.0175844 + 7200 20696.821 71.985154 0 3904.7298 3.9649146 + 7250 18456.212 487.1819 0 3904.9989 5.8280225 + 7300 17705.1 625.95928 0 3904.6816 6.8298215 + 7350 17032.039 750.96958 0 3905.051 11.833303 + 7400 20557.431 97.599213 0 3904.5308 0.43747863 + 7450 20466.847 114.5693 0 3904.7261 1.9786538 + 7500 20416.862 123.31643 0 3904.2168 -2.9094738 + 7550 18433.95 487.50767 0 3901.2022 4.0921479 + 7600 19950.107 209.92208 0 3904.3863 3.9114888 + 7650 16037.844 934.94785 0 3904.9189 -1.2183461 + 7700 20145.239 173.99945 0 3904.5993 3.1185554 + 7750 18672.579 446.35236 0 3904.2373 4.1086445 + 7800 19740.616 249.10395 0 3904.7737 4.6048428 + 7850 20801.917 52.742096 0 3904.9489 1.5978265 + 7900 20305.348 144.57749 0 3904.8272 2.7348725 + 7950 20221.086 159.31958 0 3903.9652 7.1592496 + 8000 20826.907 47.953835 0 3904.7884 6.2728901 + 8050 18646.418 452.02126 0 3905.0617 5.9716218 + 8100 20653.653 80.183024 0 3904.9336 -1.8274783 + 8150 20843.275 45.172279 0 3905.0379 -6.9445524 + 8200 20364.78 133.45082 0 3904.7064 -12.094533 + 8250 18163.745 541.08818 0 3904.7447 -2.6103997 + 8300 20889.664 36.793018 0 3905.2494 -9.2650749 + 8350 20307.367 144.33088 0 3904.9543 -0.65999546 + 8400 20485.202 111.41317 0 3904.9691 -0.42802224 + 8450 20864.395 41.146879 0 3904.9238 7.7084978 + 8500 20901.899 34.291267 0 3905.0132 -5.2070823 + 8550 20211.78 162.02611 0 3904.9484 -5.8363409 + 8600 19639.538 268.05291 0 3905.0044 3.8180903 + 8650 19919.356 216.24885 0 3905.0185 0.17130921 + 8700 19499.449 293.97522 0 3904.9843 -4.897872 + 8750 20270.687 151.1571 0 3904.9879 0.28558082 + 8800 18804.137 422.61651 0 3904.864 15.351015 + 8850 20654.443 80.110976 0 3905.0078 4.1368065 + 8900 19953.725 209.81046 0 3904.9447 10.71743 + 8950 18195.013 536.67764 0 3906.1245 21.497802 + 9000 20478.531 112.78923 0 3905.1098 -13.053056 + 9050 20866.484 40.901611 0 3905.0653 -3.6134066 + 9100 20322.595 141.61419 0 3905.0577 15.459697 + 9150 20855.456 42.94311 0 3905.0646 4.9123213 + 9200 20208.201 162.79363 0 3905.0531 2.5454472 + 9250 18394.203 498.63686 0 3904.9707 0.041811692 + 9300 18776.997 427.7118 0 3904.9335 -7.652483 + 9350 18330.751 510.07857 0 3904.6621 8.3424059 + 9400 17538.366 657.08623 0 3904.9319 8.5478668 + 9450 20309.605 143.77142 0 3904.8093 6.6831447 + 9500 19982.331 203.81545 0 3904.2471 -7.6711411 + 9550 19410.612 310.1139 0 3904.6717 5.3983286 + 9600 19198.225 349.06634 0 3904.2932 -4.107658 + 9650 19388.043 314.31566 0 3904.6939 6.1198194 + 9700 18849.37 414.1045 0 3904.7286 5.4468861 + 9750 18263.312 523.38716 0 3905.4819 -0.56480349 + 9800 20421.858 122.53973 0 3904.3653 -15.641399 + 9850 17678.959 631.15683 0 3905.0381 -1.805446 + 9900 19421.046 306.67446 0 3903.1644 7.0287747 + 9950 18460.64 483.18902 0 3901.8261 3.658774 + 10000 19781.151 239.38136 0 3902.5575 6.3312911 +Loop time of 3.21586 on 4 procs for 10000 steps with 81 atoms + +Performance: 26866.868 tau/day, 3109.591 timesteps/s, 251.877 katom-step/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0068055 | 0.017185 | 0.043838 | 11.8 | 0.53 +Neigh | 0.010594 | 0.021601 | 0.042532 | 8.5 | 0.67 +Comm | 0.068664 | 0.091849 | 0.10748 | 4.8 | 2.86 +Output | 0.0038351 | 0.0044469 | 0.0057465 | 1.1 | 0.14 +Modify | 2.8494 | 2.9033 | 2.9663 | 2.5 | 90.28 +Other | | 0.1775 | | | 5.52 + +Nlocal: 20.25 ave 36 max 0 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 38.25 ave 50 max 28 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 126.5 ave 213 max 0 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 506 +Ave neighs/atom = 6.2469136 +Neighbor list builds = 1207 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.property.g++.1 b/examples/rigid/log.25Mar24.rigid.property.g++.1 new file mode 100644 index 0000000000..0a3d0da63a --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.property.g++.1 @@ -0,0 +1,343 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +fix 0 all property/atom i_bodies + +read_data data.rigid-property fix 0 NULL Clumps +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +# assemble bodies from per-atom custom integer property bodies +fix 1 all rigid custom i_bodies + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.42 | 4.42 | 4.42 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 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5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191522 0 5269.5092 12.011013 + 9700 16735.041 1.0589881 0 5269.4979 12.062708 + 9750 16738.013 0.13550093 0 5269.5101 11.407245 + 9800 16738.512 -0.01162033 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 + 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.13897 on 1 procs for 10000 steps with 81 atoms + +Performance: 621716.264 tau/day, 71957.901 timesteps/s, 5.829 Matom-step/s +98.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0095014 | 0.0095014 | 0.0095014 | 0.0 | 6.84 +Neigh | 0.050174 | 0.050174 | 0.050174 | 0.0 | 36.10 +Comm | 0.0091698 | 0.0091698 | 0.0091698 | 0.0 | 6.60 +Output | 0.0016255 | 0.0016255 | 0.0016255 | 0.0 | 1.17 +Modify | 0.060968 | 0.060968 | 0.060968 | 0.0 | 43.87 +Other | | 0.007531 | | | 5.42 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.property.g++.4 b/examples/rigid/log.25Mar24.rigid.property.g++.4 new file mode 100644 index 0000000000..5195cd4eb6 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.property.g++.4 @@ -0,0 +1,343 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +fix 0 all property/atom i_bodies + +read_data data.rigid-property fix 0 NULL Clumps +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +# assemble bodies from per-atom custom integer property bodies +fix 1 all rigid custom i_bodies + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.3 | 4.394 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 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16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589886 0 5269.4979 12.062708 + 9750 16738.013 0.13550089 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.145717 on 4 procs for 10000 steps with 81 atoms + +Performance: 592928.932 tau/day, 68626.034 timesteps/s, 5.559 Matom-step/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0017512 | 0.002579 | 0.0032423 | 1.1 | 1.77 +Neigh | 0.01337 | 0.01442 | 0.016488 | 1.0 | 9.90 +Comm | 0.066749 | 0.068666 | 0.070799 | 0.7 | 47.12 +Output | 0.0018563 | 0.0020346 | 0.0025278 | 0.6 | 1.40 +Modify | 0.040991 | 0.042542 | 0.044042 | 0.6 | 29.19 +Other | | 0.01548 | | | 10.62 + +Nlocal: 20.25 ave 37 max 3 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.small.g++.1 b/examples/rigid/log.25Mar24.rigid.small.g++.1 new file mode 100644 index 0000000000..7c1c88364b --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.small.g++.1 @@ -0,0 +1,321 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.002 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/small molecule + create bodies CPU = 0.000 seconds + 9 rigid bodies with 81 atoms + 1.2247449 = max distance from body owner to body atom + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722853e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.05932751 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934369 0 5269.4889 12.025288 + 3750 16737.731 0.20706559 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690669 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646805 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532808 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652431 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 + 9600 16738.549 -0.026814366 0 5269.5163 12.011415 + 9650 16738.765 -0.10191522 0 5269.5092 12.011013 + 9700 16735.041 1.0589875 0 5269.4979 12.062708 + 9750 16738.013 0.13550135 0 5269.5101 11.407245 + 9800 16738.512 -0.01162033 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270544 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.159025 on 1 procs for 10000 steps with 81 atoms + +Performance: 543312.198 tau/day, 62883.356 timesteps/s, 5.094 Matom-step/s +98.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0094515 | 0.0094515 | 0.0094515 | 0.0 | 5.94 +Bond | 0.00045015 | 0.00045015 | 0.00045015 | 0.0 | 0.28 +Neigh | 0.066186 | 0.066186 | 0.066186 | 0.0 | 41.62 +Comm | 0.0097819 | 0.0097819 | 0.0097819 | 0.0 | 6.15 +Output | 0.0021947 | 0.0021947 | 0.0021947 | 0.0 | 1.38 +Modify | 0.062923 | 0.062923 | 0.062923 | 0.0 | 39.57 +Other | | 0.008038 | | | 5.05 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.small.g++.4 b/examples/rigid/log.25Mar24.rigid.small.g++.4 new file mode 100644 index 0000000000..1b0d54f7b3 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.small.g++.4 @@ -0,0 +1,321 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/small molecule + create bodies CPU = 0.000 seconds + 9 rigid bodies with 81 atoms + 1.2247449 = max distance from body owner to body atom + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 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14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722842e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554428 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 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12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690662 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532814 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.0003765244 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191524 0 5269.5092 12.011013 + 9700 16735.041 1.0589896 0 5269.4979 12.062708 + 9750 16738.013 0.13550091 0 5269.5101 11.407245 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984566 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.200426 on 4 procs for 10000 steps with 81 atoms + +Performance: 431082.236 tau/day, 49893.777 timesteps/s, 4.041 Matom-step/s +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.001863 | 0.0024669 | 0.0029246 | 0.8 | 1.23 +Bond | 0.00033475 | 0.00034422 | 0.00035273 | 0.0 | 0.17 +Neigh | 0.016097 | 0.017035 | 0.018935 | 0.9 | 8.50 +Comm | 0.066051 | 0.06822 | 0.070253 | 0.7 | 34.04 +Output | 0.0020466 | 0.0021927 | 0.0026005 | 0.5 | 1.09 +Modify | 0.094972 | 0.096687 | 0.098173 | 0.4 | 48.24 +Other | | 0.01348 | | | 6.73 + +Nlocal: 20.25 ave 37 max 3 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.small.infile.g++.1 b/examples/rigid/log.25Mar24.rigid.small.infile.g++.1 new file mode 100644 index 0000000000..8c441d5d00 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.small.infile.g++.1 @@ -0,0 +1,322 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/small molecule infile bodyinfo.dat + create bodies CPU = 0.000 seconds + 9 rigid bodies with 81 atoms + 1.2247449 = max distance from body owner to body atom + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Reading rigid body data for 4 bodies from file bodyinfo.dat +Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 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16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706559 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 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5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690667 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532809 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652433 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156155 0 5269.5203 12.011611 + 9600 16738.549 -0.026814367 0 5269.5163 12.011415 + 9650 16738.765 -0.10191522 0 5269.5092 12.011013 + 9700 16735.041 1.0589876 0 5269.4979 12.062708 + 9750 16738.013 0.13550105 0 5269.5101 11.407245 + 9800 16738.512 -0.011620331 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270584 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984576 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395074 +Loop time of 0.154542 on 1 procs for 10000 steps with 81 atoms + +Performance: 559072.380 tau/day, 64707.451 timesteps/s, 5.241 Matom-step/s +98.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0094322 | 0.0094322 | 0.0094322 | 0.0 | 6.10 +Bond | 0.00037544 | 0.00037544 | 0.00037544 | 0.0 | 0.24 +Neigh | 0.062048 | 0.062048 | 0.062048 | 0.0 | 40.15 +Comm | 0.0095533 | 0.0095533 | 0.0095533 | 0.0 | 6.18 +Output | 0.0022247 | 0.0022247 | 0.0022247 | 0.0 | 1.44 +Modify | 0.06281 | 0.06281 | 0.06281 | 0.0 | 40.64 +Other | | 0.008098 | | | 5.24 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.small.infile.g++.4 b/examples/rigid/log.25Mar24.rigid.small.infile.g++.4 new file mode 100644 index 0000000000..e4c45a4523 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.small.infile.g++.4 @@ -0,0 +1,322 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/small molecule infile bodyinfo.dat + create bodies CPU = 0.000 seconds + 9 rigid bodies with 81 atoms + 1.2247449 = max distance from body owner to body atom + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Reading rigid body data for 4 bodies from file bodyinfo.dat +Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 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12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.05932751 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934369 0 5269.4889 12.025288 + 3750 16737.731 0.20706559 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 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12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690668 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646805 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532808 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652432 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156155 0 5269.5203 12.011611 + 9600 16738.549 -0.026814366 0 5269.5163 12.011415 + 9650 16738.765 -0.10191522 0 5269.5092 12.011013 + 9700 16735.041 1.0589874 0 5269.4979 12.062708 + 9750 16738.013 0.1355012 0 5269.5101 11.407245 + 9800 16738.512 -0.011620331 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270574 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984568 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.194899 on 4 procs for 10000 steps with 81 atoms + +Performance: 443306.036 tau/day, 51308.569 timesteps/s, 4.156 Matom-step/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0017487 | 0.0024215 | 0.0028965 | 0.9 | 1.24 +Bond | 0.00032501 | 0.00033082 | 0.0003413 | 0.0 | 0.17 +Neigh | 0.015692 | 0.016603 | 0.018578 | 0.9 | 8.52 +Comm | 0.063465 | 0.066081 | 0.068061 | 0.8 | 33.91 +Output | 0.0019654 | 0.0021191 | 0.0025315 | 0.5 | 1.09 +Modify | 0.092199 | 0.094298 | 0.096149 | 0.5 | 48.38 +Other | | 0.01305 | | | 6.69 + +Nlocal: 20.25 ave 37 max 3 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 1552 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.tnr.g++.1 b/examples/rigid/log.25Mar24.rigid.tnr.g++.1 new file mode 100644 index 0000000000..be58bf94b9 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.tnr.g++.1 @@ -0,0 +1,475 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Tethered nanorods + +atom_style molecular + +read_data data.rigid.tnr +Reading data file ... + orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5600 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 1600 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.027 seconds + +# Specify bond parameters + +bond_style fene +bond_coeff 1 30.0 1.5 1.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + +# Specify initial velocities + +velocity all create 1.4 109345 + +# Specify rigid components + +group rods type 2 +4000 atoms in group rods +group tethers subtract all rods +1600 atoms in group tethers + +neigh_modify exclude molecule/intra rods delay 0 every 1 + +# Specify the pair potentials + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff * * 1.0 1.0 1.122 +pair_coeff 2 2 1.0 1.0 2.5 + +# Specify output + +thermo 100 +thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz +thermo_modify flush yes lost warn + +timestep 0.005 + +fix 1 rods rigid molecule + 800 rigid bodies with 4000 atoms +fix 2 tethers nve +fix 3 all langevin 1.4 1.4 1.0 437624 + +run 5000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 45 45 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.017 | 8.017 | 8.017 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 + 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248 + 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036 + 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998 + 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801 + 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745 + 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581 + 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883 + 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271 + 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788 + 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119 + 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748 + 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115 + 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625 + 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021 + 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242 + 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334 + 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014 + 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797 + 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268 + 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673 + 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825 + 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911 + 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296 + 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402 + 2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677 + 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948 + 2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371 + 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106 + 2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713 + 3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611 + 3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039 + 3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251 + 3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362 + 3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524 + 3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699 + 3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752 + 3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797 + 3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772 + 3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034 + 4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065 + 4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387 + 4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557 + 4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574 + 4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421 + 4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711 + 4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462 + 4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986 + 4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278 + 4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891 + 5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248 +Loop time of 5.54157 on 1 procs for 5000 steps with 5600 atoms + +Performance: 389781.415 tau/day, 902.272 timesteps/s, 5.053 Matom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.40156 | 0.40156 | 0.40156 | 0.0 | 7.25 +Bond | 0.172 | 0.172 | 0.172 | 0.0 | 3.10 +Neigh | 1.6573 | 1.6573 | 1.6573 | 0.0 | 29.91 +Comm | 0.10679 | 0.10679 | 0.10679 | 0.0 | 1.93 +Output | 0.0033706 | 0.0033706 | 0.0033706 | 0.0 | 0.06 +Modify | 3.0948 | 3.0948 | 3.0948 | 0.0 | 55.85 +Other | | 0.1058 | | | 1.91 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1351 ave 1351 max 1351 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5254 ave 5254 max 5254 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5254 +Ave neighs/atom = 0.93821429 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 766 +Dangerous builds = 0 + +# Replace fix rigid and fix langevin with new ones + +unfix 1 +unfix 3 + +fix 3 tethers langevin 1.4 1.4 1.0 198450 + +# Test different integrators for rods + +fix 1 rods rigid/nve molecule + 800 rigid bodies with 4000 atoms +print "rigid/nve" +rigid/nve +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 8.018 | 8.018 | 8.018 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575 + 5100 1.439608 5.9052128 7.0359478 0.0060989876 7.2985886 62.244 62.244 62.244 0.0087364154 0.0040228411 0.0055377063 + 5200 1.4120671 5.9102569 7.01936 0.0064301456 7.2962615 62.244 62.244 62.244 0.0082738088 0.0038925707 0.0071240574 + 5300 1.4452434 5.8842166 7.0193778 0.0081724166 7.3713067 62.244 62.244 62.244 0.0077715644 0.0068924374 0.0098532479 + 5400 1.4170243 5.887522 7.0005186 0.00086566653 7.0377968 62.244 62.244 62.244 -9.179779e-05 -0.0020237494 0.0047125468 + 5500 1.4209084 5.875892 6.9919394 0.009363414 7.3951563 62.244 62.244 62.244 0.0088769611 0.0087092372 0.010504044 + 5600 1.4132978 5.8798939 6.9899636 0.0014877902 7.0540323 62.244 62.244 62.244 -0.0023427699 0.0045593956 0.0022467449 + 5700 1.4065055 5.8875412 6.9922759 0.002808316 7.1132105 62.244 62.244 62.244 0.0025187553 0.00051088905 0.0053953037 + 5800 1.4079049 5.8940749 6.9999087 0.0015946903 7.0685809 62.244 62.244 62.244 0.0037830352 0.00021762631 0.00078340928 + 5900 1.4076048 5.8941588 6.9997569 0.0051902121 7.2232631 62.244 62.244 62.244 -0.00093181434 0.0096405899 0.0068618607 + 6000 1.4322812 5.8903503 7.0153305 0.00029722379 7.0281298 62.244 62.244 62.244 0.0019139164 -0.00073870179 -0.00028354325 +Loop time of 1.21399 on 1 procs for 1000 steps with 5600 atoms + +Performance: 355850.342 tau/day, 823.728 timesteps/s, 4.613 Matom-step/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12141 | 0.12141 | 0.12141 | 0.0 | 10.00 +Bond | 0.038739 | 0.038739 | 0.038739 | 0.0 | 3.19 +Neigh | 0.39335 | 0.39335 | 0.39335 | 0.0 | 32.40 +Comm | 0.023806 | 0.023806 | 0.023806 | 0.0 | 1.96 +Output | 0.00074295 | 0.00074295 | 0.00074295 | 0.0 | 0.06 +Modify | 0.61212 | 0.61212 | 0.61212 | 0.0 | 50.42 +Other | | 0.02383 | | | 1.96 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1347 ave 1347 max 1347 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5399 ave 5399 max 5399 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5399 +Ave neighs/atom = 0.96410714 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 153 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 + 800 rigid bodies with 4000 atoms +print "rigid/nvt" +rigid/nvt +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 8.018 | 8.018 | 8.018 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 6000 1.4322812 5.8903503 7.0153305 0.012984296 7.5744734 62.244 62.244 62.244 0.058323772 0.007366828 -0.026737713 + 6100 1.4199781 5.8764024 6.9917192 0.0054080227 7.2246049 62.244 62.244 62.244 0.0092282159 0.0019631398 0.0050327123 + 6200 1.3976803 5.8924474 6.9902504 0.00044474719 7.0094026 62.244 62.244 62.244 -0.0022979183 -0.0004943354 0.0041264952 + 6300 1.4076912 5.8847607 6.9904268 0.0066261457 7.2757686 62.244 62.244 62.244 0.0057923777 0.0091772934 0.0049087658 + 6400 1.3749242 5.8816641 6.9615934 0.0075045379 7.2847615 62.244 62.244 62.244 0.012318395 0.003979389 0.0062158299 + 6500 1.3467602 5.888001 6.945809 -6.1011018e-05 6.9431817 62.244 62.244 62.244 0.0031945051 -0.0013048764 -0.0020726618 + 6600 1.3638321 5.8744775 6.9456945 0.005780579 7.1946237 62.244 62.244 62.244 0.0060765968 0.0058486743 0.0054164658 + 6700 1.3933343 5.8833797 6.9777691 0.0026007197 7.089764 62.244 62.244 62.244 0.0029828101 0.0019631585 0.0028561905 + 6800 1.4025439 5.901019 7.0026421 0.0033759718 7.1480216 62.244 62.244 62.244 0.0059683617 0.0016890885 0.002470465 + 6900 1.4165405 5.8901618 7.0027785 0.0048537306 7.2117948 62.244 62.244 62.244 0.0031937581 0.0089194691 0.0024479647 + 7000 1.4256345 5.8979889 7.0177485 0.0076603683 7.347627 62.244 62.244 62.244 0.0064499957 0.0096400261 0.0068910831 +Loop time of 1.16587 on 1 procs for 1000 steps with 5600 atoms + +Performance: 370540.281 tau/day, 857.732 timesteps/s, 4.803 Matom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.11675 | 0.11675 | 0.11675 | 0.0 | 10.01 +Bond | 0.03628 | 0.03628 | 0.03628 | 0.0 | 3.11 +Neigh | 0.36879 | 0.36879 | 0.36879 | 0.0 | 31.63 +Comm | 0.022201 | 0.022201 | 0.022201 | 0.0 | 1.90 +Output | 0.00070791 | 0.00070791 | 0.00070791 | 0.0 | 0.06 +Modify | 0.59859 | 0.59859 | 0.59859 | 0.0 | 51.34 +Other | | 0.02255 | | | 1.93 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1284 ave 1284 max 1284 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5691 ave 5691 max 5691 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5691 +Ave neighs/atom = 1.01625 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 151 +Dangerous builds = 0 +unfix 1 + +compute myTemp all temp + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all + 800 rigid bodies with 4000 atoms +print "rigid/npt iso" +rigid/npt iso +fix_modify 1 temp myTemp + +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 8.018 | 8.018 | 8.018 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 7000 1.4256345 5.8979889 7.0177485 0.030670312 8.3385046 62.244 62.244 62.244 0.019152979 0.028037341 0.044820616 + 7100 1.4830481 5.8740667 7.0389215 0.021216954 7.7436467 57.083193 57.083193 57.083193 0.015785563 0.020078182 0.027787115 + 7200 1.5225973 5.8364439 7.0323626 0.015560962 7.3866118 50.329217 50.329217 50.329217 0.017379604 0.02205435 0.0072489313 + 7300 1.5589134 5.7874972 7.0119402 0.020613279 7.3515942 45.188285 45.188285 45.188285 0.019963793 0.02165546 0.020220585 + 7400 1.5629259 5.7523794 6.9799739 0.035363756 7.4299227 41.456971 41.456971 41.456971 0.030810521 0.041559103 0.033721646 + 7500 1.5735285 5.706087 6.9420093 0.033186427 7.2889675 38.830074 38.830074 38.830074 0.030605548 0.018770943 0.050182791 + 7600 1.5546074 5.6815832 6.902644 0.027297758 7.1446412 36.752801 36.752801 36.752801 0.027154479 0.030653039 0.024085757 + 7700 1.5396727 5.6293114 6.8386418 0.030528746 7.0744265 35.101973 35.101973 35.101973 0.022542269 0.025802901 0.043241069 + 7800 1.5249769 5.5826711 6.7804588 0.067321436 7.2458344 33.82824 33.82824 33.82824 0.063820368 0.072156874 0.065987065 + 7900 1.5017937 5.5660576 6.7456361 0.04770857 7.0497596 32.926623 32.926623 32.926623 0.035259576 0.06869573 0.039170404 + 8000 1.5105319 5.5459012 6.7323431 0.053301062 7.0487429 32.153588 32.153588 32.153588 0.076450314 0.07417732 0.0092755526 +Loop time of 2.49405 on 1 procs for 1000 steps with 5600 atoms + +Performance: 173212.568 tau/day, 400.955 timesteps/s, 2.245 Matom-step/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.29712 | 0.29712 | 0.29712 | 0.0 | 11.91 +Bond | 0.044611 | 0.044611 | 0.044611 | 0.0 | 1.79 +Neigh | 1.2735 | 1.2735 | 1.2735 | 0.0 | 51.06 +Comm | 0.048469 | 0.048469 | 0.048469 | 0.0 | 1.94 +Output | 0.0007418 | 0.0007418 | 0.0007418 | 0.0 | 0.03 +Modify | 0.7991 | 0.7991 | 0.7991 | 0.0 | 32.04 +Other | | 0.03048 | | | 1.22 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2993 ave 2993 max 2993 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25312 ave 25312 max 25312 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25312 +Ave neighs/atom = 4.52 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 335 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all + 800 rigid bodies with 4000 atoms +print "rigid/npt x" +rigid/npt x +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 8.033 | 8.033 | 8.033 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 8000 1.5105319 5.5459012 6.7323431 -0.15611622 5.8056235 32.153588 32.153588 32.153588 -0.25823552 0.036861264 -0.24697441 + 8100 1.4816536 5.5214096 6.6851691 0.051659716 6.9889314 31.85012 32.153588 32.153588 0.042525917 0.079045459 0.033407772 + 8200 1.4364335 5.5026881 6.6309297 0.030961663 6.8100555 31.337401 32.153588 32.153588 0.062969827 0.0077436471 0.022171514 + 8300 1.4159126 5.504273 6.6163965 0.050231597 6.9027629 30.879771 32.153588 32.153588 0.047512875 0.071477224 0.031704693 + 8400 1.4479331 5.4732237 6.6104975 0.037171033 6.8195306 30.460678 32.153588 32.153588 0.016306171 0.072770628 0.022436301 + 8500 1.4126922 5.4616331 6.5712271 0.069137703 6.9521816 29.846079 32.153588 32.153588 0.075972518 0.063305384 0.068135208 + 8600 1.4129562 5.4397649 6.5495663 0.068287674 6.9190398 29.306917 32.153588 32.153588 0.077820831 0.076960087 0.050082105 + 8700 1.4199417 5.408767 6.5240551 0.046952367 6.7741118 28.847632 32.153588 32.153588 0.078496327 0.013710756 0.048650018 + 8800 1.415092 5.4082456 6.5197246 0.017068201 6.6091852 28.39051 32.153588 32.153588 0.01803734 0.0086202553 0.024547008 + 8900 1.4080943 5.3806524 6.486635 0.006282149 6.5189723 27.882074 32.153588 32.153588 0.023331732 0.01130818 -0.015793465 + 9000 1.4188356 5.3687142 6.4831335 0.078333785 6.8770321 27.237322 32.153588 32.153588 0.092873218 0.033643462 0.10848468 +Loop time of 2.35076 on 1 procs for 1000 steps with 5600 atoms + +Performance: 183770.370 tau/day, 425.394 timesteps/s, 2.382 Matom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.45082 | 0.45082 | 0.45082 | 0.0 | 19.18 +Bond | 0.045157 | 0.045157 | 0.045157 | 0.0 | 1.92 +Neigh | 0.98655 | 0.98655 | 0.98655 | 0.0 | 41.97 +Comm | 0.039968 | 0.039968 | 0.039968 | 0.0 | 1.70 +Output | 0.00072296 | 0.00072296 | 0.00072296 | 0.0 | 0.03 +Modify | 0.80394 | 0.80394 | 0.80394 | 0.0 | 34.20 +Other | | 0.0236 | | | 1.00 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3422 ave 3422 max 3422 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 31084 ave 31084 max 31084 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 31084 +Ave neighs/atom = 5.5507143 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 167 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all + 800 rigid bodies with 4000 atoms +print "rigid/nph iso" +rigid/nph iso +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 8.036 | 8.036 | 8.036 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 9000 1.4188356 5.3687142 6.4831335 0.066940268 6.8197402 27.237322 32.153588 32.153588 0.020750172 0.14461869 0.035451941 + 9100 1.418441 5.3523211 6.4664305 0.016522511 6.5489637 27.17712 32.08252 32.08252 0.01137531 0.0028933886 0.035298833 + 9200 1.4433401 5.3458252 6.4794915 0.038961106 6.6708176 27.023003 31.900585 31.900585 0.012667867 0.094480325 0.0097351253 + 9300 1.4806575 5.309105 6.4720822 0.11806636 7.0379478 26.804952 31.643176 31.643176 0.063001935 0.11667303 0.17452413 + 9400 1.4835179 5.3103383 6.4755622 0.098990545 6.9362503 26.543432 31.334452 31.334452 0.13023767 0.084360197 0.08237377 + 9500 1.4855723 5.2906327 6.4574702 -0.0012789282 6.4516456 26.352845 31.109465 31.109465 0.053813822 -0.016098782 -0.041551825 + 9600 1.4959395 5.2553176 6.4302979 0.036958035 6.5952607 26.176506 30.901298 30.901298 0.077457004 -0.035314705 0.068731807 + 9700 1.4470266 5.289874 6.4264359 0.065648447 6.7177609 26.125849 30.841497 30.841497 0.064764383 0.041383889 0.090797069 + 9800 1.4525327 5.2808561 6.4217428 0.0076421133 6.4554682 26.077575 30.78451 30.78451 -0.01978363 0.013568065 0.029141905 + 9900 1.4603761 5.269343 6.4163902 0.079488558 6.7651749 26.027767 30.725712 30.725712 0.06210239 0.062690336 0.11367295 + 10000 1.4437445 5.2626116 6.3965955 0.0024175103 6.4072252 26.045744 30.746933 30.746933 0.0020903338 0.023283622 -0.018121425 +Loop time of 2.42718 on 1 procs for 1000 steps with 5600 atoms + +Performance: 177984.690 tau/day, 412.002 timesteps/s, 2.307 Matom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.52411 | 0.52411 | 0.52411 | 0.0 | 21.59 +Bond | 0.04594 | 0.04594 | 0.04594 | 0.0 | 1.89 +Neigh | 1.0079 | 1.0079 | 1.0079 | 0.0 | 41.53 +Comm | 0.040182 | 0.040182 | 0.040182 | 0.0 | 1.66 +Output | 0.00070663 | 0.00070663 | 0.00070663 | 0.0 | 0.03 +Modify | 0.78582 | 0.78582 | 0.78582 | 0.0 | 32.38 +Other | | 0.02253 | | | 0.93 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3638 ave 3638 max 3638 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 35778 ave 35778 max 35778 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 35778 +Ave neighs/atom = 6.3889286 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 161 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all + 800 rigid bodies with 4000 atoms +print "rigid/nph xy couple" +rigid/nph xy couple +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 8.041 | 8.041 | 8.041 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 10000 1.4437445 5.2626116 6.3965955 0.043852305 6.5894123 26.045744 30.746933 30.746933 -0.10594451 -0.016019605 0.25352103 + 10100 1.4544517 5.2536075 6.3960014 0.040252547 6.5723133 25.995896 30.688087 30.746933 0.036481947 0.058195014 0.026080679 + 10200 1.4465796 5.2533056 6.3895164 0.043103918 6.5797343 26.093233 30.802994 30.746933 0.047509548 0.023387048 0.058415158 + 10300 1.4703558 5.2311222 6.3860079 0.02952279 6.5179005 26.253791 30.992532 30.746933 0.067825843 -1.1742127e-05 0.020754268 + 10400 1.4264151 5.2426153 6.362988 0.043320767 6.5561801 26.230542 30.965087 30.746933 0.036437179 0.069318063 0.02420706 + 10500 1.4718495 5.213542 6.3696009 0.028876649 6.4965877 26.047535 30.749047 30.746933 0.044470994 0.03304953 0.0091094235 + 10600 1.4550996 5.2087392 6.3516419 0.049130073 6.5647387 25.868744 30.537985 30.746933 0.056613289 0.028555571 0.062221359 + 10700 1.4755834 5.1912236 6.3502153 0.0027128909 6.3617831 25.648895 30.278455 30.746933 0.035708882 0.02165412 -0.04922433 + 10800 1.4801906 5.1863989 6.3490092 0.030220134 6.4763468 25.497097 30.099256 30.746933 0.035963119 0.021549561 0.033147721 + 10900 1.4318851 5.1785312 6.3032002 0.095502071 6.7019424 25.380506 29.961622 30.746933 0.1040397 0.10708089 0.075385625 + 11000 1.4500789 5.1660716 6.3050309 0.072030914 6.6026703 25.249123 29.806525 30.746933 0.073199983 0.0091150749 0.13377768 +Loop time of 2.55647 on 1 procs for 1000 steps with 5600 atoms + +Performance: 168982.932 tau/day, 391.164 timesteps/s, 2.191 Matom-step/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.5683 | 0.5683 | 0.5683 | 0.0 | 22.23 +Bond | 0.044877 | 0.044877 | 0.044877 | 0.0 | 1.76 +Neigh | 1.0732 | 1.0732 | 1.0732 | 0.0 | 41.98 +Comm | 0.041328 | 0.041328 | 0.041328 | 0.0 | 1.62 +Output | 0.00078717 | 0.00078717 | 0.00078717 | 0.0 | 0.03 +Modify | 0.80433 | 0.80433 | 0.80433 | 0.0 | 31.46 +Other | | 0.02363 | | | 0.92 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3699 ave 3699 max 3699 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 39523 ave 39523 max 39523 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 39523 +Ave neighs/atom = 7.0576786 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 163 +Dangerous builds = 0 + +Total wall time: 0:00:17 diff --git a/examples/rigid/log.25Mar24.rigid.tnr.g++.4 b/examples/rigid/log.25Mar24.rigid.tnr.g++.4 new file mode 100644 index 0000000000..6d98088472 --- /dev/null +++ b/examples/rigid/log.25Mar24.rigid.tnr.g++.4 @@ -0,0 +1,475 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) + using 1 OpenMP thread(s) per MPI task +# Tethered nanorods + +atom_style molecular + +read_data data.rigid.tnr +Reading data file ... + orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 5600 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 1600 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.017 seconds + +# Specify bond parameters + +bond_style fene +bond_coeff 1 30.0 1.5 1.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# Specify initial velocities + +velocity all create 1.4 109345 + +# Specify rigid components + +group rods type 2 +4000 atoms in group rods +group tethers subtract all rods +1600 atoms in group tethers + +neigh_modify exclude molecule/intra rods delay 0 every 1 + +# Specify the pair potentials + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff * * 1.0 1.0 1.122 +pair_coeff 2 2 1.0 1.0 2.5 + +# Specify output + +thermo 100 +thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz +thermo_modify flush yes lost warn + +timestep 0.005 + +fix 1 rods rigid molecule + 800 rigid bodies with 4000 atoms +fix 2 tethers nve +fix 3 all langevin 1.4 1.4 1.0 437624 + +run 5000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 45 45 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.552 | 7.555 | 7.559 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 + 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624 + 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719 + 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786 + 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141 + 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529 + 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222 + 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907 + 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859 + 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971 + 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735 + 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195 + 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658 + 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474 + 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314 + 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432 + 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699 + 1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975 + 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981 + 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291 + 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901 + 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978 + 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521 + 2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595 + 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026 + 2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414204 0.0039571831 0.0048428538 + 2600 1.3876469 5.9249124 7.0148347 -0.0017777225 6.9382806 62.244 62.244 62.244 -0.00047616393 -0.0025484918 -0.0023085117 + 2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812866 0.0032048359 + 2800 1.4444643 5.9283432 7.0628925 0.0019400023 7.1464349 62.244 62.244 62.244 0.0014895078 0.0046367397 -0.00030624049 + 2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403268 -0.0046971891 + 3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147657 + 3100 1.3569137 5.9171753 6.9829583 -0.0028266769 6.8612331 62.244 62.244 62.244 -0.0069507251 0.0010084401 -0.0025377458 + 3200 1.4004275 5.905939 7.0058998 0.0054394667 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594139 0.00020680257 + 3300 1.3641217 5.9145275 6.985972 -0.0027212813 6.8687854 62.244 62.244 62.244 -0.00065933696 -0.005771301 -0.001733206 + 3400 1.3868722 5.9059546 6.9952684 0.0092591263 7.3939943 62.244 62.244 62.244 0.010690877 0.01075252 0.0063339817 + 3500 1.3939169 5.8992292 6.9940762 0.0074340014 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252538 0.0077394438 + 3600 1.3982507 5.9219461 7.0201971 0.0056794512 7.2647714 62.244 62.244 62.244 0.0023367131 0.0080592141 0.0066424266 + 3700 1.4019908 5.9059957 7.0071844 0.0065915518 7.2910365 62.244 62.244 62.244 0.0049554052 0.010827013 0.0039922376 + 3800 1.3960736 5.902079 6.9986201 0.0027763672 7.1181788 62.244 62.244 62.244 -0.0015907142 0.0025862031 0.0073336126 + 3900 1.4352825 5.8986216 7.0259591 0.003498295 7.1766062 62.244 62.244 62.244 0.0030417173 0.0027739456 0.0046792221 + 4000 1.4121845 5.9079028 7.0170981 0.0050462581 7.2344052 62.244 62.244 62.244 0.0045543085 0.0064113637 0.0041731022 + 4100 1.3989579 5.9082397 7.0070461 0.00042870391 7.0255074 62.244 62.244 62.244 0.0025733986 0.0025181076 -0.0038053944 + 4200 1.399883 5.8998147 6.9993477 0.0042777423 7.1835602 62.244 62.244 62.244 0.0013744675 0.0064699404 0.0049888191 + 4300 1.4076025 5.9044509 7.0100472 0.0066788698 7.2976595 62.244 62.244 62.244 0.007361029 0.0048139331 0.0078616474 + 4400 1.4161078 5.9064334 7.0187102 -0.0011844913 6.9677025 62.244 62.244 62.244 -0.001908963 -0.0037556847 0.0021111739 + 4500 1.429225 5.8980089 7.0205885 0.0018498822 7.10025 62.244 62.244 62.244 0.0041143046 0.0010156504 0.00041969169 + 4600 1.3958783 5.894313 6.9907006 0.0041483111 7.1693394 62.244 62.244 62.244 0.0033996217 0.0041616835 0.004883628 + 4700 1.3856609 5.8886843 6.9770467 0.0013148711 7.033669 62.244 62.244 62.244 -0.00051706505 0.0030872136 0.0013744648 + 4800 1.4016792 5.902351 7.0032949 0.0025050908 7.1111717 62.244 62.244 62.244 0.0016540384 -0.00018095286 0.0060421869 + 4900 1.4466248 5.9050606 7.0413069 -0.0026620212 6.9266722 62.244 62.244 62.244 -0.00069094879 -0.0073956145 0.00010049979 + 5000 1.4387209 5.9077482 7.0377864 0.0049404333 7.2505363 62.244 62.244 62.244 0.0042769255 0.0046681652 0.0058762093 +Loop time of 2.72962 on 4 procs for 5000 steps with 5600 atoms + +Performance: 791319.942 tau/day, 1831.759 timesteps/s, 10.258 Matom-step/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.06605 | 0.10369 | 0.14557 | 11.7 | 3.80 +Bond | 0.03005 | 0.045571 | 0.06035 | 6.5 | 1.67 +Neigh | 0.61326 | 0.61489 | 0.61678 | 0.2 | 22.53 +Comm | 0.14416 | 0.19908 | 0.25001 | 11.1 | 7.29 +Output | 0.0017405 | 0.0025188 | 0.0028143 | 0.9 | 0.09 +Modify | 1.522 | 1.6149 | 1.699 | 6.3 | 59.16 +Other | | 0.1489 | | | 5.46 + +Nlocal: 1400 ave 1868 max 905 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 648.25 ave 688 max 598 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 1202.5 ave 1821 max 698 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 4810 +Ave neighs/atom = 0.85892857 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 759 +Dangerous builds = 0 + +# Replace fix rigid and fix langevin with new ones + +unfix 1 +unfix 3 + +fix 3 tethers langevin 1.4 1.4 1.0 198450 + +# Test different integrators for rods + +fix 1 rods rigid/nve molecule + 800 rigid bodies with 4000 atoms +print "rigid/nve" +rigid/nve +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.557 | 7.566 | 7.574 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 5000 1.4387209 5.9077482 7.0377864 0.0036839327 7.1964276 62.244 62.244 62.244 0.025677952 -0.016670649 0.002044495 + 5100 1.4449629 5.8876265 7.0225675 0.0023125815 7.1221542 62.244 62.244 62.244 0.0045991271 0.0036872425 -0.0013486251 + 5200 1.4271279 5.9160281 7.0369606 0.0020315691 7.1244461 62.244 62.244 62.244 -0.0022476411 0.0039290288 0.0044133197 + 5300 1.4143266 5.9052803 7.0161581 0.0064093985 7.2921661 62.244 62.244 62.244 0.0090986577 0.0026397649 0.0074897729 + 5400 1.4426551 5.9087477 7.041876 0.0020419183 7.1298072 62.244 62.244 62.244 0.0043078454 1.5623413e-05 0.001802286 + 5500 1.4280605 5.9038941 7.0255591 0.00057730336 7.0504195 62.244 62.244 62.244 0.0058938228 0.00065558729 -0.0048175 + 5600 1.4315004 5.902394 7.0267609 0.0096531882 7.4424563 62.244 62.244 62.244 0.0054225258 0.011780272 0.011756766 + 5700 1.4074659 5.9076093 7.0130984 0.0052032455 7.2371658 62.244 62.244 62.244 0.0029612305 0.003678953 0.008969553 + 5800 1.4216898 5.9047983 7.0214595 0.0015109698 7.0865264 62.244 62.244 62.244 -6.4662019e-05 0.0023994389 0.0021981326 + 5900 1.4052133 5.8920187 6.9957385 0.0065755622 7.278902 62.244 62.244 62.244 0.0062703932 0.011367786 0.002088507 + 6000 1.3958734 5.9025061 6.9988899 0.0071783223 7.3080101 62.244 62.244 62.244 0.0088905564 0.0025533521 0.010091058 +Loop time of 0.646284 on 4 procs for 1000 steps with 5600 atoms + +Performance: 668436.315 tau/day, 1547.306 timesteps/s, 8.665 Matom-step/s +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.01802 | 0.028926 | 0.041262 | 6.4 | 4.48 +Bond | 0.0066363 | 0.0098826 | 0.012811 | 2.9 | 1.53 +Neigh | 0.14233 | 0.14273 | 0.14311 | 0.1 | 22.08 +Comm | 0.029365 | 0.044453 | 0.057955 | 6.3 | 6.88 +Output | 0.00034317 | 0.00049475 | 0.00055796 | 0.0 | 0.08 +Modify | 0.35817 | 0.37856 | 0.40064 | 2.8 | 58.57 +Other | | 0.04124 | | | 6.38 + +Nlocal: 1400 ave 1850 max 932 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 642.25 ave 730 max 550 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Neighs: 1267.25 ave 1805 max 729 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +Total # of neighbors = 5069 +Ave neighs/atom = 0.90517857 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 154 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 + 800 rigid bodies with 4000 atoms +print "rigid/nvt" +rigid/nvt +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.557 | 7.566 | 7.574 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 6000 1.3958734 5.9025061 6.9988899 0.0021028569 7.0894453 62.244 62.244 62.244 0.013626393 0.019990521 -0.027308344 + 6100 1.403297 5.9008111 7.0030257 0.0034667159 7.152313 62.244 62.244 62.244 0.00094173119 0.0074633638 0.0019950526 + 6200 1.4025256 5.8966477 6.9982564 -0.00020483779 6.9894355 62.244 62.244 62.244 -0.0064238043 0.0010245391 0.0047847518 + 6300 1.4394011 5.9052004 7.0357728 0.0054604133 7.2709147 62.244 62.244 62.244 0.0096132747 0.002164465 0.0046035003 + 6400 1.408769 5.8824709 6.9889834 0.005608612 7.2305072 62.244 62.244 62.244 0.0042736813 0.0053311794 0.0072209755 + 6500 1.3956548 5.8831208 6.9793329 0.0085962528 7.3495135 62.244 62.244 62.244 0.0082055979 0.011231962 0.0063511989 + 6600 1.3758562 5.8829365 6.9635978 0.0065047826 7.2437134 62.244 62.244 62.244 0.005468046 0.0069917695 0.0070545323 + 6700 1.3804704 5.8923062 6.9765917 0.0057976076 7.2262542 62.244 62.244 62.244 0.0052851407 0.011935403 0.00017227886 + 6800 1.396967 5.8774293 6.974672 0.0018361999 7.0537443 62.244 62.244 62.244 1.5181397e-05 0.0031700121 0.0023234062 + 6900 1.3966118 5.8872183 6.9841821 0.0029553371 7.1114478 62.244 62.244 62.244 -0.0022750426 0.0055197498 0.005621304 + 7000 1.3992657 5.8918087 6.990857 0.0033614376 7.1356106 62.244 62.244 62.244 0.0019626838 -0.0019054573 0.010027086 +Loop time of 0.627583 on 4 procs for 1000 steps with 5600 atoms + +Performance: 688355.013 tau/day, 1593.414 timesteps/s, 8.923 Matom-step/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.017522 | 0.028358 | 0.041297 | 6.2 | 4.52 +Bond | 0.0060681 | 0.0092563 | 0.012417 | 2.9 | 1.47 +Neigh | 0.13625 | 0.13667 | 0.13709 | 0.1 | 21.78 +Comm | 0.027966 | 0.043787 | 0.057522 | 6.2 | 6.98 +Output | 0.00035478 | 0.00049121 | 0.00055892 | 0.0 | 0.08 +Modify | 0.35811 | 0.37631 | 0.39333 | 2.6 | 59.96 +Other | | 0.03272 | | | 5.21 + +Nlocal: 1400 ave 1883 max 958 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 665 ave 803 max 565 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Neighs: 1272.25 ave 1895 max 762 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 5089 +Ave neighs/atom = 0.90875 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 150 +Dangerous builds = 0 +unfix 1 + +compute myTemp all temp + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all + 800 rigid bodies with 4000 atoms +print "rigid/npt iso" +rigid/npt iso +fix_modify 1 temp myTemp + +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.557 | 7.566 | 7.574 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 7000 1.3992657 5.8918087 6.990857 0.016459779 7.6996647 62.244 62.244 62.244 0.056781831 -0.019577361 0.012174866 + 7100 1.5086944 5.8706667 7.0556653 0.011656301 7.4412826 57.006966 57.006966 57.006966 0.015012728 0.015151838 0.0048043378 + 7200 1.5444857 5.8347072 7.047818 0.025893976 7.6357076 50.283831 50.283831 50.283831 0.021166084 0.027070838 0.029445006 + 7300 1.5460527 5.7950177 7.0093593 0.02162991 7.3688559 45.318555 45.318555 45.318555 0.014747735 0.037527921 0.012614075 + 7400 1.5613693 5.7516603 6.9780323 0.034798817 7.4279201 41.678228 41.678228 41.678228 0.041296806 0.025288632 0.037811012 + 7500 1.5582169 5.7359749 6.9598708 0.029878761 7.2757008 38.972622 38.972622 38.972622 0.031657651 0.020061922 0.037916711 + 7600 1.5578367 5.6988812 6.9224785 0.045695884 7.3351888 36.981577 36.981577 36.981577 0.040243029 0.039644927 0.057199697 + 7700 1.5148812 5.6528692 6.8427272 0.022439627 7.0209705 35.43196 35.43196 35.43196 0.010631952 0.017769669 0.03891726 + 7800 1.529109 5.6051059 6.8061392 0.054079172 7.1911354 34.161596 34.161596 34.161596 0.034939239 0.071325426 0.05597285 + 7900 1.5182819 5.5708546 6.7633838 0.066345571 7.1933547 33.108416 33.108416 33.108416 0.060359678 0.07068182 0.067995216 + 8000 1.4677372 5.5540248 6.7068537 0.033729921 6.90804 32.205032 32.205032 32.205032 0.049412183 0.016101823 0.035675755 +Loop time of 1.1282 on 4 procs for 1000 steps with 5600 atoms + +Performance: 382910.795 tau/day, 886.368 timesteps/s, 4.964 Matom-step/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.047245 | 0.075421 | 0.11065 | 10.1 | 6.69 +Bond | 0.0077964 | 0.011056 | 0.014794 | 2.9 | 0.98 +Neigh | 0.47306 | 0.4737 | 0.47434 | 0.1 | 41.99 +Comm | 0.047565 | 0.086613 | 0.11788 | 10.3 | 7.68 +Output | 0.00031206 | 0.00038703 | 0.00060877 | 0.0 | 0.03 +Modify | 0.43174 | 0.44726 | 0.46676 | 2.3 | 39.64 +Other | | 0.03376 | | | 2.99 + +Nlocal: 1400 ave 1845 max 1051 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1558.25 ave 1732 max 1431 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 6210.75 ave 9543 max 3698 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 24843 +Ave neighs/atom = 4.43625 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 335 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all + 800 rigid bodies with 4000 atoms +print "rigid/npt x" +rigid/npt x +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.567 | 7.579 | 7.596 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 8000 1.4677372 5.5540248 6.7068537 -0.017850632 6.6003814 32.205032 32.205032 32.205032 -0.10278017 -0.1824093 0.23163757 + 8100 1.4540331 5.5388671 6.6809322 0.022562574 6.8139144 31.823315 32.205032 32.205032 0.028408548 0.028883436 0.010395737 + 8200 1.4702497 5.4971666 6.6519689 0.031541665 6.8340274 31.164985 32.205032 32.205032 0.05198967 0.017790558 0.024844767 + 8300 1.4895576 5.4752966 6.6452643 0.049612462 6.9245663 30.396516 32.205032 32.205032 0.050583662 0.041684528 0.056569197 + 8400 1.4546023 5.4627064 6.6052185 0.014637455 6.6862795 29.901065 32.205032 32.205032 0.022874978 -0.0061332581 0.027170646 + 8500 1.4485789 5.4330137 6.5707949 0.06887386 6.9450276 29.337823 32.205032 32.205032 0.082103679 0.041682043 0.082835857 + 8600 1.4443937 5.4261726 6.5606664 0.02551672 6.6959898 28.63444 32.205032 32.205032 0.028149026 0.066325162 -0.017924027 + 8700 1.4329121 5.409813 6.5352887 0.028828984 6.6848753 28.015854 32.205032 32.205032 0.015384578 0.050827744 0.02027463 + 8800 1.4015747 5.4009279 6.5017898 0.046423411 6.7374794 27.41221 32.205032 32.205032 0.099149897 0.019633915 0.020486421 + 8900 1.411353 5.3728016 6.4813438 0.046095308 6.711069 26.908695 32.205032 32.205032 0.04716092 0.029778906 0.061346098 + 9000 1.3987178 5.3528351 6.451453 0.029891295 6.5977498 26.425959 32.205032 32.205032 0.033096258 0.039059663 0.017517965 +Loop time of 1.05732 on 4 procs for 1000 steps with 5600 atoms + +Performance: 408581.873 tau/day, 945.791 timesteps/s, 5.296 Matom-step/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.084017 | 0.12178 | 0.1674 | 10.7 | 11.52 +Bond | 0.0087866 | 0.011339 | 0.014172 | 2.1 | 1.07 +Neigh | 0.35177 | 0.35194 | 0.35221 | 0.0 | 33.29 +Comm | 0.046529 | 0.094466 | 0.13331 | 12.7 | 8.93 +Output | 0.00031081 | 0.00038714 | 0.00061511 | 0.0 | 0.04 +Modify | 0.43779 | 0.45007 | 0.46334 | 1.8 | 42.57 +Other | | 0.02734 | | | 2.59 + +Nlocal: 1400 ave 1718 max 1133 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 1700.75 ave 1793 max 1533 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Neighs: 7936.75 ave 10967 max 5250 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 31747 +Ave neighs/atom = 5.6691071 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 169 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all + 800 rigid bodies with 4000 atoms +print "rigid/nph iso" +rigid/nph iso +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.58 | 7.597 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 9000 1.3987178 5.3528351 6.451453 0.26585248 7.7526137 26.425959 32.205032 32.205032 0.02018168 0.47782722 0.29954855 + 9100 1.4351747 5.3304458 6.4576986 0.051746697 6.707501 26.305023 32.057649 32.057649 0.073064096 0.037508173 0.044667823 + 9200 1.442609 5.3185643 6.4516564 0.026933669 6.5768423 25.974904 31.655336 31.655336 0.0097800385 0.035425194 0.035595776 + 9300 1.4528107 5.2812305 6.4223354 0.074634951 6.7601945 25.747306 31.377965 31.377965 0.12937272 0.031196451 0.063335685 + 9400 1.4778194 5.2625966 6.4233445 0.0179548 6.5034822 25.626311 31.23051 31.23051 0.042627054 -0.047901197 0.059138542 + 9500 1.4406019 5.2661826 6.3976982 0.048963663 6.6143417 25.551982 31.139926 31.139926 0.097226703 -0.0051171725 0.054781458 + 9600 1.4463517 5.2420508 6.3780826 0.033338493 6.5253103 25.535743 31.120136 31.120136 0.013953126 0.066958907 0.019103444 + 9700 1.4040075 5.264089 6.3668617 0.075486855 6.6986983 25.496763 31.072631 31.072631 0.051974464 0.097239496 0.077246606 + 9800 1.4369291 5.25259 6.3812208 0.062882837 6.6532231 25.359898 30.905835 30.905835 0.088614069 0.087884794 0.012149647 + 9900 1.4426697 5.2270989 6.3602387 0.070910381 6.6603048 25.175015 30.68052 30.68052 0.081294501 0.056618911 0.07481773 + 10000 1.4714476 5.2051468 6.3608901 0.038441228 6.5234989 25.171919 30.676748 30.676748 0.021691591 0.0086967032 0.084935388 +Loop time of 1.07529 on 4 procs for 1000 steps with 5600 atoms + +Performance: 401751.573 tau/day, 929.980 timesteps/s, 5.208 Matom-step/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.10178 | 0.14349 | 0.18701 | 10.0 | 13.34 +Bond | 0.0094369 | 0.011359 | 0.01342 | 1.5 | 1.06 +Neigh | 0.35737 | 0.35764 | 0.35787 | 0.0 | 33.26 +Comm | 0.048562 | 0.093503 | 0.13651 | 12.7 | 8.70 +Output | 0.00029714 | 0.00035903 | 0.0005404 | 0.0 | 0.03 +Modify | 0.43477 | 0.44365 | 0.45263 | 1.3 | 41.26 +Other | | 0.0253 | | | 2.35 + +Nlocal: 1400 ave 1650 max 1148 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Nghost: 1770.5 ave 1864 max 1640 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 9370.75 ave 12213 max 6410 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 37483 +Ave neighs/atom = 6.6933929 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 162 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all + 800 rigid bodies with 4000 atoms +print "rigid/nph xy couple" +rigid/nph xy couple +run 1000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 7.569 | 7.58 | 7.597 Mbytes + Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 10000 1.4714476 5.2051468 6.3608901 -0.096738415 5.9516804 25.171919 30.676748 30.676748 -0.07465944 0.069571401 -0.28512721 + 10100 1.4336012 5.2129069 6.3389239 0.069305782 6.6336186 25.237381 30.756525 30.676748 0.1042358 0.062982076 0.040699467 + 10200 1.3850266 5.2255115 6.3133757 -0.026502584 6.1990129 25.423835 30.983755 30.676748 -0.018638813 -0.01225392 -0.048615018 + 10300 1.4059572 5.2273228 6.3316268 0.026841528 6.4477936 25.461278 31.029386 30.676748 0.0032748153 0.054971756 0.022278013 + 10400 1.4085811 5.2218002 6.3281652 0.087028058 6.7005137 25.315588 30.851835 30.676748 0.095488962 0.059423478 0.10617173 + 10500 1.4323046 5.1961285 6.321127 0.011963636 6.3715428 25.124329 30.61875 30.676748 0.047765438 -0.013073535 0.0011990069 + 10600 1.4401614 5.1744178 6.3055874 0.065577091 6.5770196 24.899891 30.345229 30.676748 0.05130409 0.11923748 0.026189709 + 10700 1.45262 5.1656069 6.3065622 0.019979844 6.3873914 24.616776 30.0002 30.676748 0.062077837 0.01564587 -0.017784176 + 10800 1.436593 5.1491998 6.2775666 0.06467682 6.5343926 24.388662 29.722201 30.676748 0.055509186 0.081686998 0.056834275 + 10900 1.4221057 5.1580272 6.2750151 0.10779715 6.6964287 24.198783 29.490797 30.676748 0.11821126 0.13388181 0.071298392 + 11000 1.4318097 5.1652839 6.2898937 0.12207839 6.7635101 24.106649 29.378514 30.676748 0.13281999 0.095712525 0.13770264 +Loop time of 1.05977 on 4 procs for 1000 steps with 5600 atoms + +Performance: 407635.235 tau/day, 943.600 timesteps/s, 5.284 Matom-step/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.11531 | 0.15482 | 0.18642 | 8.0 | 14.61 +Bond | 0.0095915 | 0.011316 | 0.012716 | 1.2 | 1.07 +Neigh | 0.34708 | 0.34732 | 0.34748 | 0.0 | 32.77 +Comm | 0.050629 | 0.082561 | 0.12326 | 11.1 | 7.79 +Output | 0.00029841 | 0.00036751 | 0.00057311 | 0.0 | 0.03 +Modify | 0.43421 | 0.44242 | 0.45027 | 0.9 | 41.75 +Other | | 0.02097 | | | 1.98 + +Nlocal: 1400 ave 1551 max 1205 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 1831.5 ave 1910 max 1688 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 10203.8 ave 12647 max 7619 min +Histogram: 1 0 1 0 0 0 0 1 0 1 + +Total # of neighbors = 40815 +Ave neighs/atom = 7.2883929 +Ave special neighs/atom = 0.57142857 +Neighbor list builds = 161 +Dangerous builds = 0 + +Total wall time: 0:00:08 diff --git a/examples/rigid/log.27Nov18.rigid.atomfile.g++.1 b/examples/rigid/log.27Nov18.rigid.atomfile.g++.1 deleted file mode 100644 index e3e539eada..0000000000 --- a/examples/rigid/log.27Nov18.rigid.atomfile.g++.1 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -variable bodies atomfile bodies.txt -fix 1 all rigid custom v_bodies -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.109 | 4.109 | 4.109 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 - 9550 16738.493 -0.005315616 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589885 0 5269.4979 12.062708 - 9750 16738.013 0.13550123 0 5269.5101 11.407245 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.153749 on 1 procs for 10000 steps with 81 atoms - -Performance: 561955.786 tau/day, 65041.179 timesteps/s -98.4% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0098538 | 0.0098538 | 0.0098538 | 0.0 | 6.41 -Neigh | 0.040308 | 0.040308 | 0.040308 | 0.0 | 26.22 -Comm | 0.013034 | 0.013034 | 0.013034 | 0.0 | 8.48 -Output | 0.0017202 | 0.0017202 | 0.0017202 | 0.0 | 1.12 -Modify | 0.083709 | 0.083709 | 0.083709 | 0.0 | 54.45 -Other | | 0.005123 | | | 3.33 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.atomfile.g++.4 b/examples/rigid/log.27Nov18.rigid.atomfile.g++.4 deleted file mode 100644 index 1e28766101..0000000000 --- a/examples/rigid/log.27Nov18.rigid.atomfile.g++.4 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -variable bodies atomfile bodies.txt -fix 1 all rigid custom v_bodies -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.174 | 4.455 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706557 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 - 9600 16738.549 -0.026814371 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589894 0 5269.4979 12.062708 - 9750 16738.013 0.13550109 0 5269.5101 11.407246 - 9800 16738.512 -0.011620327 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.202963 on 4 procs for 10000 steps with 81 atoms - -Performance: 425693.239 tau/day, 49270.051 timesteps/s -89.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0025978 | 0.0033882 | 0.0042055 | 1.0 | 1.67 -Neigh | 0.012025 | 0.013416 | 0.01623 | 1.4 | 6.61 -Comm | 0.080375 | 0.087468 | 0.090782 | 1.4 | 43.10 -Output | 0.0031407 | 0.0039954 | 0.0065427 | 2.3 | 1.97 -Modify | 0.086613 | 0.087285 | 0.087619 | 0.1 | 43.01 -Other | | 0.00741 | | | 3.65 - -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.atomvar.g++.1 b/examples/rigid/log.27Nov18.rigid.atomvar.g++.1 deleted file mode 100644 index 58834ebf3d..0000000000 --- a/examples/rigid/log.27Nov18.rigid.atomvar.g++.1 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) -fix 1 all rigid custom v_bodies -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.984 | 3.984 | 3.984 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 - 9550 16738.493 -0.005315616 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589885 0 5269.4979 12.062708 - 9750 16738.013 0.13550123 0 5269.5101 11.407245 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.15622 on 1 procs for 10000 steps with 81 atoms - -Performance: 553065.489 tau/day, 64012.209 timesteps/s -95.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0098181 | 0.0098181 | 0.0098181 | 0.0 | 6.28 -Neigh | 0.040912 | 0.040912 | 0.040912 | 0.0 | 26.19 -Comm | 0.013111 | 0.013111 | 0.013111 | 0.0 | 8.39 -Output | 0.0016305 | 0.0016305 | 0.0016305 | 0.0 | 1.04 -Modify | 0.085361 | 0.085361 | 0.085361 | 0.0 | 54.64 -Other | | 0.005387 | | | 3.45 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.atomvar.g++.4 b/examples/rigid/log.27Nov18.rigid.atomvar.g++.4 deleted file mode 100644 index 42b8a52768..0000000000 --- a/examples/rigid/log.27Nov18.rigid.atomvar.g++.4 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) -fix 1 all rigid custom v_bodies -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.955 | 4.049 | 4.33 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706557 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 - 9600 16738.549 -0.026814371 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589894 0 5269.4979 12.062708 - 9750 16738.013 0.13550109 0 5269.5101 11.407246 - 9800 16738.512 -0.011620327 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.199799 on 4 procs for 10000 steps with 81 atoms - -Performance: 432434.078 tau/day, 50050.241 timesteps/s -91.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.002665 | 0.0034567 | 0.0040557 | 0.9 | 1.73 -Neigh | 0.012185 | 0.013168 | 0.014083 | 0.8 | 6.59 -Comm | 0.079331 | 0.082804 | 0.084927 | 0.7 | 41.44 -Output | 0.0031595 | 0.0039212 | 0.0061827 | 2.1 | 1.96 -Modify | 0.088465 | 0.090202 | 0.091938 | 0.4 | 45.15 -Other | | 0.006247 | | | 3.13 - -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.early.g++.1 b/examples/rigid/log.27Nov18.rigid.early.g++.1 deleted file mode 100644 index 3c8022423f..0000000000 --- a/examples/rigid/log.27Nov18.rigid.early.g++.1 +++ /dev/null @@ -1,337 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -9 rigid bodies with 81 atoms - -fix_modify 1 bodyforces early - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 - 9550 16738.493 -0.005315616 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589885 0 5269.4979 12.062708 - 9750 16738.013 0.13550123 0 5269.5101 11.407245 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.152593 on 1 procs for 10000 steps with 81 atoms - -Performance: 566210.692 tau/day, 65533.645 timesteps/s -96.1% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0098324 | 0.0098324 | 0.0098324 | 0.0 | 6.44 -Neigh | 0.040376 | 0.040376 | 0.040376 | 0.0 | 26.46 -Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 8.03 -Output | 0.0016036 | 0.0016036 | 0.0016036 | 0.0 | 1.05 -Modify | 0.083605 | 0.083605 | 0.083605 | 0.0 | 54.79 -Other | | 0.00493 | | | 3.23 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.early.g++.4 b/examples/rigid/log.27Nov18.rigid.early.g++.4 deleted file mode 100644 index 91f091b799..0000000000 --- a/examples/rigid/log.27Nov18.rigid.early.g++.4 +++ /dev/null @@ -1,337 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -9 rigid bodies with 81 atoms - -fix_modify 1 bodyforces early - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706557 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 - 9600 16738.549 -0.026814371 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589894 0 5269.4979 12.062708 - 9750 16738.013 0.13550109 0 5269.5101 11.407246 - 9800 16738.512 -0.011620327 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.198859 on 4 procs for 10000 steps with 81 atoms - -Performance: 434479.274 tau/day, 50286.953 timesteps/s -91.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.002526 | 0.0034331 | 0.0041001 | 1.0 | 1.73 -Neigh | 0.012097 | 0.013092 | 0.013992 | 0.8 | 6.58 -Comm | 0.075266 | 0.07972 | 0.084679 | 1.2 | 40.09 -Output | 0.0030892 | 0.0043746 | 0.0081537 | 3.3 | 2.20 -Modify | 0.088037 | 0.091924 | 0.095021 | 0.9 | 46.23 -Other | | 0.006316 | | | 3.18 - -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.g++.1 b/examples/rigid/log.27Nov18.rigid.g++.1 deleted file mode 100644 index 9dff202069..0000000000 --- a/examples/rigid/log.27Nov18.rigid.g++.1 +++ /dev/null @@ -1,335 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 - 9550 16738.493 -0.005315616 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589885 0 5269.4979 12.062708 - 9750 16738.013 0.13550123 0 5269.5101 11.407245 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.152143 on 1 procs for 10000 steps with 81 atoms - -Performance: 567885.005 tau/day, 65727.431 timesteps/s -98.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0097773 | 0.0097773 | 0.0097773 | 0.0 | 6.43 -Neigh | 0.040602 | 0.040602 | 0.040602 | 0.0 | 26.69 -Comm | 0.012049 | 0.012049 | 0.012049 | 0.0 | 7.92 -Output | 0.0016172 | 0.0016172 | 0.0016172 | 0.0 | 1.06 -Modify | 0.083104 | 0.083104 | 0.083104 | 0.0 | 54.62 -Other | | 0.004994 | | | 3.28 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.g++.4 b/examples/rigid/log.27Nov18.rigid.g++.4 deleted file mode 100644 index 36e602f1f1..0000000000 --- a/examples/rigid/log.27Nov18.rigid.g++.4 +++ /dev/null @@ -1,335 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706557 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 - 9600 16738.549 -0.026814371 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589894 0 5269.4979 12.062708 - 9750 16738.013 0.13550109 0 5269.5101 11.407246 - 9800 16738.512 -0.011620327 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.201762 on 4 procs for 10000 steps with 81 atoms - -Performance: 428226.262 tau/day, 49563.225 timesteps/s -89.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0025356 | 0.0033935 | 0.0042305 | 1.0 | 1.68 -Neigh | 0.012009 | 0.012959 | 0.015092 | 1.1 | 6.42 -Comm | 0.07666 | 0.086213 | 0.092506 | 2.0 | 42.73 -Output | 0.0032623 | 0.0052034 | 0.011 | 4.6 | 2.58 -Modify | 0.084815 | 0.087869 | 0.089999 | 0.6 | 43.55 -Other | | 0.006125 | | | 3.04 - -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.nve.early.g++.1 b/examples/rigid/log.27Nov18.rigid.nve.early.g++.1 deleted file mode 100644 index 1e426d397e..0000000000 --- a/examples/rigid/log.27Nov18.rigid.nve.early.g++.1 +++ /dev/null @@ -1,337 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -9 rigid bodies with 81 atoms - -fix_modify 1 bodyforces early - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.69 571.70921 0 5265.8153 32.005816 - 100 16298.128 136.75661 0 5267.6488 16.449029 - 150 16682.532 17.504156 0 5269.4124 14.901186 - 200 16733.906 1.3755079 0 5269.4571 14.571305 - 250 16738.861 -0.15272039 0 5269.4886 14.498342 - 300 16738.608 -0.055216883 0 5269.5066 14.498 - 350 16738.5 -0.017457072 0 5269.5104 14.498392 - 400 16738.451 -0.0060161309 0 5269.5063 14.49851 - 450 16738.435 -0.001271965 0 5269.5059 14.498571 - 500 16738.443 -0.00081074175 0 5269.509 14.498598 - 550 16738.452 -0.00083208965 0 5269.5118 14.498618 - 600 16738.45 -0.00058358431 0 5269.5116 14.498617 - 650 16738.443 -0.00047228525 0 5269.5093 14.4986 - 700 16738.444 0 0 5269.5102 14.498612 - 750 16738.461 0 0 5269.5157 14.498654 - 800 16738.479 0 0 5269.521 14.498697 - 850 16738.473 0 0 5269.5192 14.498683 - 900 16738.449 0 0 5269.5116 14.498624 - 950 16738.438 -0.0035324203 0 5269.5046 14.498537 - 1000 16738.562 -0.051134242 0 5269.4963 14.498093 - 1050 16737.343 0.32970192 0 5269.4934 14.527634 - 1100 16737.878 0.16213235 0 5269.4941 14.533864 - 1150 16738.682 -0.089236256 0 5269.4959 14.511765 - 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 - 1250 16738.45 0 0 5269.5119 14.512611 - 1300 16738.475 0 0 5269.5199 14.512673 - 1350 16738.484 0 0 5269.5228 14.512696 - 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 - 1450 16738.45 -0.0010933363 0 5269.511 14.512595 - 1500 16738.445 -0.00057484239 0 5269.51 14.512591 - 1550 16738.451 0 0 5269.5123 14.512615 - 1600 16738.452 0 0 5269.5127 14.512618 - 1650 16738.443 0 0 5269.5099 14.512596 - 1700 16738.433 0 0 5269.5068 14.512572 - 1750 16738.438 0 0 5269.5084 14.512584 - 1800 16738.459 0 0 5269.5149 14.512635 - 1850 16738.473 0 0 5269.5193 14.51267 - 1900 16738.462 0 0 5269.5159 14.512644 - 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 - 2000 16738.463 -0.013425408 0 5269.5027 14.512382 - 2050 16738.535 -0.036964311 0 5269.5017 14.512152 - 2100 16738.621 -0.063490509 0 5269.5023 14.512108 - 2150 16738.594 -0.056143934 0 5269.5012 14.512117 - 2200 16738.536 -0.038486645 0 5269.5007 14.512277 - 2250 16738.496 -0.023712406 0 5269.503 14.51242 - 2300 16738.488 -0.013209094 0 5269.5109 14.51255 - 2350 16738.486 -0.0045244524 0 5269.519 14.512693 - 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 - 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 - 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 - 2550 16738.552 -0.04420046 0 5269.4998 14.512177 - 2600 16738.42 -0.004347531 0 5269.4982 14.512783 - 2650 16734.241 1.3131302 0 5269.5 14.577195 - 2700 16738.737 -0.10612056 0 5269.4961 14.503874 - 2750 16732.705 1.7939719 0 5269.4974 14.629294 - 2800 16738.558 -0.042867033 0 5269.5032 14.519893 - 2850 16738.499 -0.01271227 0 5269.5146 14.518524 - 2900 16738.486 -0.0032778045 0 5269.52 14.518712 - 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 - 3000 16738.647 -0.070862542 0 5269.5031 14.51803 - 3050 16678.313 18.829038 0 5269.409 15.533426 - 3100 16632.312 33.399217 0 5269.4975 14.588597 - 3150 16739.318 -0.31388148 0 5269.4715 13.520782 - 3200 16727.951 3.26736 0 5269.4741 12.288358 - 3250 16686.364 16.353793 0 5269.4682 14.152517 - 3300 16738.532 -0.031574462 0 5269.5064 13.310615 - 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 - 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 - 3450 16738.489 -0.021623738 0 5269.5026 13.308001 - 3500 16737.78 0.19719043 0 5269.4983 13.325999 - 3550 16658.578 25.116206 0 5269.4834 13.778249 - 3600 16738.51 -0.032864725 0 5269.4981 12.392389 - 3650 16738.899 -0.15952703 0 5269.4938 12.383503 - 3700 16738.879 -0.16025994 0 5269.487 12.382575 - 3750 16738.878 -0.16608251 0 5269.4806 12.382765 - 3800 16738.591 -0.078679341 0 5269.4776 12.383227 - 3850 16738.429 -0.024729409 0 5269.4807 12.382942 - 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 - 3950 16738.428 -0.002521266 0 5269.5027 12.383324 - 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 - 4050 16738.488 0 0 5269.5241 12.383531 - 4100 16738.468 0 0 5269.5178 12.383482 - 4150 16738.422 0 0 5269.5033 12.383369 - 4200 16738.387 0 0 5269.4921 12.383281 - 4250 16738.383 0 0 5269.4908 12.38327 - 4300 16738.4 0 0 5269.4964 12.383314 - 4350 16738.423 0 0 5269.5036 12.38337 - 4400 16738.441 0 0 5269.5092 12.383414 - 4450 16738.45 0 0 5269.5121 12.383437 - 4500 16738.45 0 0 5269.5122 12.383438 - 4550 16738.442 0 0 5269.5095 12.383417 - 4600 16738.425 0 0 5269.5042 12.383376 - 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 - 4700 16738.444 -0.024020551 0 5269.4862 12.382975 - 4750 16738.49 -0.04852143 0 5269.4761 12.385777 - 4800 16735.057 1.0347216 0 5269.4786 12.43543 - 4850 16735.441 0.92650925 0 5269.4913 12.418653 - 4900 16723.839 4.5908974 0 5269.5033 13.410103 - 4950 16738.531 -0.02153767 0 5269.5159 13.089982 - 5000 16738.45 -0.0042589697 0 5269.5077 13.090062 - 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 - 5100 16738.404 0 0 5269.4976 13.090032 - 5150 16738.421 0 0 5269.5029 13.090073 - 5200 16738.44 0 0 5269.5087 13.090119 - 5250 16738.448 -0.001279392 0 5269.5102 13.090114 - 5300 16738.456 -0.0064376391 0 5269.5075 13.090026 - 5350 16738.479 -0.020383841 0 5269.5007 13.089897 - 5400 16735.845 0.7988947 0 5269.4909 13.136244 - 5450 16735.558 0.87620022 0 5269.4778 12.324482 - 5500 16711.494 8.4724178 0 5269.4984 12.656579 - 5550 16454.525 89.074815 0 5269.2031 16.996503 - 5600 16713.084 7.9801418 0 5269.5065 13.774979 - 5650 16738.676 -0.079987748 0 5269.5033 13.168297 - 5700 16446.281 91.866085 0 5269.399 23.764663 - 5750 16738.549 -0.039869084 0 5269.5034 13.378122 - 5800 16738.487 -0.014994478 0 5269.5086 13.378399 - 5850 16738.466 -0.0051267616 0 5269.512 13.37856 - 5900 16738.462 -0.0043690142 0 5269.5113 13.378573 - 5950 16738.528 -0.032727415 0 5269.5039 13.378197 - 6000 16702.774 10.969438 0 5269.2502 13.788852 - 6050 16682.271 17.483137 0 5269.3092 13.353101 - 6100 16738.508 -0.028838222 0 5269.5016 12.521084 - 6150 16738.425 -0.0067595536 0 5269.4974 12.521223 - 6200 16738.401 -0.0011499893 0 5269.4955 12.521254 - 6250 16738.455 0 0 5269.5135 12.52141 - 6300 16738.523 0 0 5269.5352 12.52158 - 6350 16738.503 0 0 5269.5287 12.521531 - 6400 16738.427 0 0 5269.5047 12.521344 - 6450 16738.399 0 0 5269.496 12.521274 - 6500 16738.425 0 0 5269.5042 12.521337 - 6550 16738.441 0 0 5269.5093 12.521378 - 6600 16738.42 0 0 5269.5025 12.521326 - 6650 16738.398 0 0 5269.4957 12.521272 - 6700 16738.435 0 0 5269.5074 12.521362 - 6750 16738.505 0 0 5269.5293 12.521534 - 6800 16738.508 0 0 5269.5303 12.521543 - 6850 16738.446 0 0 5269.5108 12.521391 - 6900 16738.414 0 0 5269.5009 12.521312 - 6950 16738.432 0 0 5269.5063 12.521354 - 7000 16738.444 0 0 5269.5102 12.521385 - 7050 16738.421 0 0 5269.5029 12.521329 - 7100 16738.393 0 0 5269.4941 12.521259 - 7150 16738.419 0 0 5269.5022 12.521322 - 7200 16738.489 0 0 5269.5244 12.521495 - 7250 16738.505 0 0 5269.5293 12.521535 - 7300 16738.443 0 0 5269.5098 12.521383 - 7350 16738.404 0 0 5269.4976 12.521287 - 7400 16738.43 0 0 5269.5058 12.52135 - 7450 16738.461 0 0 5269.5156 12.521427 - 7500 16738.447 0 0 5269.5109 12.521392 - 7550 16738.407 0 0 5269.4986 12.521295 - 7600 16738.412 0 0 5269.5002 12.521306 - 7650 16738.478 0 0 5269.5208 12.521467 - 7700 16738.51 0 0 5269.5309 12.521547 - 7750 16738.454 0 0 5269.5135 12.521412 - 7800 16738.398 0 0 5269.4958 12.521273 - 7850 16738.407 -0.0002118108 0 5269.4982 12.521289 - 7900 16738.441 -0.00021679711 0 5269.509 12.521373 - 7950 16738.446 -0.00023848139 0 5269.5107 12.521386 - 8000 16738.423 0 0 5269.5035 12.521333 - 8050 16738.423 0 0 5269.5034 12.521332 - 8100 16738.478 -0.00069622994 0 5269.52 12.521454 - 8150 16738.523 -0.0040058408 0 5269.531 12.521501 - 8200 16738.486 -0.0092298229 0 5269.5142 12.521334 - 8250 16738.458 -0.023189671 0 5269.4914 12.521014 - 8300 16738.513 -0.045845677 0 5269.4861 12.520779 - 8350 16723.745 4.5690412 0 5269.4516 12.849325 - 8400 16738.466 -0.020158442 0 5269.497 12.835773 - 8450 16738.437 -0.012822892 0 5269.4952 12.829936 - 8500 16738.408 -0.0016837088 0 5269.4972 12.830061 - 8550 16738.464 -0.00097379467 0 5269.5155 12.830216 - 8600 16738.669 -0.050578079 0 5269.5304 12.829934 - 8650 15917.563 250.28318 0 5261.3678 24.54572 - 8700 16738.445 0.0012168759 0 5269.5117 10.589499 - 8750 16738.473 -0.010164589 0 5269.509 10.588414 - 8800 16738.468 0 0 5269.5177 10.588633 - 8850 16738.508 0 0 5269.5304 10.588733 - 8900 16738.509 0 0 5269.5307 10.588736 - 8950 16738.496 0 0 5269.5266 10.588705 - 9000 16738.477 0 0 5269.5204 10.588656 - 9050 16738.455 0 0 5269.5135 10.588602 - 9100 16738.477 0 0 5269.5206 10.588656 - 9150 16738.512 0 0 5269.5316 10.588743 - 9200 16738.502 0 0 5269.5285 10.58872 - 9250 16738.493 0 0 5269.5255 10.588696 - 9300 16738.482 0 0 5269.522 10.588669 - 9350 16738.46 0 0 5269.5151 10.588615 - 9400 16738.481 0 0 5269.5217 10.588665 - 9450 16738.509 0 0 5269.5307 10.588736 - 9500 16738.491 0 0 5269.5248 10.58869 - 9550 16738.484 0 0 5269.5227 10.588674 - 9600 16738.483 0 0 5269.5223 10.588671 - 9650 16738.464 0 0 5269.5166 10.588626 - 9700 16738.484 0 0 5269.5229 10.588674 - 9750 16738.507 0 0 5269.5301 10.588731 - 9800 16738.482 0 0 5269.5221 10.588669 - 9850 16738.478 0 0 5269.5208 10.588659 - 9900 16738.487 -0.00030979474 0 5269.5233 10.588675 - 9950 16738.476 -0.00095968581 0 5269.5193 10.588632 - 10000 16738.494 -0.00062717822 0 5269.5253 10.588684 -Loop time of 0.168577 on 1 procs for 10000 steps with 81 atoms - -Performance: 512524.843 tau/day, 59320.005 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.010812 | 0.010812 | 0.010812 | 0.0 | 6.41 -Neigh | 0.04144 | 0.04144 | 0.04144 | 0.0 | 24.58 -Comm | 0.012082 | 0.012082 | 0.012082 | 0.0 | 7.17 -Output | 0.0016394 | 0.0016394 | 0.0016394 | 0.0 | 0.97 -Modify | 0.097466 | 0.097466 | 0.097466 | 0.0 | 57.82 -Other | | 0.005139 | | | 3.05 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 49 ave 49 max 49 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3 ave 3 max 3 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3 -Ave neighs/atom = 0.037037 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.nve.early.g++.4 b/examples/rigid/log.27Nov18.rigid.nve.early.g++.4 deleted file mode 100644 index 5b775d969a..0000000000 --- a/examples/rigid/log.27Nov18.rigid.nve.early.g++.4 +++ /dev/null @@ -1,337 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -9 rigid bodies with 81 atoms - -fix_modify 1 bodyforces early - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.69 571.70921 0 5265.8153 32.005816 - 100 16298.128 136.75661 0 5267.6488 16.449029 - 150 16682.532 17.504156 0 5269.4124 14.901186 - 200 16733.906 1.3755079 0 5269.4571 14.571305 - 250 16738.861 -0.15272039 0 5269.4886 14.498342 - 300 16738.608 -0.055216883 0 5269.5066 14.498 - 350 16738.5 -0.017457072 0 5269.5104 14.498392 - 400 16738.451 -0.0060161309 0 5269.5063 14.49851 - 450 16738.435 -0.001271965 0 5269.5059 14.498571 - 500 16738.443 -0.00081074175 0 5269.509 14.498598 - 550 16738.452 -0.00083208965 0 5269.5118 14.498618 - 600 16738.45 -0.00058358431 0 5269.5116 14.498617 - 650 16738.443 -0.00047228525 0 5269.5093 14.4986 - 700 16738.444 0 0 5269.5102 14.498612 - 750 16738.461 0 0 5269.5157 14.498654 - 800 16738.479 0 0 5269.521 14.498697 - 850 16738.473 0 0 5269.5192 14.498683 - 900 16738.449 0 0 5269.5116 14.498624 - 950 16738.438 -0.0035324203 0 5269.5046 14.498537 - 1000 16738.562 -0.051134242 0 5269.4963 14.498093 - 1050 16737.343 0.32970192 0 5269.4934 14.527634 - 1100 16737.878 0.16213235 0 5269.4941 14.533864 - 1150 16738.682 -0.089236256 0 5269.4959 14.511765 - 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 - 1250 16738.45 0 0 5269.5119 14.512611 - 1300 16738.475 0 0 5269.5199 14.512673 - 1350 16738.484 0 0 5269.5228 14.512696 - 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 - 1450 16738.45 -0.0010933363 0 5269.511 14.512595 - 1500 16738.445 -0.00057484239 0 5269.51 14.512591 - 1550 16738.451 0 0 5269.5123 14.512615 - 1600 16738.452 0 0 5269.5127 14.512618 - 1650 16738.443 0 0 5269.5099 14.512596 - 1700 16738.433 0 0 5269.5068 14.512572 - 1750 16738.438 0 0 5269.5084 14.512584 - 1800 16738.459 0 0 5269.5149 14.512635 - 1850 16738.473 0 0 5269.5193 14.51267 - 1900 16738.462 0 0 5269.5159 14.512644 - 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 - 2000 16738.463 -0.013425408 0 5269.5027 14.512382 - 2050 16738.535 -0.036964311 0 5269.5017 14.512152 - 2100 16738.621 -0.063490509 0 5269.5023 14.512108 - 2150 16738.594 -0.056143934 0 5269.5012 14.512117 - 2200 16738.536 -0.038486645 0 5269.5007 14.512277 - 2250 16738.496 -0.023712406 0 5269.503 14.51242 - 2300 16738.488 -0.013209094 0 5269.5109 14.51255 - 2350 16738.486 -0.0045244524 0 5269.519 14.512693 - 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 - 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 - 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 - 2550 16738.552 -0.04420046 0 5269.4998 14.512177 - 2600 16738.42 -0.004347531 0 5269.4982 14.512783 - 2650 16734.241 1.3131302 0 5269.5 14.577195 - 2700 16738.737 -0.10612056 0 5269.4961 14.503874 - 2750 16732.705 1.7939719 0 5269.4974 14.629294 - 2800 16738.558 -0.042867033 0 5269.5032 14.519893 - 2850 16738.499 -0.01271227 0 5269.5146 14.518524 - 2900 16738.486 -0.0032778045 0 5269.52 14.518712 - 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 - 3000 16738.647 -0.070862542 0 5269.5031 14.51803 - 3050 16678.313 18.829038 0 5269.409 15.533426 - 3100 16632.312 33.399217 0 5269.4975 14.588597 - 3150 16739.318 -0.31388148 0 5269.4715 13.520782 - 3200 16727.951 3.26736 0 5269.4741 12.288358 - 3250 16686.364 16.353793 0 5269.4682 14.152517 - 3300 16738.532 -0.031574462 0 5269.5064 13.310615 - 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 - 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 - 3450 16738.489 -0.021623738 0 5269.5026 13.308001 - 3500 16737.78 0.19719043 0 5269.4983 13.325999 - 3550 16658.578 25.116206 0 5269.4834 13.778249 - 3600 16738.51 -0.032864725 0 5269.4981 12.392389 - 3650 16738.899 -0.15952703 0 5269.4938 12.383503 - 3700 16738.879 -0.16025994 0 5269.487 12.382575 - 3750 16738.878 -0.16608251 0 5269.4806 12.382765 - 3800 16738.591 -0.078679341 0 5269.4776 12.383227 - 3850 16738.429 -0.024729409 0 5269.4807 12.382942 - 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 - 3950 16738.428 -0.002521266 0 5269.5027 12.383324 - 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 - 4050 16738.488 0 0 5269.5241 12.383531 - 4100 16738.468 0 0 5269.5178 12.383482 - 4150 16738.422 0 0 5269.5033 12.383369 - 4200 16738.387 0 0 5269.4921 12.383281 - 4250 16738.383 0 0 5269.4908 12.38327 - 4300 16738.4 0 0 5269.4964 12.383314 - 4350 16738.423 0 0 5269.5036 12.38337 - 4400 16738.441 0 0 5269.5092 12.383414 - 4450 16738.45 0 0 5269.5121 12.383437 - 4500 16738.45 0 0 5269.5122 12.383438 - 4550 16738.442 0 0 5269.5095 12.383417 - 4600 16738.425 0 0 5269.5042 12.383376 - 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 - 4700 16738.444 -0.024020551 0 5269.4862 12.382975 - 4750 16738.49 -0.048521428 0 5269.4761 12.385777 - 4800 16735.057 1.0347217 0 5269.4786 12.43543 - 4850 16735.441 0.92650925 0 5269.4913 12.418653 - 4900 16723.839 4.5908973 0 5269.5033 13.410103 - 4950 16738.531 -0.02153767 0 5269.5159 13.089982 - 5000 16738.45 -0.0042589696 0 5269.5077 13.090062 - 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 - 5100 16738.404 0 0 5269.4976 13.090032 - 5150 16738.421 0 0 5269.5029 13.090073 - 5200 16738.44 0 0 5269.5087 13.090119 - 5250 16738.448 -0.001279392 0 5269.5102 13.090114 - 5300 16738.456 -0.0064376392 0 5269.5075 13.090026 - 5350 16738.479 -0.020383842 0 5269.5007 13.089897 - 5400 16735.845 0.79889474 0 5269.4909 13.136244 - 5450 16735.558 0.87619992 0 5269.4778 12.324482 - 5500 16711.494 8.4724208 0 5269.4984 12.656579 - 5550 16454.525 89.074816 0 5269.2031 16.996503 - 5600 16713.084 7.9801334 0 5269.5065 13.774977 - 5650 16738.676 -0.079987764 0 5269.5033 13.168295 - 5700 16446.281 91.866085 0 5269.399 23.764662 - 5750 16738.549 -0.039869084 0 5269.5034 13.378121 - 5800 16738.487 -0.014994475 0 5269.5086 13.378397 - 5850 16738.466 -0.0051267556 0 5269.512 13.378559 - 5900 16738.462 -0.0043690097 0 5269.5113 13.378572 - 5950 16738.528 -0.03272741 0 5269.5039 13.378195 - 6000 16702.774 10.969434 0 5269.2502 13.788851 - 6050 16682.271 17.483158 0 5269.3092 13.3531 - 6100 16738.508 -0.028838239 0 5269.5016 12.521082 - 6150 16738.425 -0.0067595542 0 5269.4974 12.521221 - 6200 16738.401 -0.0011499896 0 5269.4955 12.521252 - 6250 16738.455 0 0 5269.5135 12.521408 - 6300 16738.523 0 0 5269.5352 12.521578 - 6350 16738.503 0 0 5269.5287 12.52153 - 6400 16738.427 0 0 5269.5047 12.521342 - 6450 16738.399 0 0 5269.496 12.521273 - 6500 16738.425 0 0 5269.5042 12.521336 - 6550 16738.441 0 0 5269.5093 12.521377 - 6600 16738.42 0 0 5269.5025 12.521324 - 6650 16738.398 0 0 5269.4957 12.52127 - 6700 16738.435 0 0 5269.5074 12.52136 - 6750 16738.505 0 0 5269.5293 12.521532 - 6800 16738.508 0 0 5269.5303 12.521541 - 6850 16738.446 0 0 5269.5108 12.521389 - 6900 16738.414 0 0 5269.5009 12.521311 - 6950 16738.432 0 0 5269.5063 12.521353 - 7000 16738.444 0 0 5269.5102 12.521383 - 7050 16738.421 0 0 5269.5029 12.521327 - 7100 16738.393 0 0 5269.4941 12.521258 - 7150 16738.419 0 0 5269.5022 12.52132 - 7200 16738.489 0 0 5269.5244 12.521494 - 7250 16738.505 0 0 5269.5293 12.521533 - 7300 16738.443 0 0 5269.5098 12.521381 - 7350 16738.404 0 0 5269.4976 12.521285 - 7400 16738.43 0 0 5269.5058 12.521348 - 7450 16738.461 0 0 5269.5156 12.521425 - 7500 16738.447 0 0 5269.5109 12.52139 - 7550 16738.407 0 0 5269.4986 12.521293 - 7600 16738.412 0 0 5269.5002 12.521305 - 7650 16738.478 0 0 5269.5208 12.521465 - 7700 16738.51 0 0 5269.5309 12.521546 - 7750 16738.454 0 0 5269.5135 12.52141 - 7800 16738.398 0 0 5269.4958 12.521272 - 7850 16738.407 -0.00021180981 0 5269.4982 12.521288 - 7900 16738.441 -0.0002167964 0 5269.509 12.521371 - 7950 16738.446 -0.00023848065 0 5269.5107 12.521385 - 8000 16738.423 0 0 5269.5035 12.521331 - 8050 16738.423 0 0 5269.5034 12.52133 - 8100 16738.478 -0.00069623408 0 5269.52 12.521452 - 8150 16738.523 -0.0040058355 0 5269.531 12.521499 - 8200 16738.486 -0.0092298325 0 5269.5142 12.521332 - 8250 16738.458 -0.023189665 0 5269.4914 12.521012 - 8300 16738.513 -0.045846242 0 5269.4861 12.520778 - 8350 16723.742 4.5698786 0 5269.4516 12.849386 - 8400 16738.466 -0.02016972 0 5269.497 12.835784 - 8450 16738.437 -0.012822703 0 5269.4952 12.829948 - 8500 16738.408 -0.0016836132 0 5269.4972 12.830073 - 8550 16738.464 -0.00097380297 0 5269.5155 12.830227 - 8600 16738.669 -0.050578946 0 5269.5304 12.829946 - 8650 15917.707 250.24016 0 5261.3702 24.544744 - 8700 16738.445 0.0010615265 0 5269.5117 10.589987 - 8750 16738.473 -0.010158834 0 5269.509 10.588904 - 8800 16738.468 0 0 5269.5176 10.589124 - 8850 16738.508 0 0 5269.5304 10.589223 - 8900 16738.509 0 0 5269.5306 10.589226 - 8950 16738.496 0 0 5269.5266 10.589195 - 9000 16738.477 0 0 5269.5204 10.589147 - 9050 16738.455 0 0 5269.5135 10.589092 - 9100 16738.477 0 0 5269.5206 10.589146 - 9150 16738.512 0 0 5269.5316 10.589233 - 9200 16738.502 0 0 5269.5285 10.58921 - 9250 16738.493 0 0 5269.5255 10.589186 - 9300 16738.482 0 0 5269.522 10.589159 - 9350 16738.46 0 0 5269.5151 10.589105 - 9400 16738.481 0 0 5269.5217 10.589155 - 9450 16738.509 0 0 5269.5307 10.589226 - 9500 16738.491 0 0 5269.5248 10.589181 - 9550 16738.484 0 0 5269.5227 10.589164 - 9600 16738.483 0 0 5269.5223 10.589161 - 9650 16738.464 0 0 5269.5166 10.589116 - 9700 16738.484 0 0 5269.5228 10.589164 - 9750 16738.507 0 0 5269.5301 10.589221 - 9800 16738.482 0 0 5269.5221 10.589159 - 9850 16738.478 0 0 5269.5208 10.589149 - 9900 16738.487 -0.00030979591 0 5269.5233 10.589165 - 9950 16738.476 -0.0009596827 0 5269.5193 10.589123 - 10000 16738.494 -0.0006271698 0 5269.5253 10.589175 -Loop time of 0.213152 on 4 procs for 10000 steps with 81 atoms - -Performance: 405345.239 tau/day, 46914.958 timesteps/s -91.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0029514 | 0.0038354 | 0.005348 | 1.5 | 1.80 -Neigh | 0.01178 | 0.013139 | 0.0167 | 1.8 | 6.16 -Comm | 0.073879 | 0.078553 | 0.081131 | 1.0 | 36.85 -Output | 0.0031943 | 0.0037987 | 0.0055451 | 1.6 | 1.78 -Modify | 0.10553 | 0.10763 | 0.1096 | 0.4 | 50.49 -Other | | 0.0062 | | | 2.91 - -Nlocal: 20.25 ave 34 max 9 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 38.5 ave 43 max 26 min -Histogram: 1 0 0 0 0 0 0 0 0 3 -Neighs: 0.75 ave 2 max 0 min -Histogram: 2 0 0 0 0 1 0 0 0 1 - -Total # of neighbors = 3 -Ave neighs/atom = 0.037037 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.nve.g++.1 b/examples/rigid/log.27Nov18.rigid.nve.g++.1 deleted file mode 100644 index c3805dc42e..0000000000 --- a/examples/rigid/log.27Nov18.rigid.nve.g++.1 +++ /dev/null @@ -1,335 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.69 571.70921 0 5265.8153 32.005816 - 100 16298.128 136.75661 0 5267.6488 16.449029 - 150 16682.532 17.504156 0 5269.4124 14.901186 - 200 16733.906 1.3755079 0 5269.4571 14.571305 - 250 16738.861 -0.15272039 0 5269.4886 14.498342 - 300 16738.608 -0.055216883 0 5269.5066 14.498 - 350 16738.5 -0.017457072 0 5269.5104 14.498392 - 400 16738.451 -0.0060161309 0 5269.5063 14.49851 - 450 16738.435 -0.001271965 0 5269.5059 14.498571 - 500 16738.443 -0.00081074175 0 5269.509 14.498598 - 550 16738.452 -0.00083208965 0 5269.5118 14.498618 - 600 16738.45 -0.00058358431 0 5269.5116 14.498617 - 650 16738.443 -0.00047228525 0 5269.5093 14.4986 - 700 16738.444 0 0 5269.5102 14.498612 - 750 16738.461 0 0 5269.5157 14.498654 - 800 16738.479 0 0 5269.521 14.498697 - 850 16738.473 0 0 5269.5192 14.498683 - 900 16738.449 0 0 5269.5116 14.498624 - 950 16738.438 -0.0035324203 0 5269.5046 14.498537 - 1000 16738.562 -0.051134242 0 5269.4963 14.498093 - 1050 16737.343 0.32970192 0 5269.4934 14.527634 - 1100 16737.878 0.16213235 0 5269.4941 14.533864 - 1150 16738.682 -0.089236256 0 5269.4959 14.511765 - 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 - 1250 16738.45 0 0 5269.5119 14.512611 - 1300 16738.475 0 0 5269.5199 14.512673 - 1350 16738.484 0 0 5269.5228 14.512696 - 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 - 1450 16738.45 -0.0010933363 0 5269.511 14.512595 - 1500 16738.445 -0.00057484239 0 5269.51 14.512591 - 1550 16738.451 0 0 5269.5123 14.512615 - 1600 16738.452 0 0 5269.5127 14.512618 - 1650 16738.443 0 0 5269.5099 14.512596 - 1700 16738.433 0 0 5269.5068 14.512572 - 1750 16738.438 0 0 5269.5084 14.512584 - 1800 16738.459 0 0 5269.5149 14.512635 - 1850 16738.473 0 0 5269.5193 14.51267 - 1900 16738.462 0 0 5269.5159 14.512644 - 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 - 2000 16738.463 -0.013425408 0 5269.5027 14.512382 - 2050 16738.535 -0.036964311 0 5269.5017 14.512152 - 2100 16738.621 -0.063490509 0 5269.5023 14.512108 - 2150 16738.594 -0.056143934 0 5269.5012 14.512117 - 2200 16738.536 -0.038486645 0 5269.5007 14.512277 - 2250 16738.496 -0.023712406 0 5269.503 14.51242 - 2300 16738.488 -0.013209094 0 5269.5109 14.51255 - 2350 16738.486 -0.0045244524 0 5269.519 14.512693 - 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 - 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 - 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 - 2550 16738.552 -0.04420046 0 5269.4998 14.512177 - 2600 16738.42 -0.004347531 0 5269.4982 14.512783 - 2650 16734.241 1.3131302 0 5269.5 14.577195 - 2700 16738.737 -0.10612056 0 5269.4961 14.503874 - 2750 16732.705 1.7939719 0 5269.4974 14.629294 - 2800 16738.558 -0.042867033 0 5269.5032 14.519893 - 2850 16738.499 -0.01271227 0 5269.5146 14.518524 - 2900 16738.486 -0.0032778045 0 5269.52 14.518712 - 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 - 3000 16738.647 -0.070862542 0 5269.5031 14.51803 - 3050 16678.313 18.829038 0 5269.409 15.533426 - 3100 16632.312 33.399217 0 5269.4975 14.588597 - 3150 16739.318 -0.31388148 0 5269.4715 13.520782 - 3200 16727.951 3.26736 0 5269.4741 12.288358 - 3250 16686.364 16.353793 0 5269.4682 14.152517 - 3300 16738.532 -0.031574462 0 5269.5064 13.310615 - 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 - 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 - 3450 16738.489 -0.021623738 0 5269.5026 13.308001 - 3500 16737.78 0.19719043 0 5269.4983 13.325999 - 3550 16658.578 25.116206 0 5269.4834 13.778249 - 3600 16738.51 -0.032864725 0 5269.4981 12.392389 - 3650 16738.899 -0.15952703 0 5269.4938 12.383503 - 3700 16738.879 -0.16025994 0 5269.487 12.382575 - 3750 16738.878 -0.16608251 0 5269.4806 12.382765 - 3800 16738.591 -0.078679341 0 5269.4776 12.383227 - 3850 16738.429 -0.024729409 0 5269.4807 12.382942 - 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 - 3950 16738.428 -0.002521266 0 5269.5027 12.383324 - 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 - 4050 16738.488 0 0 5269.5241 12.383531 - 4100 16738.468 0 0 5269.5178 12.383482 - 4150 16738.422 0 0 5269.5033 12.383369 - 4200 16738.387 0 0 5269.4921 12.383281 - 4250 16738.383 0 0 5269.4908 12.38327 - 4300 16738.4 0 0 5269.4964 12.383314 - 4350 16738.423 0 0 5269.5036 12.38337 - 4400 16738.441 0 0 5269.5092 12.383414 - 4450 16738.45 0 0 5269.5121 12.383437 - 4500 16738.45 0 0 5269.5122 12.383438 - 4550 16738.442 0 0 5269.5095 12.383417 - 4600 16738.425 0 0 5269.5042 12.383376 - 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 - 4700 16738.444 -0.024020551 0 5269.4862 12.382975 - 4750 16738.49 -0.04852143 0 5269.4761 12.385777 - 4800 16735.057 1.0347216 0 5269.4786 12.43543 - 4850 16735.441 0.92650925 0 5269.4913 12.418653 - 4900 16723.839 4.5908974 0 5269.5033 13.410103 - 4950 16738.531 -0.02153767 0 5269.5159 13.089982 - 5000 16738.45 -0.0042589697 0 5269.5077 13.090062 - 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 - 5100 16738.404 0 0 5269.4976 13.090032 - 5150 16738.421 0 0 5269.5029 13.090073 - 5200 16738.44 0 0 5269.5087 13.090119 - 5250 16738.448 -0.001279392 0 5269.5102 13.090114 - 5300 16738.456 -0.0064376391 0 5269.5075 13.090026 - 5350 16738.479 -0.020383841 0 5269.5007 13.089897 - 5400 16735.845 0.7988947 0 5269.4909 13.136244 - 5450 16735.558 0.87620022 0 5269.4778 12.324482 - 5500 16711.494 8.4724178 0 5269.4984 12.656579 - 5550 16454.525 89.074815 0 5269.2031 16.996503 - 5600 16713.084 7.9801418 0 5269.5065 13.774979 - 5650 16738.676 -0.079987748 0 5269.5033 13.168297 - 5700 16446.281 91.866085 0 5269.399 23.764663 - 5750 16738.549 -0.039869084 0 5269.5034 13.378122 - 5800 16738.487 -0.014994478 0 5269.5086 13.378399 - 5850 16738.466 -0.0051267616 0 5269.512 13.37856 - 5900 16738.462 -0.0043690142 0 5269.5113 13.378573 - 5950 16738.528 -0.032727415 0 5269.5039 13.378197 - 6000 16702.774 10.969438 0 5269.2502 13.788852 - 6050 16682.271 17.483137 0 5269.3092 13.353101 - 6100 16738.508 -0.028838222 0 5269.5016 12.521084 - 6150 16738.425 -0.0067595536 0 5269.4974 12.521223 - 6200 16738.401 -0.0011499893 0 5269.4955 12.521254 - 6250 16738.455 0 0 5269.5135 12.52141 - 6300 16738.523 0 0 5269.5352 12.52158 - 6350 16738.503 0 0 5269.5287 12.521531 - 6400 16738.427 0 0 5269.5047 12.521344 - 6450 16738.399 0 0 5269.496 12.521274 - 6500 16738.425 0 0 5269.5042 12.521337 - 6550 16738.441 0 0 5269.5093 12.521378 - 6600 16738.42 0 0 5269.5025 12.521326 - 6650 16738.398 0 0 5269.4957 12.521272 - 6700 16738.435 0 0 5269.5074 12.521362 - 6750 16738.505 0 0 5269.5293 12.521534 - 6800 16738.508 0 0 5269.5303 12.521543 - 6850 16738.446 0 0 5269.5108 12.521391 - 6900 16738.414 0 0 5269.5009 12.521312 - 6950 16738.432 0 0 5269.5063 12.521354 - 7000 16738.444 0 0 5269.5102 12.521385 - 7050 16738.421 0 0 5269.5029 12.521329 - 7100 16738.393 0 0 5269.4941 12.521259 - 7150 16738.419 0 0 5269.5022 12.521322 - 7200 16738.489 0 0 5269.5244 12.521495 - 7250 16738.505 0 0 5269.5293 12.521535 - 7300 16738.443 0 0 5269.5098 12.521383 - 7350 16738.404 0 0 5269.4976 12.521287 - 7400 16738.43 0 0 5269.5058 12.52135 - 7450 16738.461 0 0 5269.5156 12.521427 - 7500 16738.447 0 0 5269.5109 12.521392 - 7550 16738.407 0 0 5269.4986 12.521295 - 7600 16738.412 0 0 5269.5002 12.521306 - 7650 16738.478 0 0 5269.5208 12.521467 - 7700 16738.51 0 0 5269.5309 12.521547 - 7750 16738.454 0 0 5269.5135 12.521412 - 7800 16738.398 0 0 5269.4958 12.521273 - 7850 16738.407 -0.0002118108 0 5269.4982 12.521289 - 7900 16738.441 -0.00021679711 0 5269.509 12.521373 - 7950 16738.446 -0.00023848139 0 5269.5107 12.521386 - 8000 16738.423 0 0 5269.5035 12.521333 - 8050 16738.423 0 0 5269.5034 12.521332 - 8100 16738.478 -0.00069622994 0 5269.52 12.521454 - 8150 16738.523 -0.0040058408 0 5269.531 12.521501 - 8200 16738.486 -0.0092298229 0 5269.5142 12.521334 - 8250 16738.458 -0.023189671 0 5269.4914 12.521014 - 8300 16738.513 -0.045845677 0 5269.4861 12.520779 - 8350 16723.745 4.5690412 0 5269.4516 12.849325 - 8400 16738.466 -0.020158442 0 5269.497 12.835773 - 8450 16738.437 -0.012822892 0 5269.4952 12.829936 - 8500 16738.408 -0.0016837088 0 5269.4972 12.830061 - 8550 16738.464 -0.00097379467 0 5269.5155 12.830216 - 8600 16738.669 -0.050578079 0 5269.5304 12.829934 - 8650 15917.563 250.28318 0 5261.3678 24.54572 - 8700 16738.445 0.0012168759 0 5269.5117 10.589499 - 8750 16738.473 -0.010164589 0 5269.509 10.588414 - 8800 16738.468 0 0 5269.5177 10.588633 - 8850 16738.508 0 0 5269.5304 10.588733 - 8900 16738.509 0 0 5269.5307 10.588736 - 8950 16738.496 0 0 5269.5266 10.588705 - 9000 16738.477 0 0 5269.5204 10.588656 - 9050 16738.455 0 0 5269.5135 10.588602 - 9100 16738.477 0 0 5269.5206 10.588656 - 9150 16738.512 0 0 5269.5316 10.588743 - 9200 16738.502 0 0 5269.5285 10.58872 - 9250 16738.493 0 0 5269.5255 10.588696 - 9300 16738.482 0 0 5269.522 10.588669 - 9350 16738.46 0 0 5269.5151 10.588615 - 9400 16738.481 0 0 5269.5217 10.588665 - 9450 16738.509 0 0 5269.5307 10.588736 - 9500 16738.491 0 0 5269.5248 10.58869 - 9550 16738.484 0 0 5269.5227 10.588674 - 9600 16738.483 0 0 5269.5223 10.588671 - 9650 16738.464 0 0 5269.5166 10.588626 - 9700 16738.484 0 0 5269.5229 10.588674 - 9750 16738.507 0 0 5269.5301 10.588731 - 9800 16738.482 0 0 5269.5221 10.588669 - 9850 16738.478 0 0 5269.5208 10.588659 - 9900 16738.487 -0.00030979474 0 5269.5233 10.588675 - 9950 16738.476 -0.00095968581 0 5269.5193 10.588632 - 10000 16738.494 -0.00062717822 0 5269.5253 10.588684 -Loop time of 0.171181 on 1 procs for 10000 steps with 81 atoms - -Performance: 504728.317 tau/day, 58417.629 timesteps/s -97.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.011004 | 0.011004 | 0.011004 | 0.0 | 6.43 -Neigh | 0.041984 | 0.041984 | 0.041984 | 0.0 | 24.53 -Comm | 0.012262 | 0.012262 | 0.012262 | 0.0 | 7.16 -Output | 0.0017002 | 0.0017002 | 0.0017002 | 0.0 | 0.99 -Modify | 0.098894 | 0.098894 | 0.098894 | 0.0 | 57.77 -Other | | 0.005337 | | | 3.12 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 49 ave 49 max 49 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3 ave 3 max 3 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3 -Ave neighs/atom = 0.037037 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.nve.g++.4 b/examples/rigid/log.27Nov18.rigid.nve.g++.4 deleted file mode 100644 index bc79d9730f..0000000000 --- a/examples/rigid/log.27Nov18.rigid.nve.g++.4 +++ /dev/null @@ -1,335 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.69 571.70921 0 5265.8153 32.005816 - 100 16298.128 136.75661 0 5267.6488 16.449029 - 150 16682.532 17.504156 0 5269.4124 14.901186 - 200 16733.906 1.3755079 0 5269.4571 14.571305 - 250 16738.861 -0.15272039 0 5269.4886 14.498342 - 300 16738.608 -0.055216883 0 5269.5066 14.498 - 350 16738.5 -0.017457072 0 5269.5104 14.498392 - 400 16738.451 -0.0060161309 0 5269.5063 14.49851 - 450 16738.435 -0.001271965 0 5269.5059 14.498571 - 500 16738.443 -0.00081074175 0 5269.509 14.498598 - 550 16738.452 -0.00083208965 0 5269.5118 14.498618 - 600 16738.45 -0.00058358431 0 5269.5116 14.498617 - 650 16738.443 -0.00047228525 0 5269.5093 14.4986 - 700 16738.444 0 0 5269.5102 14.498612 - 750 16738.461 0 0 5269.5157 14.498654 - 800 16738.479 0 0 5269.521 14.498697 - 850 16738.473 0 0 5269.5192 14.498683 - 900 16738.449 0 0 5269.5116 14.498624 - 950 16738.438 -0.0035324203 0 5269.5046 14.498537 - 1000 16738.562 -0.051134242 0 5269.4963 14.498093 - 1050 16737.343 0.32970192 0 5269.4934 14.527634 - 1100 16737.878 0.16213235 0 5269.4941 14.533864 - 1150 16738.682 -0.089236256 0 5269.4959 14.511765 - 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 - 1250 16738.45 0 0 5269.5119 14.512611 - 1300 16738.475 0 0 5269.5199 14.512673 - 1350 16738.484 0 0 5269.5228 14.512696 - 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 - 1450 16738.45 -0.0010933363 0 5269.511 14.512595 - 1500 16738.445 -0.00057484239 0 5269.51 14.512591 - 1550 16738.451 0 0 5269.5123 14.512615 - 1600 16738.452 0 0 5269.5127 14.512618 - 1650 16738.443 0 0 5269.5099 14.512596 - 1700 16738.433 0 0 5269.5068 14.512572 - 1750 16738.438 0 0 5269.5084 14.512584 - 1800 16738.459 0 0 5269.5149 14.512635 - 1850 16738.473 0 0 5269.5193 14.51267 - 1900 16738.462 0 0 5269.5159 14.512644 - 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 - 2000 16738.463 -0.013425408 0 5269.5027 14.512382 - 2050 16738.535 -0.036964311 0 5269.5017 14.512152 - 2100 16738.621 -0.063490509 0 5269.5023 14.512108 - 2150 16738.594 -0.056143934 0 5269.5012 14.512117 - 2200 16738.536 -0.038486645 0 5269.5007 14.512277 - 2250 16738.496 -0.023712406 0 5269.503 14.51242 - 2300 16738.488 -0.013209094 0 5269.5109 14.51255 - 2350 16738.486 -0.0045244524 0 5269.519 14.512693 - 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 - 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 - 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 - 2550 16738.552 -0.04420046 0 5269.4998 14.512177 - 2600 16738.42 -0.004347531 0 5269.4982 14.512783 - 2650 16734.241 1.3131302 0 5269.5 14.577195 - 2700 16738.737 -0.10612056 0 5269.4961 14.503874 - 2750 16732.705 1.7939719 0 5269.4974 14.629294 - 2800 16738.558 -0.042867033 0 5269.5032 14.519893 - 2850 16738.499 -0.01271227 0 5269.5146 14.518524 - 2900 16738.486 -0.0032778045 0 5269.52 14.518712 - 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 - 3000 16738.647 -0.070862542 0 5269.5031 14.51803 - 3050 16678.313 18.829038 0 5269.409 15.533426 - 3100 16632.312 33.399217 0 5269.4975 14.588597 - 3150 16739.318 -0.31388148 0 5269.4715 13.520782 - 3200 16727.951 3.26736 0 5269.4741 12.288358 - 3250 16686.364 16.353793 0 5269.4682 14.152517 - 3300 16738.532 -0.031574462 0 5269.5064 13.310615 - 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 - 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 - 3450 16738.489 -0.021623738 0 5269.5026 13.308001 - 3500 16737.78 0.19719043 0 5269.4983 13.325999 - 3550 16658.578 25.116206 0 5269.4834 13.778249 - 3600 16738.51 -0.032864725 0 5269.4981 12.392389 - 3650 16738.899 -0.15952703 0 5269.4938 12.383503 - 3700 16738.879 -0.16025994 0 5269.487 12.382575 - 3750 16738.878 -0.16608251 0 5269.4806 12.382765 - 3800 16738.591 -0.078679341 0 5269.4776 12.383227 - 3850 16738.429 -0.024729409 0 5269.4807 12.382942 - 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 - 3950 16738.428 -0.002521266 0 5269.5027 12.383324 - 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 - 4050 16738.488 0 0 5269.5241 12.383531 - 4100 16738.468 0 0 5269.5178 12.383482 - 4150 16738.422 0 0 5269.5033 12.383369 - 4200 16738.387 0 0 5269.4921 12.383281 - 4250 16738.383 0 0 5269.4908 12.38327 - 4300 16738.4 0 0 5269.4964 12.383314 - 4350 16738.423 0 0 5269.5036 12.38337 - 4400 16738.441 0 0 5269.5092 12.383414 - 4450 16738.45 0 0 5269.5121 12.383437 - 4500 16738.45 0 0 5269.5122 12.383438 - 4550 16738.442 0 0 5269.5095 12.383417 - 4600 16738.425 0 0 5269.5042 12.383376 - 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 - 4700 16738.444 -0.024020551 0 5269.4862 12.382975 - 4750 16738.49 -0.048521428 0 5269.4761 12.385777 - 4800 16735.057 1.0347217 0 5269.4786 12.43543 - 4850 16735.441 0.92650925 0 5269.4913 12.418653 - 4900 16723.839 4.5908973 0 5269.5033 13.410103 - 4950 16738.531 -0.02153767 0 5269.5159 13.089982 - 5000 16738.45 -0.0042589696 0 5269.5077 13.090062 - 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 - 5100 16738.404 0 0 5269.4976 13.090032 - 5150 16738.421 0 0 5269.5029 13.090073 - 5200 16738.44 0 0 5269.5087 13.090119 - 5250 16738.448 -0.001279392 0 5269.5102 13.090114 - 5300 16738.456 -0.0064376392 0 5269.5075 13.090026 - 5350 16738.479 -0.020383842 0 5269.5007 13.089897 - 5400 16735.845 0.79889474 0 5269.4909 13.136244 - 5450 16735.558 0.87619992 0 5269.4778 12.324482 - 5500 16711.494 8.4724208 0 5269.4984 12.656579 - 5550 16454.525 89.074816 0 5269.2031 16.996503 - 5600 16713.084 7.9801334 0 5269.5065 13.774977 - 5650 16738.676 -0.079987764 0 5269.5033 13.168295 - 5700 16446.281 91.866085 0 5269.399 23.764662 - 5750 16738.549 -0.039869084 0 5269.5034 13.378121 - 5800 16738.487 -0.014994475 0 5269.5086 13.378397 - 5850 16738.466 -0.0051267556 0 5269.512 13.378559 - 5900 16738.462 -0.0043690097 0 5269.5113 13.378572 - 5950 16738.528 -0.03272741 0 5269.5039 13.378195 - 6000 16702.774 10.969434 0 5269.2502 13.788851 - 6050 16682.271 17.483158 0 5269.3092 13.3531 - 6100 16738.508 -0.028838239 0 5269.5016 12.521082 - 6150 16738.425 -0.0067595542 0 5269.4974 12.521221 - 6200 16738.401 -0.0011499896 0 5269.4955 12.521252 - 6250 16738.455 0 0 5269.5135 12.521408 - 6300 16738.523 0 0 5269.5352 12.521578 - 6350 16738.503 0 0 5269.5287 12.52153 - 6400 16738.427 0 0 5269.5047 12.521342 - 6450 16738.399 0 0 5269.496 12.521273 - 6500 16738.425 0 0 5269.5042 12.521336 - 6550 16738.441 0 0 5269.5093 12.521377 - 6600 16738.42 0 0 5269.5025 12.521324 - 6650 16738.398 0 0 5269.4957 12.52127 - 6700 16738.435 0 0 5269.5074 12.52136 - 6750 16738.505 0 0 5269.5293 12.521532 - 6800 16738.508 0 0 5269.5303 12.521541 - 6850 16738.446 0 0 5269.5108 12.521389 - 6900 16738.414 0 0 5269.5009 12.521311 - 6950 16738.432 0 0 5269.5063 12.521353 - 7000 16738.444 0 0 5269.5102 12.521383 - 7050 16738.421 0 0 5269.5029 12.521327 - 7100 16738.393 0 0 5269.4941 12.521258 - 7150 16738.419 0 0 5269.5022 12.52132 - 7200 16738.489 0 0 5269.5244 12.521494 - 7250 16738.505 0 0 5269.5293 12.521533 - 7300 16738.443 0 0 5269.5098 12.521381 - 7350 16738.404 0 0 5269.4976 12.521285 - 7400 16738.43 0 0 5269.5058 12.521348 - 7450 16738.461 0 0 5269.5156 12.521425 - 7500 16738.447 0 0 5269.5109 12.52139 - 7550 16738.407 0 0 5269.4986 12.521293 - 7600 16738.412 0 0 5269.5002 12.521305 - 7650 16738.478 0 0 5269.5208 12.521465 - 7700 16738.51 0 0 5269.5309 12.521546 - 7750 16738.454 0 0 5269.5135 12.52141 - 7800 16738.398 0 0 5269.4958 12.521272 - 7850 16738.407 -0.00021180981 0 5269.4982 12.521288 - 7900 16738.441 -0.0002167964 0 5269.509 12.521371 - 7950 16738.446 -0.00023848065 0 5269.5107 12.521385 - 8000 16738.423 0 0 5269.5035 12.521331 - 8050 16738.423 0 0 5269.5034 12.52133 - 8100 16738.478 -0.00069623408 0 5269.52 12.521452 - 8150 16738.523 -0.0040058355 0 5269.531 12.521499 - 8200 16738.486 -0.0092298325 0 5269.5142 12.521332 - 8250 16738.458 -0.023189665 0 5269.4914 12.521012 - 8300 16738.513 -0.045846242 0 5269.4861 12.520778 - 8350 16723.742 4.5698786 0 5269.4516 12.849386 - 8400 16738.466 -0.02016972 0 5269.497 12.835784 - 8450 16738.437 -0.012822703 0 5269.4952 12.829948 - 8500 16738.408 -0.0016836132 0 5269.4972 12.830073 - 8550 16738.464 -0.00097380297 0 5269.5155 12.830227 - 8600 16738.669 -0.050578946 0 5269.5304 12.829946 - 8650 15917.707 250.24016 0 5261.3702 24.544744 - 8700 16738.445 0.0010615265 0 5269.5117 10.589987 - 8750 16738.473 -0.010158834 0 5269.509 10.588904 - 8800 16738.468 0 0 5269.5176 10.589124 - 8850 16738.508 0 0 5269.5304 10.589223 - 8900 16738.509 0 0 5269.5306 10.589226 - 8950 16738.496 0 0 5269.5266 10.589195 - 9000 16738.477 0 0 5269.5204 10.589147 - 9050 16738.455 0 0 5269.5135 10.589092 - 9100 16738.477 0 0 5269.5206 10.589146 - 9150 16738.512 0 0 5269.5316 10.589233 - 9200 16738.502 0 0 5269.5285 10.58921 - 9250 16738.493 0 0 5269.5255 10.589186 - 9300 16738.482 0 0 5269.522 10.589159 - 9350 16738.46 0 0 5269.5151 10.589105 - 9400 16738.481 0 0 5269.5217 10.589155 - 9450 16738.509 0 0 5269.5307 10.589226 - 9500 16738.491 0 0 5269.5248 10.589181 - 9550 16738.484 0 0 5269.5227 10.589164 - 9600 16738.483 0 0 5269.5223 10.589161 - 9650 16738.464 0 0 5269.5166 10.589116 - 9700 16738.484 0 0 5269.5228 10.589164 - 9750 16738.507 0 0 5269.5301 10.589221 - 9800 16738.482 0 0 5269.5221 10.589159 - 9850 16738.478 0 0 5269.5208 10.589149 - 9900 16738.487 -0.00030979591 0 5269.5233 10.589165 - 9950 16738.476 -0.0009596827 0 5269.5193 10.589123 - 10000 16738.494 -0.0006271698 0 5269.5253 10.589175 -Loop time of 0.212511 on 4 procs for 10000 steps with 81 atoms - -Performance: 406566.385 tau/day, 47056.295 timesteps/s -91.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0032909 | 0.0039915 | 0.0048544 | 0.9 | 1.88 -Neigh | 0.011434 | 0.01325 | 0.016991 | 1.9 | 6.24 -Comm | 0.076038 | 0.082493 | 0.088069 | 1.5 | 38.82 -Output | 0.0031183 | 0.0045295 | 0.0086036 | 3.5 | 2.13 -Modify | 0.099662 | 0.10206 | 0.10679 | 0.9 | 48.02 -Other | | 0.00619 | | | 2.91 - -Nlocal: 20.25 ave 34 max 9 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 38.5 ave 43 max 26 min -Histogram: 1 0 0 0 0 0 0 0 0 3 -Neighs: 0.75 ave 2 max 0 min -Histogram: 2 0 0 0 0 1 0 0 0 1 - -Total # of neighbors = 3 -Ave neighs/atom = 0.037037 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.property.g++.1 b/examples/rigid/log.27Nov18.rigid.property.g++.1 deleted file mode 100644 index e6ab4ed102..0000000000 --- a/examples/rigid/log.27Nov18.rigid.property.g++.1 +++ /dev/null @@ -1,340 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -fix 0 all property/atom i_bodies - -read_data data.rigid-property fix 0 NULL Bodies - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -# assemble bodies from per-atom custom integer property bodies -fix 1 all rigid custom i_bodies -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.046 | 4.046 | 4.046 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 - 9550 16738.493 -0.005315616 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589885 0 5269.4979 12.062708 - 9750 16738.013 0.13550123 0 5269.5101 11.407245 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.156049 on 1 procs for 10000 steps with 81 atoms - -Performance: 553673.043 tau/day, 64082.528 timesteps/s -97.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.010187 | 0.010187 | 0.010187 | 0.0 | 6.53 -Neigh | 0.040601 | 0.040601 | 0.040601 | 0.0 | 26.02 -Comm | 0.013221 | 0.013221 | 0.013221 | 0.0 | 8.47 -Output | 0.0016611 | 0.0016611 | 0.0016611 | 0.0 | 1.06 -Modify | 0.085107 | 0.085107 | 0.085107 | 0.0 | 54.54 -Other | | 0.005271 | | | 3.38 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.property.g++.4 b/examples/rigid/log.27Nov18.rigid.property.g++.4 deleted file mode 100644 index f63e34bc4b..0000000000 --- a/examples/rigid/log.27Nov18.rigid.property.g++.4 +++ /dev/null @@ -1,340 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -fix 0 all property/atom i_bodies - -read_data data.rigid-property fix 0 NULL Bodies - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -# assemble bodies from per-atom custom integer property bodies -fix 1 all rigid custom i_bodies -9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.017 | 4.111 | 4.392 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706557 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 - 9600 16738.549 -0.026814371 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589894 0 5269.4979 12.062708 - 9750 16738.013 0.13550109 0 5269.5101 11.407246 - 9800 16738.512 -0.011620327 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.198069 on 4 procs for 10000 steps with 81 atoms - -Performance: 436211.675 tau/day, 50487.462 timesteps/s -91.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0026007 | 0.0034987 | 0.0043218 | 1.0 | 1.77 -Neigh | 0.012213 | 0.013261 | 0.014237 | 0.8 | 6.70 -Comm | 0.073581 | 0.082048 | 0.087982 | 2.1 | 41.42 -Output | 0.0047908 | 0.0058783 | 0.009093 | 2.4 | 2.97 -Modify | 0.081998 | 0.086993 | 0.09176 | 1.4 | 43.92 -Other | | 0.00639 | | | 3.23 - -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 998 -Dangerous builds = 997 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.tnr.g++.1 b/examples/rigid/log.27Nov18.rigid.tnr.g++.1 deleted file mode 100644 index bf29e0b94b..0000000000 --- a/examples/rigid/log.27Nov18.rigid.tnr.g++.1 +++ /dev/null @@ -1,458 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Tethered nanorods - -atom_style molecular - -read_data data.rigid.tnr - orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 5600 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 1600 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -# Specify bond parameters - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 - -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - -# Specify initial velocities - -velocity all create 1.4 109345 - -# Specify rigid components - -group rods type 2 -4000 atoms in group rods -group tethers subtract all rods -1600 atoms in group tethers - -neigh_modify exclude molecule/intra rods delay 0 every 1 - -# Specify the pair potentials - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff * * 1.0 1.0 1.122 -pair_coeff 2 2 1.0 1.0 2.5 - -# Specify output - -thermo 100 -thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz -thermo_modify flush yes lost warn - -timestep 0.005 - -fix 1 rods rigid molecule -800 rigid bodies with 4000 atoms -fix 2 tethers nve -fix 3 all langevin 1.4 1.4 1.0 437624 - -run 5000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 45 45 45 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 - 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248 - 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036 - 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998 - 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801 - 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745 - 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581 - 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883 - 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271 - 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788 - 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119 - 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748 - 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115 - 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625 - 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021 - 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242 - 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334 - 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014 - 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797 - 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268 - 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673 - 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825 - 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911 - 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296 - 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402 - 2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677 - 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948 - 2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371 - 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106 - 2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713 - 3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611 - 3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039 - 3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251 - 3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362 - 3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524 - 3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699 - 3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752 - 3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797 - 3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772 - 3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034 - 4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065 - 4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387 - 4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557 - 4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574 - 4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421 - 4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711 - 4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462 - 4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986 - 4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278 - 4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891 - 5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248 -Loop time of 6.84203 on 1 procs for 5000 steps with 5600 atoms - -Performance: 315695.745 tau/day, 730.777 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.53182 | 0.53182 | 0.53182 | 0.0 | 7.77 -Bond | 0.18231 | 0.18231 | 0.18231 | 0.0 | 2.66 -Neigh | 1.8709 | 1.8709 | 1.8709 | 0.0 | 27.34 -Comm | 0.18452 | 0.18452 | 0.18452 | 0.0 | 2.70 -Output | 0.0043087 | 0.0043087 | 0.0043087 | 0.0 | 0.06 -Modify | 3.8809 | 3.8809 | 3.8809 | 0.0 | 56.72 -Other | | 0.1873 | | | 2.74 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1351 ave 1351 max 1351 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5254 ave 5254 max 5254 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5254 -Ave neighs/atom = 0.938214 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 766 -Dangerous builds = 0 - -# Replace fix rigid and fix langevin with new ones - -unfix 1 -unfix 3 - -fix 3 tethers langevin 1.4 1.4 1.0 198450 - -# Test different integrators for rods - -fix 1 rods rigid/nve molecule -800 rigid bodies with 4000 atoms -print "rigid/nve" -rigid/nve -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575 - 5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041 - 5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551 - 5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518 - 5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493 - 5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038 - 5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751 - 5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035 - 5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927 - 5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509 - 6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075 -Loop time of 1.40593 on 1 procs for 1000 steps with 5600 atoms - -Performance: 307270.224 tau/day, 711.274 timesteps/s -99.1% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.14844 | 0.14844 | 0.14844 | 0.0 | 10.56 -Bond | 0.036852 | 0.036852 | 0.036852 | 0.0 | 2.62 -Neigh | 0.40537 | 0.40537 | 0.40537 | 0.0 | 28.83 -Comm | 0.036592 | 0.036592 | 0.036592 | 0.0 | 2.60 -Output | 0.00085831 | 0.00085831 | 0.00085831 | 0.0 | 0.06 -Modify | 0.74053 | 0.74053 | 0.74053 | 0.0 | 52.67 -Other | | 0.03729 | | | 2.65 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1347 ave 1347 max 1347 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5399 ave 5399 max 5399 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5399 -Ave neighs/atom = 0.964107 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 153 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 -800 rigid bodies with 4000 atoms -print "rigid/nvt" -rigid/nvt -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547 - 6100 1.4199699 5.8764035 6.9917138 0.0054065561 7.2245364 62.244 62.244 62.244 0.009227645 0.0019623802 0.0050296432 - 6200 1.3976825 5.8924426 6.9902474 0.00043900876 7.0091524 62.244 62.244 62.244 -0.0023073124 -0.00049925318 0.0041235918 - 6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018934 0.0091933877 0.0049242093 - 6400 1.3749203 5.8817073 6.9616336 0.0074967162 7.2844648 62.244 62.244 62.244 0.012281887 0.0039781589 0.0062301027 - 6500 1.3467096 5.8881264 6.9458946 -0.00011926349 6.9407588 62.244 62.244 62.244 0.0030721967 -0.0013265863 -0.0021034009 - 6600 1.3646558 5.8739857 6.9458497 0.0056064043 7.1872784 62.244 62.244 62.244 0.0059660337 0.0057680048 0.0050851745 - 6700 1.3927251 5.883612 6.9775229 0.0025583824 7.0876946 62.244 62.244 62.244 0.0030974706 0.0018499606 0.002727716 - 6800 1.4016999 5.9015886 7.0025488 0.0039070678 7.1707989 62.244 62.244 62.244 0.0068320586 0.0020056859 0.002883459 - 6900 1.4136745 5.8914714 7.001837 0.0051755091 7.22471 62.244 62.244 62.244 0.0028467792 0.0094052519 0.0032744962 - 7000 1.4286639 5.893567 7.0157059 0.0062957476 7.2868198 62.244 62.244 62.244 0.0047242086 0.0093408867 0.0048221474 -Loop time of 1.41045 on 1 procs for 1000 steps with 5600 atoms - -Performance: 306284.404 tau/day, 708.992 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.1497 | 0.1497 | 0.1497 | 0.0 | 10.61 -Bond | 0.036719 | 0.036719 | 0.036719 | 0.0 | 2.60 -Neigh | 0.40272 | 0.40272 | 0.40272 | 0.0 | 28.55 -Comm | 0.036315 | 0.036315 | 0.036315 | 0.0 | 2.57 -Output | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 0.06 -Modify | 0.747 | 0.747 | 0.747 | 0.0 | 52.96 -Other | | 0.03715 | | | 2.63 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1284 ave 1284 max 1284 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5677 ave 5677 max 5677 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5677 -Ave neighs/atom = 1.01375 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 151 -Dangerous builds = 0 -unfix 1 - -compute myTemp all temp - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt iso" -rigid/npt iso -fix_modify 1 temp myTemp - -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 7000 1.4286639 5.893567 7.0157059 0.032101512 8.3980939 62.244 62.244 62.244 0.0040045405 0.040447803 0.051852194 - 7100 1.4709161 5.8870949 7.0424207 0.019697134 7.6953761 57.045689 57.045689 57.045689 0.012929484 0.020492532 0.025669387 - 7200 1.5163078 5.8421187 7.0330973 0.018916867 7.46241 50.277171 50.277171 50.277171 0.017823354 0.026688031 0.012239218 - 7300 1.5675309 5.7752739 7.0064855 0.022899743 7.3829781 45.154874 45.154874 45.154874 0.019324617 0.024318577 0.025056034 - 7400 1.5432228 5.7513096 6.9634284 0.024381819 7.272744 41.416613 41.416613 41.416613 0.032026791 0.022254425 0.018864241 - 7500 1.5511419 5.7072564 6.9255953 0.030632381 7.2405167 38.613262 38.613262 38.613262 0.041572196 0.012539031 0.037785916 - 7600 1.5437461 5.6656571 6.8781869 0.031293788 7.1486082 36.440994 36.440994 36.440994 0.036220762 0.02125772 0.036402883 - 7700 1.5873874 5.6134986 6.8603063 0.04807003 7.221002 34.765744 34.765744 34.765744 0.031608235 0.053442472 0.059159381 - 7800 1.5079648 5.601961 6.7863866 0.031128515 6.9971673 33.59594 33.59594 33.59594 0.032932226 0.015950578 0.044502741 - 7900 1.4737447 5.5644198 6.7219673 0.099246661 7.3415696 32.698542 32.698542 32.698542 0.071386679 0.10758014 0.11877317 - 8000 1.4727947 5.5161158 6.6729171 0.072190554 7.0973199 32.050043 32.050043 32.050043 0.072806068 0.06277287 0.080992723 -Loop time of 3.15299 on 1 procs for 1000 steps with 5600 atoms - -Performance: 137012.841 tau/day, 317.159 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.37069 | 0.37069 | 0.37069 | 0.0 | 11.76 -Bond | 0.05046 | 0.05046 | 0.05046 | 0.0 | 1.60 -Neigh | 1.4844 | 1.4844 | 1.4844 | 0.0 | 47.08 -Comm | 0.081178 | 0.081178 | 0.081178 | 0.0 | 2.57 -Output | 0.00083494 | 0.00083494 | 0.00083494 | 0.0 | 0.03 -Modify | 1.1163 | 1.1163 | 1.1163 | 0.0 | 35.41 -Other | | 0.0491 | | | 1.56 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2954 ave 2954 max 2954 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 25585 ave 25585 max 25585 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 25585 -Ave neighs/atom = 4.56875 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 334 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt x" -rigid/npt x -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.785 | 7.785 | 7.785 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 8000 1.4727947 5.5161158 6.6729171 0.13628586 7.4741313 32.050043 32.050043 32.050043 -0.030897367 0.27196335 0.1677916 - 8100 1.4522497 5.5136331 6.6542974 0.057107124 6.9895036 32.000184 32.050043 32.050043 0.049932793 0.056130194 0.065258384 - 8200 1.4407937 5.5014539 6.6331202 0.024119241 6.7733276 31.691157 32.050043 32.050043 0.041526366 0.022503949 0.0083274089 - 8300 1.4542258 5.496977 6.6391934 0.043395674 6.887667 31.215092 32.050043 32.050043 0.025407647 0.075227689 0.029551686 - 8400 1.4375595 5.4901345 6.6192605 0.013578023 6.6952098 30.494249 32.050043 32.050043 -0.0045150608 0.033500673 0.011748456 - 8500 1.4410736 5.4540565 6.5859426 0.017121222 6.679397 29.757445 32.050043 32.050043 0.035675932 -0.032105 0.047792733 - 8600 1.4372413 5.4150437 6.5439197 0.084045699 6.9949237 29.254706 32.050043 32.050043 0.10347392 0.073148157 0.075515024 - 8700 1.4299119 5.3982284 6.5213476 0.00045273296 6.5237411 28.822481 32.050043 32.050043 0.0093093459 0.0081538479 -0.016104995 - 8800 1.4677947 5.3637715 6.5166456 0.028621833 6.6651924 28.294159 32.050043 32.050043 0.033527613 0.036046563 0.016291323 - 8900 1.4625499 5.3483914 6.4971459 0.032843022 6.6649394 27.852402 32.050043 32.050043 0.040751528 0.055865445 0.0019120942 - 9000 1.4488382 5.3486741 6.4866589 0.087522574 6.9279711 27.488856 32.050043 32.050043 0.059432129 0.10936517 0.093770421 -Loop time of 3.09429 on 1 procs for 1000 steps with 5600 atoms - -Performance: 139611.779 tau/day, 323.175 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.57714 | 0.57714 | 0.57714 | 0.0 | 18.65 -Bond | 0.051715 | 0.051715 | 0.051715 | 0.0 | 1.67 -Neigh | 1.223 | 1.223 | 1.223 | 0.0 | 39.52 -Comm | 0.066183 | 0.066183 | 0.066183 | 0.0 | 2.14 -Output | 0.00086594 | 0.00086594 | 0.00086594 | 0.0 | 0.03 -Modify | 1.1355 | 1.1355 | 1.1355 | 0.0 | 36.70 -Other | | 0.03994 | | | 1.29 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3381 ave 3381 max 3381 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 31737 ave 31737 max 31737 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 31737 -Ave neighs/atom = 5.66732 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 169 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph iso" -rigid/nph iso -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.788 | 7.788 | 7.788 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 9000 1.4488382 5.3486741 6.4866589 0.20124138 7.5013717 27.488856 32.050043 32.050043 0.22160189 0.42145658 -0.039334342 - 9100 1.4408457 5.3612674 6.4929746 0.076331412 6.8758499 27.440968 31.994208 31.994208 0.083838068 0.041724506 0.10343166 - 9200 1.4870445 5.3340546 6.5020483 0.01010773 6.5521592 27.334266 31.869802 31.869802 0.024563803 -0.0068003493 0.012559737 - 9300 1.4376808 5.3295183 6.4587396 0.10720051 6.9752889 27.076116 31.568817 31.568817 0.11844426 0.10444301 0.09871425 - 9400 1.4621325 5.3011274 6.4495541 0.071127232 6.7846388 26.873295 31.332342 31.332342 0.091608834 0.02680694 0.094965923 - 9500 1.4463444 5.3005044 6.4365304 0.0011545049 6.4418432 26.664 31.088319 31.088319 -0.030551889 0.036011952 -0.0019965484 - 9600 1.4473406 5.2912939 6.4281024 0.066132857 6.7281169 26.537276 30.940568 30.940568 0.12276096 0.013455525 0.06218208 - 9700 1.4520445 5.2707214 6.4112246 0.077219765 6.757956 26.446587 30.834832 30.834832 0.073829267 0.11047347 0.047356559 - 9800 1.4825713 5.246644 6.4111243 0.061402527 6.6831281 26.327581 30.696078 30.696078 0.091860222 0.022619578 0.06972778 - 9900 1.4795219 5.2344495 6.3965347 0.086345107 6.7729623 26.187615 30.532888 30.532888 0.077396265 0.11142542 0.07021363 - 10000 1.4527053 5.2126819 6.3537041 0.045117764 6.5474705 26.057038 30.380645 30.380645 0.011087188 0.058029185 0.066236921 -Loop time of 3.25046 on 1 procs for 1000 steps with 5600 atoms - -Performance: 132904.162 tau/day, 307.649 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.68223 | 0.68223 | 0.68223 | 0.0 | 20.99 -Bond | 0.05211 | 0.05211 | 0.05211 | 0.0 | 1.60 -Neigh | 1.2617 | 1.2617 | 1.2617 | 0.0 | 38.82 -Comm | 0.069407 | 0.069407 | 0.069407 | 0.0 | 2.14 -Output | 0.00085688 | 0.00085688 | 0.00085688 | 0.0 | 0.03 -Modify | 1.1438 | 1.1438 | 1.1438 | 0.0 | 35.19 -Other | | 0.04037 | | | 1.24 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3756 ave 3756 max 3756 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 37360 ave 37360 max 37360 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 37360 -Ave neighs/atom = 6.67143 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 158 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph xy couple" -rigid/nph xy couple -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.795 | 7.795 | 7.795 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 10000 1.4527053 5.2126819 6.3537041 0.056937886 6.5982342 26.057038 30.380645 30.380645 -0.37001102 0.18554825 0.35527643 - 10100 1.4606958 5.2220088 6.3693071 0.10308269 6.8132489 26.093341 30.422971 30.380645 0.12567436 0.057087258 0.12648646 - 10200 1.4429187 5.2134399 6.3467753 0.022637194 6.4450326 26.195743 30.542365 30.380645 0.010739012 0.071921542 -0.014748971 - 10300 1.4559104 5.2293511 6.3728908 0.0079467818 6.4073504 26.182966 30.527467 30.380645 -0.014274944 0.032205181 0.0059101087 - 10400 1.4741126 5.2072221 6.3650586 0.095611559 6.7814715 26.240156 30.594148 30.380645 0.073579289 0.092441893 0.12081349 - 10500 1.4411698 5.2173262 6.3492878 0.010458046 6.3947259 26.208633 30.557393 30.380645 0.036794882 -0.0051462954 -0.00027444949 - 10600 1.4492728 5.1940541 6.3323802 0.042602534 6.5163992 26.132032 30.468083 30.380645 0.090116773 0.0022769844 0.035413845 - 10700 1.4599974 5.1895935 6.3363432 0.05533717 6.573197 26.013045 30.329352 30.380645 0.070180878 0.08084881 0.014981824 - 10800 1.4781084 5.1724704 6.3334454 0.031843587 6.4690539 25.947295 30.252692 30.380645 0.0041524129 0.077618702 0.013759645 - 10900 1.4410507 5.1708846 6.3027527 0.020221033 6.3881531 25.839719 30.127267 30.380645 -0.0014092876 0.014833141 0.047239245 - 11000 1.4150286 5.1756927 6.2871219 0.039768792 6.45242 25.63435 29.887821 30.380645 0.034930907 0.032278926 0.052096542 -Loop time of 3.43774 on 1 procs for 1000 steps with 5600 atoms - -Performance: 125663.855 tau/day, 290.889 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.75066 | 0.75066 | 0.75066 | 0.0 | 21.84 -Bond | 0.053177 | 0.053177 | 0.053177 | 0.0 | 1.55 -Neigh | 1.3577 | 1.3577 | 1.3577 | 0.0 | 39.49 -Comm | 0.07294 | 0.07294 | 0.07294 | 0.0 | 2.12 -Output | 0.00086403 | 0.00086403 | 0.00086403 | 0.0 | 0.03 -Modify | 1.1612 | 1.1612 | 1.1612 | 0.0 | 33.78 -Other | | 0.0412 | | | 1.20 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3904 ave 3904 max 3904 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 39666 ave 39666 max 39666 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 39666 -Ave neighs/atom = 7.08321 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 159 -Dangerous builds = 0 - -Total wall time: 0:00:22 diff --git a/examples/rigid/log.27Nov18.rigid.tnr.g++.4 b/examples/rigid/log.27Nov18.rigid.tnr.g++.4 deleted file mode 100644 index 1fa53eb8d3..0000000000 --- a/examples/rigid/log.27Nov18.rigid.tnr.g++.4 +++ /dev/null @@ -1,458 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Tethered nanorods - -atom_style molecular - -read_data data.rigid.tnr - orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 5600 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 1600 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -# Specify bond parameters - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 - -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - -# Specify initial velocities - -velocity all create 1.4 109345 - -# Specify rigid components - -group rods type 2 -4000 atoms in group rods -group tethers subtract all rods -1600 atoms in group tethers - -neigh_modify exclude molecule/intra rods delay 0 every 1 - -# Specify the pair potentials - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff * * 1.0 1.0 1.122 -pair_coeff 2 2 1.0 1.0 2.5 - -# Specify output - -thermo 100 -thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz -thermo_modify flush yes lost warn - -timestep 0.005 - -fix 1 rods rigid molecule -800 rigid bodies with 4000 atoms -fix 2 tethers nve -fix 3 all langevin 1.4 1.4 1.0 437624 - -run 5000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 45 45 45 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 - 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624 - 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719 - 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786 - 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141 - 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529 - 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222 - 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907 - 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859 - 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971 - 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735 - 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195 - 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658 - 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474 - 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314 - 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432 - 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699 - 1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975 - 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981 - 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291 - 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901 - 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978 - 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521 - 2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595 - 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026 - 2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538 - 2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116 - 2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359 - 2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055 - 2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189 - 3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657 - 3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458 - 3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265 - 3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057 - 3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981 - 3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447 - 3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317 - 3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268 - 3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977 - 3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851 - 4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779 - 4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267 - 4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436 - 4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353 - 4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015 - 4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655 - 4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475 - 4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828 - 4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007 - 4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05 - 5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114 -Loop time of 3.70354 on 4 procs for 5000 steps with 5600 atoms - -Performance: 583225.455 tau/day, 1350.059 timesteps/s -92.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.081073 | 0.13498 | 0.20108 | 14.4 | 3.64 -Bond | 0.032352 | 0.048566 | 0.066671 | 7.0 | 1.31 -Neigh | 0.71345 | 0.72477 | 0.73658 | 1.3 | 19.57 -Comm | 0.29998 | 0.37027 | 0.42722 | 8.9 | 10.00 -Output | 0.0026417 | 0.0048325 | 0.0085185 | 3.2 | 0.13 -Modify | 1.9807 | 2.1035 | 2.263 | 8.1 | 56.80 -Other | | 0.3166 | | | 8.55 - -Nlocal: 1400 ave 1868 max 905 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Nghost: 648.25 ave 688 max 598 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Neighs: 1202.5 ave 1821 max 698 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 4810 -Ave neighs/atom = 0.858929 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 759 -Dangerous builds = 0 - -# Replace fix rigid and fix langevin with new ones - -unfix 1 -unfix 3 - -fix 3 tethers langevin 1.4 1.4 1.0 198450 - -# Test different integrators for rods - -fix 1 rods rigid/nve molecule -800 rigid bodies with 4000 atoms -print "rigid/nve" -rigid/nve -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407 - 5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113 - 5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599 - 5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984 - 5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427 - 5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784 - 5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228 - 5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215 - 5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708 - 5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003 - 6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208 -Loop time of 0.84847 on 4 procs for 1000 steps with 5600 atoms - -Performance: 509151.820 tau/day, 1178.592 timesteps/s -94.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.020741 | 0.03547 | 0.053064 | 7.5 | 4.18 -Bond | 0.0064373 | 0.0096895 | 0.013065 | 3.0 | 1.14 -Neigh | 0.14992 | 0.15174 | 0.15392 | 0.4 | 17.88 -Comm | 0.068751 | 0.081259 | 0.10084 | 4.2 | 9.58 -Output | 0.00054288 | 0.00096381 | 0.0017593 | 0.0 | 0.11 -Modify | 0.45914 | 0.48587 | 0.51316 | 2.8 | 57.26 -Other | | 0.08348 | | | 9.84 - -Nlocal: 1400 ave 1868 max 935 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 633.75 ave 695 max 541 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Neighs: 1263 ave 1799 max 710 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 5052 -Ave neighs/atom = 0.902143 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 153 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 -800 rigid bodies with 4000 atoms -print "rigid/nvt" -rigid/nvt -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535 - 6100 1.3829575 5.9055308 6.9917699 0.0022904842 7.090405 62.244 62.244 62.244 -0.00045870123 0.0040556461 0.0032745076 - 6200 1.3942692 5.90506 7.0001838 0.0046406766 7.2000253 62.244 62.244 62.244 0.0042263485 0.0051632793 0.0045324021 - 6300 1.4009885 5.902399 7.0028005 0.0077682466 7.3373246 62.244 62.244 62.244 0.0071636876 0.0098268446 0.0063142075 - 6400 1.3627532 5.9075588 6.9779284 0.0093180831 7.3791932 62.244 62.244 62.244 0.0062401458 0.01302262 0.0086914833 - 6500 1.3341203 5.9012967 6.9491767 0.01010805 7.3844599 62.244 62.244 62.244 0.0031876185 0.011099561 0.01603697 - 6600 1.3572847 5.8915298 6.9576042 -0.00034416901 6.9427833 62.244 62.244 62.244 0.0025579012 -0.0011308802 -0.0024595281 - 6700 1.366374 5.8985277 6.9717413 0.0029472772 7.0986599 62.244 62.244 62.244 0.0022469424 -0.00042869772 0.0070235868 - 6800 1.381673 5.8909304 6.9761606 -9.1063397e-05 6.9722391 62.244 62.244 62.244 -0.0048194377 -0.00080972169 0.0053559692 - 6900 1.4011472 5.8881927 6.9887188 0.0010086058 7.0321524 62.244 62.244 62.244 0.0012132619 -0.0025916747 0.0044042301 - 7000 1.3973658 5.8867938 6.9843498 0.0070015187 7.2858563 62.244 62.244 62.244 0.0058913402 0.0076802028 0.0074330131 -Loop time of 0.902266 on 4 procs for 1000 steps with 5600 atoms - -Performance: 478794.425 tau/day, 1108.320 timesteps/s -92.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.022644 | 0.037091 | 0.054025 | 7.4 | 4.11 -Bond | 0.0066526 | 0.0098482 | 0.012934 | 2.8 | 1.09 -Neigh | 0.15815 | 0.16028 | 0.16242 | 0.5 | 17.76 -Comm | 0.086046 | 0.10069 | 0.11568 | 3.7 | 11.16 -Output | 0.00047731 | 0.00090772 | 0.0016732 | 0.0 | 0.10 -Modify | 0.46692 | 0.49338 | 0.52973 | 3.5 | 54.68 -Other | | 0.1001 | | | 11.09 - -Nlocal: 1400 ave 1832 max 970 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 652.5 ave 749 max 561 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 1407.5 ave 2071 max 748 min -Histogram: 1 1 0 0 0 0 0 0 1 1 - -Total # of neighbors = 5630 -Ave neighs/atom = 1.00536 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 149 -Dangerous builds = 0 -unfix 1 - -compute myTemp all temp - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt iso" -rigid/npt iso -fix_modify 1 temp myTemp - -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 7000 1.3973658 5.8867938 6.9843498 0.0026564535 7.0987447 62.244 62.244 62.244 0.033711862 -0.0068580786 -0.018884423 - 7100 1.463906 5.861189 7.0110088 0.011521299 7.3924648 57.022165 57.022165 57.022165 0.010788399 0.0093706759 0.014404821 - 7200 1.4950346 5.817724 6.9919936 0.023104537 7.516484 50.28164 50.28164 50.28164 0.023252537 0.018108267 0.027952807 - 7300 1.5103539 5.7757334 6.9620355 0.02265972 7.3367664 45.242961 45.242961 45.242961 0.023588139 0.022279352 0.022111669 - 7400 1.5583184 5.7576833 6.9816589 0.028383162 7.3460731 41.582206 41.582206 41.582206 0.027312172 0.029876235 0.027961079 - 7500 1.5988886 5.6930714 6.9489127 0.046500933 7.4415595 39.00204 39.00204 39.00204 0.057497139 0.031007247 0.050998413 - 7600 1.5458926 5.6844397 6.8986555 0.034168406 7.2068206 36.96428 36.96428 36.96428 0.037874991 0.027247969 0.037382258 - 7700 1.5179913 5.6416448 6.8339457 0.070322183 7.3856048 35.284894 35.284894 35.284894 0.054248771 0.10402305 0.052694729 - 7800 1.4797888 5.6045532 6.7668481 0.07801402 7.3126319 33.963465 33.963465 33.963465 0.096058241 0.061172194 0.076811627 - 7900 1.4846305 5.54982 6.7159177 0.065303374 7.1325712 32.936376 32.936376 32.936376 0.089117046 0.06069295 0.046100127 - 8000 1.4352665 5.5157472 6.6430722 0.065962965 7.0326574 32.099391 32.099391 32.099391 0.032126133 0.070109418 0.095653344 -Loop time of 1.72334 on 4 procs for 1000 steps with 5600 atoms - -Performance: 250675.661 tau/day, 580.268 timesteps/s -92.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.060282 | 0.099801 | 0.13824 | 10.8 | 5.79 -Bond | 0.0095227 | 0.013491 | 0.017217 | 3.2 | 0.78 -Neigh | 0.58793 | 0.59546 | 0.60654 | 1.0 | 34.55 -Comm | 0.17903 | 0.21403 | 0.24615 | 6.5 | 12.42 -Output | 0.00045562 | 0.00076783 | 0.0017018 | 0.0 | 0.04 -Modify | 0.64959 | 0.68513 | 0.70671 | 2.8 | 39.76 -Other | | 0.1147 | | | 6.65 - -Nlocal: 1400 ave 1768 max 981 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 1574 ave 1663 max 1447 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Neighs: 6338 ave 9521 max 3068 min -Histogram: 1 0 1 0 0 0 0 0 1 1 - -Total # of neighbors = 25352 -Ave neighs/atom = 4.52714 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 337 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt x" -rigid/npt x -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.226 | 7.412 | 7.597 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 8000 1.4352665 5.5157472 6.6430722 0.073641793 7.0780095 32.099391 32.099391 32.099391 0.13359913 0.13991003 -0.052583787 - 8100 1.4385682 5.5149882 6.6449064 0.092621097 7.1894426 31.952972 32.099391 32.099391 0.10729401 0.11619987 0.054369411 - 8200 1.42735 5.5149024 6.6360094 0.023903894 6.7756304 31.745099 32.099391 32.099391 0.051524189 0.013370811 0.006816681 - 8300 1.4335369 5.5031396 6.629106 0.024536474 6.7705237 31.324638 32.099391 32.099391 0.042356568 -0.0039258365 0.035178692 - 8400 1.4502714 5.4659017 6.6050122 0.06575457 6.9774701 30.785462 32.099391 32.099391 0.056998298 0.084852971 0.055412441 - 8500 1.4432366 5.4541505 6.5877355 0.03322226 6.7725932 30.241461 32.099391 32.099391 0.045871758 0.024443739 0.029351281 - 8600 1.436491 5.4272043 6.5554911 0.039811655 6.7732608 29.729098 32.099391 32.099391 0.037709456 0.060942551 0.020782958 - 8700 1.4099251 5.4106713 6.5180919 0.013490442 6.590596 29.209958 32.099391 32.099391 0.025833003 -0.0021161354 0.016754458 - 8800 1.3801478 5.3926425 6.4766747 0.028808964 6.6280205 28.552039 32.099391 32.099391 0.012603549 0.018713073 0.055110271 - 8900 1.4411695 5.3583474 6.4903088 0.053464468 6.7655624 27.980937 32.099391 32.099391 0.055084927 0.073292013 0.032016464 - 9000 1.4264395 5.3680298 6.4884216 0.066557314 6.8276318 27.69922 32.099391 32.099391 0.05380086 0.069450871 0.076420212 -Loop time of 1.45936 on 4 procs for 1000 steps with 5600 atoms - -Performance: 296020.704 tau/day, 685.233 timesteps/s -96.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.097855 | 0.1563 | 0.20542 | 12.5 | 10.71 -Bond | 0.010222 | 0.01371 | 0.016844 | 2.6 | 0.94 -Neigh | 0.43646 | 0.44419 | 0.4668 | 2.0 | 30.44 -Comm | 0.10136 | 0.14589 | 0.19563 | 11.6 | 10.00 -Output | 0.00046229 | 0.00076181 | 0.0016556 | 0.0 | 0.05 -Modify | 0.59971 | 0.62524 | 0.65776 | 2.9 | 42.84 -Other | | 0.07327 | | | 5.02 - -Nlocal: 1400 ave 1680 max 1049 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 1627.25 ave 1775 max 1488 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 7842 ave 10600 max 4326 min -Histogram: 1 0 1 0 0 0 0 0 0 2 - -Total # of neighbors = 31368 -Ave neighs/atom = 5.60143 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 166 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph iso" -rigid/nph iso -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.412 | 7.597 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 9000 1.4264395 5.3680298 6.4884216 0.0098629166 6.5386881 27.69922 32.099391 32.099391 -0.32352455 -0.020288613 0.37340191 - 9100 1.4501008 5.3468478 6.4858243 0.059250929 6.7846766 27.60347 31.988431 31.988431 0.076039445 0.051409059 0.050304282 - 9200 1.4635102 5.3406895 6.4901983 0.035210102 6.6656151 27.490192 31.857158 31.857158 0.0079484246 0.066653954 0.031027926 - 9300 1.4503713 5.3595734 6.4987624 0.020794 6.6013231 27.398334 31.750708 31.750708 0.053098983 0.0019379163 0.0073450997 - 9400 1.4701421 5.3186993 6.4734172 0.039118143 6.6618027 27.181055 31.498913 31.498913 0.076457868 -0.0028405762 0.043737137 - 9500 1.4495442 5.323167 6.4617063 0.073591495 6.8091096 27.000921 31.290164 31.290164 0.037777789 0.097624306 0.085372389 - 9600 1.4668438 5.3002222 6.4523494 0.06758294 6.7648428 26.814997 31.074705 31.074705 0.057941415 0.09775976 0.047047645 - 9700 1.4926839 5.2883964 6.4608196 0.059125916 6.7288224 26.637713 30.869258 30.869258 0.049817515 0.032285203 0.095275031 - 9800 1.4644558 5.2702597 6.4205112 0.0076221617 6.4543756 26.460515 30.663911 30.663911 -0.0060723629 0.010616271 0.018322577 - 9900 1.4669549 5.2511861 6.4034006 0.044167302 6.5961243 26.30195 30.480157 30.480157 0.026274163 0.013826125 0.092401618 - 10000 1.460983 5.2470476 6.3945715 0.10536479 6.8483021 26.186495 30.346361 30.346361 0.088951294 0.11273872 0.11440435 -Loop time of 1.61361 on 4 procs for 1000 steps with 5600 atoms - -Performance: 267722.758 tau/day, 619.729 timesteps/s -93.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.13322 | 0.18643 | 0.259 | 12.5 | 11.55 -Bond | 0.012367 | 0.014462 | 0.016771 | 1.6 | 0.90 -Neigh | 0.46284 | 0.46471 | 0.46675 | 0.3 | 28.80 -Comm | 0.10183 | 0.17241 | 0.22246 | 12.4 | 10.68 -Output | 0.00044584 | 0.00074542 | 0.0016396 | 0.0 | 0.05 -Modify | 0.691 | 0.7057 | 0.72761 | 1.8 | 43.73 -Other | | 0.06915 | | | 4.29 - -Nlocal: 1400 ave 1633 max 1183 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 1747.75 ave 1847 max 1624 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 9290.75 ave 12454 max 6621 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 37163 -Ave neighs/atom = 6.63625 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 162 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph xy couple" -rigid/nph xy couple -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 10000 1.460983 5.2470476 6.3945715 0.18376191 7.1859023 26.186495 30.346361 30.346361 0.015959435 0.68341409 -0.14808778 - 10100 1.4487259 5.2485513 6.3864479 0.060157728 6.6465409 26.238844 30.407026 30.346361 0.10289596 0.022823411 0.05475381 - 10200 1.4335646 5.2420513 6.3680395 0.013676852 6.4271554 26.235255 30.402867 30.346361 -0.017328522 0.040786509 0.017572569 - 10300 1.4334952 5.2377534 6.3636871 0.030978458 6.4967192 26.150168 30.304264 30.346361 0.044154015 0.036133394 0.012647966 - 10400 1.4209473 5.2242736 6.3403516 -0.00094467594 6.3363148 26.085773 30.22964 30.346361 0.030664991 0.018005544 -0.051504563 - 10500 1.4262805 5.2044624 6.3247294 0.045042501 6.5149748 25.934148 30.053928 30.346361 0.031103656 0.045410964 0.058612885 - 10600 1.4516048 5.2017459 6.3419036 0.069565209 6.6313867 25.741959 29.831208 30.346361 0.021768778 0.11302833 0.073898515 - 10700 1.4841074 5.1911212 6.356808 0.046866825 6.5493087 25.574636 29.637306 30.346361 0.073969059 0.064901506 0.0017299084 - 10800 1.4646257 5.1958815 6.3462665 0.050747116 6.5534926 25.500146 29.550982 30.346361 0.076646556 0.070734108 0.004860682 - 10900 1.461356 5.1821605 6.3299773 0.069060447 6.610166 25.417723 29.455466 30.346361 0.051399011 0.065631311 0.090151019 - 11000 1.4395386 5.1786243 6.3093047 -0.0087983274 6.2737059 25.383039 29.415273 30.346361 -0.060891892 0.037235898 -0.0027389884 -Loop time of 1.56065 on 4 procs for 1000 steps with 5600 atoms - -Performance: 276807.605 tau/day, 640.758 timesteps/s -94.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.15892 | 0.20364 | 0.2564 | 9.2 | 13.05 -Bond | 0.011486 | 0.014652 | 0.01918 | 2.6 | 0.94 -Neigh | 0.43915 | 0.43981 | 0.44125 | 0.1 | 28.18 -Comm | 0.093711 | 0.14431 | 0.18183 | 9.9 | 9.25 -Output | 0.00044441 | 0.00073904 | 0.0016198 | 0.0 | 0.05 -Modify | 0.66889 | 0.68497 | 0.70418 | 1.5 | 43.89 -Other | | 0.07254 | | | 4.65 - -Nlocal: 1400 ave 1610 max 1237 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 1832 ave 1919 max 1765 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Neighs: 10008.2 ave 12428 max 7982 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 40033 -Ave neighs/atom = 7.14875 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 157 -Dangerous builds = 0 - -Total wall time: 0:00:11 diff --git a/src/math_eigen.cpp b/src/math_eigen.cpp index 65c3fa806a..99c8d38290 100644 --- a/src/math_eigen.cpp +++ b/src/math_eigen.cpp @@ -44,7 +44,7 @@ int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v1 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_DECREASING_EVALS); + int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_INCREASING_EVALS); // transpose the evec matrix @@ -67,7 +67,7 @@ int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v2 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_DECREASING_EVALS); + int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_INCREASING_EVALS); // transpose the evec matrix diff --git a/unittest/force-styles/tests/fix-timestep-rigid_group.yaml b/unittest/force-styles/tests/fix-timestep-rigid_group.yaml index e28e0abb08..b5c77af975 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_group.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_group.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:00:59 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,65 +15,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4245356937318884e+03 -1.4496493315649691e+03 -3.6144360984224995e+03 8.4840626828644076e+02 2.0318336761611761e+02 -6.0622397707970140e+02 -global_scalar: 15.711521423178082 + -1.4245356937318909e+03 -1.4496493315649632e+03 -3.6144360984225123e+03 8.4840626828644361e+02 2.0318336761612773e+02 -6.0622397707969583e+02 +global_scalar: 15.711521423178084 run_pos: ! |2 - 1 -2.7899546863891400e-01 2.4731857340328229e+00 -1.7290667740242271e-01 - 2 3.0296221610264262e-01 2.9517129916957545e+00 -8.5798904387773245e-01 - 3 -6.9368802364134741e-01 1.2445115421754194e+00 -6.2281111198650418e-01 - 4 -1.5764879647103154e+00 1.4919714415841279e+00 -1.2492069414674623e+00 - 5 -8.9434512967429969e-01 9.3651699743511030e-01 4.0191726558261276e-01 - 6 2.9454439634451712e-01 2.2724545792544038e-01 -1.2845195053960268e+00 - 7 3.4049112903270051e-01 -9.4655678322458359e-03 -2.4634480020857055e+00 - 8 1.1644354555804874e+00 -4.8367776650961336e-01 -6.7663643940735863e-01 - 9 1.3781717822696469e+00 -2.5332509530010694e-01 2.6864954436590061e-01 - 10 2.0186368606041896e+00 -1.4285861423625796e+00 -9.6712491252780131e-01 - 11 1.7929137227577452e+00 -1.9875455388407426e+00 -1.8836565352266534e+00 - 12 3.0032775230399604e+00 -4.8983022415174027e-01 -1.6190248017343642e+00 - 13 4.0448964162125947e+00 -9.0213155122391020e-01 -1.6385398399479558e+00 - 14 2.6035151245015822e+00 -4.0874995493219213e-01 -2.6555999074786607e+00 - 15 2.9761196776172318e+00 5.6287237454108674e-01 -1.2442626196083388e+00 - 16 2.6517373021566168e+00 -2.3957035508393707e+00 3.3389262100692263e-02 - 17 2.2311114924744970e+00 -2.1018393228798513e+00 1.1496088522377543e+00 - 18 2.1390642573201784e+00 3.0164773560693781e+00 -3.5143984803853878e+00 - 19 1.5353246655146278e+00 2.6305911186316133e+00 -4.2455871034737074e+00 - 20 2.7649421538938390e+00 3.6818603528430849e+00 -3.9364115785985550e+00 - 21 4.9043112657298877e+00 -4.0774268210397882e+00 -3.6200836396129836e+00 - 22 4.3665322424283310e+00 -4.2075138112953594e+00 -4.4636587264885881e+00 - 23 5.7355405581985188e+00 -3.5789558641908918e+00 -3.8805763324089981e+00 - 24 2.0692780332810115e+00 3.1504920436416004e+00 3.1571131300668789e+00 - 25 1.3007297593169076e+00 3.2745259354179481e+00 2.5110163874103675e+00 - 26 2.5819416446099739e+00 4.0104903120756576e+00 3.2150249624526035e+00 + 1 -2.7899546863891755e-01 2.4731857340328198e+00 -1.7290667740241461e-01 + 2 3.0296221610263996e-01 2.9517129916957550e+00 -8.5798904387772190e-01 + 3 -6.9368802364134963e-01 1.2445115421754176e+00 -6.2281111198650141e-01 + 4 -1.5764879647103172e+00 1.4919714415841279e+00 -1.2492069414674598e+00 + 5 -8.9434512967430235e-01 9.3651699743510453e-01 4.0191726558261442e-01 + 6 2.9454439634451712e-01 2.2724545792544146e-01 -1.2845195053960266e+00 + 7 3.4049112903270240e-01 -9.4655678322404235e-03 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8.4222594596602409e-04 + 19 2.0572616567799204e-04 -5.0334424271726607e-04 8.4953929443210702e-04 + 20 4.1224811789513060e-04 -7.4115205416011543e-04 8.3678612337507964e-04 + 21 -1.0671858777656406e-03 -1.1531171045499533e-03 7.3720674900162007e-04 + 22 -1.1066511338291734e-03 -1.0433933757600477e-03 7.4544544325708432e-04 + 23 -9.7629260480941644e-04 -1.3100872491594124e-03 7.2687284219704641e-04 + 24 4.3308126651259382e-04 -6.6527658087322671e-04 8.4451298670663671e-04 + 25 4.4565811905442982e-04 -5.1298436273584133e-04 8.5878867884521635e-04 + 26 5.9865972692022961e-04 -7.6385263287080262e-04 8.4259943226842242e-04 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml b/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml index d667942e49..a73c8cd112 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:00:59 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00 -global_scalar: 18.3405601674144 + -4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00 +global_scalar: 18.340560167414402 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588271301e+00 3.0171068018412779e+00 -3.5144628518856349e+00 - 19 1.5366124997074571e+00 2.6286809834111748e+00 -4.2452547844370221e+00 - 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352554e+00 - 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515904e+00 - 22 4.3655322291888483e+00 -4.2084949965552561e+00 -4.4622011117402334e+00 - 23 5.7380414793463101e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 + 18 2.1392027588271301e+00 3.0171068018412783e+00 -3.5144628518856353e+00 + 19 1.5366124997074575e+00 2.6286809834111740e+00 -4.2452547844370221e+00 + 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 + 21 4.9036621347791236e+00 -4.0757648442838548e+00 -3.6192617654515908e+00 + 22 4.3655322291888474e+00 -4.2084949965552561e+00 -4.4622011117402343e+00 + 23 5.7380414793463110e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 24 2.0701314765323930e+00 3.1499370533342330e+00 3.1565324852522938e+00 - 25 1.3030170721374779e+00 3.2711173927682249e+00 2.5081940917429768e+00 - 26 2.5776230782480045e+00 4.0127347068243875e+00 3.2182355138709275e+00 + 25 1.3030170721374787e+00 3.2711173927682244e+00 2.5081940917429759e+00 + 26 2.5776230782480041e+00 4.0127347068243884e+00 3.2182355138709284e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704914e-04 -3.1032459262908286e-04 8.1043030117346052e-04 - 19 8.5103884665345452e-04 -1.4572280596788108e-03 1.0163621287634116e-03 - 20 -6.5204659278590683e-04 4.3989037444289853e-04 4.9909839028507901e-04 - 21 -1.3888125881903923e-03 -3.1978049143082385e-04 1.1455681499836646e-03 - 22 -1.6084223477729510e-03 -1.5355394240821117e-03 1.4772010826232375e-03 - 23 2.6392672378805124e-04 -3.9375414431174821e-03 -3.6991583139728095e-04 - 24 8.6062827067890247e-04 -9.4179873474469237e-04 5.5396395550012453e-04 - 25 1.5933645477487538e-03 -2.2139156625681695e-03 -5.5078029695647401e-04 - 26 -1.5679561743998840e-03 3.5146224354726100e-04 2.4446924193334478e-03 + 18 3.6149625095704849e-04 -3.1032459262908286e-04 8.1043030117346052e-04 + 19 8.5103884665345473e-04 -1.4572280596788095e-03 1.0163621287634121e-03 + 20 -6.5204659278590661e-04 4.3989037444289755e-04 4.9909839028507901e-04 + 21 -1.3888125881903906e-03 -3.1978049143082342e-04 1.1455681499836646e-03 + 22 -1.6084223477729526e-03 -1.5355394240821163e-03 1.4772010826232394e-03 + 23 2.6392672378804821e-04 -3.9375414431174795e-03 -3.6991583139728377e-04 + 24 8.6062827067890269e-04 -9.4179873474469291e-04 5.5396395550012388e-04 + 25 1.5933645477487551e-03 -2.2139156625681673e-03 -5.5078029695647250e-04 + 26 -1.5679561743998888e-03 3.5146224354726068e-04 2.4446924193334487e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml index 304db9fd60..9e362dd3ac 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:00 2024 epsilon: 5e-12 skip_tests: prerequisites: ! | @@ -15,8 +16,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134788658e+01 -2.6907707565985344e+01 -6.0080860422268874e+00 -2.5620423972099733e+01 -1.3450224059983656e+01 -1.4947288487000705e+00 -global_scalar: 18.340560167414306 + -4.9200116134789653e+01 -2.6907707565986087e+01 -6.0080860422267843e+00 -2.5620423972100063e+01 -1.3450224059983270e+01 -1.4947288486998982e+00 +global_scalar: 18.340560167414335 run_pos: ! |2 1 -2.7993683669226854e-01 2.4726588069312836e+00 -1.7200860244148508e-01 2 3.0197083955402171e-01 2.9515239068888608e+00 -8.5689735572907555e-01 @@ -36,14 +37,14 @@ run_pos: ! |2 16 2.6517554244980301e+00 -2.3957110424978438e+00 3.2908335999177751e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 18 2.1392027588271310e+00 3.0171068018412779e+00 -3.5144628518856349e+00 - 19 1.5366124997074566e+00 2.6286809834111740e+00 -4.2452547844370239e+00 + 19 1.5366124997074584e+00 2.6286809834111722e+00 -4.2452547844370230e+00 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 - 21 4.9036621347791245e+00 -4.0757648442838557e+00 -3.6192617654515900e+00 - 22 4.3655322291888465e+00 -4.2084949965552569e+00 -4.4622011117402334e+00 + 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515900e+00 + 22 4.3655322291888465e+00 -4.2084949965552578e+00 -4.4622011117402343e+00 23 5.7380414793463101e+00 -3.5841969195032686e+00 -3.8827839830470232e+00 24 2.0701314765323913e+00 3.1499370533342308e+00 3.1565324852522920e+00 - 25 1.3030170721374770e+00 3.2711173927682236e+00 2.5081940917429755e+00 - 26 2.5776230782480054e+00 4.0127347068243875e+00 3.2182355138709262e+00 + 25 1.3030170721374779e+00 3.2711173927682236e+00 2.5081940917429755e+00 + 26 2.5776230782480036e+00 4.0127347068243875e+00 3.2182355138709280e+00 27 -1.9613581876744357e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678509e+00 29 -1.3108232656499084e+00 -3.5992986322410765e+00 2.2680459788743512e+00 @@ -65,15 +66,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704681e-04 -3.1032459262907857e-04 8.1043030117346074e-04 - 19 8.5103884665345820e-04 -1.4572280596788108e-03 1.0163621287634073e-03 - 20 -6.5204659278590271e-04 4.3989037444289630e-04 4.9909839028508215e-04 - 21 -1.3888125881903852e-03 -3.1978049143082049e-04 1.1455681499836594e-03 - 22 -1.6084223477729513e-03 -1.5355394240820970e-03 1.4772010826232351e-03 - 23 2.6392672378803975e-04 -3.9375414431174569e-03 -3.6991583139727910e-04 - 24 8.6062827067889835e-04 -9.4179873474469346e-04 5.5396395550012518e-04 - 25 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-1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml index c80a70b428..420e54be25 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:00 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,38 +15,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |2- - 4.3578059172167876e+01 1.7275105166465000e+01 6.7372361276631054e+01 5.1985075049901745e+01 -2.0990677389800993e+01 -7.5321398101844359e+00 -global_scalar: 29.023636440847998 + 4.3578059175768836e+01 1.7275105168781163e+01 6.7372361277896715e+01 5.1985075050485008e+01 -2.0990677388216337e+01 -7.5321398110797180e+00 +global_scalar: 29.023636439584656 run_pos: ! |2 - 1 -6.3472039825517168e-01 3.0113983126282058e+00 -8.8148450172235826e-02 - 2 6.4798884173500326e-02 3.5870486860057795e+00 -9.1146271255434463e-01 - 3 -1.1328967478840362e+00 1.5344674077762583e+00 -6.2949567786977667e-01 - 4 -2.1941320441841130e+00 1.8319737599530370e+00 -1.3824693495474225e+00 - 5 -1.3741175247360697e+00 1.1637763350569887e+00 6.0220861483086097e-01 - 6 5.5368589242158706e-02 3.1209253712244411e-01 -1.4252606627467266e+00 - 7 1.1075313780270069e-01 2.8008314824797154e-02 -2.8425552056438050e+00 - 8 1.1011987966104080e+00 -5.4254536577068713e-01 -6.9472264392660854e-01 - 9 1.3580030945401020e+00 -2.6595138115345840e-01 4.4172536708297194e-01 - 10 2.1282964643831388e+00 -1.6781145595676907e+00 -1.0442216631471304e+00 - 11 1.8571593172391605e+00 -2.3497452731071471e+00 -2.1462323657665392e+00 - 12 3.3117732698469986e+00 -5.4913311816190635e-01 -1.8274356036322548e+00 - 13 4.5640183918453143e+00 -1.0445083545907554e+00 -1.8509716390298214e+00 - 14 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3.8953804330779889e+00 + 25 1.3973696115700545e+00 3.9794119229082359e+00 3.2321313265764022e+00 + 26 2.7018361229436465e+00 4.7379517630364116e+00 3.9583193477161114e+00 + 27 -2.6559803075362858e+00 -5.1969823689084436e+00 2.6552621488559236e+00 + 28 -3.5927802460212725e+00 -4.7943885088607452e+00 2.0214142204098309e+00 + 29 -1.8739632618342856e+00 -4.2877858778718556e+00 2.8450749793922920e+00 run_vel: ! |2 1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04 2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.0094600491564739e-04 -2.4312792027781263e-04 6.5542049134062323e-04 - 19 7.4731683462770076e-04 -1.2894119671278408e-03 8.4327024053533397e-04 - 20 -6.2333686369976551e-04 4.4115361641690044e-04 3.7135656431834220e-04 - 21 -1.1457423793218525e-03 -1.7337748161437940e-04 9.4510018429417686e-04 - 22 -1.3457150581639313e-03 -1.2816797357047471e-03 1.2470992250388096e-03 - 23 3.6277645415306518e-04 -3.4719859048227848e-03 -4.3796817853449118e-04 - 24 7.2410992462873655e-04 -7.6012809744767037e-04 4.3327155128124943e-04 - 25 1.3921349892629666e-03 -1.9207002802664867e-03 -5.7453335109528090e-04 - 26 -1.4901465947638008e-03 4.2012923457099966e-04 2.1578545404178418e-03 + 18 3.0094600492089644e-04 -2.4312792028464785e-04 6.5542049134054972e-04 + 19 7.4731683460624917e-04 -1.2894119671240515e-03 8.4327024053305281e-04 + 20 -6.2333686369944134e-04 4.4115361644063580e-04 3.7135656432041769e-04 + 21 -1.1457423794330429e-03 -1.7337748206069275e-04 9.4510018428907005e-04 + 22 -1.3457150585185161e-03 -1.2816797348700177e-03 1.2470992253076274e-03 + 23 3.6277645495226573e-04 -3.4719859038751704e-03 -4.3796817878355291e-04 + 24 7.2410992459670032e-04 -7.6012809759399148e-04 4.3327155120505761e-04 + 25 1.3921349891892136e-03 -1.9207002802470530e-03 -5.7453335098663809e-04 + 26 -1.4901465945625111e-03 4.2012923513626559e-04 2.1578545406129137e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml index 3894815950..4d16fc12a0 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:00 2024 epsilon: 6.5e-13 skip_tests: prerequisites: ! | @@ -14,38 +15,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |2- - 2.7340318973870396e+01 4.7963870091858283e+00 6.8884396847592512e+01 2.9853310007358935e+01 -1.0857139901347722e+01 -5.1889756561454785e+00 -global_scalar: 9.77678786310451 + 2.7340318979717416e+01 4.7963870104375275e+00 6.8884396847589585e+01 2.9853310005453281e+01 -1.0857139898599751e+01 -5.1889756547311965e+00 +global_scalar: 9.776787862991728 run_pos: ! |2 - 1 -5.1121862036604515e-01 2.8134872171079977e+00 -4.8993015395518924e-02 - 2 1.4735952488047133e-01 3.3535825972277546e+00 -9.3694001270735150e-01 - 3 -9.8023793775378820e-01 1.4277788160410712e+00 -6.3283768722999234e-01 - 4 -1.9793617512974304e+00 1.7069097152779946e+00 -1.4449221382955635e+00 - 5 -1.2073406578712120e+00 1.0799834439081337e+00 6.9555923026692668e-01 - 6 1.3848116183742931e-01 2.8090381873852976e-01 -1.4910727029127884e+00 - 7 1.9062418946016990e-01 1.4366032742456625e-02 -3.0196292835199614e+00 - 8 1.1231015082845541e+00 -5.2094745136401599e-01 -7.0318517336042774e-01 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-3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.1638284997073272e-04 -2.6313163919070405e-04 6.1054395248656961e-04 - 19 7.6494647252307673e-04 -1.3190724749214326e-03 7.9947132612985723e-04 - 20 -6.1620104632513929e-04 4.2577138774295274e-04 3.2526261653548693e-04 - 21 -1.2063428871524097e-03 -2.2879409878999576e-04 8.9132836538734445e-04 - 22 -1.4151473871894464e-03 -1.3502255393198256e-03 1.1972773109437849e-03 - 23 3.1280366109607172e-04 -3.5563936893394407e-03 -4.9548546532774958e-04 - 24 7.5594375541558026e-04 -8.1321043994394464e-04 3.9340911295780739e-04 - 25 1.4373446731689036e-03 -1.9778020567486213e-03 -6.1842201918304478e-04 - 26 -1.4806168650325999e-03 3.7766934274110835e-04 2.1280924225288342e-03 + 18 3.1638284997600319e-04 -2.6313163919763335e-04 6.1054395248685519e-04 + 19 7.6494647250110288e-04 -1.3190724749175438e-03 7.9947132612783736e-04 + 20 -6.1620104632483571e-04 4.2577138776739548e-04 3.2526261653790590e-04 + 21 -1.2063428872614197e-03 -2.2879409923923591e-04 8.9132836537741717e-04 + 22 -1.4151473875545966e-03 -1.3502255384792933e-03 1.1972773112250280e-03 + 23 3.1280366189902534e-04 -3.5563936883846667e-03 -4.9548546556753227e-04 + 24 7.5594375538112746e-04 -8.1321044009394260e-04 3.9340911288157350e-04 + 25 1.4373446730968913e-03 -1.9778020567293151e-03 -6.1842201907436371e-04 + 26 -1.4806168648243687e-03 3.7766934332225264e-04 2.1280924227258073e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml index f5965e53ff..5504ed4686 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:01 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -13,65 +14,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.6326314448663306e+03 -1.4727331978532295e+03 -3.8557370515932275e+03 5.5052891601644615e+02 4.7346742977310657e+02 -6.2035591882122355e+02 -global_scalar: 106.86683072474125 + -1.6326314448662429e+03 -1.4727331978532245e+03 -3.8557370515929042e+03 5.5052891601619581e+02 4.7346742977256520e+02 -6.2035591882208064e+02 +global_scalar: 106.86683072474244 run_pos: ! |2 - 1 -2.6314711410922875e-01 2.4664715027241684e+00 -1.7093568570875561e-01 - 2 3.1632911015968190e-01 2.9434731493852482e+00 -8.5432214735778889e-01 - 3 -6.7623447816593885e-01 1.2410822625695044e+00 -6.1935152269903870e-01 - 4 -1.5552134736906362e+00 1.4878541800991378e+00 -1.2440909745466859e+00 - 5 -8.7601967096402067e-01 9.3417436540572218e-01 4.0272031680440712e-01 - 6 3.0755837780638462e-01 2.2629147986241449e-01 -1.2791162680673960e+00 - 7 3.5322094628053069e-01 -1.0043890952307954e-02 -2.4548503163676365e+00 - 8 1.1736205127907979e+00 -4.8269091330540537e-01 -6.7273784266507608e-01 - 9 1.3865071239751696e+00 -2.5278331076620741e-01 2.6996653369766221e-01 - 10 2.0239883243193546e+00 -1.4252201368162511e+00 -9.6228264545891751e-01 - 11 1.7991233925769246e+00 -1.9828365722517098e+00 -1.8762366544355809e+00 - 12 3.0044710092992837e+00 -4.8928363303895761e-01 -1.6126944183951402e+00 - 13 4.0415308387392486e+00 -9.0061411581930262e-01 -1.6321139880363660e+00 - 14 2.6064005411338655e+00 -4.0859653026870735e-01 -2.6465043951812621e+00 - 15 2.9775904824773907e+00 5.6065407887877150e-01 -1.2391617757503752e+00 - 16 2.6542663248057963e+00 -2.3895844048756363e+00 3.5746598094128501e-02 - 17 2.2355490747046538e+00 -2.0962135127180099e+00 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-7.9980833669012115e-04 -2.0274707260294341e-04 - 13 2.0597404142686670e-04 -1.0865778699535151e-03 -1.1731137935658918e-04 - 14 2.4719215573349161e-04 -1.1410575874168858e-03 -2.0209037936298231e-04 - 15 6.3286464043726845e-04 -6.3068988069288313e-04 -6.5527927471360488e-04 - 16 -4.4100406048953834e-05 8.6869240444187047e-06 6.5198761255923199e-04 - 17 1.3407421346950653e-04 6.0357565278263911e-04 5.6233596575975121e-04 - 18 7.9277804690569076e-04 -1.5618239874425175e-03 2.1367192719678593e-03 - 19 5.6167660797942776e-04 -1.2371794194922848e-03 2.1562222137424714e-03 - 20 1.1137406410123489e-03 -1.8729421751430327e-03 2.1222207985340819e-03 - 21 -2.8426953558137740e-03 -2.9730185469781381e-03 1.8564402246257748e-03 - 22 -2.9480844379790165e-03 -2.6797216173769360e-03 1.8784164631754769e-03 - 23 -2.5997293519674958e-03 -3.3926375081633348e-03 1.8288830284141459e-03 - 24 1.1689404599043950e-03 -1.6701257754515662e-03 2.1428138286394673e-03 - 25 1.2027302640333160e-03 -1.2630861421196525e-03 2.1808987508670514e-03 - 26 1.6116362268906780e-03 -1.9337182438138849e-03 2.1377249582867843e-03 + 1 1.2393084479632162e-03 7.0215195817134601e-04 -1.1910956210642444e-03 + 2 1.3060936199989690e-03 2.5041119719309234e-04 -1.4496302699052684e-03 + 3 8.7069732478170037e-04 6.1866591813752230e-04 -6.2317312592555772e-04 + 4 8.8100215742026918e-04 5.8380213791525335e-04 -6.5145037264832683e-04 + 5 8.7979303398017070e-04 1.1152950208763543e-03 -4.7231382224773813e-04 + 6 5.3965146863306555e-04 6.8643008418797912e-05 -2.7149223435837187e-04 + 7 3.7117679682156736e-04 -4.5322194777208414e-04 -1.7317402888817444e-04 + 8 4.0378854177637320e-04 9.9015358993721983e-05 -4.1783685861266425e-05 + 9 5.4970639315557207e-04 4.5048022318731326e-04 -1.6045108899939207e-04 + 10 1.2521448037938158e-04 -2.5472783650525840e-04 2.9052485920884211e-04 + 11 -1.0599027352512348e-04 -5.9051612835367331e-04 5.5226010155827335e-04 + 12 3.1798607399607243e-04 -7.9980833669034384e-04 -2.0274707260289267e-04 + 13 2.0597404142668038e-04 -1.0865778699538143e-03 -1.1731137935657286e-04 + 14 2.4719215573317579e-04 -1.1410575874171004e-03 -2.0209037936272953e-04 + 15 6.3286464043720871e-04 -6.3068988069325653e-04 -6.5527927471369335e-04 + 16 -4.4100406048914694e-05 8.6869240445997393e-06 6.5198761255915100e-04 + 17 1.3407421346973834e-04 6.0357565278286712e-04 5.6233596575947994e-04 + 18 7.9277804690533363e-04 -1.5618239874416928e-03 2.1367192719678658e-03 + 19 5.6167660797890148e-04 -1.2371794194914493e-03 2.1562222137424727e-03 + 20 1.1137406410120911e-03 -1.8729421751419769e-03 2.1222207985341088e-03 + 21 -2.8426953558134235e-03 -2.9730185469789214e-03 1.8564402246258563e-03 + 22 -2.9480844379788334e-03 -2.6797216173776307e-03 1.8784164631755556e-03 + 23 -2.5997293519669897e-03 -3.3926375081639489e-03 1.8288830284142509e-03 + 24 1.1689404599044329e-03 -1.6701257754517325e-03 2.1428138286393884e-03 + 25 1.2027302640331447e-03 -1.2630861421197028e-03 2.1808987508669616e-03 + 26 1.6116362268908176e-03 -1.9337182438138503e-03 2.1377249582867175e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml index 3b13658e19..d04c58e083 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:01 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -13,38 +14,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -8.7531774769722489e+01 5.5811525017966304e+00 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b/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:02 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,65 +15,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4245356938011610e+03 -1.4496493316650424e+03 -3.6144360982532016e+03 8.4840626794792252e+02 2.0318336802442886e+02 -6.0622397695978805e+02 -global_scalar: 15.711521423178128 + -1.4245356938011316e+03 -1.4496493316650758e+03 -3.6144360982530934e+03 8.4840626794790273e+02 2.0318336802433893e+02 -6.0622397695991208e+02 +global_scalar: 15.711521423178162 run_pos: ! |2 - 1 -2.7899546863905123e-01 2.4731857340327181e+00 -1.7290667740231969e-01 - 2 3.0296221610252227e-01 2.9517129916957194e+00 -8.5798904387756503e-01 - 3 -6.9368802364141247e-01 1.2445115421753310e+00 -6.2281111198650718e-01 - 4 -1.5764879647103560e+00 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3.7774817121242263e-06 2.4035199548835337e-04 + 17 5.7507224523620660e-05 2.2629217444845357e-04 2.0686920072685659e-04 + 18 2.9220264989356375e-04 -6.2478376436786377e-04 8.4222594596602756e-04 + 19 2.0572616567793704e-04 -5.0334424271716611e-04 8.4953929443210886e-04 + 20 4.1224811789511017e-04 -7.4115205415999053e-04 8.3678612337508690e-04 + 21 -1.0671858777656028e-03 -1.1531171045500558e-03 7.3720674900162051e-04 + 22 -1.1066511338291541e-03 -1.0433933757601397e-03 7.4544544325708389e-04 + 23 -9.7629260480935768e-04 -1.3100872491594961e-03 7.2687284219705075e-04 + 24 4.3308126651259366e-04 -6.6527658087323755e-04 8.4451298670663172e-04 + 25 4.4565811905440515e-04 -5.1298436273583775e-04 8.5878867884520984e-04 + 26 5.9865972692024294e-04 -7.6385263287079004e-04 8.4259943226842036e-04 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml index 839ac060a5..0f36c31a95 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:02 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00 -global_scalar: 18.340560167364448 + -4.9200114760030708e+01 -2.6907707699312748e+01 -6.0080872440179061e+00 -2.5620425767600064e+01 -1.3450222535184853e+01 -1.4947348700253382e+00 +global_scalar: 18.340560165889197 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588270928e+00 3.0171068018423082e+00 -3.5144628518853867e+00 - 19 1.5366124996934336e+00 2.6286809834236959e+00 -4.2452547844313493e+00 - 20 2.7628161763597592e+00 3.6842251687468450e+00 -3.9370881219419189e+00 - 21 4.9036621348471368e+00 -4.0757648444604762e+00 -3.6192617654906609e+00 - 22 4.3655322292129357e+00 -4.2084949964269480e+00 -4.4622011117992786e+00 - 23 5.7380414790507261e+00 -3.5841969189265162e+00 -3.8827839828320116e+00 - 24 2.0701314764933532e+00 3.1499370533556008e+00 3.1565324853054118e+00 - 25 1.3030170721038390e+00 3.2711173927738786e+00 2.5081940917867680e+00 - 26 2.5776230784374867e+00 4.0127347067334345e+00 3.2182355136150917e+00 + 18 2.1392027588241729e+00 3.0171068018404634e+00 -3.5144628518858858e+00 + 19 1.5366124996944652e+00 2.6286809834366300e+00 -4.2452547844429631e+00 + 20 2.7628161763703827e+00 3.6842251687412753e+00 -3.9370881219283147e+00 + 21 4.9036621349084646e+00 -4.0757648444931904e+00 -3.6192617654848509e+00 + 22 4.3655322292057255e+00 -4.2084949967079632e+00 -4.4622011117106153e+00 + 23 5.7380414788131207e+00 -3.5841969185149058e+00 -3.8827839829438688e+00 + 24 2.0701314764430685e+00 3.1499370533656190e+00 3.1565324853444698e+00 + 25 1.3030170721374645e+00 3.2711173928413317e+00 2.5081940917372791e+00 + 26 2.5776230786045939e+00 4.0127347066259897e+00 3.2182355135086644e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625094898067e-04 -3.1032459262177040e-04 8.1043030117471950e-04 - 19 8.5103884664914254e-04 -1.4572280597118469e-03 1.0163621287571445e-03 - 20 -6.5204659274939057e-04 4.3989037444674739e-04 4.9909839028631532e-04 - 21 -1.3888125888095134e-03 -3.1978049191290817e-04 1.1455681505629727e-03 - 22 -1.6084223473476296e-03 -1.5355394235202363e-03 1.4772010819351844e-03 - 23 2.6392672583440717e-04 -3.9375414417551127e-03 -3.6991583302200246e-04 - 24 8.6062827046548790e-04 -9.4179873487668705e-04 5.5396395555797203e-04 - 25 1.5933645478462865e-03 -2.2139156628290975e-03 -5.5078029723780941e-04 - 26 -1.5679561736454237e-03 3.5146224433513641e-04 2.4446924193838983e-03 + 18 3.6149625095571725e-04 -3.1032459263052550e-04 8.1043030117473349e-04 + 19 8.5103884662188244e-04 -1.4572280597071525e-03 1.0163621287543638e-03 + 20 -6.5204659274901945e-04 4.3989037447700791e-04 4.9909839028904252e-04 + 21 -1.3888125889514069e-03 -3.1978049248194420e-04 1.1455681505565557e-03 + 22 -1.6084223477996385e-03 -1.5355394224557757e-03 1.4772010822781041e-03 + 23 2.6392672685288674e-04 -3.9375414405480738e-03 -3.6991583333937880e-04 + 24 8.6062827042478370e-04 -9.4179873506334828e-04 5.5396395546095014e-04 + 25 1.5933645477524167e-03 -2.2139156628045932e-03 -5.5078029709943691e-04 + 26 -1.5679561733890424e-03 3.5146224505578228e-04 2.4446924196328459e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml index 854e8b4d45..6a8c54f4a9 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:03 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,26 +15,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3754817467882767e+03 -1.4228425246441275e+03 -3.6087196200592489e+03 8.7407043142559303e+02 2.1665316510426268e+02 -6.0480791467747542e+02 -global_scalar: 4.531423038570333 + -1.3754817467882813e+03 -1.4228425246442055e+03 -3.6087196200592184e+03 8.7407043142559792e+02 2.1665316510417179e+02 -6.0480791467761571e+02 +global_scalar: 4.531423038570381 run_pos: ! |2 - 1 -2.7899546859706881e-01 2.4731857340427750e+00 -1.7290667720866193e-01 - 2 3.0296221616781649e-01 2.9517129917211218e+00 -8.5798904365338713e-01 - 3 -6.9368802362172777e-01 1.2445115422148878e+00 -6.2281111185285920e-01 - 4 -1.5764879646739900e+00 1.4919714416721197e+00 -1.2492069413381908e+00 - 5 -8.9434512967965252e-01 9.3651699743522254e-01 4.0191726569953845e-01 - 6 2.9454439635066831e-01 2.2724545796942719e-01 -1.2845195052894431e+00 - 7 3.4049112905319934e-01 -9.4655677384814507e-03 -2.4634480019885556e+00 - 8 1.1644354555589707e+00 -4.8367776651303718e-01 -6.7663643931662931e-01 - 9 1.3781717822376129e+00 -2.5332509534954067e-01 2.6864954447021949e-01 - 10 2.0186368605646337e+00 -1.4285861423742481e+00 -9.6712491246329535e-01 - 11 1.7929137227202196e+00 -1.9875455388073511e+00 -1.8836565351901273e+00 - 12 3.0032775230343667e+00 -4.8983022415922672e-01 -1.6190248016125368e+00 - 13 4.0448964161972993e+00 -9.0213155125590028e-01 -1.6385398398261621e+00 - 14 2.6035151245156412e+00 -4.0874995488520105e-01 -2.6555999073601511e+00 - 15 2.9761196776308623e+00 5.6287237451808192e-01 -1.2442626194415292e+00 - 16 2.6517373020764632e+00 -2.3957035509096389e+00 3.3389262134244646e-02 - 17 2.2311114923824555e+00 -2.1018393229880719e+00 1.1496088522768189e+00 + 1 -2.7899546859705771e-01 2.4731857340428069e+00 -1.7290667720877784e-01 + 2 3.0296221616781072e-01 2.9517129917211151e+00 -8.5798904365354312e-01 + 3 -6.9368802362172532e-01 1.2445115422148945e+00 -6.2281111185289584e-01 + 4 -1.5764879646740031e+00 1.4919714416720897e+00 -1.2492069413382207e+00 + 5 -8.9434512967962521e-01 9.3651699743528616e-01 4.0191726569952280e-01 + 6 2.9454439635065666e-01 2.2724545796939852e-01 -1.2845195052894454e+00 + 7 3.4049112905316026e-01 -9.4655677385761805e-03 -2.4634480019885459e+00 + 8 1.1644354555589742e+00 -4.8367776651303018e-01 -6.7663643931661244e-01 + 9 1.3781717822376380e+00 -2.5332509534948033e-01 2.6864954447021760e-01 + 10 2.0186368605646310e+00 -1.4285861423742554e+00 -9.6712491246324517e-01 + 11 1.7929137227201968e+00 -1.9875455388074099e+00 -1.8836565351900401e+00 + 12 3.0032775230343471e+00 -4.8983022415926980e-01 -1.6190248016125621e+00 + 13 4.0448964161972807e+00 -9.0213155125594269e-01 -1.6385398398261892e+00 + 14 2.6035151245155976e+00 -4.0874995488530264e-01 -2.6555999073601715e+00 + 15 2.9761196776308503e+00 5.6287237451805949e-01 -1.2442626194416131e+00 + 16 2.6517373020764849e+00 -2.3957035509095892e+00 3.3389262134333686e-02 + 17 2.2311114923825035e+00 -2.1018393229879604e+00 1.1496088522769004e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -47,23 +48,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093296226164550e-04 2.6351124312060223e-04 -4.4905063547613568e-04 - 2 4.9594635271876775e-04 9.4561409237174846e-05 -5.4581325723053790e-04 - 3 3.3306088119081919e-04 2.3224949911015709e-04 -2.3659435306899653e-04 - 4 3.3692332940285361e-04 2.1926824120528752e-04 -2.4716611858555457e-04 - 5 3.3642541894622217e-04 4.1797578053944250e-04 -1.8011323945926332e-04 - 6 2.0926870695908031e-04 2.6449376032433555e-05 -1.0508922741401509e-04 - 7 1.4629046128363305e-04 -1.6873362379725323e-04 -6.8353900724087087e-05 - 8 1.5844098346817862e-04 3.7728756087615553e-05 -1.9162577392847385e-05 - 9 2.1299357198252531e-04 1.6917133003967874e-04 -6.3528006071188683e-05 - 10 5.4261569071251603e-05 -9.4655546204709643e-05 1.0511372702289179e-04 - 11 -3.2194218121513917e-05 -2.2025090185605342e-04 2.0300208519291412e-04 - 12 1.2640585449265036e-04 -2.9851081600945991e-04 -7.9476186245599681e-05 - 13 8.4523551795123310e-05 -4.0583140303606936e-04 -4.7550925831962545e-05 - 14 9.9954071734181717e-05 -4.2610809338914382e-04 -7.9255453072696249e-05 - 15 2.4417483202631243e-04 -2.3521005781666407e-04 -2.4875292755154228e-04 - 16 -9.0959360838797421e-06 3.7773746063106756e-06 2.4035204669042973e-04 - 17 5.7507084250803101e-05 2.2629200960629499e-04 2.0686926033796699e-04 + 1 4.7093296226165618e-04 2.6351124312058857e-04 -4.4905063547614403e-04 + 2 4.9594635271877252e-04 9.4561409237151983e-05 -5.4581325723054321e-04 + 3 3.3306088119082413e-04 2.3224949911015692e-04 -2.3659435306899455e-04 + 4 3.3692332940285378e-04 2.1926824120529077e-04 -2.4716611858554389e-04 + 5 3.3642541894623611e-04 4.1797578053944765e-04 -1.8011323945926958e-04 + 6 2.0926870695907706e-04 2.6449376032434591e-05 -1.0508922741400673e-04 + 7 1.4629046128361865e-04 -1.6873362379725188e-04 -6.8353900724066446e-05 + 8 1.5844098346817927e-04 3.7728756087617390e-05 -1.9162577392845779e-05 + 9 2.1299357198253474e-04 1.6917133003967807e-04 -6.3528006071197993e-05 + 10 5.4261569071247645e-05 -9.4655546204705848e-05 1.0511372702289633e-04 + 11 -3.2194218121526927e-05 -2.2025090185604412e-04 2.0300208519293052e-04 + 12 1.2640585449264128e-04 -2.9851081600947238e-04 -7.9476186245595616e-05 + 13 8.4523551795112752e-05 -4.0583140303608579e-04 -4.7550925831960783e-05 + 14 9.9954071734163598e-05 -4.2610809338915548e-04 -7.9255453072680826e-05 + 15 2.4417483202630842e-04 -2.3521005781668527e-04 -2.4875292755154548e-04 + 16 -9.0959360838764895e-06 3.7773746063197473e-06 2.4035204669042547e-04 + 17 5.7507084250817169e-05 2.2629200960630572e-04 2.0686926033795233e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml index 664921b147..7b702a4f2a 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:03 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00 -global_scalar: 0.5007318719663203 + -4.9200114760030708e+01 -2.6907707699312748e+01 -6.0080872440179061e+00 -2.5620425767600064e+01 -1.3450222535184853e+01 -1.4947348700253382e+00 +global_scalar: 0.5007318719399354 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588270928e+00 3.0171068018423082e+00 -3.5144628518853867e+00 - 19 1.5366124996934336e+00 2.6286809834236959e+00 -4.2452547844313493e+00 - 20 2.7628161763597592e+00 3.6842251687468450e+00 -3.9370881219419189e+00 - 21 4.9036621348471368e+00 -4.0757648444604762e+00 -3.6192617654906609e+00 - 22 4.3655322292129357e+00 -4.2084949964269480e+00 -4.4622011117992786e+00 - 23 5.7380414790507261e+00 -3.5841969189265162e+00 -3.8827839828320116e+00 - 24 2.0701314764933532e+00 3.1499370533556008e+00 3.1565324853054118e+00 - 25 1.3030170721038390e+00 3.2711173927738786e+00 2.5081940917867680e+00 - 26 2.5776230784374867e+00 4.0127347067334345e+00 3.2182355136150917e+00 + 18 2.1392027588241729e+00 3.0171068018404634e+00 -3.5144628518858858e+00 + 19 1.5366124996944652e+00 2.6286809834366300e+00 -4.2452547844429631e+00 + 20 2.7628161763703827e+00 3.6842251687412753e+00 -3.9370881219283147e+00 + 21 4.9036621349084646e+00 -4.0757648444931904e+00 -3.6192617654848509e+00 + 22 4.3655322292057255e+00 -4.2084949967079632e+00 -4.4622011117106153e+00 + 23 5.7380414788131207e+00 -3.5841969185149058e+00 -3.8827839829438688e+00 + 24 2.0701314764430685e+00 3.1499370533656190e+00 3.1565324853444698e+00 + 25 1.3030170721374645e+00 3.2711173928413317e+00 2.5081940917372791e+00 + 26 2.5776230786045939e+00 4.0127347066259897e+00 3.2182355135086644e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625094898067e-04 -3.1032459262177040e-04 8.1043030117471950e-04 - 19 8.5103884664914254e-04 -1.4572280597118469e-03 1.0163621287571445e-03 - 20 -6.5204659274939057e-04 4.3989037444674739e-04 4.9909839028631532e-04 - 21 -1.3888125888095134e-03 -3.1978049191290817e-04 1.1455681505629727e-03 - 22 -1.6084223473476296e-03 -1.5355394235202363e-03 1.4772010819351844e-03 - 23 2.6392672583440717e-04 -3.9375414417551127e-03 -3.6991583302200246e-04 - 24 8.6062827046548790e-04 -9.4179873487668705e-04 5.5396395555797203e-04 - 25 1.5933645478462865e-03 -2.2139156628290975e-03 -5.5078029723780941e-04 - 26 -1.5679561736454237e-03 3.5146224433513641e-04 2.4446924193838983e-03 + 18 3.6149625095571725e-04 -3.1032459263052550e-04 8.1043030117473349e-04 + 19 8.5103884662188244e-04 -1.4572280597071525e-03 1.0163621287543638e-03 + 20 -6.5204659274901945e-04 4.3989037447700791e-04 4.9909839028904252e-04 + 21 -1.3888125889514069e-03 -3.1978049248194420e-04 1.1455681505565557e-03 + 22 -1.6084223477996385e-03 -1.5355394224557757e-03 1.4772010822781041e-03 + 23 2.6392672685288674e-04 -3.9375414405480738e-03 -3.6991583333937880e-04 + 24 8.6062827042478370e-04 -9.4179873506334828e-04 5.5396395546095014e-04 + 25 1.5933645477524167e-03 -2.2139156628045932e-03 -5.5078029709943691e-04 + 26 -1.5679561733890424e-03 3.5146224505578228e-04 2.4446924196328459e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml index a49508ca15..b8ec6036a3 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml @@ -1,7 +1,8 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 -epsilon: 5e-13 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:03 2024 +epsilon: 1e-12 skip_tests: prerequisites: ! | atom full @@ -13,26 +14,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3123962047757550e+03 -1.3675423591710460e+03 -3.5468492999583855e+03 7.8271738572396373e+02 2.6480486115495069e+02 -7.6950536863736306e+02 -global_scalar: 68.08659647423171 + -1.3123962047758187e+03 -1.3675423591720764e+03 -3.5468492999580299e+03 7.8271738572394452e+02 2.6480486115379637e+02 -7.6950536863892899e+02 +global_scalar: 68.08659647424867 run_pos: ! |2 - 1 -2.7802951913990959e-01 2.4737132264311215e+00 -1.7381271738602289e-01 - 2 3.0397800832473609e-01 2.9519031941431444e+00 -8.5908822750267100e-01 - 3 -6.9299720296404743e-01 1.2449766685866726e+00 -6.2329294828335358e-01 - 4 -1.5757894675975461e+00 1.4924105480974301e+00 -1.2497098747240374e+00 - 5 -8.9364750934418624e-01 9.3735293261000852e-01 4.0154813851989335e-01 - 6 2.9498813449175199e-01 2.2729986882976547e-01 -1.2847387164260673e+00 - 7 3.4080910885027837e-01 -9.8008218359699473e-03 -2.4635938021179546e+00 - 8 1.1647778042705452e+00 -4.8360070140706557e-01 -6.7668409924218165e-01 - 9 1.3786230528159027e+00 -2.5298559880150862e-01 2.6851325883861188e-01 - 10 2.0187712935465942e+00 -1.4287732348422091e+00 -9.6692440387148870e-01 - 11 1.7928755785831587e+00 -1.9879833661313322e+00 -1.8832605388690278e+00 - 12 3.0035558347419657e+00 -4.9042429038271507e-01 -1.6191927838346238e+00 - 13 4.0450911337530959e+00 -9.0293975523160919e-01 -1.6386440514135796e+00 - 14 2.6037405819194577e+00 -4.0959881564101863e-01 -2.6557674031621108e+00 - 15 2.9766330093335447e+00 5.6240461100771322e-01 -1.2447686007433758e+00 - 16 2.6517453810147344e+00 -2.3956939898026426e+00 3.3859750042781744e-02 - 17 2.2312525656149020e+00 -2.1013855689264771e+00 1.1500124166835219e+00 + 1 -2.7802951913978302e-01 2.4737132264315886e+00 -1.7381271738770820e-01 + 2 3.0397800832462774e-01 2.9519031941430738e+00 -8.5908822750493219e-01 + 3 -6.9299720296403144e-01 1.2449766685867643e+00 -6.2329294828390935e-01 + 4 -1.5757894675977402e+00 1.4924105480969891e+00 -1.2497098747245081e+00 + 5 -8.9364750934382919e-01 9.3735293261092456e-01 4.0154813851965188e-01 + 6 2.9498813449158368e-01 2.2729986882934847e-01 -1.2847387164261186e+00 + 7 3.4080910884973536e-01 -9.8008218373410172e-03 -2.4635938021178290e+00 + 8 1.1647778042705941e+00 -4.8360070140696521e-01 -6.7668409924193851e-01 + 9 1.3786230528162504e+00 -2.5298559880063631e-01 2.6851325883859889e-01 + 10 2.0187712935465760e+00 -1.4287732348423197e+00 -9.6692440387075651e-01 + 11 1.7928755785828601e+00 -1.9879833661321924e+00 -1.8832605388677695e+00 + 12 3.0035558347417104e+00 -4.9042429038332558e-01 -1.6191927838349707e+00 + 13 4.0450911337528455e+00 -9.0293975523220671e-01 -1.6386440514139291e+00 + 14 2.6037405819188639e+00 -4.0959881564248080e-01 -2.6557674031623937e+00 + 15 2.9766330093333795e+00 5.6240461100740513e-01 -1.2447686007445669e+00 + 16 2.6517453810150675e+00 -2.3956939898019254e+00 3.3859750044092363e-02 + 17 2.2312525656155877e+00 -2.1013855689248668e+00 1.1500124166847305e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -46,23 +47,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 1.8443993556501188e-03 1.0121779580014884e-03 -1.7361326034900006e-03 - 2 1.9401022924558343e-03 3.6428754787592733e-04 -2.1069540627804634e-03 - 3 1.3158623602983108e-03 8.9265747656461540e-04 -9.2144725682164657e-04 - 4 1.3306255280096089e-03 8.4281508655990054e-04 -9.6194026572564146e-04 - 5 1.3289682243410692e-03 1.6048237018834067e-03 -7.0511232123071470e-04 - 6 8.4113718611833661e-04 1.0389683283144290e-04 -4.1697370456873913e-04 - 7 5.9950574545626287e-04 -6.4437674895215604e-04 -2.7586696717582678e-04 - 8 6.4634547270651834e-04 1.4734228826522431e-04 -8.7540766366730972e-05 - 9 8.5561404484505246e-04 6.5123532540338036e-04 -2.5782947158524498e-04 - 10 2.4688038968480818e-04 -3.5995975344065565e-04 3.8912416843275122e-04 - 11 -8.4672359473208624e-05 -8.4134349031640394e-04 7.6463157764214873e-04 - 12 5.2321633256319569e-04 -1.1418047427480882e-03 -3.1842516233562688e-04 - 13 3.6258187754908603e-04 -1.5531581259494627e-03 -1.9590476904013767e-04 - 14 4.2166181631324117e-04 -1.6310415916630540e-03 -3.1740232809360453e-04 - 15 9.7471807923383321e-04 -8.9939841790992827e-04 -9.6757308853409824e-04 - 16 4.1534888649229478e-06 1.7705740202856454e-05 9.0753010117813394e-04 - 17 2.5969943716026096e-04 8.7075266710270492e-04 7.7887058799645239e-04 + 1 1.8443993556507550e-03 1.0121779580008364e-03 -1.7361326034906117e-03 + 2 1.9401022924561704e-03 3.6428754787474148e-04 -2.1069540627809144e-03 + 3 1.3158623602986111e-03 8.9265747656469769e-04 -9.2144725682167822e-04 + 4 1.3306255280096579e-03 8.4281508656016844e-04 -9.6194026572521364e-04 + 5 1.3289682243418409e-03 1.6048237018838117e-03 -7.0511232123120064e-04 + 6 8.4113718611817723e-04 1.0389683283156166e-04 -4.1697370456838980e-04 + 7 5.9950574545550414e-04 -6.4437674895204296e-04 -2.7586696717479603e-04 + 8 6.4634547270655271e-04 1.4734228826538870e-04 -8.7540766366732192e-05 + 9 8.5561404484556399e-04 6.5123532540342654e-04 -2.5782947158584915e-04 + 10 2.4688038968457540e-04 -3.5995975344040265e-04 3.8912416843293944e-04 + 11 -8.4672359473939376e-05 -8.4134349031586390e-04 7.6463157764299549e-04 + 12 5.2321633256271539e-04 -1.1418047427487572e-03 -3.1842516233546950e-04 + 13 3.6258187754852045e-04 -1.5531581259503574e-03 -1.9590476904008422e-04 + 14 4.2166181631227780e-04 -1.6310415916636891e-03 -3.1740232809282303e-04 + 15 9.7471807923364706e-04 -8.9939841791107037e-04 -9.6757308853435780e-04 + 16 4.1534888650543531e-06 1.7705740203412426e-05 9.0753010117785768e-04 + 17 2.5969943716097897e-04 8.7075266710338634e-04 7.7887058799558893e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml index 6068993094..deeee40b52 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:04 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -13,8 +14,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4827261116680472e+02 -1.8411194349753309e+01 -1.0752762859308649e+02 -2.1814511477016276e+02 1.7027764307147623e+02 2.1058942244057214e+01 -global_scalar: 0.9532609554739606 + -1.4827261099624999e+02 -1.8411194282828326e+01 -1.0752762861573947e+02 -2.1814511471949461e+02 1.7027764305079162e+02 2.1058942246396320e+01 +global_scalar: 0.9532609552151339 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -33,15 +34,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1395635672981443e+00 3.0168023048492310e+00 -3.5136606977867388e+00 - 19 1.5374727853253387e+00 2.6272080572819609e+00 -4.2442423140467360e+00 - 20 2.7621434607990372e+00 3.6846842324743214e+00 -3.9366036441030396e+00 - 21 4.9022821625125470e+00 -4.0760572704380627e+00 -3.6181235130909242e+00 - 22 4.3639257458824501e+00 -4.2100277325126187e+00 -4.4607219430080747e+00 - 23 5.7383384133351401e+00 -3.5881799317362106e+00 -3.8831848688588710e+00 - 24 2.0709922902331592e+00 3.1490053461169678e+00 3.1570777020268803e+00 - 25 1.3046262534530633e+00 3.2688902575528282e+00 2.5076144141701078e+00 - 26 2.5760050685080813e+00 4.0131166912605272e+00 3.2207051913215210e+00 + 18 2.1395635672857165e+00 3.0168023048413781e+00 -3.5136606977888540e+00 + 19 1.5374727853296883e+00 2.6272080573369379e+00 -4.2442423140961818e+00 + 20 2.7621434608442974e+00 3.6846842324506923e+00 -3.9366036440451500e+00 + 21 4.9022821627727593e+00 -4.0760572705753884e+00 -3.6181235130648650e+00 + 22 4.3639257458473608e+00 -4.2100277337137149e+00 -4.4607219426242057e+00 + 23 5.7383384123314833e+00 -3.5881799299869201e+00 -3.8831848693467652e+00 + 24 2.0709922900187268e+00 3.1490053461587983e+00 3.1570777021928031e+00 + 25 1.3046262535950772e+00 3.2688902578410239e+00 2.5076144139609013e+00 + 26 2.5760050692220648e+00 4.0131166908053464e+00 3.2207051908683750e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -63,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 7.8522439440007537e-04 -6.6826115062653757e-04 1.7528441282153480e-03 - 19 1.8628941719211862e-03 -3.1840047051916367e-03 2.2062694140207390e-03 - 20 -1.4430972531298200e-03 9.7564145841628493e-04 1.0686492192569898e-03 - 21 -3.0047717246574385e-03 -6.6139343888744974e-04 2.4784169377340712e-03 - 22 -3.4980341571643784e-03 -3.3380963325931002e-03 3.2191613979274040e-03 - 23 5.9333930569297746e-04 -8.6231086219834968e-03 -8.2692040355627789e-04 - 24 1.8727912311097641e-03 -2.0349136820274911e-03 1.1951471753018509e-03 - 25 3.4887365958745920e-03 -4.8232966889391266e-03 -1.2263764490291313e-03 - 26 -3.4770258010749858e-03 7.8662050223200905e-04 5.3381090661352298e-03 + 18 7.8522439447394326e-04 -6.6826115070004464e-04 1.7528441282176825e-03 + 19 1.8628941717384645e-03 -3.1840047052822556e-03 2.2062694140226819e-03 + 20 -1.4430972532419690e-03 9.7564145880034414e-04 1.0686492192457362e-03 + 21 -3.0047717260078453e-03 -6.6139344410253201e-04 2.4784169376928207e-03 + 22 -3.4980341614361554e-03 -3.3380963226435131e-03 3.2191614012082861e-03 + 23 5.9333931535562748e-04 -8.6231086111150188e-03 -8.2692040667271425e-04 + 24 1.8727912307694413e-03 -2.0349136837727452e-03 1.1951471743788897e-03 + 25 3.4887365951187166e-03 -4.8232966888750181e-03 -1.2263764478999317e-03 + 26 -3.4770257989604671e-03 7.8662050913487318e-04 5.3381090686904524e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml index 02acb437d9..a8087adef5 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:04 2024 epsilon: 7.5e-13 skip_tests: prerequisites: ! | @@ -14,26 +15,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3754817466835989e+03 -1.4228425246166137e+03 -3.6087196201914348e+03 8.7407043149698916e+02 2.1665316519769885e+02 -6.0480791462033073e+02 -global_scalar: 4.531423038570297 + -1.3754817466835991e+03 -1.4228425246166084e+03 -3.6087196201914162e+03 8.7407043149699155e+02 2.1665316519769920e+02 -6.0480791462032153e+02 +global_scalar: 4.531423038570312 run_pos: ! |2 - 1 -2.7899546859693136e-01 2.4731857340428784e+00 -1.7290667720876285e-01 - 2 3.0296221616793728e-01 2.9517129917211546e+00 -8.5798904365355155e-01 - 3 -6.9368802362166204e-01 1.2445115422149751e+00 -6.2281111185285498e-01 - 4 -1.5764879646739487e+00 1.4919714416722010e+00 -1.2492069413381564e+00 - 5 -8.9434512967954416e-01 9.3651699743538730e-01 4.0191726569957442e-01 - 6 2.9454439635065910e-01 2.2724545796943096e-01 -1.2845195052894232e+00 - 7 3.4049112905311751e-01 -9.4655677385591108e-03 -2.4634480019885228e+00 - 8 1.1644354555589662e+00 -4.8367776651302724e-01 -6.7663643931660777e-01 - 9 1.3781717822376680e+00 -2.5332509534947545e-01 2.6864954447021416e-01 - 10 2.0186368605645764e+00 -1.4285861423742918e+00 -9.6712491246325605e-01 - 11 1.7929137227200918e+00 -1.9875455388074483e+00 -1.8836565351900385e+00 - 12 3.0032775230343125e+00 -4.8983022415935312e-01 -1.6190248016126132e+00 - 13 4.0448964161972283e+00 -9.0213155125606947e-01 -1.6385398398262669e+00 - 14 2.6035151245155355e+00 -4.0874995488538129e-01 -2.6555999073602123e+00 - 15 2.9761196776308694e+00 5.6287237451798222e-01 -1.2442626194416753e+00 - 16 2.6517373020764219e+00 -2.3957035509096407e+00 3.3389262134315700e-02 - 17 2.2311114923824857e+00 -2.1018393229879817e+00 1.1496088522768926e+00 + 1 -2.7899546859693225e-01 2.4731857340428771e+00 -1.7290667720876018e-01 + 2 3.0296221616793617e-01 2.9517129917211538e+00 -8.5798904365354822e-01 + 3 -6.9368802362166271e-01 1.2445115422149740e+00 -6.2281111185285387e-01 + 4 -1.5764879646739496e+00 1.4919714416722003e+00 -1.2492069413381550e+00 + 5 -8.9434512967954460e-01 9.3651699743538508e-01 4.0191726569957453e-01 + 6 2.9454439635065910e-01 2.2724545796943096e-01 -1.2845195052894227e+00 + 7 3.4049112905311785e-01 -9.4655677385578896e-03 -2.4634480019885232e+00 + 8 1.1644354555589664e+00 -4.8367776651302741e-01 -6.7663643931660822e-01 + 9 1.3781717822376678e+00 -2.5332509534947639e-01 2.6864954447021405e-01 + 10 2.0186368605645768e+00 -1.4285861423742912e+00 -9.6712491246325705e-01 + 11 1.7929137227200933e+00 -1.9875455388074468e+00 -1.8836565351900401e+00 + 12 3.0032775230343129e+00 -4.8983022415935129e-01 -1.6190248016126136e+00 + 13 4.0448964161972292e+00 -9.0213155125606781e-01 -1.6385398398262672e+00 + 14 2.6035151245155359e+00 -4.0874995488537874e-01 -2.6555999073602123e+00 + 15 2.9761196776308694e+00 5.6287237451798344e-01 -1.2442626194416739e+00 + 16 2.6517373020764223e+00 -2.3957035509096416e+00 3.3389262134313369e-02 + 17 2.2311114923824853e+00 -2.1018393229879830e+00 1.1496088522768906e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -47,23 +48,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093296226165759e-04 2.6351124312057290e-04 -4.4905063547614669e-04 - 2 4.9594635271877263e-04 9.4561409237138512e-05 -5.4581325723053421e-04 - 3 3.3306088119083101e-04 2.3224949911015481e-04 -2.3659435306900835e-04 - 4 3.3692332940286717e-04 2.1926824120529722e-04 -2.4716611858556465e-04 - 5 3.3642541894624077e-04 4.1797578053943724e-04 -1.8011323945929064e-04 - 6 2.0926870695908283e-04 2.6449376032441855e-05 -1.0508922741401397e-04 - 7 1.4629046128362884e-04 -1.6873362379723068e-04 -6.8353900724071325e-05 - 8 1.5844098346817943e-04 3.7728756087619084e-05 -1.9162577392849316e-05 - 9 2.1299357198253002e-04 1.6917133003966749e-04 -6.3528006071200284e-05 - 10 5.4261569071245856e-05 -9.4655546204698666e-05 1.0511372702289738e-04 - 11 -3.2194218121523431e-05 -2.2025090185602293e-04 2.0300208519292805e-04 - 12 1.2640585449263546e-04 -2.9851081600946745e-04 -7.9476186245575585e-05 - 13 8.4523551795102263e-05 -4.0583140303608199e-04 -4.7550925831931374e-05 - 14 9.9954071734163435e-05 -4.2610809338913835e-04 -7.9255453072661880e-05 - 15 2.4417483202629980e-04 -2.3521005781669047e-04 -2.4875292755152005e-04 - 16 -9.0959360838836724e-06 3.7773746063194780e-06 2.4035204669042463e-04 - 17 5.7507084250807628e-05 2.2629200960629336e-04 2.0686926033794547e-04 + 1 4.7093296226165726e-04 2.6351124312057366e-04 -4.4905063547614750e-04 + 2 4.9594635271877263e-04 9.4561409237139244e-05 -5.4581325723053519e-04 + 3 3.3306088119083079e-04 2.3224949911015511e-04 -2.3659435306900900e-04 + 4 3.3692332940286722e-04 2.1926824120529738e-04 -2.4716611858556574e-04 + 5 3.3642541894624012e-04 4.1797578053943767e-04 -1.8011323945929113e-04 + 6 2.0926870695908297e-04 2.6449376032441903e-05 -1.0508922741401427e-04 + 7 1.4629046128362941e-04 -1.6873362379723111e-04 -6.8353900724071745e-05 + 8 1.5844098346817935e-04 3.7728756087619165e-05 -1.9162577392849147e-05 + 9 2.1299357198252962e-04 1.6917133003966793e-04 -6.3528006071199972e-05 + 10 5.4261569071245965e-05 -9.4655546204698774e-05 1.0511372702289789e-04 + 11 -3.2194218121522970e-05 -2.2025090185602350e-04 2.0300208519292848e-04 + 12 1.2640585449263589e-04 -2.9851081600946756e-04 -7.9476186245575178e-05 + 13 8.4523551795102697e-05 -4.0583140303608210e-04 -4.7550925831930561e-05 + 14 9.9954071734164248e-05 -4.2610809338913878e-04 -7.9255453072661758e-05 + 15 2.4417483202630007e-04 -2.3521005781669015e-04 -2.4875292755151984e-04 + 16 -9.0959360838839976e-06 3.7773746063194848e-06 2.4035204669042588e-04 + 17 5.7507084250806896e-05 2.2629200960629374e-04 2.0686926033794661e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml index 92754f85f5..0eae9f7559 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Mon Mar 25 20:01:05 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00 -global_scalar: 18.3405601674144 + -4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00 +global_scalar: 18.340560167414402 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588271301e+00 3.0171068018412779e+00 -3.5144628518856349e+00 - 19 1.5366124997074571e+00 2.6286809834111748e+00 -4.2452547844370221e+00 - 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352554e+00 - 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515904e+00 - 22 4.3655322291888483e+00 -4.2084949965552561e+00 -4.4622011117402334e+00 - 23 5.7380414793463101e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 + 18 2.1392027588271301e+00 3.0171068018412783e+00 -3.5144628518856353e+00 + 19 1.5366124997074575e+00 2.6286809834111740e+00 -4.2452547844370221e+00 + 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 + 21 4.9036621347791236e+00 -4.0757648442838548e+00 -3.6192617654515908e+00 + 22 4.3655322291888474e+00 -4.2084949965552561e+00 -4.4622011117402343e+00 + 23 5.7380414793463110e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 24 2.0701314765323930e+00 3.1499370533342330e+00 3.1565324852522938e+00 - 25 1.3030170721374779e+00 3.2711173927682249e+00 2.5081940917429768e+00 - 26 2.5776230782480045e+00 4.0127347068243875e+00 3.2182355138709275e+00 + 25 1.3030170721374787e+00 3.2711173927682244e+00 2.5081940917429759e+00 + 26 2.5776230782480041e+00 4.0127347068243884e+00 3.2182355138709284e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704914e-04 -3.1032459262908286e-04 8.1043030117346052e-04 - 19 8.5103884665345452e-04 -1.4572280596788108e-03 1.0163621287634116e-03 - 20 -6.5204659278590683e-04 4.3989037444289853e-04 4.9909839028507901e-04 - 21 -1.3888125881903923e-03 -3.1978049143082385e-04 1.1455681499836646e-03 - 22 -1.6084223477729510e-03 -1.5355394240821117e-03 1.4772010826232375e-03 - 23 2.6392672378805124e-04 -3.9375414431174821e-03 -3.6991583139728095e-04 - 24 8.6062827067890247e-04 -9.4179873474469237e-04 5.5396395550012453e-04 - 25 1.5933645477487538e-03 -2.2139156625681695e-03 -5.5078029695647401e-04 - 26 -1.5679561743998840e-03 3.5146224354726100e-04 2.4446924193334478e-03 + 18 3.6149625095704849e-04 -3.1032459262908286e-04 8.1043030117346052e-04 + 19 8.5103884665345473e-04 -1.4572280596788095e-03 1.0163621287634121e-03 + 20 -6.5204659278590661e-04 4.3989037444289755e-04 4.9909839028507901e-04 + 21 -1.3888125881903906e-03 -3.1978049143082342e-04 1.1455681499836646e-03 + 22 -1.6084223477729526e-03 -1.5355394240821163e-03 1.4772010826232394e-03 + 23 2.6392672378804821e-04 -3.9375414431174795e-03 -3.6991583139728377e-04 + 24 8.6062827067890269e-04 -9.4179873474469291e-04 5.5396395550012388e-04 + 25 1.5933645477487551e-03 -2.2139156625681673e-03 -5.5078029695647250e-04 + 26 -1.5679561743998888e-03 3.5146224354726068e-04 2.4446924193334487e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index 1da2dfa33c..15ce3ae605 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -1922,70 +1922,58 @@ TEST_F(AtomStyleTest, tri) EXPECT_NEAR(radius[GETIDX(5)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(6)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 13.982119044342252, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 13.982119044342252, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 13.945895752275419, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 0.10811427523057447, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 0.10811427523057447, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 0.23541253382609079, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 19.018309360029388, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 19.018309360029388, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 18.948744087979012, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 0.36886008861549813, EPSILON); - EXPECT_NEAR(bonus[0].quat[0], 0.66466395261228639, EPSILON); - EXPECT_NEAR(bonus[0].quat[1], -0.26579965871355399, EPSILON); - EXPECT_NEAR(bonus[0].quat[2], -0.64169714094040209, EPSILON); - EXPECT_NEAR(bonus[0].quat[3], -0.27531282359251713, EPSILON); - EXPECT_NEAR(bonus[1].quat[0], 0.63718542087921404, EPSILON); - EXPECT_NEAR(bonus[1].quat[1], 0.66984067651944412, EPSILON); - EXPECT_NEAR(bonus[1].quat[2], -0.26272786480888066, EPSILON); - EXPECT_NEAR(bonus[1].quat[3], -0.27619246288035992, EPSILON); - EXPECT_NEAR(bonus[2].quat[0], 0.70865471105868871, EPSILON); - EXPECT_NEAR(bonus[2].quat[1], 0.40297854431552654, EPSILON); - EXPECT_NEAR(bonus[2].quat[2], -0.56684324752832238, EPSILON); - EXPECT_NEAR(bonus[2].quat[3], 0.11876668744732566, EPSILON); - EXPECT_NEAR(bonus[3].quat[0], 0.55997606330452898, EPSILON); - EXPECT_NEAR(bonus[3].quat[1], 0.69182747953492685, EPSILON); - EXPECT_NEAR(bonus[3].quat[2], 0.072026021657128514, EPSILON); - EXPECT_NEAR(bonus[3].quat[3], 0.45012642589672475, EPSILON); - EXPECT_NEAR(bonus[0].c1[0], -0.0052525338293288905, EPSILON); - EXPECT_NEAR(bonus[0].c1[1], -0.55767753582520529, EPSILON); - EXPECT_NEAR(bonus[0].c1[2], 0.14933690186163631, EPSILON); - EXPECT_NEAR(bonus[1].c1[0], 0.18561232929671426, EPSILON); - EXPECT_NEAR(bonus[1].c1[1], 0.51379191773154387, EPSILON); - EXPECT_NEAR(bonus[1].c1[2], 0.18681344121910506, EPSILON); - EXPECT_NEAR(bonus[2].c1[0], -0.22123552085772166, EPSILON); - EXPECT_NEAR(bonus[2].c1[1], -0.28372571379613187, EPSILON); - EXPECT_NEAR(bonus[2].c1[2], 0.78775285695558617, EPSILON); - EXPECT_NEAR(bonus[3].c1[0], -0.69845793336676587, EPSILON); - EXPECT_NEAR(bonus[3].c1[1], 0.18083523090249506, EPSILON); - EXPECT_NEAR(bonus[3].c1[2], 0.47901475403318056, EPSILON); - EXPECT_NEAR(bonus[0].c2[0], 0.019602723119529659, EPSILON); - EXPECT_NEAR(bonus[0].c2[1], 0.14942924536134222, EPSILON); - EXPECT_NEAR(bonus[0].c2[2], -0.55733290519255385, EPSILON); - EXPECT_NEAR(bonus[1].c2[0], 0.2208094914375279, EPSILON); - EXPECT_NEAR(bonus[1].c2[1], -0.4849604211463005, EPSILON); - EXPECT_NEAR(bonus[1].c2[2], 0.22223836695322477, EPSILON); - EXPECT_NEAR(bonus[2].c2[0], 0.17705460333259249, EPSILON); - EXPECT_NEAR(bonus[2].c2[1], -0.56674478453558153, EPSILON); - EXPECT_NEAR(bonus[2].c2[2], -0.6304379562181005, EPSILON); - EXPECT_NEAR(bonus[3].c2[0], 0.22007613459534958, EPSILON); - EXPECT_NEAR(bonus[3].c2[1], -0.82388470022624394, EPSILON); - EXPECT_NEAR(bonus[3].c2[2], -0.15093208974463557, EPSILON); - EXPECT_NEAR(bonus[0].c3[0], -0.014350189290200811, EPSILON); - EXPECT_NEAR(bonus[0].c3[1], 0.40824829046386302, EPSILON); - EXPECT_NEAR(bonus[0].c3[2], 0.40799600333091751, EPSILON); - EXPECT_NEAR(bonus[1].c3[0], -0.40642182073424188, EPSILON); - EXPECT_NEAR(bonus[1].c3[1], -0.028831496585242929, EPSILON); - EXPECT_NEAR(bonus[1].c3[2], -0.40905180817232945, EPSILON); - EXPECT_NEAR(bonus[2].c3[0], 0.044180917525129149, EPSILON); - EXPECT_NEAR(bonus[2].c3[1], 0.85047049833171351, EPSILON); - EXPECT_NEAR(bonus[2].c3[2], -0.15731490073748589, EPSILON); - EXPECT_NEAR(bonus[3].c3[0], 0.47838179877141634, EPSILON); - EXPECT_NEAR(bonus[3].c3[1], 0.64304946932374796, EPSILON); - EXPECT_NEAR(bonus[3].c3[2], -0.32808266428854477, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 0.36886008861549813, EPSILON); + EXPECT_NEAR(bonus[0].quat[0], 0.92373678792937974, EPSILON); + EXPECT_NEAR(bonus[0].quat[1], 0.0067268233964605136, EPSILON); + EXPECT_NEAR(bonus[0].quat[2], 0.016239988275423622, EPSILON); + EXPECT_NEAR(bonus[0].quat[3], -0.38262430562330857, EPSILON); + EXPECT_NEAR(bonus[1].quat[0], 0.63633478678991862, EPSILON); + EXPECT_NEAR(bonus[1].quat[1], 0.66894644809679971, EPSILON); + EXPECT_NEAR(bonus[1].quat[2], 0.26478147716387457, EPSILON); + EXPECT_NEAR(bonus[1].quat[3], 0.27835132126616718, EPSILON); + EXPECT_NEAR(bonus[2].quat[0], 0.90191325590647375, EPSILON); + EXPECT_NEAR(bonus[2].quat[1], 0.2009681312851252, EPSILON); + EXPECT_NEAR(bonus[2].quat[2], 0.1002758475123109, EPSILON); + EXPECT_NEAR(bonus[2].quat[3], 0.36892959143125958, EPSILON); + EXPECT_NEAR(bonus[3].quat[0], 0.34503278332913523, EPSILON); + EXPECT_NEAR(bonus[3].quat[1], 0.17090845404750615, EPSILON); + EXPECT_NEAR(bonus[3].quat[2], 0.44689296000042461, EPSILON); + EXPECT_NEAR(bonus[3].quat[3], 0.80748335033318219, EPSILON); + EXPECT_NEAR(bonus[0].c1[0], -0.14933690186163626, EPSILON); + EXPECT_NEAR(bonus[0].c1[2], -0.0052525338293288879, EPSILON); + EXPECT_NEAR(bonus[1].c1[0], -0.18681344121910512, EPSILON); + EXPECT_NEAR(bonus[1].c1[2], 0.18561232929671317, EPSILON); + EXPECT_NEAR(bonus[2].c1[0], -0.78775285695558628, EPSILON); + EXPECT_NEAR(bonus[2].c1[2], -0.22123552085772158, EPSILON); + EXPECT_NEAR(bonus[3].c1[0], -0.47901475403318072, EPSILON); + EXPECT_NEAR(bonus[3].c1[2], -0.69845793336676587, EPSILON); + EXPECT_NEAR(bonus[0].c2[0], 0.55733290519255363, EPSILON); + EXPECT_NEAR(bonus[0].c2[2], 0.019602723119529656, EPSILON); + EXPECT_NEAR(bonus[1].c2[0], -0.22223836695322477, EPSILON); + EXPECT_NEAR(bonus[1].c2[2], 0.22080949143752887, EPSILON); + EXPECT_NEAR(bonus[2].c2[0], 0.63043795621810073, EPSILON); + EXPECT_NEAR(bonus[2].c2[2], 0.17705460333259254, EPSILON); + EXPECT_NEAR(bonus[3].c2[0], 0.15093208974463557, EPSILON); + EXPECT_NEAR(bonus[3].c2[2], 0.22007613459534847, EPSILON); + EXPECT_NEAR(bonus[0].c3[0], -0.4079960033309174, EPSILON); + EXPECT_NEAR(bonus[0].c3[2], -0.014350189290200809, EPSILON); + EXPECT_NEAR(bonus[1].c3[0], 0.40905180817232961, EPSILON); + EXPECT_NEAR(bonus[1].c3[2], -0.40642182073424171, EPSILON); + EXPECT_NEAR(bonus[2].c3[0], 0.15731490073748589, EPSILON); + EXPECT_NEAR(bonus[2].c3[2], 0.044180917525128927, EPSILON); + EXPECT_NEAR(bonus[3].c3[0], 0.32808266428854477, EPSILON); + EXPECT_NEAR(bonus[3].c3[2], 0.4783817987714174, EPSILON); BEGIN_HIDE_OUTPUT(); command("group two id 2:4:2"); @@ -2048,70 +2036,58 @@ TEST_F(AtomStyleTest, tri) EXPECT_NEAR(radius[GETIDX(11)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(12)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 0.23541253382609079, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 0.23541253382609079, EPSILON); - EXPECT_NEAR(bonus[0].quat[0], 0.66466395261228639, EPSILON); - EXPECT_NEAR(bonus[0].quat[1], -0.26579965871355399, EPSILON); - EXPECT_NEAR(bonus[0].quat[2], -0.64169714094040209, EPSILON); - EXPECT_NEAR(bonus[0].quat[3], -0.27531282359251713, EPSILON); - EXPECT_NEAR(bonus[1].quat[0], 0.70865471105868871, EPSILON); - EXPECT_NEAR(bonus[1].quat[1], 0.40297854431552654, EPSILON); - EXPECT_NEAR(bonus[1].quat[2], -0.56684324752832238, EPSILON); - EXPECT_NEAR(bonus[1].quat[3], 0.11876668744732566, EPSILON); - EXPECT_NEAR(bonus[2].quat[0], 0.66466395261228639, EPSILON); - EXPECT_NEAR(bonus[2].quat[1], -0.26579965871355399, EPSILON); - EXPECT_NEAR(bonus[2].quat[2], -0.64169714094040209, EPSILON); - EXPECT_NEAR(bonus[2].quat[3], -0.27531282359251713, EPSILON); - EXPECT_NEAR(bonus[3].quat[0], 0.70865471105868871, EPSILON); - EXPECT_NEAR(bonus[3].quat[1], 0.40297854431552654, EPSILON); - EXPECT_NEAR(bonus[3].quat[2], -0.56684324752832238, EPSILON); - EXPECT_NEAR(bonus[3].quat[3], 0.11876668744732566, EPSILON); - EXPECT_NEAR(bonus[0].c1[0], -0.0052525338293288879, EPSILON); - EXPECT_NEAR(bonus[0].c1[1], -0.55767753582520529, EPSILON); - EXPECT_NEAR(bonus[0].c1[2], 0.14933690186163626, EPSILON); - EXPECT_NEAR(bonus[1].c1[0], -0.22123552085772158, EPSILON); - EXPECT_NEAR(bonus[1].c1[1], -0.28372571379613187, EPSILON); - EXPECT_NEAR(bonus[1].c1[2], 0.78775285695558628, EPSILON); - EXPECT_NEAR(bonus[2].c1[0], -0.0052525338293288905, EPSILON); - EXPECT_NEAR(bonus[2].c1[1], -0.55767753582520529, EPSILON); - EXPECT_NEAR(bonus[2].c1[2], 0.14933690186163631, EPSILON); - EXPECT_NEAR(bonus[3].c1[0], -0.22123552085772166, EPSILON); - EXPECT_NEAR(bonus[3].c1[1], -0.28372571379613187, EPSILON); - EXPECT_NEAR(bonus[3].c1[2], 0.78775285695558617, EPSILON); - EXPECT_NEAR(bonus[0].c2[0], 0.019602723119529659, EPSILON); - EXPECT_NEAR(bonus[0].c2[1], 0.14942924536134222, EPSILON); - EXPECT_NEAR(bonus[0].c2[2], -0.55733290519255385, EPSILON); - EXPECT_NEAR(bonus[1].c2[0], 0.17705460333259249, EPSILON); - EXPECT_NEAR(bonus[1].c2[1], -0.56674478453558153, EPSILON); - EXPECT_NEAR(bonus[1].c2[2], -0.6304379562181005, EPSILON); - EXPECT_NEAR(bonus[2].c2[0], 0.019602723119529659, EPSILON); - EXPECT_NEAR(bonus[2].c2[1], 0.14942924536134222, EPSILON); - EXPECT_NEAR(bonus[2].c2[2], -0.55733290519255385, EPSILON); - EXPECT_NEAR(bonus[3].c2[0], 0.17705460333259249, EPSILON); - EXPECT_NEAR(bonus[3].c2[1], -0.56674478453558153, EPSILON); - EXPECT_NEAR(bonus[3].c2[2], -0.6304379562181005, EPSILON); - EXPECT_NEAR(bonus[0].c3[0], -0.014350189290200811, EPSILON); - EXPECT_NEAR(bonus[0].c3[1], 0.40824829046386302, EPSILON); - EXPECT_NEAR(bonus[0].c3[2], 0.40799600333091751, EPSILON); - EXPECT_NEAR(bonus[1].c3[0], 0.044180917525129149, EPSILON); - EXPECT_NEAR(bonus[1].c3[1], 0.85047049833171351, EPSILON); - EXPECT_NEAR(bonus[1].c3[2], -0.15731490073748589, EPSILON); - EXPECT_NEAR(bonus[2].c3[0], -0.014350189290200811, EPSILON); - EXPECT_NEAR(bonus[2].c3[1], 0.40824829046386302, EPSILON); - EXPECT_NEAR(bonus[2].c3[2], 0.40799600333091751, EPSILON); - EXPECT_NEAR(bonus[3].c3[0], 0.044180917525129149, EPSILON); - EXPECT_NEAR(bonus[3].c3[1], 0.85047049833171351, EPSILON); - EXPECT_NEAR(bonus[3].c3[2], -0.15731490073748589, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[0].quat[0], 0.92373678792937974, EPSILON); + EXPECT_NEAR(bonus[0].quat[1], 0.0067268233964605136, EPSILON); + EXPECT_NEAR(bonus[0].quat[2], 0.016239988275423622, EPSILON); + EXPECT_NEAR(bonus[0].quat[3], -0.38262430562330857, EPSILON); + EXPECT_NEAR(bonus[1].quat[0], 0.90191325590647375, EPSILON); + EXPECT_NEAR(bonus[1].quat[1], 0.2009681312851252, EPSILON); + EXPECT_NEAR(bonus[1].quat[2], 0.1002758475123109, EPSILON); + EXPECT_NEAR(bonus[1].quat[3], 0.36892959143125958, EPSILON); + EXPECT_NEAR(bonus[2].quat[0], 0.92373678792937974, EPSILON); + EXPECT_NEAR(bonus[2].quat[1], 0.0067268233964605136, EPSILON); + EXPECT_NEAR(bonus[2].quat[2], 0.016239988275423622, EPSILON); + EXPECT_NEAR(bonus[2].quat[3], -0.38262430562330857, EPSILON); + EXPECT_NEAR(bonus[3].quat[0], 0.90191325590647375, EPSILON); + EXPECT_NEAR(bonus[3].quat[1], 0.2009681312851252, EPSILON); + EXPECT_NEAR(bonus[3].quat[2], 0.1002758475123109, EPSILON); + EXPECT_NEAR(bonus[3].quat[3], 0.36892959143125958, EPSILON); + EXPECT_NEAR(bonus[0].c1[0], -0.14933690186163626, EPSILON); + EXPECT_NEAR(bonus[0].c1[2], -0.0052525338293288879, EPSILON); + EXPECT_NEAR(bonus[1].c1[0], -0.78775285695558628, EPSILON); + EXPECT_NEAR(bonus[1].c1[2], -0.22123552085772158, EPSILON); + EXPECT_NEAR(bonus[2].c1[0], -0.14933690186163626, EPSILON); + EXPECT_NEAR(bonus[2].c1[2], -0.0052525338293288879, EPSILON); + EXPECT_NEAR(bonus[3].c1[0], -0.78775285695558628, EPSILON); + EXPECT_NEAR(bonus[3].c1[2], -0.22123552085772158, EPSILON); + EXPECT_NEAR(bonus[0].c2[0], 0.55733290519255363, EPSILON); + EXPECT_NEAR(bonus[0].c2[2], 0.019602723119529656, EPSILON); + EXPECT_NEAR(bonus[1].c2[0], 0.63043795621810073, EPSILON); + EXPECT_NEAR(bonus[1].c2[2], 0.17705460333259254, EPSILON); + EXPECT_NEAR(bonus[2].c2[0], 0.55733290519255363, EPSILON); + EXPECT_NEAR(bonus[2].c2[2], 0.019602723119529656, EPSILON); + EXPECT_NEAR(bonus[3].c2[0], 0.63043795621810073, EPSILON); + EXPECT_NEAR(bonus[3].c2[2], 0.17705460333259254, EPSILON); + EXPECT_NEAR(bonus[0].c3[0], -0.4079960033309174, EPSILON); + EXPECT_NEAR(bonus[0].c3[2], -0.014350189290200809, EPSILON); + EXPECT_NEAR(bonus[1].c3[0], 0.15731490073748589, EPSILON); + EXPECT_NEAR(bonus[1].c3[2], 0.044180917525128927, EPSILON); + EXPECT_NEAR(bonus[2].c3[0], -0.4079960033309174, EPSILON); + EXPECT_NEAR(bonus[2].c3[2], -0.014350189290200809, EPSILON); + EXPECT_NEAR(bonus[3].c3[0], 0.15731490073748589, EPSILON); + EXPECT_NEAR(bonus[3].c3[2], 0.044180917525128927, EPSILON); BEGIN_HIDE_OUTPUT(); command("reset_atoms id"); @@ -2140,18 +2116,18 @@ TEST_F(AtomStyleTest, tri) ASSERT_EQ(tri[GETIDX(6)], -1); ASSERT_EQ(tri[GETIDX(7)], 3); ASSERT_EQ(tri[GETIDX(8)], -1); - EXPECT_NEAR(bonus[0].inertia[0], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 0.23541253382609079, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 0.23541253382609079, EPSILON); } TEST_F(AtomStyleTest, body_nparticle) @@ -2347,18 +2323,18 @@ TEST_F(AtomStyleTest, body_nparticle) EXPECT_NEAR(radius[GETIDX(5)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(6)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 2.0, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 2.0, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 2.0, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 0.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 4.5, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 0.0, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 4.5, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 4.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 0.5, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 1.7746273249544022, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 0.5, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 1.7746273249544022, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 1.67188, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 0.49099767504559777, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 12.0, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 0.49099767504559777, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 12.0, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 12.0, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 0.0, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[0], 1.0, EPSILON); EXPECT_NEAR(bonus[0].quat[1], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[2], 0.0, EPSILON); @@ -2519,18 +2495,18 @@ TEST_F(AtomStyleTest, body_nparticle) EXPECT_NEAR(radius[GETIDX(5)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(6)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 2.0, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 2.0, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 2.0, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 0.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 4.5, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 0.0, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 4.5, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 4.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 0.5, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 1.7746273249544022, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 0.5, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 1.7746273249544022, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 1.67188, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 0.49099767504559777, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 12.0, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 0.49099767504559777, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 12.0, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 12.0, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 0.0, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[0], 1.0, EPSILON); EXPECT_NEAR(bonus[0].quat[1], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[2], 0.0, EPSILON); @@ -2543,10 +2519,10 @@ TEST_F(AtomStyleTest, body_nparticle) EXPECT_NEAR(bonus[2].quat[1], 0.25056280708573159, EPSILON); EXPECT_NEAR(bonus[2].quat[2], 0.0, EPSILON); EXPECT_NEAR(bonus[2].quat[3], 0.25056280708573148, EPSILON); - EXPECT_NEAR(bonus[3].quat[0], 0.62499650256800654, EPSILON); - EXPECT_NEAR(bonus[3].quat[1], 0.47323774316465234, EPSILON); - EXPECT_NEAR(bonus[3].quat[2], 0.33072552332373728, EPSILON); - EXPECT_NEAR(bonus[3].quat[3], 0.52540083597613996, EPSILON); + EXPECT_NEAR(bonus[3].quat[0], 0.070424771223903379, EPSILON); + EXPECT_NEAR(bonus[3].quat[1], 0.81345375914352225, EPSILON); + EXPECT_NEAR(bonus[3].quat[2], 0.56848787755882768, EPSILON); + EXPECT_NEAR(bonus[3].quat[3], -0.10077135705145905, EPSILON); ASSERT_EQ(bonus[0].ilocal, 0); ASSERT_EQ(bonus[1].ilocal, 1); ASSERT_EQ(bonus[2].ilocal, 2); @@ -2634,18 +2610,18 @@ TEST_F(AtomStyleTest, body_nparticle) EXPECT_NEAR(radius[GETIDX(9)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(11)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(12)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 2.0, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 2.0, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 2.0, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 0.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 1.7746273249544022, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 0.0, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 1.7746273249544022, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 1.67188, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 0.49099767504559777, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 2.0, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 0.49099767504559777, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 2.0, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 2.0, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 0.0, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 1.7746273249544022, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 0.0, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 1.7746273249544022, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 1.67188, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 0.49099767504559777, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 0.49099767504559777, EPSILON); EXPECT_NEAR(bonus[0].quat[0], 1.0, EPSILON); EXPECT_NEAR(bonus[0].quat[1], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[2], 0.0, EPSILON); From b01efd96a52b35ed6065a5c80817e52800337bae Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Mar 2024 23:27:44 -0400 Subject: [PATCH 04/40] add missing link and expand docs for Unknown identifier in data file error --- doc/src/Errors_details.rst | 32 ++++++++++++++++++++++---------- src/read_data.cpp | 3 ++- 2 files changed, 24 insertions(+), 11 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index b63d80a9ae..2a08a308f4 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -13,15 +13,27 @@ discussions of such cases. Unknown identifier in data file ------------------------------- -This error happens when LAMMPS encounters a line of text in an unexpected format -while reading a data file. This is most commonly cause by inconsistent header and -section data. The header section informs LAMMPS how many entries or lines are expected in the -various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file. -If there is a mismatch, LAMMPS will either keep reading beyond the end of a section -or stop reading before the section has ended. +This error happens when LAMMPS encounters a line of text with an +unexpected keyword while :doc:`reading a data file `. This +would be either header keywords or section header keywords. This is +most commonly due to a mistyped keyword or due to a keyword that is +inconsistent with the :doc:`atom style ` used. -Such a mismatch can happen unexpectedly when the first line of the data -is *not* a comment as required by the format. That would result in -LAMMPS expecting, for instance, 0 atoms because the "atoms" header line -is treated as a comment. +The header section informs LAMMPS how many entries or lines are expected +in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of +the data file. If there is a mismatch, LAMMPS will either keep reading +beyond the end of a section or stop reading before the section has +ended. In that case the next line will not contain a recognized keyword. +Such a mismatch can also happen when the first line of the data +is *not* a comment as required by the format, but a line with a valid +header keyword. That would result in LAMMPS expecting, for instance, +0 atoms because the "atoms" header line is the first line and thus +treated as a comment. + +Another possibility to trigger this error is to have a keyword in the +data file that corresponds to a fix (e.g. :doc:`fix cmap `) +but the :doc:`read_data ` command is missing the (optional) +arguments that identify the fix and the header keyword and section +keyword or those arguments are inconsistent with the keywords in the +data file. diff --git a/src/read_data.cpp b/src/read_data.cpp index 657369d5d0..36bbce605f 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1360,7 +1360,8 @@ void ReadData::header(int firstpass) // check that exiting string is a valid section keyword parse_keyword(1); - if (!is_data_section(keyword)) error->all(FLERR, "Unknown identifier in data file: {}", keyword); + if (!is_data_section(keyword)) + error->all(FLERR, "Unknown identifier in data file: {}{}", keyword, utils::errorurl(1)); // error checks on header values // must be consistent with atom style and other header values From cd154abe73018b8c45a7e3b06ad7cd2ac0a537d9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 26 Mar 2024 23:56:38 -0400 Subject: [PATCH 05/40] add "Incorrect format in ... section of data file" to Error_details and url --- doc/src/Errors_details.rst | 17 +++++++++++++++++ src/MOLECULE/fix_cmap.cpp | 3 ++- src/atom.cpp | 28 ++++++++++++++++++++-------- src/fix_property_atom.cpp | 5 +++-- 4 files changed, 42 insertions(+), 11 deletions(-) diff --git a/doc/src/Errors_details.rst b/doc/src/Errors_details.rst index 2a08a308f4..c798784106 100644 --- a/doc/src/Errors_details.rst +++ b/doc/src/Errors_details.rst @@ -37,3 +37,20 @@ but the :doc:`read_data ` command is missing the (optional) arguments that identify the fix and the header keyword and section keyword or those arguments are inconsistent with the keywords in the data file. + +.. _err0002: + +Incorrect format in ... section of data file +-------------------------------------------- + +This error happens when LAMMPS reads the contents of a section of a +:doc:`data file ` and the number of parameters in the line +differs from what is expected. This most commonly happens, when the +atom style is different from what is expected for a specific data file +since changing the atom style usually changes the format of the line. + +This error can also happen when the number of entries indicated in the +header of a data file (e.g. the number of atoms) is larger than the +number of lines provided (e.g. in the corresponding Atoms section) +and then LAMMPS will continue reading into the next section and that +would have a completely different format. diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index cb4cb8cadc..bc220da30e 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -970,7 +970,8 @@ void FixCMAP::read_data_section(char * /*keyword*/, int /*n*/, char *buf, atom5 = values.next_tagint(); if (values.has_next()) throw TokenizerException("too many items",line); } catch (std::exception &e) { - error->all(FLERR,"Incorrect format of CMAP section: {}", e.what()); + error->all(FLERR,"Incorrect format of CMAP section in data file: {}{}", + e.what(), utils::errorurl(2)); } atom1 += id_offset; diff --git a/src/atom.cpp b/src/atom.cpp index 085ca88b4e..7edf4760d2 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1068,7 +1068,8 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, } if ((nwords != avec->size_data_atom) && (nwords != avec->size_data_atom + 3)) - error->all(FLERR,"Incorrect format in {}: {}", location, utils::trim(buf)); + error->all(FLERR,"Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); *next = '\n'; // set bounds for my proc @@ -1149,7 +1150,8 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, // skip over empty or comment lines } else if ((nvalues < nwords) || ((nvalues > nwords) && (!utils::strmatch(values[nwords],"^#")))) { - error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); } else { int imx = 0, imy = 0, imz = 0; if (imageflag) { @@ -1243,7 +1245,8 @@ void Atom::data_vels(int n, char *buf, tagint id_offset) if (values.size() == 0) { // skip over empty or comment lines } else if ((int)values.size() != avec->size_data_vel) { - error->all(FLERR, "Incorrect velocity format in data file: {}", utils::trim(buf)); + error->all(FLERR, "Incorrect format in Velocities section of data file: {}{}", + utils::trim(buf), utils::errorurl(2)); } else { tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset; if (tagdata <= 0 || tagdata > map_tag_max) @@ -1287,7 +1290,9 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, // skip over empty or comment lines // Bonds line is: number(ignored), bond type, atomID 1, atomID 2 if (nwords > 0) { - if (nwords != 4) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + if (nwords != 4) + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); typestr = utils::utf8_subst(values[1]); atom1 = utils::tnumeric(FLERR, values[2], false, lmp); atom2 = utils::tnumeric(FLERR, values[3], false, lmp); @@ -1378,7 +1383,9 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset, // skip over empty or comment lines // Angles line is: number(ignored), angle type, atomID 1, atomID 2, atomID 3 if (nwords > 0) { - if (nwords != 5) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + if (nwords != 5) + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); typestr = utils::utf8_subst(values[1]); atom1 = utils::tnumeric(FLERR, values[2], false, lmp); atom2 = utils::tnumeric(FLERR, values[3], false, lmp); @@ -1485,7 +1492,9 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset, // skip over empty or comment lines // Dihedrals line is: number(ignored), bond type, atomID 1, atomID 2, atomID 3, atomID 4 if (nwords > 0) { - if (nwords != 6) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + if (nwords != 6) + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); typestr = utils::utf8_subst(values[1]); atom1 = utils::tnumeric(FLERR, values[2], false, lmp); atom2 = utils::tnumeric(FLERR, values[3], false, lmp); @@ -1611,7 +1620,9 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset, // skip over empty or comment lines // Impropers line is: number(ignored), bond type, atomID 1, atomID 2, atomID 3, atomID 4 if (nwords > 0) { - if (nwords != 6) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf)); + if (nwords != 6) + error->all(FLERR, "Incorrect format in {}: {}{}", location, + utils::trim(buf), utils::errorurl(2)); typestr = utils::utf8_subst(values[1]); atom1 = utils::tnumeric(FLERR, values[2], false, lmp); atom2 = utils::tnumeric(FLERR, values[3], false, lmp); @@ -1727,7 +1738,8 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset) if (values.size() == 0) { // skip over empty or comment lines } else if ((int)values.size() != avec_bonus->size_data_bonus) { - error->all(FLERR, "Incorrect bonus data format in data file: {}", utils::trim(buf)); + error->all(FLERR, "Incorrect format in Bonus section of data file: {}{}", + utils::trim(buf), utils::errorurl(2)); } else { tagint tagdata = utils::tnumeric(FLERR,values[0],false,lmp) + id_offset; if (tagdata <= 0 || tagdata > map_tag_max) diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index de96b5c39d..2cbdb44ab0 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -328,8 +328,9 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint try { ValueTokenizer values(buf); if ((int) values.count() != values_peratom + 1) - error->all(FLERR, "Incorrect format in {} section of data file: {} expected {} and got {}", - keyword, buf, values_peratom + 1, values.count()); + error->all(FLERR, "Incorrect format in {} section of data file: {}\n" + "expected {} parameters and got {}{}", keyword, utils::trim(buf), + values_peratom + 1, values.count(), utils::errorurl(2)); itag = values.next_tagint() + id_offset; if (itag <= 0 || itag > map_tag_max) From e5ea8c2670227934a0cb20a565432a5ef045fa83 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Mar 2024 06:04:56 -0400 Subject: [PATCH 06/40] silence compiler warnings --- src/KOKKOS/fft3d_kokkos.cpp | 3 +++ src/KOKKOS/pair_kokkos.h | 4 ++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index 5caed42f43..202d46e788 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -39,8 +39,11 @@ FFT3dKokkos::FFT3dKokkos(LAMMPS *lmp, MPI_Comm comm, int nfast, int Pointers(lmp) { int nthreads = lmp->kokkos->nthreads; + +#if defined(LMP_KOKKOS_GPU) int ngpus = lmp->kokkos->ngpus; ExecutionSpace execution_space = ExecutionSpaceFromDevice::space; +#endif #if defined(FFT_KOKKOS_MKL) if (ngpus > 0 && execution_space == Device) diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index 15417d7620..c4bd603041 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -950,10 +950,10 @@ EV_FLOAT pair_compute_neighlist (PairStyle* fpair, std::enable_if_t<(NEIGHFLAG&P static int vectorsize = 0; static int atoms_per_team = 0; - static int teamsize_max_for = 0; - static int teamsize_max_reduce = 0; #if defined(LMP_KOKKOS_GPU) + static int teamsize_max_for = 0; + static int teamsize_max_reduce = 0; static int lastcall = -1; if (!vectorsize || lastcall < fpair->lmp->neighbor->lastcall) { lastcall = fpair->lmp->update->ntimestep; From edcbd2e7618518e6bb1a5d843081474d7176872d Mon Sep 17 00:00:00 2001 From: Stan Gerald Moore Date: Wed, 27 Mar 2024 13:04:23 -0600 Subject: [PATCH 07/40] Fix bug in Kokkos when shrink-wrapping with no atoms --- src/KOKKOS/domain_kokkos.cpp | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/KOKKOS/domain_kokkos.cpp b/src/KOKKOS/domain_kokkos.cpp index aecc12cd12..d0865c6afb 100644 --- a/src/KOKKOS/domain_kokkos.cpp +++ b/src/KOKKOS/domain_kokkos.cpp @@ -22,7 +22,7 @@ using namespace LAMMPS_NS; -static constexpr double BIG = 1.0e20; +static constexpr double BIG = 1.0e20; /* ---------------------------------------------------------------------- */ @@ -80,6 +80,11 @@ public: void DomainKokkos::reset_box() { // perform shrink-wrapping + + // nothing to do for empty systems + + if (atom->natoms == 0) return; + // compute extent of atoms on this proc // for triclinic, this is done in lamda space From 3c8ba3d37612025687c8069deb345bbbcca92033 Mon Sep 17 00:00:00 2001 From: Stan Gerald Moore Date: Wed, 27 Mar 2024 13:14:52 -0600 Subject: [PATCH 08/40] Update codeowners so changes to domain can be ported to KOKKOS package --- .github/CODEOWNERS | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index ed37fa80b9..0e42635244 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -83,7 +83,7 @@ src/bond.* @sjplimp src/comm*.* @sjplimp src/compute.* @sjplimp src/dihedral.* @sjplimp -src/domain.* @sjplimp +src/domain.* @sjplimp @stanmoore1 src/dump*.* @sjplimp src/error.* @sjplimp src/finish.* @sjplimp From f8d8ed094659f24d3a4a96d9eae32997148d23bc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Mar 2024 17:52:13 -0400 Subject: [PATCH 09/40] use correct character class escapes --- unittest/force-styles/check_tests.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/unittest/force-styles/check_tests.py b/unittest/force-styles/check_tests.py index df71640789..4dba8f9b9e 100755 --- a/unittest/force-styles/check_tests.py +++ b/unittest/force-styles/check_tests.py @@ -54,7 +54,7 @@ improper = {} kspace = {} pair = {} -style_pattern = re.compile("(.+)Style\((.+),(.+)\)") +style_pattern = re.compile("(.+)Style\\((.+),(.+)\\)") upper = re.compile("[A-Z]+") gpu = re.compile("(.+)/gpu$") intel = re.compile("(.+)/intel$") @@ -176,19 +176,19 @@ def check_tests(name,styles,yaml,search,skip=()): counter = 0 counter += check_tests('pair',pair,'*-pair-*.yaml', - '.*pair_style:\s*((\S+).*)?',skip=('meam','lj/sf')) + '.*pair_style:\\s*((\\S+).*)?',skip=('meam','lj/sf')) counter += check_tests('bond',bond,'bond-*.yaml', - '.*bond_style:\s*((\S+).*)?') + '.*bond_style:\\s*((\\S+).*)?') counter += check_tests('angle',angle,'angle-*.yaml', - '.*angle_style:\s*((\S+).*)?') + '.*angle_style:\\s*((\\S+).*)?') counter += check_tests('dihedral',dihedral,'dihedral-*.yaml', - '.*dihedral_style:\s*((\S+).*)?') + '.*dihedral_style:\\s*((\\S+).*)?') counter += check_tests('improper',improper,'improper-*.yaml', - '.*improper_style:\s*((\S+).*)?') + '.*improper_style:\\s*((\\S+).*)?') counter += check_tests('kspace',kspace,'kspace-*.yaml', - '.*kspace_style\s*((\S+).*)?') + '.*kspace_style\\s*((\\S+).*)?') counter += check_tests('fix',fix,'fix-*.yaml', - ' fix\s+((\S+)\s*)?') + ' fix\\s+((\\S+)\\s*)?') total = len(pair)+len(bond)+len(angle)+len(dihedral)+len(improper)+len(kspace)+len(fix) print(f"\nTotal tests missing: {counter} of {total}") From a13d53dd65a435df205a727f77efe752c1f8c986 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 28 Mar 2024 16:14:44 -0400 Subject: [PATCH 10/40] disable references to cuFFT (which is not yet used) --- lib/gpu/lal_base_amoeba.h | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/lib/gpu/lal_base_amoeba.h b/lib/gpu/lal_base_amoeba.h index f415b30334..7255b8770f 100644 --- a/lib/gpu/lal_base_amoeba.h +++ b/lib/gpu/lal_base_amoeba.h @@ -33,6 +33,7 @@ //#define ASYNC_DEVICE_COPY +#if 0 #if !defined(USE_OPENCL) && !defined(USE_HIP) // temporary workaround for int2 also defined in cufft #ifdef int2 @@ -40,6 +41,7 @@ #endif #include "cufft.h" #endif +#endif namespace LAMMPS_AL { @@ -313,10 +315,11 @@ class BaseAmoeba { virtual int fphi_mpole(); virtual int polar_real(const int eflag, const int vflag) = 0; - +#if 0 #if !defined(USE_OPENCL) && !defined(USE_HIP) cufftHandle plan; #endif +#endif bool fft_plan_created; }; From 996f5b9d52cf5e186d496ed0df81d33f9c510cea Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 29 Mar 2024 02:50:30 -0400 Subject: [PATCH 11/40] fix ttm doc formatting fixes --- doc/src/fix_ttm.rst | 75 +++++++++++++++++++++++---------------------- 1 file changed, 38 insertions(+), 37 deletions(-) diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 5a7f864686..f3e6a08d61 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -136,23 +136,23 @@ transfer between the subsystems: \bigtriangledown (\kappa_e \bigtriangledown T_e) - g_p (T_e - T_a) + g_s T_a' -where C_e is the specific heat, rho_e is the density, kappa_e is the -thermal conductivity, T is temperature, the "e" and "a" subscripts -represent electronic and atomic subsystems respectively, g_p is the -coupling constant for the electron-ion interaction, and g_s is the -electron stopping coupling parameter. C_e, rho_e, and kappa_e are -specified as parameters to the fix. The other quantities are derived. -The form of the heat diffusion equation used here is almost the same -as that in equation 6 of :ref:`(Duffy) `, with the exception that the -electronic density is explicitly represented, rather than being part -of the specific heat parameter. +where :math:`C_e` is the specific heat, :math:`\rho_e` is the density, +:math:`\kappa_e` is the thermal conductivity, *T* is temperature, the +"e" and "a" subscripts represent electronic and atomic subsystems +respectively, :math:`g_p` is the coupling constant for the electron-ion +interaction, and :math:`g_s` is the electron stopping coupling +parameter. :math:`C_e`, :math:`\rho_e`, and :math:`\kappa_e` are +specified as parameters to the fix *ttm* or *ttm/grid*. The other +quantities are derived. The form of the heat diffusion equation used +here is almost the same as that in equation 6 of :ref:`(Duffy) `, +with the exception that the electronic density is explicitly +represented, rather than being part of the specific heat parameter. Currently, the TTM fixes assume that none of the user-supplied -parameters will vary with temperature. Note that :ref:`(Duffy) -` used a tanh() functional form for the temperature dependence -of the electronic specific heat, but ignored temperature dependencies -of any of the other parameters. See more discussion below for fix -ttm/mod. +parameters will vary with temperature. Note that :ref:`(Duffy) ` +used a tanh() functional form for the temperature dependence of the +electronic specific heat, but ignored temperature dependencies of any of +the other parameters. See more discussion below for fix *ttm/mod*. .. note:: @@ -265,27 +265,27 @@ heat sources (e.g. laser heating in ablation simulations): \bigtriangledown (\kappa_e \bigtriangledown T_e) - g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin}) -where theta is the Heaviside step function, I_0 is the (absorbed) -laser pulse intensity for ablation simulations, l_skin is the depth -of skin-layer, and all other designations have the same meaning as in -the former equation. The duration of the pulse is set by the parameter -*tau* in the *init_file*. +where :math:`\theta` is the Heaviside step function, :math:`I_0` is the +(absorbed) laser pulse intensity for ablation simulations, +:math:`l_{skin}` is the depth of the skin-layer, and all other +designations have the same meaning as in the former equation. The +duration of the pulse is set by the parameter *tau* in the *init_file*. -Fix ttm/mod also allows users to specify the dependencies of C_e and -kappa_e on the electronic temperature. The specific heat is expressed -as +Fix *ttm/mod* also allows users to specify the dependencies of +:math:`C_e` and :math:`\kappa_e` on the electronic temperature. The +specific heat is expressed as .. math:: C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2) -where *X* = T_e/1000, and the thermal conductivity is defined as -kappa_e = D_e\*rho_e\*C_e, where D_e is the thermal diffusion -coefficient. +where :math:`X = \frac{T_e}{1000}`, and the thermal conductivity is +defined as :math:`\kappa_e = D_e \cdot rho_e \cdot C_e`, where +:math:`D_e` is the thermal diffusion coefficient. -Electronic pressure effects are included in the TTM model to account -for the blast force acting on ions because of electronic pressure -gradient (see :ref:`(Chen) `, :ref:`(Norman) `). The total force +Electronic pressure effects are included in the TTM model to account for +the blast force acting on ions because of electronic pressure gradient +(see :ref:`(Chen) `, :ref:`(Norman) `). The total force acting on an ion is: .. math:: @@ -293,13 +293,14 @@ acting on an ion is: {\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec F}_{langevin} - \nabla P_e/n_{ion} -where F_langevin is a force from Langevin thermostat simulating -electron-phonon coupling, and nabla P_e/n_ion is the electron blast -force. +where :math:`F_{langevin}` is a force from Langevin thermostat +simulating electron-phonon coupling, and :math:`\nabla P_e/n_{ion}` is +the electron blast force. -The electronic pressure is taken to be P_e = B\*rho_e\*C_e\*T_e +The electronic pressure is taken to be :math:`P_e = B \cdot rho_e \cdot +C_e \cdot T_e` -The current fix ttm/mod implementation allows TTM simulations with a +The current fix *ttm/mod* implementation allows TTM simulations with a vacuum. The vacuum region is defined as the grid cells with zero electronic temperature. The numerical scheme does not allow energy exchange with such cells. Since the material can expand to previously @@ -319,10 +320,10 @@ electronic pressure gradient is calculated as \frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta x}-(C_e{}T_e)_{x}}{\Delta x} \right] -where lambda is the electron mean free path (see :ref:`(Norman) `, -:ref:`(Pisarev) `) +where :math:`\lambda` is the electron mean free path (see :ref:`(Norman) +`, :ref:`(Pisarev) `) -The fix ttm/mod parameter file *init_file* has the following syntax. +The fix *ttm/mod* parameter file *init_file* has the following syntax. Every line with an odd number is considered as a comment and ignored. The lines with the even numbers are treated as follows: From 9c85e5a99bb7369589a5d05c1e655074dd6697c5 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 29 Mar 2024 14:27:43 -0600 Subject: [PATCH 12/40] fix bug in option arg parsing of fix ave/correlate, also update doc page for fix ave/correlate/long --- doc/src/fix_ave_correlate.rst | 1 - doc/src/fix_ave_correlate_long.rst | 13 ++++++++----- src/fix_ave_correlate.cpp | 16 ++++++++-------- 3 files changed, 16 insertions(+), 14 deletions(-) diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 1aff749048..659e15105c 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -65,7 +65,6 @@ Examples fix 1 all ave/correlate 1 50 10000 & c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] & type upper ave running title1 "My correlation data" - fix 1 all ave/correlate 1 50 10000 c_thermo_press[*] Description diff --git a/doc/src/fix_ave_correlate_long.rst b/doc/src/fix_ave_correlate_long.rst index e2b23248f2..003bdf897d 100644 --- a/doc/src/fix_ave_correlate_long.rst +++ b/doc/src/fix_ave_correlate_long.rst @@ -20,11 +20,11 @@ Syntax .. parsed-literal:: c_ID = global scalar calculated by a compute with ID - c_ID[I] = Ith component of global vector calculated by a compute with ID + c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below) f_ID = global scalar calculated by a fix with ID - f_ID[I] = Ith component of global vector calculated by a fix with ID + f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below) v_name = global value calculated by an equal-style variable with name - v_name[I] = Ith component of global vector calculated by a vector-style variable with name + v_name[I] = Ith component of a vector-style variable with name, I can include wildcard (see below) * zero or more keyword/arg pairs may be appended * keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount* @@ -63,6 +63,7 @@ Examples fix 1 all ave/correlate/long 1 10000 & c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] & type upper title1 "My correlation data" nlen 15 ncount 3 + fix 1 all ave/correlate/long 1 10000 c_thermo_press[*] Description """"""""""" @@ -80,8 +81,10 @@ specified values may represent calculations performed by computes and fixes which store their own "group" definitions. Each listed value can be the result of a compute or fix or the -evaluation of an equal-style variable. See the -:doc:`fix ave/correlate ` page for details. +evaluation of an equal-style or vector-style variable. For +vector-style variables, the specified indices can include a wildcard +character. See the :doc:`fix ave/correlate ` page +for details. The *Nevery* and *Nfreq* arguments specify on what time steps the input values will be used to calculate correlation data and the frequency diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index d506e17761..4b9e316b9d 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -97,7 +97,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS *lmp, int narg, char **arg) : while (iarg < nargnew) { if (strcmp(arg[iarg],"type") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate type", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate type", error); if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO; else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER; else if (strcmp(arg[iarg+1],"lower") == 0) type = LOWER; @@ -107,21 +107,21 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS *lmp, int narg, char **arg) : else error->all(FLERR,"Unknown fix ave/correlate type: {}"); iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate ave", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate ave", error); if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING; else error->all(FLERR,"Unknown fix ave/correlate ave mode: {}", arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"start") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate start", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate start", error); startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"prefactor") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate prefactor", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate prefactor", error); prefactor = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate file", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate file", error); if (comm->me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) @@ -133,17 +133,17 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS *lmp, int narg, char **arg) : overwrite = 1; iarg += 1; } else if (strcmp(arg[iarg],"title1") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate title1", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate title1", error); delete[] title1; title1 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title2") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate title2", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate title2", error); delete[] title2; title2 = utils::strdup(arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title3") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate title3", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate title3", error); delete[] title3; title3 = utils::strdup(arg[iarg+1]); iarg += 2; From 30f330718af1856bc01cfd23163fe08a1961677d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 29 Mar 2024 16:53:18 -0600 Subject: [PATCH 13/40] more consistent error checks on variable length global vecs and arrays --- src/fix_ave_correlate.cpp | 2 +- src/fix_ave_time.cpp | 2 +- src/thermo.cpp | 20 +++++++-------- src/variable.cpp | 51 ++++++++++++++++++++++----------------- 4 files changed, 41 insertions(+), 34 deletions(-) diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index d506e17761..50ea6a5614 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -121,7 +121,7 @@ FixAveCorrelate::FixAveCorrelate(LAMMPS *lmp, int narg, char **arg) : prefactor = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; } else if (strcmp(arg[iarg],"file") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix ave/correlate file", error); + if (iarg+2 > nargnew) utils::missing_cmd_args(FLERR, "fix ave/correlate file", error); if (comm->me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == nullptr) diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 5219a4de3d..c88d8e1659 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -178,7 +178,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) : if (val.argindex && (val.val.f->array_flag == 0)) error->all(FLERR,"Fix ave/time fix {} does not calculate an array", val.id); if (val.argindex && (val.val.f->size_array_rows_variable)) - error->all(FLERR,"Fix ave/time fix {} array cannot be variable length", val.id); + error->all(FLERR,"Fix ave/time fix {} array cannot have variable row length", val.id); if (val.argindex && (val.argindex > val.val.f->size_array_cols)) error->all(FLERR,"Fix ave/time fix {} array is accessed out-of-range", val.id); if (nevery % val.val.f->global_freq) diff --git a/src/thermo.cpp b/src/thermo.cpp index efc5f984fc..dbb8b2530e 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -1490,9 +1490,8 @@ void Thermo::compute_compute() if (normflag && compute->extscalar) dvalue /= natoms; } else if (compute_which[m] == VECTOR) { if (compute->size_vector_variable && argindex1[ifield] > compute->size_vector) - dvalue = 0.0; - else - dvalue = compute->vector[argindex1[ifield] - 1]; + error->all(FLERR, "Thermo compute vector is accessed out-of-range"); + dvalue = compute->vector[argindex1[ifield] - 1]; if (normflag) { if (compute->extvector == 0) return; @@ -1503,9 +1502,8 @@ void Thermo::compute_compute() } } else { if (compute->size_array_rows_variable && argindex1[ifield] > compute->size_array_rows) - dvalue = 0.0; - else - dvalue = compute->array[argindex1[ifield] - 1][argindex2[ifield] - 1]; + error->all(FLERR, "Thermo compute array is accessed out-of-range"); + dvalue = compute->array[argindex1[ifield] - 1][argindex2[ifield] - 1]; if (normflag && compute->extarray) dvalue /= natoms; } } @@ -1521,6 +1519,8 @@ void Thermo::compute_fix() dvalue = fix->compute_scalar(); if (normflag && fix->extscalar) dvalue /= natoms; } else if (argindex2[ifield] == 0) { + if (fix->size_vector_variable && argindex1[ifield] > fix->size_vector) + error->all(FLERR, "Thermo fix vector is accessed out-of-range"); dvalue = fix->compute_vector(argindex1[ifield] - 1); if (normflag) { if (fix->extvector == 0) @@ -1531,6 +1531,8 @@ void Thermo::compute_fix() dvalue /= natoms; } } else { + if (fix->size_array_rows_variable && argindex1[ifield] > fix->size_array_rows) + error->all(FLERR, "Thermo fix array is accessed out-of-range"); dvalue = fix->compute_array(argindex1[ifield] - 1, argindex2[ifield] - 1); if (normflag && fix->extarray) dvalue /= natoms; } @@ -1547,10 +1549,8 @@ void Thermo::compute_variable() else { double *varvec; int nvec = input->variable->compute_vector(variables[field2index[ifield]], &varvec); - if (nvec < iarg) - dvalue = 0.0; - else - dvalue = varvec[iarg - 1]; + if (iarg > nvec) error->all(FLERR, "Thermo vector-style variable is accessed out-of-range"); + dvalue = varvec[iarg - 1]; } } diff --git a/src/variable.cpp b/src/variable.cpp index 8124d9c4a1..a6a194779c 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -1225,7 +1225,6 @@ int Variable::compute_vector(int ivar, double **result) int nlen = size_tree_vector(tree); if (nlen == 0) print_var_error(FLERR,"Vector-style variable has zero length",ivar); - if (nlen < 0) print_var_error(FLERR,"Inconsistent lengths in vector-style variable",ivar); @@ -1535,9 +1534,6 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->vector_flag) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); - if (index1 > compute->size_vector && - compute->size_vector_variable == 0) - print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0); if (!compute->is_initialized()) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); @@ -1546,10 +1542,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) compute->invoked_flag |= Compute::INVOKED_VECTOR; } - if (compute->size_vector_variable && - index1 > compute->size_vector) value1 = 0.0; - else value1 = compute->vector[index1-1]; - argstack[nargstack++] = value1; + // wait to check index1 until after compute invocation + // to allow for computes with size_vector_variable == 1 + + if (index1 > compute->size_vector) + print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0); + + value1 = compute->vector[index1-1]; + argstack[nargstack++] = value1; // c_ID[i][j] = scalar from global array @@ -1557,9 +1557,6 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->array_flag) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); - if (index1 > compute->size_array_rows && - compute->size_array_rows_variable == 0) - print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); if (index2 > compute->size_array_cols) print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); if (!compute->is_initialized()) @@ -1570,9 +1567,13 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) compute->invoked_flag |= Compute::INVOKED_ARRAY; } - if (compute->size_array_rows_variable && - index1 > compute->size_array_rows) value1 = 0.0; - else value1 = compute->array[index1-1][index2-1]; + // wait to check index1 until after compute invocation + // to allow for computes with size_array_rows_variable == 1 + + if (index1 > compute->size_array_rows) + print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); + + value1 = compute->array[index1-1][index2-1]; argstack[nargstack++] = value1; // C_ID[i] = scalar element of per-atom vector, note uppercase "C" @@ -1634,8 +1635,6 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->vector_flag) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); - if (compute->size_vector == 0) - print_var_error(FLERR,"Variable formula compute vector is zero length",ivar); if (!compute->is_initialized()) print_var_error(FLERR,"Variable formula compute cannot be invoked before " "initialization by a run",ivar); @@ -1644,6 +1643,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) compute->invoked_flag |= Compute::INVOKED_VECTOR; } + // wait to check vector size until after compute invocation + // to allow for computes with size_vector_variable == 1 + + if (compute->size_vector == 0) + print_var_error(FLERR,"Variable formula compute vector is zero length",ivar); + auto newtree = new Tree(); newtree->type = VECTORARRAY; newtree->array = compute->vector; @@ -1657,8 +1662,6 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!compute->array_flag) print_var_error(FLERR,"Mismatched compute in variable formula",ivar); - if (compute->size_array_rows == 0) - print_var_error(FLERR,"Variable formula compute array is zero length",ivar); if (index1 > compute->size_array_cols) print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); if (!compute->is_initialized()) @@ -1669,6 +1672,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) compute->invoked_flag |= Compute::INVOKED_ARRAY; } + // wait to check row count until after compute invocation + // to allow for computes with size_array_rows_variable == 1 + + if (compute->size_array_rows == 0) + print_var_error(FLERR,"Variable formula compute array has zero rows",ivar); + auto newtree = new Tree(); newtree->type = VECTORARRAY; newtree->array = &compute->array[0][index1-1]; @@ -1798,8 +1807,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!fix->vector_flag) print_var_error(FLERR,"Mismatched fix in variable formula",ivar); - if (index1 > fix->size_vector && - fix->size_vector_variable == 0) + if (index1 > fix->size_vector) print_var_error(FLERR,"Variable formula fix vector is accessed out-of-range",ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar); @@ -1813,8 +1821,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (!fix->array_flag) print_var_error(FLERR,"Mismatched fix in variable formula",ivar); - if (index1 > fix->size_array_rows && - fix->size_array_rows_variable == 0) + if (index1 > fix->size_array_rows) print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0); if (index2 > fix->size_array_cols) print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar,0); From dcc791621044d0e42303e0bb5c34d5f42f434204 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 29 Mar 2024 21:32:08 -0400 Subject: [PATCH 14/40] reorder header --- src/OPENMP/angle_cosine_squared_omp.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/OPENMP/angle_cosine_squared_omp.cpp b/src/OPENMP/angle_cosine_squared_omp.cpp index 9b849c62a3..f70e167d36 100644 --- a/src/OPENMP/angle_cosine_squared_omp.cpp +++ b/src/OPENMP/angle_cosine_squared_omp.cpp @@ -16,14 +16,16 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "angle_cosine_squared_omp.h" -#include + #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" +#include + +#include "omp_compat.h" #include "suffix.h" using namespace LAMMPS_NS; From f6bdc05c242c39adf35e6acfa08674a6e27383f3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 30 Mar 2024 19:19:47 -0400 Subject: [PATCH 15/40] alternate fix to PR #4116 --- src/fix_ave_histo_weight.cpp | 228 +++++++++++++++++------------------ 1 file changed, 114 insertions(+), 114 deletions(-) diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 7a5458bd3d..cccfc86d59 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -113,256 +113,256 @@ void FixAveHistoWeight::end_of_step() double weight = 0.0; double *weights = nullptr; int stride = 0; - auto &val = values[1]; - int j = val.argindex; + auto &val1 = values[1]; + int j = val1.argindex; // atom attributes - if (val.which == ArgInfo::X) { + if (val1.which == ArgInfo::X) { weights = &atom->x[0][j]; stride = 3; - } else if (val.which == ArgInfo::V) { + } else if (val1.which == ArgInfo::V) { weights = &atom->v[0][j]; stride = 3; bin_atoms(&atom->v[0][j],3); - } else if (val.which == ArgInfo::F) { + } else if (val1.which == ArgInfo::F) { weights = &atom->f[0][j]; stride = 3; } // invoke compute if not previously invoked - if (val.which == ArgInfo::COMPUTE) { + if (val1.which == ArgInfo::COMPUTE) { if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { - val.val.c->compute_scalar(); - val.val.c->invoked_flag |= Compute::INVOKED_SCALAR; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { + val1.val.c->compute_scalar(); + val1.val.c->invoked_flag |= Compute::INVOKED_SCALAR; } - weight = val.val.c->scalar; + weight = val1.val.c->scalar; } else { - if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { - val.val.c->compute_vector(); - val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val1.val.c->compute_vector(); + val1.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - weight = val.val.c->vector[j-1]; + weight = val1.val.c->vector[j-1]; } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { - val.val.c->compute_vector(); - val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val1.val.c->compute_vector(); + val1.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - weights = val.val.c->vector; + weights = val1.val.c->vector; stride = 1; } else { - if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { - val.val.c->compute_array(); - val.val.c->invoked_flag |= Compute::INVOKED_ARRAY; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { + val1.val.c->compute_array(); + val1.val.c->invoked_flag |= Compute::INVOKED_ARRAY; } - if (val.val.c->array) weights = &val.val.c->array[0][j-1]; - stride = val.val.c->size_array_cols; + if (val1.val.c->array) weights = &val1.val.c->array[0][j-1]; + stride = val1.val.c->size_array_cols; } } else if (kind == PERATOM) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { - val.val.c->compute_peratom(); - val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val1.val.c->compute_peratom(); + val1.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } if (j == 0) { - weights = val.val.c->vector_atom; + weights = val1.val.c->vector_atom; stride = 1; - } else if (val.val.c->array_atom) { - weights = &val.val.c->array_atom[0][j-1]; - stride = val.val.c->size_peratom_cols; + } else if (val1.val.c->array_atom) { + weights = &val1.val.c->array_atom[0][j-1]; + stride = val1.val.c->size_peratom_cols; } } else if (kind == LOCAL) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { - val.val.c->compute_local(); - val.val.c->invoked_flag |= Compute::INVOKED_LOCAL; + if (!(val1.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { + val1.val.c->compute_local(); + val1.val.c->invoked_flag |= Compute::INVOKED_LOCAL; } if (j == 0) { - weights = val.val.c->vector_local; + weights = val1.val.c->vector_local; stride = 1; - } else if (val.val.c->array_local) { - weights = &val.val.c->array_local[0][j-1]; - stride = val.val.c->size_local_cols; + } else if (val1.val.c->array_local) { + weights = &val1.val.c->array_local[0][j-1]; + stride = val1.val.c->size_local_cols; } } // access fix fields, guaranteed to be ready - } else if (val.which == ArgInfo::FIX) { + } else if (val1.which == ArgInfo::FIX) { if (kind == GLOBAL && mode == SCALAR) { - if (j == 0) weight = val.val.f->compute_scalar(); - else weight = val.val.f->compute_vector(j-1); + if (j == 0) weight = val1.val.f->compute_scalar(); + else weight = val1.val.f->compute_vector(j-1); } else if (kind == GLOBAL && mode == VECTOR) { error->all(FLERR,"Fix ave/histo/weight option not yet supported"); // NOTE: need to allocate local storage if (j == 0) { - int n = val.val.f->size_vector; - for (int i = 0; i < n; i++) weights[n] = val.val.f->compute_vector(i); + int n = val1.val.f->size_vector; + for (int i = 0; i < n; i++) weights[n] = val1.val.f->compute_vector(i); } else { - int n = val.val.f->size_vector; - for (int i = 0; i < n; i++) weights[n] = val.val.f->compute_array(i,j-1); + int n = val1.val.f->size_vector; + for (int i = 0; i < n; i++) weights[n] = val1.val.f->compute_array(i,j-1); } } else if (kind == PERATOM) { if (j == 0) { - weights = val.val.f->vector_atom; + weights = val1.val.f->vector_atom; stride = 1; - } else if (val.val.f->array_atom) { - weights = &val.val.f->array_atom[0][j-1]; - stride = val.val.f->size_peratom_cols; + } else if (val1.val.f->array_atom) { + weights = &val1.val.f->array_atom[0][j-1]; + stride = val1.val.f->size_peratom_cols; } } else if (kind == LOCAL) { if (j == 0) { - weights = val.val.f->vector_local; + weights = val1.val.f->vector_local; stride = 1; - } else if (val.val.f->array_local) { - weights = &val.val.f->array_local[0][j-1]; - stride = val.val.f->size_local_cols; + } else if (val1.val.f->array_local) { + weights = &val1.val.f->array_local[0][j-1]; + stride = val1.val.f->size_local_cols; } } // evaluate equal-style variable - } else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL) { - weight = input->variable->compute_equal(val.val.v); + } else if (val1.which == ArgInfo::VARIABLE && kind == GLOBAL) { + weight = input->variable->compute_equal(val1.val.v); - } else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) { + } else if (val1.which == ArgInfo::VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo/weight:vector"); } - input->variable->compute_atom(val.val.v,igroup,vector,1,0); + input->variable->compute_atom(val1.val.v,igroup,vector,1,0); weights = vector; stride = 1; } // bin values using weights, values are 1st value (i = 0) - val = values[0]; - j = val.argindex; + auto &val0 = values[0]; + j = val0.argindex; // atom attributes - if (val.which == ArgInfo::X && weights != nullptr) + if (val0.which == ArgInfo::X && weights != nullptr) bin_atoms_weights(&atom->x[0][j],3,weights,stride); - else if (val.which == ArgInfo::V && weights != nullptr) + else if (val0.which == ArgInfo::V && weights != nullptr) bin_atoms_weights(&atom->v[0][j],3,weights,stride); - else if (val.which == ArgInfo::F && weights != nullptr) + else if (val0.which == ArgInfo::F && weights != nullptr) bin_atoms_weights(&atom->f[0][j],3,weights,stride); // invoke compute if not previously invoked - if (val.which == ArgInfo::COMPUTE) { + if (val0.which == ArgInfo::COMPUTE) { if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { - val.val.c->compute_scalar(); - val.val.c->invoked_flag |= Compute::INVOKED_SCALAR; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_SCALAR)) { + val0.val.c->compute_scalar(); + val0.val.c->invoked_flag |= Compute::INVOKED_SCALAR; } - bin_one_weights(val.val.c->scalar,weight); + bin_one_weights(val0.val.c->scalar,weight); } else { - if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { - val.val.c->compute_vector(); - val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val0.val.c->compute_vector(); + val0.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - bin_one_weights(val.val.c->vector[j-1],weight); + bin_one_weights(val0.val.c->vector[j-1],weight); } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { - val.val.c->compute_vector(); - val.val.c->invoked_flag |= Compute::INVOKED_VECTOR; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_VECTOR)) { + val0.val.c->compute_vector(); + val0.val.c->invoked_flag |= Compute::INVOKED_VECTOR; } - bin_vector_weights(val.val.c->size_vector,val.val.c->vector,1, + bin_vector_weights(val0.val.c->size_vector,val0.val.c->vector,1, weights,stride); } else { - if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { - val.val.c->compute_array(); - val.val.c->invoked_flag |= Compute::INVOKED_ARRAY; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_ARRAY)) { + val0.val.c->compute_array(); + val0.val.c->invoked_flag |= Compute::INVOKED_ARRAY; } - if (val.val.c->array) - bin_vector_weights(val.val.c->size_array_rows,&val.val.c->array[0][j-1], - val.val.c->size_array_cols,weights,stride); + if (val0.val.c->array) + bin_vector_weights(val0.val.c->size_array_rows,&val0.val.c->array[0][j-1], + val0.val.c->size_array_cols,weights,stride); } } else if (kind == PERATOM) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { - val.val.c->compute_peratom(); - val.val.c->invoked_flag |= Compute::INVOKED_PERATOM; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_PERATOM)) { + val0.val.c->compute_peratom(); + val0.val.c->invoked_flag |= Compute::INVOKED_PERATOM; } if (j == 0) - bin_atoms_weights(val.val.c->vector_atom,1,weights, stride); - else if (val.val.c->array_atom) - bin_atoms_weights(&val.val.c->array_atom[0][j-1], - val.val.c->size_peratom_cols,weights,stride); + bin_atoms_weights(val0.val.c->vector_atom,1,weights, stride); + else if (val0.val.c->array_atom) + bin_atoms_weights(&val0.val.c->array_atom[0][j-1], + val0.val.c->size_peratom_cols,weights,stride); } else if (kind == LOCAL) { - if (!(val.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { - val.val.c->compute_local(); - val.val.c->invoked_flag |= Compute::INVOKED_LOCAL; + if (!(val0.val.c->invoked_flag & Compute::INVOKED_LOCAL)) { + val0.val.c->compute_local(); + val0.val.c->invoked_flag |= Compute::INVOKED_LOCAL; } if (j == 0) - bin_vector_weights(val.val.c->size_local_rows, - val.val.c->vector_local,1,weights,stride); - else if (val.val.c->array_local) - bin_vector_weights(val.val.c->size_local_rows, - &val.val.c->array_local[0][j-1], - val.val.c->size_local_cols,weights,stride); + bin_vector_weights(val0.val.c->size_local_rows, + val0.val.c->vector_local,1,weights,stride); + else if (val0.val.c->array_local) + bin_vector_weights(val0.val.c->size_local_rows, + &val0.val.c->array_local[0][j-1], + val0.val.c->size_local_cols,weights,stride); } // access fix fields, guaranteed to be ready - } else if (val.which == ArgInfo::FIX) { + } else if (val0.which == ArgInfo::FIX) { if (kind == GLOBAL && mode == SCALAR) { - if (j == 0) bin_one_weights(val.val.f->compute_scalar(),weight); - else bin_one_weights(val.val.f->compute_vector(j-1),weight); + if (j == 0) bin_one_weights(val0.val.f->compute_scalar(),weight); + else bin_one_weights(val0.val.f->compute_vector(j-1),weight); } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { - int n = val.val.f->size_vector; + int n = val0.val.f->size_vector; for (int i = 0; i < n; i++) - bin_one_weights(val.val.f->compute_vector(i),weights[i*stride]); + bin_one_weights(val0.val.f->compute_vector(i),weights[i*stride]); } else { - int n = val.val.f->size_vector; + int n = val0.val.f->size_vector; for (int i = 0; i < n; i++) - bin_one_weights(val.val.f->compute_array(i,j-1),weights[i*stride]); + bin_one_weights(val0.val.f->compute_array(i,j-1),weights[i*stride]); } } else if (kind == PERATOM) { if (j == 0) - bin_atoms_weights(val.val.f->vector_atom,1,weights,stride); - else if (val.val.f->array_atom) - bin_atoms_weights(&val.val.f->array_atom[0][j-1],val.val.f->size_peratom_cols, + bin_atoms_weights(val0.val.f->vector_atom,1,weights,stride); + else if (val0.val.f->array_atom) + bin_atoms_weights(&val0.val.f->array_atom[0][j-1],val0.val.f->size_peratom_cols, weights,stride); } else if (kind == LOCAL) { - if (j == 0) bin_vector_weights(val.val.f->size_local_rows,val.val.f->vector_local,1, + if (j == 0) bin_vector_weights(val0.val.f->size_local_rows,val0.val.f->vector_local,1, weights,stride); - else if (val.val.f->array_local) - bin_vector_weights(val.val.f->size_local_rows,&val.val.f->array_local[0][j-1], - val.val.f->size_local_cols,weights,stride); + else if (val0.val.f->array_local) + bin_vector_weights(val0.val.f->size_local_rows,&val0.val.f->array_local[0][j-1], + val0.val.f->size_local_cols,weights,stride); } // evaluate equal-style variable - } else if (val.which == ArgInfo::VARIABLE && kind == GLOBAL) { - bin_one_weights(input->variable->compute_equal(val.val.v),weight); + } else if (val0.which == ArgInfo::VARIABLE && kind == GLOBAL) { + bin_one_weights(input->variable->compute_equal(val0.val.v),weight); - } else if (val.which == ArgInfo::VARIABLE && kind == PERATOM) { + } else if (val0.which == ArgInfo::VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo/weight:vector"); } - input->variable->compute_atom(val.val.v,igroup,vector,1,0); + input->variable->compute_atom(val0.val.v,igroup,vector,1,0); bin_atoms_weights(vector,1,weights,stride); } From ae6247d3be85e49f1243229b64ca92be108dcf74 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 31 Mar 2024 17:41:35 -0400 Subject: [PATCH 16/40] remove xdr_compat.h include and pimplify XDR struct, silence compiler warnings --- src/EXTRA-DUMP/dump_xtc.cpp | 45 ++++++++++++++++++++----------------- src/EXTRA-DUMP/dump_xtc.h | 4 ++-- 2 files changed, 27 insertions(+), 22 deletions(-) diff --git a/src/EXTRA-DUMP/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp index 798bdcb391..9d4ec1b9bb 100644 --- a/src/EXTRA-DUMP/dump_xtc.cpp +++ b/src/EXTRA-DUMP/dump_xtc.cpp @@ -35,6 +35,8 @@ #include "output.h" #include "update.h" +#include "xdr_compat.h" + #include #include #include @@ -47,15 +49,15 @@ using namespace LAMMPS_NS; #define MYMIN(a,b) ((a) < (b) ? (a) : (b)) #define MYMAX(a,b) ((a) > (b) ? (a) : (b)) -int xdropen(XDR *, const char *, const char *); -int xdrclose(XDR *); -void xdrfreebuf(); -int xdr3dfcoord(XDR *, float *, int *, float *); +static int xdropen(XDR *, const char *, const char *); +static int xdrclose(XDR *); +static void xdrfreebuf(); +static int xdr3dfcoord(XDR *, float *, int *, float *); /* ---------------------------------------------------------------------- */ -DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg), - coords(nullptr) +DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) + : Dump(lmp, narg, arg), coords(nullptr), xd(nullptr) { if (narg != 5) error->all(FLERR,"Illegal dump xtc command"); if (binary || compressed || multifile || multiproc) @@ -68,6 +70,7 @@ DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg), flush_flag = 0; unwrap_flag = 0; precision = 1000.0; + xd = new XDR; // allocate global array for atom coords @@ -105,9 +108,10 @@ DumpXTC::~DumpXTC() memory->destroy(coords); if (me == 0) { - xdrclose(&xd); + xdrclose(xd); xdrfreebuf(); } + delete xd; } /* ---------------------------------------------------------------------- */ @@ -150,7 +154,8 @@ void DumpXTC::openfile() fp = nullptr; if (me == 0) - if (xdropen(&xd,filename,"w") == 0) error->one(FLERR,"Cannot open dump file"); + if (xdropen(xd,filename,"w") == 0) + error->one(FLERR,"Cannot open XTC format dump file {}: {}", filename, utils::getsyserror()); } /* ---------------------------------------------------------------------- */ @@ -176,11 +181,11 @@ void DumpXTC::write_header(bigint nbig) if (me != 0) return; int tmp = XTC_MAGIC; - xdr_int(&xd,&tmp); - xdr_int(&xd,&n); - xdr_int(&xd,&ntimestep); + xdr_int(xd,&tmp); + xdr_int(xd,&n); + xdr_int(xd,&ntimestep); float time_value = ntimestep * tfactor * update->dt; - xdr_float(&xd,&time_value); + xdr_float(xd,&time_value); // cell basis vectors if (domain->triclinic) { @@ -192,18 +197,18 @@ void DumpXTC::write_header(bigint nbig) float xz = sfactor * domain->xz; float yz = sfactor * domain->yz; - xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero); - xdr_float(&xd,&xy ); xdr_float(&xd,&ydim); xdr_float(&xd,&zero); - xdr_float(&xd,&xz ); xdr_float(&xd,&yz ); xdr_float(&xd,&zdim); + xdr_float(xd,&xdim); xdr_float(xd,&zero); xdr_float(xd,&zero); + xdr_float(xd,&xy ); xdr_float(xd,&ydim); xdr_float(xd,&zero); + xdr_float(xd,&xz ); xdr_float(xd,&yz ); xdr_float(xd,&zdim); } else { float zero = 0.0; float xdim = sfactor * (domain->boxhi[0] - domain->boxlo[0]); float ydim = sfactor * (domain->boxhi[1] - domain->boxlo[1]); float zdim = sfactor * (domain->boxhi[2] - domain->boxlo[2]); - xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero); - xdr_float(&xd,&zero); xdr_float(&xd,&ydim); xdr_float(&xd,&zero); - xdr_float(&xd,&zero); xdr_float(&xd,&zero); xdr_float(&xd,&zdim); + xdr_float(xd,&xdim); xdr_float(xd,&zero); xdr_float(xd,&zero); + xdr_float(xd,&zero); xdr_float(xd,&ydim); xdr_float(xd,&zero); + xdr_float(xd,&zero); xdr_float(xd,&zero); xdr_float(xd,&zdim); } } @@ -328,7 +333,7 @@ double DumpXTC::memory_usage() void DumpXTC::write_frame() { - xdr3dfcoord(&xd,coords,&natoms,&precision); + xdr3dfcoord(xd,coords,&natoms,&precision); } // ---------------------------------------------------------------------- @@ -406,7 +411,7 @@ static int magicints[] = { | | xdropen - open xdr file | - | This versions differs from xdrstdio_create, because I need to know + | This version differs from xdrstdio_create, because I need to know | the state of the file (read or write) so I can use xdr3dfcoord | in eigther read or write mode, and the file descriptor | so I can close the file (something xdr_destroy doesn't do). diff --git a/src/EXTRA-DUMP/dump_xtc.h b/src/EXTRA-DUMP/dump_xtc.h index 74147be06b..0a27cc67dd 100644 --- a/src/EXTRA-DUMP/dump_xtc.h +++ b/src/EXTRA-DUMP/dump_xtc.h @@ -21,8 +21,8 @@ DumpStyle(xtc,DumpXTC); #define LMP_DUMP_XTC_H #include "dump.h" -#include "xdr_compat.h" +struct XDR; namespace LAMMPS_NS { class DumpXTC : public Dump { @@ -37,7 +37,7 @@ class DumpXTC : public Dump { float precision; // user-adjustable precision setting float *coords; double sfactor, tfactor; // scaling factors for positions and time unit - XDR xd; + XDR *xd; void init_style() override; int modify_param(int, char **) override; From 0cdbcc801ef72ef9017a5e9aeae24c68e4f1dd87 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 31 Mar 2024 17:42:41 -0400 Subject: [PATCH 17/40] switch to BSD 3-clause licensed XDR version, use c++11 portability, cleanups --- src/EXTRA-DUMP/xdr_compat.cpp | 258 +++++++++++++++++----------------- src/EXTRA-DUMP/xdr_compat.h | 106 +++++--------- 2 files changed, 164 insertions(+), 200 deletions(-) diff --git a/src/EXTRA-DUMP/xdr_compat.cpp b/src/EXTRA-DUMP/xdr_compat.cpp index e29bbe8334..0d1e38d901 100644 --- a/src/EXTRA-DUMP/xdr_compat.cpp +++ b/src/EXTRA-DUMP/xdr_compat.cpp @@ -3,52 +3,68 @@ #include #include -/* This file is needed for systems, that do not provide XDR support - * in their system libraries. It was written for windows, but will - * most probably work on other platforms too. better make sure you - * test that the xtc files produced are ok before using it. +/* + * This file contains an implementation of the Sun External Data Representation (XDR) + * routines. They have been adapted specifically for the use with the LAMMPS xtc dump + * style to produce compressed trajectory files in the Gromacs XTC format. * - * It is also needed on BG/L and Cray XT3/XT4 as we don't have - * XDR support in the lightweight kernel runtimes either. + * The XDR sources are avaiable under the BSD 3-clause license for example in + * the MIT Kerberos 5 distribution with the following copyright notice and license. * - * This file contains the definitions for Sun External Data - * Representation (XDR) headers and routines. + * @(#)xdr.h 2.2 88/07/29 4.0 RPCSRC * - * Although the rest of LAMPPS is GPL, you can copy and use the XDR - * routines in any way you want as long as you obey Sun's license: + * Copyright (c) 2010, Oracle America, Inc. * - * Sun RPC is a product of Sun Microsystems, Inc. and is provided for - * unrestricted use provided that this legend is included on all tape - * media and as a part of the software program in whole or part. Users - * may copy or modify Sun RPC without charge, but are not authorized - * to license or distribute it to anyone else except as part of a product or - * program developed by the user. + * All rights reserved. * - * SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE - * WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR - * PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE. + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: * - * Sun RPC is provided with no support and without any obligation on the - * part of Sun Microsystems, Inc. to assist in its use, correction, - * modification or enhancement. + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. * - * SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE - * INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC - * OR ANY PART THEREOF. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in + * the documentation and/or other materials provided with the + * distribution. * - * In no event will Sun Microsystems, Inc. be liable for any lost revenue - * or profits or other special, indirect and consequential damages, even if - * Sun has been advised of the possibility of such damages. + * * Neither the name of the "Oracle America, Inc." nor the names of + * its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. * - * Sun Microsystems, Inc. - * 2550 Garcia Avenue - * Mountain View, California 94043 + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS + * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED + * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A + * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR + * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF + * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifdef __cplusplus extern "C" { #endif +/* compatibility typedefs */ +#if defined(_WIN32) || defined(__APPLE__) || defined(__FreeBSD__) || defined(__DragonFly__) || \ + defined(__OpenBSD__) || defined(__NetBSD__) || (defined(__linux__) && !defined(__GLIBC_MINOR__)) +typedef char *caddr_t; +typedef unsigned int u_int; +#endif + +#ifndef FALSE +#define FALSE (0) +#endif +#ifndef TRUE +#define TRUE (1) +#endif + +#define BYTES_PER_XDR_UNIT (4) + /* * for unit alignment */ @@ -96,20 +112,18 @@ static xdr_uint32_t xdr_ntohl(xdr_uint32_t x) * Free a data structure using XDR * Not a filter, but a convenient utility nonetheless */ -void -xdr_free (xdrproc_t proc, char *objp) +void xdr_free(xdrproc_t proc, char *objp) { XDR x; x.x_op = XDR_FREE; - (*proc) (&x, objp); + (*proc)(&x, objp); } /* * XDR nothing */ -bool_t -xdr_void (void) +bool_t xdr_void(void) { return TRUE; } @@ -117,23 +131,21 @@ xdr_void (void) /* * XDR integers */ -bool_t -xdr_int (XDR *xdrs, int *ip) +bool_t xdr_int(XDR *xdrs, int *ip) { xdr_int32_t l; switch (xdrs->x_op) { case XDR_ENCODE: - l = (xdr_int32_t) (*ip); - return xdr_putint32 (xdrs, &l); + l = (xdr_int32_t)(*ip); + return xdr_putint32(xdrs, &l); case XDR_DECODE: - if (!xdr_getint32 (xdrs, &l)) - { + if (!xdr_getint32(xdrs, &l)) return FALSE; - } *ip = (int) l; + return TRUE; case XDR_FREE: return TRUE; @@ -145,23 +157,21 @@ xdr_int (XDR *xdrs, int *ip) /* * XDR unsigned integers */ -bool_t -xdr_u_int (XDR *xdrs, unsigned int *up) +bool_t xdr_u_int(XDR *xdrs, unsigned int *up) { xdr_uint32_t l; switch (xdrs->x_op) { case XDR_ENCODE: - l = (xdr_uint32_t) (*up); - return xdr_putuint32 (xdrs, &l); + l = (xdr_uint32_t)(*up); + return xdr_putuint32(xdrs, &l); case XDR_DECODE: - if (!xdr_getuint32 (xdrs, &l)) - { + if (!xdr_getuint32(xdrs, &l)) return FALSE; - } *up = (unsigned int) l; + return TRUE; case XDR_FREE: return TRUE; @@ -176,7 +186,7 @@ xdr_u_int (XDR *xdrs, unsigned int *up) * XDR short integers */ bool_t -xdr_short (XDR *xdrs, short *sp) +xdr_short(XDR *xdrs, short *sp) { xdr_int32_t l; @@ -184,10 +194,10 @@ xdr_short (XDR *xdrs, short *sp) { case XDR_ENCODE: l = (xdr_int32_t) *sp; - return xdr_putint32 (xdrs, &l); + return xdr_putint32(xdrs, &l); case XDR_DECODE: - if (!xdr_getint32 (xdrs, &l)) + if (!xdr_getint32(xdrs, &l)) { return FALSE; } @@ -205,7 +215,7 @@ xdr_short (XDR *xdrs, short *sp) * XDR unsigned short integers */ bool_t -xdr_u_short (XDR *xdrs, unsigned short *usp) +xdr_u_short(XDR *xdrs, unsigned short *usp) { xdr_uint32_t l; @@ -213,10 +223,10 @@ xdr_u_short (XDR *xdrs, unsigned short *usp) { case XDR_ENCODE: l = (xdr_uint32_t) *usp; - return xdr_putuint32 (xdrs, &l); + return xdr_putuint32(xdrs, &l); case XDR_DECODE: - if (!xdr_getuint32 (xdrs, &l)) + if (!xdr_getuint32(xdrs, &l)) { return FALSE; } @@ -234,12 +244,12 @@ xdr_u_short (XDR *xdrs, unsigned short *usp) * XDR a char */ bool_t -xdr_char (XDR *xdrs, char *cp) +xdr_char(XDR *xdrs, char *cp) { int i; i = (*cp); - if (!xdr_int (xdrs, &i)) + if (!xdr_int(xdrs, &i)) { return FALSE; } @@ -251,12 +261,12 @@ xdr_char (XDR *xdrs, char *cp) * XDR an unsigned char */ bool_t -xdr_u_char (XDR *xdrs, unsigned char *cp) +xdr_u_char(XDR *xdrs, unsigned char *cp) { unsigned int u; u = (*cp); - if (!xdr_u_int (xdrs, &u)) + if (!xdr_u_int(xdrs, &u)) { return FALSE; } @@ -268,7 +278,7 @@ xdr_u_char (XDR *xdrs, unsigned char *cp) * XDR booleans */ bool_t -xdr_bool (XDR *xdrs, int *bp) +xdr_bool(XDR *xdrs, int *bp) { #define XDR_FALSE ((xdr_int32_t) 0) #define XDR_TRUE ((xdr_int32_t) 1) @@ -279,10 +289,10 @@ xdr_bool (XDR *xdrs, int *bp) { case XDR_ENCODE: lb = *bp ? XDR_TRUE : XDR_FALSE; - return xdr_putint32 (xdrs, &lb); + return xdr_putint32(xdrs, &lb); case XDR_DECODE: - if (!xdr_getint32 (xdrs, &lb)) + if (!xdr_getint32(xdrs, &lb)) { return FALSE; } @@ -305,7 +315,7 @@ xdr_bool (XDR *xdrs, int *bp) * cp points to the opaque object and cnt gives the byte length. */ bool_t -xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt) +xdr_opaque(XDR *xdrs, char *cp, unsigned int cnt) { unsigned int rndup; static char crud[BYTES_PER_XDR_UNIT]; @@ -326,22 +336,22 @@ xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt) switch (xdrs->x_op) { case XDR_DECODE: - if (!xdr_getbytes (xdrs, cp, cnt)) + if (!xdr_getbytes(xdrs, cp, cnt)) { return FALSE; } if (rndup == 0) return TRUE; - return xdr_getbytes (xdrs, (char *)crud, rndup); + return xdr_getbytes(xdrs, (char *)crud, rndup); case XDR_ENCODE: - if (!xdr_putbytes (xdrs, cp, cnt)) + if (!xdr_putbytes(xdrs, cp, cnt)) { return FALSE; } if (rndup == 0) return TRUE; - return xdr_putbytes (xdrs, xdr_zero, rndup); + return xdr_putbytes(xdrs, xdr_zero, rndup); case XDR_FREE: return TRUE; @@ -359,7 +369,7 @@ xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt) * of the string as specified by a protocol. */ bool_t -xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize) +xdr_string(XDR *xdrs, char **cpp, unsigned int maxsize) { char *sp = *cpp; /* sp is the actual string pointer */ unsigned int size = 0; @@ -379,13 +389,13 @@ xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize) case XDR_ENCODE: if (sp == nullptr) return FALSE; - size = strlen (sp); + size = strlen(sp); break; case XDR_DECODE: break; } - if (!xdr_u_int (xdrs, &size)) + if (!xdr_u_int(xdrs, &size)) { return FALSE; } @@ -406,20 +416,20 @@ xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize) return TRUE; } if (sp == nullptr) - *cpp = sp = (char *) malloc (nodesize); + *cpp = sp = (char *) malloc(nodesize); if (sp == nullptr) { - (void) fputs ("xdr_string: out of memory\n", stderr); + (void) fputs("xdr_string: out of memory\n", stderr); return FALSE; } sp[size] = 0; - /* fall into ... */ + return xdr_opaque(xdrs, sp, size); case XDR_ENCODE: - return xdr_opaque (xdrs, sp, size); + return xdr_opaque(xdrs, sp, size); case XDR_FREE: - free (sp); + free(sp); *cpp = nullptr; return TRUE; } @@ -446,15 +456,15 @@ xdr_float(XDR *xdrs, float *fp) case XDR_DECODE: if (xdr_getint32(xdrs, &tmp)) { *(xdr_int32_t *)fp = tmp; - return (TRUE); + return TRUE; } break; case XDR_FREE: - return (TRUE); + return TRUE; } - return (FALSE); + return FALSE; } @@ -515,15 +525,15 @@ xdr_double(XDR *xdrs, double *dp) xdr_getint32(xdrs, tmp+LSW)) { ip[0] = tmp[0]; ip[1] = tmp[1]; - return (TRUE); + return TRUE; } break; case XDR_FREE: - return (TRUE); + return TRUE; } - return (FALSE); + return FALSE; } @@ -540,7 +550,7 @@ xdr_double(XDR *xdrs, double *dp) * > xdr_elem: routine to XDR each element */ bool_t -xdr_vector (XDR *xdrs, char *basep, unsigned int nelem, +xdr_vector(XDR *xdrs, char *basep, unsigned int nelem, unsigned int elemsize, xdrproc_t xdr_elem) { #define LASTUNSIGNED ((unsigned int)0-1) @@ -550,7 +560,7 @@ xdr_vector (XDR *xdrs, char *basep, unsigned int nelem, elptr = basep; for (i = 0; i < nelem; i++) { - if (!(*xdr_elem) (xdrs, elptr, LASTUNSIGNED)) + if (!(*xdr_elem)(xdrs, elptr, LASTUNSIGNED)) { return FALSE; } @@ -560,18 +570,16 @@ xdr_vector (XDR *xdrs, char *basep, unsigned int nelem, #undef LASTUNSIGNED } - - -static bool_t xdrstdio_getbytes (XDR *, char *, unsigned int); -static bool_t xdrstdio_putbytes (XDR *, char *, unsigned int); -static unsigned int xdrstdio_getpos (XDR *); -static bool_t xdrstdio_setpos (XDR *, unsigned int); -static xdr_int32_t *xdrstdio_inline (XDR *, int); -static void xdrstdio_destroy (XDR *); -static bool_t xdrstdio_getint32 (XDR *, xdr_int32_t *); -static bool_t xdrstdio_putint32 (XDR *, xdr_int32_t *); -static bool_t xdrstdio_getuint32 (XDR *, xdr_uint32_t *); -static bool_t xdrstdio_putuint32 (XDR *, xdr_uint32_t *); +static bool_t xdrstdio_getbytes(XDR *, char *, unsigned int); +static bool_t xdrstdio_putbytes(XDR *, char *, unsigned int); +static unsigned int xdrstdio_getpos(XDR *); +static bool_t xdrstdio_setpos(XDR *, unsigned int); +static xdr_int32_t *xdrstdio_inline(XDR *, int); +static void xdrstdio_destroy(XDR *); +static bool_t xdrstdio_getint32(XDR *, xdr_int32_t *); +static bool_t xdrstdio_putint32(XDR *, xdr_int32_t *); +static bool_t xdrstdio_getuint32(XDR *, xdr_uint32_t *); +static bool_t xdrstdio_putuint32(XDR *, xdr_uint32_t *); /* * Ops vector for stdio type XDR @@ -595,8 +603,7 @@ static const struct xdr_ops xdrstdio_ops = * Sets the xdr stream handle xdrs for use on the stream file. * Operation flag is set to op. */ -void -xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op) +void xdrstdio_create(XDR *xdrs, FILE *file, enum xdr_op op) { xdrs->x_op = op; /* We have to add the const since the `struct xdr_ops' in `struct XDR' @@ -611,46 +618,38 @@ xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op) * Destroy a stdio xdr stream. * Cleans up the xdr stream handle xdrs previously set up by xdrstdio_create. */ -static void -xdrstdio_destroy (XDR *xdrs) +static void xdrstdio_destroy(XDR *xdrs) { - (void) fflush ((FILE *) xdrs->x_private); + (void) fflush((FILE *) xdrs->x_private); /* xx should we close the file ?? */ } -static bool_t -xdrstdio_getbytes (XDR *xdrs, char *addr, unsigned int len) +static bool_t xdrstdio_getbytes(XDR *xdrs, char *addr, unsigned int len) { - if ((len != 0) && (fread (addr, (int) len, 1, - (FILE *) xdrs->x_private) != 1)) + if ((len != 0) && (fread(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) return FALSE; return TRUE; } -static bool_t -xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len) +static bool_t xdrstdio_putbytes(XDR *xdrs, char *addr, unsigned int len) { - if ((len != 0) && (fwrite (addr, (int) len, 1, - (FILE *) xdrs->x_private) != 1)) + if ((len != 0) && (fwrite(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) return FALSE; return TRUE; } -static unsigned int -xdrstdio_getpos (XDR *xdrs) +static unsigned int xdrstdio_getpos(XDR *xdrs) { - return (unsigned int) ftell ((FILE *) xdrs->x_private); + return (unsigned int) ftell((FILE *) xdrs->x_private); } -static bool_t -xdrstdio_setpos (XDR *xdrs, unsigned int pos) +static bool_t xdrstdio_setpos(XDR *xdrs, unsigned int pos) { - return fseek ((FILE *) xdrs->x_private, (xdr_int32_t) pos, 0) < 0 ? FALSE : TRUE; + return fseek((FILE *) xdrs->x_private, (xdr_int32_t) pos, 0) < 0 ? FALSE : TRUE; } -static xdr_int32_t * -xdrstdio_inline (XDR * /*xdrs*/, int /*len*/) +static xdr_int32_t *xdrstdio_inline(XDR * /*xdrs*/, int /*len*/) { /* * Must do some work to implement this: must ensure @@ -664,46 +663,42 @@ xdrstdio_inline (XDR * /*xdrs*/, int /*len*/) return nullptr; } -static bool_t -xdrstdio_getint32 (XDR *xdrs, xdr_int32_t *ip) +static bool_t xdrstdio_getint32(XDR *xdrs, xdr_int32_t *ip) { xdr_int32_t mycopy; - if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) + if (fread((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE; - *ip = xdr_ntohl (mycopy); + *ip = xdr_ntohl(mycopy); return TRUE; } -static bool_t -xdrstdio_putint32 (XDR *xdrs, xdr_int32_t *ip) +static bool_t xdrstdio_putint32(XDR *xdrs, xdr_int32_t *ip) { - xdr_int32_t mycopy = xdr_htonl (*ip); + xdr_int32_t mycopy = xdr_htonl(*ip); ip = &mycopy; - if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) + if (fwrite((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE; return TRUE; } -static bool_t -xdrstdio_getuint32 (XDR *xdrs, xdr_uint32_t *ip) +static bool_t xdrstdio_getuint32(XDR *xdrs, xdr_uint32_t *ip) { xdr_uint32_t mycopy; - if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) + if (fread((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE; *ip = xdr_ntohl (mycopy); return TRUE; } -static bool_t -xdrstdio_putuint32 (XDR *xdrs, xdr_uint32_t *ip) +static bool_t xdrstdio_putuint32(XDR *xdrs, xdr_uint32_t *ip) { xdr_uint32_t mycopy = xdr_htonl (*ip); ip = &mycopy; - if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) + if (fwrite((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE; return TRUE; } @@ -711,4 +706,3 @@ xdrstdio_putuint32 (XDR *xdrs, xdr_uint32_t *ip) #ifdef __cplusplus } #endif - diff --git a/src/EXTRA-DUMP/xdr_compat.h b/src/EXTRA-DUMP/xdr_compat.h index 55dc22e9f9..b63e13f6d8 100644 --- a/src/EXTRA-DUMP/xdr_compat.h +++ b/src/EXTRA-DUMP/xdr_compat.h @@ -1,7 +1,7 @@ #ifndef LMP_XDR_COMPAT_H #define LMP_XDR_COMPAT_H -#include +#include #include #ifdef __cplusplus @@ -9,47 +9,53 @@ extern "C" { #endif /* - * This file is needed for systems, that do not provide XDR support - * in their system libraries. It was written for windows, but will - * most probably work on other platforms too. better make sure you - * test that the xtc files produced are ok before using it. + * This file contains the definitions for Sun External Data Representation (XDR). + * They have been adapted specifically for the use with the LAMMPS xtc dump style + * to produce compressed trajectory files in the Gromacs XTC format. * - * It is also needed on BG/L, BG/P and Cray XT3/XT4/XT5 as we don't - * have XDR support in the lightweight kernel runtimes either. + * The XDR sources are avaiable under the BSD 3-clause license for example in + * the MIT Kerberos 5 distribution with the following copyright notice and license. * - * This file contains the definitions for Sun External Data - * Representation (XDR) headers and routines. + * @(#)xdr.h 2.2 88/07/29 4.0 RPCSRC * - * Although the rest of LAMPPS is GPL, you can copy and use the XDR - * routines in any way you want as long as you obey Sun's license: - * Sun RPC is a product of Sun Microsystems, Inc. and is provided for - * unrestricted use provided that this legend is included on all tape - * media and as a part of the software program in whole or part. Users - * may copy or modify Sun RPC without charge, but are not authorized - * to license or distribute it to anyone else except as part of a product or - * program developed by the user. + * Copyright (c) 2010, Oracle America, Inc. * - * SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE - * WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR - * PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE. + * All rights reserved. * - * Sun RPC is provided with no support and without any obligation on the - * part of Sun Microsystems, Inc. to assist in its use, correction, - * modification or enhancement. + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions are met: * - * SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE - * INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC - * OR ANY PART THEREOF. + * * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. * - * In no event will Sun Microsystems, Inc. be liable for any lost revenue - * or profits or other special, indirect and consequential damages, even if - * Sun has been advised of the possibility of such damages. + * * Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in + * the documentation and/or other materials provided with the + * distribution. * - * Sun Microsystems, Inc. - * 2550 Garcia Avenue - * Mountain View, California 94043 + * * Neither the name of the "Oracle America, Inc." nor the names of + * its contributors may be used to endorse or promote products + * derived from this software without specific prior written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS + * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED + * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A + * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR + * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF + * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ +/* compatibility typedefs */ +typedef int bool_t; + +typedef int32_t xdr_int32_t; +typedef uint32_t xdr_uint32_t; + /* * Xdr operations. XDR_ENCODE causes the type to be encoded into the * stream. XDR_DECODE causes the type to be extracted from the stream. @@ -57,44 +63,8 @@ extern "C" { * XDR_DECODE request. */ -typedef int bool_t; - -#if defined(_WIN32) || defined(__APPLE__) || defined(__FreeBSD__) || defined(__DragonFly__) || \ - defined(__OpenBSD__) || defined(__NetBSD__) || (defined(__linux__) && !defined(__GLIBC_MINOR__)) -typedef char *caddr_t; -typedef unsigned int u_int; -#endif - -/* - * Aninteger type that is 32 bits wide. Check if int, - * long or short is 32 bits and die if none of them is :-) - */ -#if (INT_MAX == 2147483647) -typedef int xdr_int32_t; -typedef unsigned int xdr_uint32_t; -#elif (LONG_MAX == 2147483647L) -typedef long xdr_int32_t; -typedef unsigned long xdr_uint32_t; -#elif (SHRT_MAX == 2147483647) -typedef short xdr_int32_t; -typedef unsigned short xdr_uint32_t; -#else -#error ERROR: No 32 bit wide integer type found! -#endif - enum xdr_op { XDR_ENCODE = 0, XDR_DECODE = 1, XDR_FREE = 2 }; -#ifndef FALSE -#define FALSE (0) -#endif -#ifndef TRUE -#define TRUE (1) -#endif - -#define BYTES_PER_XDR_UNIT (4) -/* Macro to round up to units of 4. */ -#define XDR_RNDUP(x) (((x) + BYTES_PER_XDR_UNIT - 1) & ~(BYTES_PER_XDR_UNIT - 1)) - /* * The XDR handle. * Contains operation which is being applied to the stream, From ff91728587bc995f2a0a07e76ea25aa1abc8f161 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 31 Mar 2024 18:09:40 -0400 Subject: [PATCH 18/40] reduce XDR compatibility code to only those routines that are used by dump xtc --- src/EXTRA-DUMP/xdr_compat.cpp | 400 +--------------------------------- src/EXTRA-DUMP/xdr_compat.h | 45 +--- 2 files changed, 14 insertions(+), 431 deletions(-) diff --git a/src/EXTRA-DUMP/xdr_compat.cpp b/src/EXTRA-DUMP/xdr_compat.cpp index 0d1e38d901..e69a2b72e9 100644 --- a/src/EXTRA-DUMP/xdr_compat.cpp +++ b/src/EXTRA-DUMP/xdr_compat.cpp @@ -107,27 +107,6 @@ static xdr_uint32_t xdr_ntohl(xdr_uint32_t x) } } - -/* - * Free a data structure using XDR - * Not a filter, but a convenient utility nonetheless - */ -void xdr_free(xdrproc_t proc, char *objp) -{ - XDR x; - - x.x_op = XDR_FREE; - (*proc)(&x, objp); -} - -/* - * XDR nothing - */ -bool_t xdr_void(void) -{ - return TRUE; -} - /* * XDR integers */ @@ -153,169 +132,12 @@ bool_t xdr_int(XDR *xdrs, int *ip) return FALSE; } - -/* - * XDR unsigned integers - */ -bool_t xdr_u_int(XDR *xdrs, unsigned int *up) -{ - xdr_uint32_t l; - - switch (xdrs->x_op) - { - case XDR_ENCODE: - l = (xdr_uint32_t)(*up); - return xdr_putuint32(xdrs, &l); - - case XDR_DECODE: - if (!xdr_getuint32(xdrs, &l)) - return FALSE; - *up = (unsigned int) l; - return TRUE; - - case XDR_FREE: - return TRUE; - } - return FALSE; -} - - - - -/* - * XDR short integers - */ -bool_t -xdr_short(XDR *xdrs, short *sp) -{ - xdr_int32_t l; - - switch (xdrs->x_op) - { - case XDR_ENCODE: - l = (xdr_int32_t) *sp; - return xdr_putint32(xdrs, &l); - - case XDR_DECODE: - if (!xdr_getint32(xdrs, &l)) - { - return FALSE; - } - *sp = (short) l; - return TRUE; - - case XDR_FREE: - return TRUE; - } - return FALSE; -} - - -/* - * XDR unsigned short integers - */ -bool_t -xdr_u_short(XDR *xdrs, unsigned short *usp) -{ - xdr_uint32_t l; - - switch (xdrs->x_op) - { - case XDR_ENCODE: - l = (xdr_uint32_t) *usp; - return xdr_putuint32(xdrs, &l); - - case XDR_DECODE: - if (!xdr_getuint32(xdrs, &l)) - { - return FALSE; - } - *usp = (unsigned short) l; - return TRUE; - - case XDR_FREE: - return TRUE; - } - return FALSE; -} - - -/* - * XDR a char - */ -bool_t -xdr_char(XDR *xdrs, char *cp) -{ - int i; - - i = (*cp); - if (!xdr_int(xdrs, &i)) - { - return FALSE; - } - *cp = i; - return TRUE; -} - -/* - * XDR an unsigned char - */ -bool_t -xdr_u_char(XDR *xdrs, unsigned char *cp) -{ - unsigned int u; - - u = (*cp); - if (!xdr_u_int(xdrs, &u)) - { - return FALSE; - } - *cp = u; - return TRUE; -} - -/* - * XDR booleans - */ -bool_t -xdr_bool(XDR *xdrs, int *bp) -{ -#define XDR_FALSE ((xdr_int32_t) 0) -#define XDR_TRUE ((xdr_int32_t) 1) - - xdr_int32_t lb; - - switch (xdrs->x_op) - { - case XDR_ENCODE: - lb = *bp ? XDR_TRUE : XDR_FALSE; - return xdr_putint32(xdrs, &lb); - - case XDR_DECODE: - if (!xdr_getint32(xdrs, &lb)) - { - return FALSE; - } - *bp = (lb == XDR_FALSE) ? FALSE : TRUE; - return TRUE; - - case XDR_FREE: - return TRUE; - } - return FALSE; -#undef XDR_FALSE -#undef XDR_TRUE -} - - - /* * XDR opaque data * Allows the specification of a fixed size sequence of opaque bytes. * cp points to the opaque object and cnt gives the byte length. */ -bool_t -xdr_opaque(XDR *xdrs, char *cp, unsigned int cnt) +bool_t xdr_opaque(XDR *xdrs, char *cp, unsigned int cnt) { unsigned int rndup; static char crud[BYTES_PER_XDR_UNIT]; @@ -360,88 +182,9 @@ xdr_opaque(XDR *xdrs, char *cp, unsigned int cnt) } -/* - * XDR null terminated ASCII strings - * xdr_string deals with "C strings" - arrays of bytes that are - * terminated by a nullptr character. The parameter cpp references a - * pointer to storage; If the pointer is null, then the necessary - * storage is allocated. The last parameter is the max allowed length - * of the string as specified by a protocol. - */ -bool_t -xdr_string(XDR *xdrs, char **cpp, unsigned int maxsize) -{ - char *sp = *cpp; /* sp is the actual string pointer */ - unsigned int size = 0; - unsigned int nodesize = 0; - - /* - * first deal with the length since xdr strings are counted-strings - */ - switch (xdrs->x_op) - { - case XDR_FREE: - if (sp == nullptr) - { - return TRUE; /* already free */ - } - /* fall through... */ - case XDR_ENCODE: - if (sp == nullptr) - return FALSE; - size = strlen(sp); - break; - case XDR_DECODE: - break; - } - - if (!xdr_u_int(xdrs, &size)) - { - return FALSE; - } - if (size > maxsize) - { - return FALSE; - } - nodesize = size + 1; - - /* - * now deal with the actual bytes - */ - switch (xdrs->x_op) - { - case XDR_DECODE: - if (nodesize == 0) - { - return TRUE; - } - if (sp == nullptr) - *cpp = sp = (char *) malloc(nodesize); - if (sp == nullptr) - { - (void) fputs("xdr_string: out of memory\n", stderr); - return FALSE; - } - sp[size] = 0; - return xdr_opaque(xdrs, sp, size); - - case XDR_ENCODE: - return xdr_opaque(xdrs, sp, size); - - case XDR_FREE: - free(sp); - *cpp = nullptr; - return TRUE; - } - return FALSE; -} - - - /* Floating-point stuff */ -bool_t -xdr_float(XDR *xdrs, float *fp) +bool_t xdr_float(XDR *xdrs, float *fp) { xdr_int32_t tmp; @@ -467,76 +210,6 @@ xdr_float(XDR *xdrs, float *fp) return FALSE; } - -bool_t -xdr_double(XDR *xdrs, double *dp) -{ - - /* Windows and some other systems dont define double-precision - * word order in the header files, so unfortunately we have - * to calculate it! - */ - static int LSW=-1; /* Least significant fp word */ - int *ip; - xdr_int32_t tmp[2]; - - if (LSW<0) { - double x=0.987654321; /* Just a number */ - - /* Possible representations in IEEE double precision: - * (S=small endian, B=big endian) - * - * Byte order, Word order, Hex - * S S b8 56 0e 3c dd 9a ef 3f - * B S 3c 0e 56 b8 3f ef 9a dd - * S B dd 9a ef 3f b8 56 0e 3c - * B B 3f ef 9a dd 3c 0e 56 b8 - */ - - unsigned char ix = *((char *)&x); - - if (ix==0xdd || ix==0x3f) - LSW=1; /* Big endian word order */ - else if (ix==0xb8 || ix==0x3c) - LSW=0; /* Small endian word order */ - else { /* Catch strange errors */ - printf("Error when detecting floating-point word order.\n" - "Do you have a non-IEEE system?\n" - "If possible, use the XDR libraries provided with your system,\n" - "instead of the Gromacs fallback XDR source.\n"); - exit(0); - } - } - - switch (xdrs->x_op) { - - case XDR_ENCODE: - ip = (int *)dp; - tmp[0] = ip[!LSW]; - tmp[1] = ip[LSW]; - return (xdr_putint32(xdrs, tmp) && - xdr_putint32(xdrs, tmp+1)); - - break; - - case XDR_DECODE: - ip = (int *)dp; - if (xdr_getint32(xdrs, tmp+!LSW) && - xdr_getint32(xdrs, tmp+LSW)) { - ip[0] = tmp[0]; - ip[1] = tmp[1]; - return TRUE; - } - - break; - - case XDR_FREE: - return TRUE; - } - return FALSE; -} - - /* Array routines */ /* @@ -549,8 +222,7 @@ xdr_double(XDR *xdrs, double *dp) * > elemsize: size of each element * > xdr_elem: routine to XDR each element */ -bool_t -xdr_vector(XDR *xdrs, char *basep, unsigned int nelem, +bool_t xdr_vector(XDR *xdrs, char *basep, unsigned int nelem, unsigned int elemsize, xdrproc_t xdr_elem) { #define LASTUNSIGNED ((unsigned int)0-1) @@ -572,30 +244,20 @@ xdr_vector(XDR *xdrs, char *basep, unsigned int nelem, static bool_t xdrstdio_getbytes(XDR *, char *, unsigned int); static bool_t xdrstdio_putbytes(XDR *, char *, unsigned int); -static unsigned int xdrstdio_getpos(XDR *); -static bool_t xdrstdio_setpos(XDR *, unsigned int); -static xdr_int32_t *xdrstdio_inline(XDR *, int); static void xdrstdio_destroy(XDR *); static bool_t xdrstdio_getint32(XDR *, xdr_int32_t *); static bool_t xdrstdio_putint32(XDR *, xdr_int32_t *); -static bool_t xdrstdio_getuint32(XDR *, xdr_uint32_t *); -static bool_t xdrstdio_putuint32(XDR *, xdr_uint32_t *); /* * Ops vector for stdio type XDR */ static const struct xdr_ops xdrstdio_ops = { - xdrstdio_getbytes, /* deserialize counted bytes */ - xdrstdio_putbytes, /* serialize counted bytes */ - xdrstdio_getpos, /* get offset in the stream */ - xdrstdio_setpos, /* set offset in the stream */ - xdrstdio_inline, /* prime stream for inline macros */ - xdrstdio_destroy, /* destroy stream */ - xdrstdio_getint32, /* deserialize a int */ - xdrstdio_putint32, /* serialize a int */ - xdrstdio_getuint32, /* deserialize a int */ - xdrstdio_putuint32 /* serialize a int */ + xdrstdio_getbytes, /* deserialize counted bytes */ + xdrstdio_putbytes, /* serialize counted bytes */ + xdrstdio_destroy, /* destroy stream */ + xdrstdio_getint32, /* deserialize a int */ + xdrstdio_putint32, /* serialize a int */ }; /* @@ -639,31 +301,7 @@ static bool_t xdrstdio_putbytes(XDR *xdrs, char *addr, unsigned int len) return TRUE; } -static unsigned int xdrstdio_getpos(XDR *xdrs) -{ - return (unsigned int) ftell((FILE *) xdrs->x_private); -} - -static bool_t xdrstdio_setpos(XDR *xdrs, unsigned int pos) -{ - return fseek((FILE *) xdrs->x_private, (xdr_int32_t) pos, 0) < 0 ? FALSE : TRUE; -} - -static xdr_int32_t *xdrstdio_inline(XDR * /*xdrs*/, int /*len*/) -{ - /* - * Must do some work to implement this: must ensure - * enough data in the underlying stdio buffer, - * that the buffer is aligned so that we can indirect through a - * long *, and stuff this pointer in xdrs->x_buf. Doing - * a fread or fwrite to a scratch buffer would defeat - * most of the gains to be had here and require storage - * management on this buffer, so we don't do this. - */ - return nullptr; -} - -static bool_t xdrstdio_getint32(XDR *xdrs, xdr_int32_t *ip) + static bool_t xdrstdio_getint32(XDR *xdrs, xdr_int32_t *ip) { xdr_int32_t mycopy; @@ -683,26 +321,6 @@ static bool_t xdrstdio_putint32(XDR *xdrs, xdr_int32_t *ip) return TRUE; } -static bool_t xdrstdio_getuint32(XDR *xdrs, xdr_uint32_t *ip) -{ - xdr_uint32_t mycopy; - - if (fread((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) - return FALSE; - *ip = xdr_ntohl (mycopy); - return TRUE; -} - -static bool_t xdrstdio_putuint32(XDR *xdrs, xdr_uint32_t *ip) -{ - xdr_uint32_t mycopy = xdr_htonl (*ip); - - ip = &mycopy; - if (fwrite((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) - return FALSE; - return TRUE; -} - #ifdef __cplusplus } #endif diff --git a/src/EXTRA-DUMP/xdr_compat.h b/src/EXTRA-DUMP/xdr_compat.h index b63e13f6d8..fdac35ea9c 100644 --- a/src/EXTRA-DUMP/xdr_compat.h +++ b/src/EXTRA-DUMP/xdr_compat.h @@ -83,26 +83,16 @@ struct XDR { }; struct xdr_ops { + /* get some bytes from XDR stream */ bool_t (*x_getbytes)(XDR *__xdrs, char *__addr, unsigned int __len); - /* get some bytes from " */ + /* put some bytes to XDR stream */ bool_t (*x_putbytes)(XDR *__xdrs, char *__addr, unsigned int __len); - /* put some bytes to " */ - unsigned int (*x_getpostn)(XDR *__xdrs); - /* returns bytes off from beginning */ - bool_t (*x_setpostn)(XDR *__xdrs, unsigned int __pos); - /* lets you reposition the stream */ - xdr_int32_t *(*x_inline)(XDR *__xdrs, int __len); - /* buf quick ptr to buffered data */ - void (*x_destroy)(XDR *__xdrs); /* free privates of this xdr_stream */ + void (*x_destroy)(XDR *__xdrs); + /* get a int from XDR stream */ bool_t (*x_getint32)(XDR *__xdrs, xdr_int32_t *__ip); - /* get a int from underlying stream */ + /* put a int to XDR stream */ bool_t (*x_putint32)(XDR *__xdrs, xdr_int32_t *__ip); - /* put a int to " */ - bool_t (*x_getuint32)(XDR *__xdrs, xdr_uint32_t *__ip); - /* get a unsigned int from underlying stream */ - bool_t (*x_putuint32)(XDR *__xdrs, xdr_uint32_t *__ip); - /* put a int to " */ }; /* @@ -128,46 +118,21 @@ typedef bool_t (*xdrproc_t)(XDR *, void *, ...); */ #define xdr_getint32(xdrs, int32p) (*(xdrs)->x_ops->x_getint32)(xdrs, int32p) - #define xdr_putint32(xdrs, int32p) (*(xdrs)->x_ops->x_putint32)(xdrs, int32p) - -#define xdr_getuint32(xdrs, uint32p) (*(xdrs)->x_ops->x_getuint32)(xdrs, uint32p) - -#define xdr_putuint32(xdrs, uint32p) (*(xdrs)->x_ops->x_putuint32)(xdrs, uint32p) - #define xdr_getbytes(xdrs, addr, len) (*(xdrs)->x_ops->x_getbytes)(xdrs, addr, len) - #define xdr_putbytes(xdrs, addr, len) (*(xdrs)->x_ops->x_putbytes)(xdrs, addr, len) - -#define xdr_getpos(xdrs) (*(xdrs)->x_ops->x_getpostn)(xdrs) - -#define xdr_setpos(xdrs, pos) (*(xdrs)->x_ops->x_setpostn)(xdrs, pos) - -#define xdr_inline(xdrs, len) (*(xdrs)->x_ops->x_inline)(xdrs, len) - #define xdr_destroy(xdrs) \ do { \ if ((xdrs)->x_ops->x_destroy) (*(xdrs)->x_ops->x_destroy)(xdrs); \ } while (0) extern bool_t xdr_int(XDR *__xdrs, int *__ip); -extern bool_t xdr_u_int(XDR *__xdrs, unsigned int *__ip); -extern bool_t xdr_short(XDR *__xdrs, short *__ip); -extern bool_t xdr_u_short(XDR *__xdrs, unsigned short *__ip); -extern bool_t xdr_bool(XDR *__xdrs, int *__bp); extern bool_t xdr_opaque(XDR *__xdrs, char *__cp, unsigned int __cnt); -extern bool_t xdr_string(XDR *__xdrs, char **__cpp, unsigned int __maxsize); -extern bool_t xdr_char(XDR *__xdrs, char *__cp); -extern bool_t xdr_u_char(XDR *__xdrs, unsigned char *__cp); extern bool_t xdr_vector(XDR *__xdrs, char *__basep, unsigned int __nelem, unsigned int __elemsize, xdrproc_t __xdr_elem); extern bool_t xdr_float(XDR *__xdrs, float *__fp); -extern bool_t xdr_double(XDR *__xdrs, double *__dp); extern void xdrstdio_create(XDR *__xdrs, FILE *__file, enum xdr_op __xop); -/* free memory buffers for xdr */ -extern void xdr_free(xdrproc_t __proc, char *__objp); - #ifdef __cplusplus } #endif From 0296ca75fb2295432e300764f132c69b927193f2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 31 Mar 2024 18:20:11 -0400 Subject: [PATCH 19/40] remove tabs --- src/EXTRA-DUMP/xdr_compat.cpp | 2 +- src/EXTRA-DUMP/xdr_compat.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/EXTRA-DUMP/xdr_compat.cpp b/src/EXTRA-DUMP/xdr_compat.cpp index e69a2b72e9..f55a415b7d 100644 --- a/src/EXTRA-DUMP/xdr_compat.cpp +++ b/src/EXTRA-DUMP/xdr_compat.cpp @@ -11,7 +11,7 @@ * The XDR sources are avaiable under the BSD 3-clause license for example in * the MIT Kerberos 5 distribution with the following copyright notice and license. * - * @(#)xdr.h 2.2 88/07/29 4.0 RPCSRC + * @(#)xdr.h 2.2 88/07/29 4.0 RPCSRC * * Copyright (c) 2010, Oracle America, Inc. * diff --git a/src/EXTRA-DUMP/xdr_compat.h b/src/EXTRA-DUMP/xdr_compat.h index fdac35ea9c..4f41ade0a0 100644 --- a/src/EXTRA-DUMP/xdr_compat.h +++ b/src/EXTRA-DUMP/xdr_compat.h @@ -16,7 +16,7 @@ extern "C" { * The XDR sources are avaiable under the BSD 3-clause license for example in * the MIT Kerberos 5 distribution with the following copyright notice and license. * - * @(#)xdr.h 2.2 88/07/29 4.0 RPCSRC + * @(#)xdr.h 2.2 88/07/29 4.0 RPCSRC * * Copyright (c) 2010, Oracle America, Inc. * From 3da6a7bdb085d88334b235a6ac9c09f2eafe100f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 31 Mar 2024 19:29:09 -0400 Subject: [PATCH 20/40] eliminate compatibility typedefs --- src/EXTRA-DUMP/dump_xtc.cpp | 4 ++-- src/EXTRA-DUMP/xdr_compat.cpp | 7 ------- 2 files changed, 2 insertions(+), 9 deletions(-) diff --git a/src/EXTRA-DUMP/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp index 9d4ec1b9bb..3d84ff67ef 100644 --- a/src/EXTRA-DUMP/dump_xtc.cpp +++ b/src/EXTRA-DUMP/dump_xtc.cpp @@ -1053,7 +1053,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) } if (buf[1] != 0) buf[0]++; xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */ - return errval * (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0])); + return errval * (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0])); } else { /* xdrs is open for reading */ @@ -1134,7 +1134,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision) if (xdr_int(xdrs, &(buf[0])) == 0) return 0; - if (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]) == 0) + if (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0]) == 0) return 0; buf[0] = buf[1] = buf[2] = 0; diff --git a/src/EXTRA-DUMP/xdr_compat.cpp b/src/EXTRA-DUMP/xdr_compat.cpp index f55a415b7d..0c8ba199ce 100644 --- a/src/EXTRA-DUMP/xdr_compat.cpp +++ b/src/EXTRA-DUMP/xdr_compat.cpp @@ -49,13 +49,6 @@ extern "C" { #endif -/* compatibility typedefs */ -#if defined(_WIN32) || defined(__APPLE__) || defined(__FreeBSD__) || defined(__DragonFly__) || \ - defined(__OpenBSD__) || defined(__NetBSD__) || (defined(__linux__) && !defined(__GLIBC_MINOR__)) -typedef char *caddr_t; -typedef unsigned int u_int; -#endif - #ifndef FALSE #define FALSE (0) #endif From 051c8185969bacd2b6ebe6dabc40f65c60179afb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 31 Mar 2024 19:39:21 -0400 Subject: [PATCH 21/40] enable and apply clang-format --- src/EXTRA-DUMP/xdr_compat.cpp | 133 ++++++++++++++-------------------- 1 file changed, 54 insertions(+), 79 deletions(-) diff --git a/src/EXTRA-DUMP/xdr_compat.cpp b/src/EXTRA-DUMP/xdr_compat.cpp index 0c8ba199ce..c37f821a4e 100644 --- a/src/EXTRA-DUMP/xdr_compat.cpp +++ b/src/EXTRA-DUMP/xdr_compat.cpp @@ -1,5 +1,5 @@ -// clang-format off #include "xdr_compat.h" + #include #include @@ -67,19 +67,18 @@ static xdr_uint32_t xdr_swapbytes(xdr_uint32_t x) { xdr_uint32_t y; int i; - char *px=(char *)&x; - char *py=(char *)&y; + char *px = (char *) &x; + char *py = (char *) &y; - for (i=0;i<4;i++) - py[i]=px[3-i]; + for (i = 0; i < 4; i++) py[i] = px[3 - i]; return y; } static xdr_uint32_t xdr_htonl(xdr_uint32_t x) { - short s=0x0F00; - if (*((char *)&s)==(char)0x0F) { + short s = 0x0F00; + if (*((char *) &s) == (char) 0x0F) { /* bigendian, do nothing */ return x; } else { @@ -90,8 +89,8 @@ static xdr_uint32_t xdr_htonl(xdr_uint32_t x) static xdr_uint32_t xdr_ntohl(xdr_uint32_t x) { - short s=0x0F00; - if (*((char *)&s)==(char)0x0F) { + short s = 0x0F00; + if (*((char *) &s) == (char) 0x0F) { /* bigendian, do nothing */ return x; } else { @@ -107,15 +106,13 @@ bool_t xdr_int(XDR *xdrs, int *ip) { xdr_int32_t l; - switch (xdrs->x_op) - { + switch (xdrs->x_op) { case XDR_ENCODE: - l = (xdr_int32_t)(*ip); + l = (xdr_int32_t) (*ip); return xdr_putint32(xdrs, &l); case XDR_DECODE: - if (!xdr_getint32(xdrs, &l)) - return FALSE; + if (!xdr_getint32(xdrs, &l)) return FALSE; *ip = (int) l; return TRUE; @@ -138,69 +135,57 @@ bool_t xdr_opaque(XDR *xdrs, char *cp, unsigned int cnt) /* * if no data we are done */ - if (cnt == 0) - return TRUE; + if (cnt == 0) return TRUE; /* * round byte count to full xdr units */ rndup = cnt % BYTES_PER_XDR_UNIT; - if (rndup > 0) - rndup = BYTES_PER_XDR_UNIT - rndup; + if (rndup > 0) rndup = BYTES_PER_XDR_UNIT - rndup; - switch (xdrs->x_op) - { + switch (xdrs->x_op) { case XDR_DECODE: - if (!xdr_getbytes(xdrs, cp, cnt)) - { - return FALSE; - } - if (rndup == 0) - return TRUE; - return xdr_getbytes(xdrs, (char *)crud, rndup); + if (!xdr_getbytes(xdrs, cp, cnt)) { return FALSE; } + if (rndup == 0) return TRUE; + return xdr_getbytes(xdrs, (char *) crud, rndup); case XDR_ENCODE: - if (!xdr_putbytes(xdrs, cp, cnt)) - { - return FALSE; - } - if (rndup == 0) - return TRUE; + if (!xdr_putbytes(xdrs, cp, cnt)) { return FALSE; } + if (rndup == 0) return TRUE; return xdr_putbytes(xdrs, xdr_zero, rndup); case XDR_FREE: return TRUE; - } + } return FALSE; } - /* Floating-point stuff */ bool_t xdr_float(XDR *xdrs, float *fp) { - xdr_int32_t tmp; + xdr_int32_t tmp; - switch (xdrs->x_op) { + switch (xdrs->x_op) { - case XDR_ENCODE: - tmp = *(xdr_int32_t *)fp; - return (xdr_putint32(xdrs, &tmp)); + case XDR_ENCODE: + tmp = *(xdr_int32_t *) fp; + return (xdr_putint32(xdrs, &tmp)); - break; + break; - case XDR_DECODE: - if (xdr_getint32(xdrs, &tmp)) { - *(xdr_int32_t *)fp = tmp; - return TRUE; - } + case XDR_DECODE: + if (xdr_getint32(xdrs, &tmp)) { + *(xdr_int32_t *) fp = tmp; + return TRUE; + } - break; + break; - case XDR_FREE: - return TRUE; - } - return FALSE; + case XDR_FREE: + return TRUE; + } + return FALSE; } /* Array routines */ @@ -215,22 +200,18 @@ bool_t xdr_float(XDR *xdrs, float *fp) * > elemsize: size of each element * > xdr_elem: routine to XDR each element */ -bool_t xdr_vector(XDR *xdrs, char *basep, unsigned int nelem, - unsigned int elemsize, xdrproc_t xdr_elem) +bool_t xdr_vector(XDR *xdrs, char *basep, unsigned int nelem, unsigned int elemsize, + xdrproc_t xdr_elem) { -#define LASTUNSIGNED ((unsigned int)0-1) +#define LASTUNSIGNED ((unsigned int) 0 - 1) unsigned int i; char *elptr; elptr = basep; - for (i = 0; i < nelem; i++) - { - if (!(*xdr_elem)(xdrs, elptr, LASTUNSIGNED)) - { - return FALSE; - } - elptr += elemsize; - } + for (i = 0; i < nelem; i++) { + if (!(*xdr_elem)(xdrs, elptr, LASTUNSIGNED)) { return FALSE; } + elptr += elemsize; + } return TRUE; #undef LASTUNSIGNED } @@ -244,13 +225,12 @@ static bool_t xdrstdio_putint32(XDR *, xdr_int32_t *); /* * Ops vector for stdio type XDR */ -static const struct xdr_ops xdrstdio_ops = -{ - xdrstdio_getbytes, /* deserialize counted bytes */ - xdrstdio_putbytes, /* serialize counted bytes */ - xdrstdio_destroy, /* destroy stream */ - xdrstdio_getint32, /* deserialize a int */ - xdrstdio_putint32, /* serialize a int */ +static const struct xdr_ops xdrstdio_ops = { + xdrstdio_getbytes, /* deserialize counted bytes */ + xdrstdio_putbytes, /* serialize counted bytes */ + xdrstdio_destroy, /* destroy stream */ + xdrstdio_getint32, /* deserialize a int */ + xdrstdio_putint32, /* serialize a int */ }; /* @@ -279,27 +259,23 @@ static void xdrstdio_destroy(XDR *xdrs) /* xx should we close the file ?? */ } - static bool_t xdrstdio_getbytes(XDR *xdrs, char *addr, unsigned int len) { - if ((len != 0) && (fread(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) - return FALSE; + if ((len != 0) && (fread(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) return FALSE; return TRUE; } static bool_t xdrstdio_putbytes(XDR *xdrs, char *addr, unsigned int len) { - if ((len != 0) && (fwrite(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) - return FALSE; + if ((len != 0) && (fwrite(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) return FALSE; return TRUE; } - static bool_t xdrstdio_getint32(XDR *xdrs, xdr_int32_t *ip) +static bool_t xdrstdio_getint32(XDR *xdrs, xdr_int32_t *ip) { xdr_int32_t mycopy; - if (fread((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) - return FALSE; + if (fread((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE; *ip = xdr_ntohl(mycopy); return TRUE; } @@ -309,8 +285,7 @@ static bool_t xdrstdio_putint32(XDR *xdrs, xdr_int32_t *ip) xdr_int32_t mycopy = xdr_htonl(*ip); ip = &mycopy; - if (fwrite((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) - return FALSE; + if (fwrite((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE; return TRUE; } From 4eaf257e526b0e1a2cbbe0240ec0419b2beb7b1e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 31 Mar 2024 19:49:01 -0400 Subject: [PATCH 22/40] small cleanups --- src/EXTRA-DUMP/dump_xtc.cpp | 6 +++--- src/EXTRA-DUMP/xdr_compat.h | 3 --- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/src/EXTRA-DUMP/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp index 3d84ff67ef..3119a470dc 100644 --- a/src/EXTRA-DUMP/dump_xtc.cpp +++ b/src/EXTRA-DUMP/dump_xtc.cpp @@ -14,7 +14,7 @@ /* ---------------------------------------------------------------------- Contributing authors: Naveen Michaud-Agrawal (Johns Hopkins U) - open-source XDR routines from + Open Source XDR based I/O routines from Frans van Hoesel (https://www.rug.nl/staff/f.h.j.van.hoesel/) are included in this file Axel Kohlmeyer (Temple U) @@ -43,8 +43,8 @@ using namespace LAMMPS_NS; -#define EPS 1e-5 -#define XTC_MAGIC 1995 +static constexpr double EPS = 1.0e-5; +static constexpr int XTC_MAGIC = 1995; #define MYMIN(a,b) ((a) < (b) ? (a) : (b)) #define MYMAX(a,b) ((a) > (b) ? (a) : (b)) diff --git a/src/EXTRA-DUMP/xdr_compat.h b/src/EXTRA-DUMP/xdr_compat.h index 4f41ade0a0..d600a4a404 100644 --- a/src/EXTRA-DUMP/xdr_compat.h +++ b/src/EXTRA-DUMP/xdr_compat.h @@ -111,10 +111,7 @@ typedef bool_t (*xdrproc_t)(XDR *, void *, ...); * * XDR *xdrs; * xdr_int32_t *int32p; - * long *longp; - * char *addr; * unsigned int len; - * unsigned int pos; */ #define xdr_getint32(xdrs, int32p) (*(xdrs)->x_ops->x_getint32)(xdrs, int32p) From 2ddd940a3e4978b2af99ac78c38a0085062cab6d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 31 Mar 2024 20:31:25 -0400 Subject: [PATCH 23/40] minor cosmetic changes --- src/EXTRA-DUMP/xdr_compat.cpp | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/src/EXTRA-DUMP/xdr_compat.cpp b/src/EXTRA-DUMP/xdr_compat.cpp index c37f821a4e..3caa38663c 100644 --- a/src/EXTRA-DUMP/xdr_compat.cpp +++ b/src/EXTRA-DUMP/xdr_compat.cpp @@ -107,17 +107,21 @@ bool_t xdr_int(XDR *xdrs, int *ip) xdr_int32_t l; switch (xdrs->x_op) { + case XDR_ENCODE: l = (xdr_int32_t) (*ip); return xdr_putint32(xdrs, &l); + break; case XDR_DECODE: if (!xdr_getint32(xdrs, &l)) return FALSE; *ip = (int) l; return TRUE; + break; case XDR_FREE: return TRUE; + break; } return FALSE; } @@ -144,18 +148,22 @@ bool_t xdr_opaque(XDR *xdrs, char *cp, unsigned int cnt) if (rndup > 0) rndup = BYTES_PER_XDR_UNIT - rndup; switch (xdrs->x_op) { + case XDR_DECODE: if (!xdr_getbytes(xdrs, cp, cnt)) { return FALSE; } if (rndup == 0) return TRUE; return xdr_getbytes(xdrs, (char *) crud, rndup); + break; case XDR_ENCODE: if (!xdr_putbytes(xdrs, cp, cnt)) { return FALSE; } if (rndup == 0) return TRUE; return xdr_putbytes(xdrs, xdr_zero, rndup); + break; case XDR_FREE: return TRUE; + break; } return FALSE; } @@ -171,7 +179,6 @@ bool_t xdr_float(XDR *xdrs, float *fp) case XDR_ENCODE: tmp = *(xdr_int32_t *) fp; return (xdr_putint32(xdrs, &tmp)); - break; case XDR_DECODE: @@ -179,11 +186,11 @@ bool_t xdr_float(XDR *xdrs, float *fp) *(xdr_int32_t *) fp = tmp; return TRUE; } - break; case XDR_FREE: return TRUE; + break; } return FALSE; } From 05562ad5e9f42473d2f3e6c40b67f6edf040dc80 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 1 Apr 2024 21:35:35 -0600 Subject: [PATCH 24/40] testing 2d rigid changes --- src/RIGID/fix_rigid.cpp | 82 ++++++++++++++++++++++++++++++++++++++++- src/math_eigen.cpp | 4 +- 2 files changed, 83 insertions(+), 3 deletions(-) diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 7a63c52220..9553d0b9fc 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -38,6 +38,9 @@ #include #include +// DEBUG +#define IBODY 42 + using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; @@ -893,9 +896,12 @@ void FixRigid::setup(int vflag) // set velocities from angmom & omega - for (ibody = 0; ibody < nbody; ibody++) + for (ibody = 0; ibody < nbody; ibody++) { MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody], ez_space[ibody],inertia[ibody],omega[ibody]); + if (ibody == IBODY) printf("SETUP omega: %g %g %g\n", + omega[ibody][0],omega[ibody][1],omega[ibody][2]); + } set_v(); @@ -944,10 +950,68 @@ void FixRigid::initial_integrate(int vflag) MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody], ez_space[ibody],inertia[ibody],omega[ibody]); + + if (update->ntimestep % 1 == 0 && ibody == IBODY) { + printf("BODY %d: start of step %ld\n",ibody,update->ntimestep); + printf(" interia %g %g %g\n", + inertia[ibody][0],inertia[ibody][1],inertia[ibody][2]); + printf(" angmom %g %g %g\n", + angmom[ibody][0],angmom[ibody][1],angmom[ibody][2]); + printf(" omega %g %g %g\n", + omega[ibody][0],omega[ibody][1],omega[ibody][2]); + printf(" ex %g %g %g\n", + ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2]); + printf(" ey %g %g %g\n", + ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2]); + printf(" ez %g %g %g\n", + ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); + printf(" quat %15.12g %15.12g %15.12g %15.12g\n", + quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3]); + } + MathExtra::richardson(quat[ibody],angmom[ibody],omega[ibody], inertia[ibody],dtq); + + if (update->ntimestep % 1 == 0 && ibody == IBODY) { + printf(" richardson omega %g %g %g\n", + omega[ibody][0],omega[ibody][1],omega[ibody][2]); + printf(" richardson quat %15.12g %15.12g %15.12g %15.12g\n", + quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3]); + } + MathExtra::q_to_exyz(quat[ibody], ex_space[ibody],ey_space[ibody],ez_space[ibody]); + + if (update->ntimestep % 1 == 0 && ibody == IBODY) { + printf(" exnew %g %g %g\n", + ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2]); + printf(" eynew %g %g %g\n", + ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2]); + printf(" eznew %g %g %g\n", + ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); + } + + /* + if (ibody == 42) { + ex_space[ibody][0] = ex_space[ibody][1] = 0.0; + ex_space[ibody][2] = 1.0; + ey_space[ibody][2] = ez_space[ibody][2] = 0.0; + MathExtra::norm3(ey_space[ibody]); + MathExtra::norm3(ez_space[ibody]); + MathExtra::exyz_to_q(ex_space[ibody],ey_space[ibody],ez_space[ibody],quat[ibody]); + } + */ + + if (update->ntimestep % 1 == 0 && ibody == IBODY) { + printf(" quatnew2 %15.12g %15.12g %15.12g %15.12g\n", + quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3]); + printf(" exnew2 %g %g %g\n", + ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2]); + printf(" eynew2 %g %g %g\n", + ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2]); + printf(" eznew2 %g %g %g\n", + ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); + } } // virial setup before call to set_xv @@ -1025,6 +1089,22 @@ void FixRigid::final_integrate() MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody], ez_space[ibody],inertia[ibody],omega[ibody]); + + if (update->ntimestep % 1 == 0 && ibody == IBODY) { + printf("BODY %d: end of step %ld\n",ibody,update->ntimestep); + printf(" interia %g %g %g\n", + inertia[ibody][0],inertia[ibody][1],inertia[ibody][2]); + printf(" angmom %g %g %g\n", + angmom[ibody][0],angmom[ibody][1],angmom[ibody][2]); + printf(" omega %g %g %g\n", + omega[ibody][0],omega[ibody][1],omega[ibody][2]); + printf(" ex %g %g %g\n", + ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2]); + printf(" ey %g %g %g\n", + ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2]); + printf(" ez %g %g %g\n", + ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); + } } // set velocity/rotation of atoms in rigid bodies diff --git a/src/math_eigen.cpp b/src/math_eigen.cpp index 65c3fa806a..42d95a1288 100644 --- a/src/math_eigen.cpp +++ b/src/math_eigen.cpp @@ -44,7 +44,7 @@ int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v1 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_DECREASING_EVALS); + int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_INCREASING_EVAL); // transpose the evec matrix @@ -67,7 +67,7 @@ int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v2 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_DECREASING_EVALS); + int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_INCREASING_EVALS); // transpose the evec matrix From 21745538a76b2e421c4229503bd22539c5389816 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Apr 2024 23:02:04 -0400 Subject: [PATCH 25/40] Revert "change ordering of eigenvalues in jacobi3() function. update tests." This reverts commit c4eadd3a5966a0103afe8236273408a5c68a1df7. --- examples/micelle/in.micelle | 76 +-- examples/micelle/in.micelle-rigid | 90 ++-- .../micelle/log.25Mar24.micelle-rigid.g++.1 | 272 ---------- .../micelle/log.25Mar24.micelle-rigid.g++.4 | 272 ---------- examples/micelle/log.25Mar24.micelle.g++.1 | 229 --------- examples/micelle/log.25Mar24.micelle.g++.4 | 229 --------- .../micelle/log.29Mar2019.micelle-rigid.g++.1 | 260 ++++++++++ .../micelle/log.29Mar2019.micelle-rigid.g++.4 | 260 ++++++++++ examples/micelle/log.29Mar2019.micelle.g++.1 | 218 ++++++++ examples/micelle/log.29Mar2019.micelle.g++.4 | 218 ++++++++ examples/rigid/log.20Mar22.rigid.infile.g++.1 | 312 ++++++++++++ examples/rigid/log.20Mar22.rigid.infile.g++.4 | 312 ++++++++++++ .../rigid/log.20Mar22.rigid.molecule.g++.1 | 349 +++++++++++++ .../rigid/log.20Mar22.rigid.molecule.g++.4 | 349 +++++++++++++ examples/rigid/log.20Mar22.rigid.poems.g++.1 | 328 ++++++++++++ examples/rigid/log.20Mar22.rigid.poems.g++.4 | 328 ++++++++++++ examples/rigid/log.20Mar22.rigid.poems2.g++.1 | 330 ++++++++++++ examples/rigid/log.20Mar22.rigid.poems2.g++.4 | 330 ++++++++++++ examples/rigid/log.20Mar22.rigid.poems3.g++.1 | 329 ++++++++++++ examples/rigid/log.20Mar22.rigid.poems3.g++.4 | 329 ++++++++++++ examples/rigid/log.20Mar22.rigid.poems4.g++.1 | 328 ++++++++++++ examples/rigid/log.20Mar22.rigid.poems4.g++.4 | 328 ++++++++++++ examples/rigid/log.20Mar22.rigid.poems5.g++.1 | 329 ++++++++++++ examples/rigid/log.20Mar22.rigid.poems5.g++.4 | 329 ++++++++++++ .../log.20Mar22.rigid.rigid.molecule.g++.1 | 0 .../log.20Mar22.rigid.rigid.molecule.g++.4 | 0 examples/rigid/log.20Mar22.rigid.small.g++.1 | 322 ++++++++++++ examples/rigid/log.20Mar22.rigid.small.g++.4 | 322 ++++++++++++ .../log.20Mar22.rigid.small.infile.g++.1 | 323 ++++++++++++ .../log.20Mar22.rigid.small.infile.g++.4 | 323 ++++++++++++ .../rigid/log.25Mar24.rigid.atomfile.g++.1 | 341 ------------- .../rigid/log.25Mar24.rigid.atomfile.g++.4 | 341 ------------- .../rigid/log.25Mar24.rigid.atomvar.g++.1 | 341 ------------- .../rigid/log.25Mar24.rigid.atomvar.g++.4 | 341 ------------- examples/rigid/log.25Mar24.rigid.early.g++.1 | 340 ------------- examples/rigid/log.25Mar24.rigid.early.g++.4 | 340 ------------- examples/rigid/log.25Mar24.rigid.g++.1 | 338 ------------- examples/rigid/log.25Mar24.rigid.g++.4 | 338 ------------- .../rigid/log.25Mar24.rigid.gravity.g++.1 | 228 --------- .../rigid/log.25Mar24.rigid.gravity.g++.4 | 228 --------- examples/rigid/log.25Mar24.rigid.infile.g++.1 | 310 ------------ examples/rigid/log.25Mar24.rigid.infile.g++.4 | 310 ------------ .../rigid/log.25Mar24.rigid.molecule.g++.1 | 319 ------------ .../rigid/log.25Mar24.rigid.molecule.g++.4 | 319 ------------ .../rigid/log.25Mar24.rigid.nve.early.g++.1 | 340 ------------- .../rigid/log.25Mar24.rigid.nve.early.g++.4 | 340 ------------- examples/rigid/log.25Mar24.rigid.nve.g++.1 | 338 ------------- examples/rigid/log.25Mar24.rigid.nve.g++.4 | 338 ------------- examples/rigid/log.25Mar24.rigid.poems.g++.1 | 328 ------------ examples/rigid/log.25Mar24.rigid.poems.g++.4 | 328 ------------ examples/rigid/log.25Mar24.rigid.poems2.g++.1 | 330 ------------ examples/rigid/log.25Mar24.rigid.poems2.g++.4 | 330 ------------ examples/rigid/log.25Mar24.rigid.poems3.g++.1 | 329 ------------ examples/rigid/log.25Mar24.rigid.poems3.g++.4 | 329 ------------ examples/rigid/log.25Mar24.rigid.poems4.g++.1 | 328 ------------ examples/rigid/log.25Mar24.rigid.poems4.g++.4 | 328 ------------ examples/rigid/log.25Mar24.rigid.poems5.g++.1 | 329 ------------ examples/rigid/log.25Mar24.rigid.poems5.g++.4 | 329 ------------ .../rigid/log.25Mar24.rigid.property.g++.1 | 343 ------------- .../rigid/log.25Mar24.rigid.property.g++.4 | 343 ------------- examples/rigid/log.25Mar24.rigid.small.g++.1 | 321 ------------ examples/rigid/log.25Mar24.rigid.small.g++.4 | 321 ------------ .../log.25Mar24.rigid.small.infile.g++.1 | 322 ------------ .../log.25Mar24.rigid.small.infile.g++.4 | 322 ------------ examples/rigid/log.25Mar24.rigid.tnr.g++.1 | 475 ------------------ examples/rigid/log.25Mar24.rigid.tnr.g++.4 | 475 ------------------ .../rigid/log.27Nov18.rigid.atomfile.g++.1 | 338 +++++++++++++ .../rigid/log.27Nov18.rigid.atomfile.g++.4 | 338 +++++++++++++ .../rigid/log.27Nov18.rigid.atomvar.g++.1 | 338 +++++++++++++ .../rigid/log.27Nov18.rigid.atomvar.g++.4 | 338 +++++++++++++ examples/rigid/log.27Nov18.rigid.early.g++.1 | 337 +++++++++++++ examples/rigid/log.27Nov18.rigid.early.g++.4 | 337 +++++++++++++ examples/rigid/log.27Nov18.rigid.g++.1 | 335 ++++++++++++ examples/rigid/log.27Nov18.rigid.g++.4 | 335 ++++++++++++ .../rigid/log.27Nov18.rigid.nve.early.g++.1 | 337 +++++++++++++ .../rigid/log.27Nov18.rigid.nve.early.g++.4 | 337 +++++++++++++ examples/rigid/log.27Nov18.rigid.nve.g++.1 | 335 ++++++++++++ examples/rigid/log.27Nov18.rigid.nve.g++.4 | 335 ++++++++++++ .../rigid/log.27Nov18.rigid.property.g++.1 | 340 +++++++++++++ .../rigid/log.27Nov18.rigid.property.g++.4 | 340 +++++++++++++ examples/rigid/log.27Nov18.rigid.tnr.g++.1 | 458 +++++++++++++++++ examples/rigid/log.27Nov18.rigid.tnr.g++.4 | 458 +++++++++++++++++ src/math_eigen.cpp | 4 +- .../tests/fix-timestep-rigid_group.yaml | 113 +++-- .../tests/fix-timestep-rigid_molecule.yaml | 43 +- .../fix-timestep-rigid_molecule_tri.yaml | 37 +- .../tests/fix-timestep-rigid_nph.yaml | 85 ++-- .../tests/fix-timestep-rigid_nph_small.yaml | 85 ++-- .../tests/fix-timestep-rigid_npt.yaml | 119 +++-- .../tests/fix-timestep-rigid_npt_small.yaml | 85 ++-- .../tests/fix-timestep-rigid_nve_group.yaml | 113 +++-- .../fix-timestep-rigid_nve_molecule.yaml | 45 +- .../tests/fix-timestep-rigid_nve_single.yaml | 77 ++- .../tests/fix-timestep-rigid_nve_small.yaml | 45 +- .../tests/fix-timestep-rigid_nvt.yaml | 79 ++- .../tests/fix-timestep-rigid_nvt_small.yaml | 45 +- .../tests/fix-timestep-rigid_single.yaml | 77 ++- .../tests/fix-timestep-rigid_small.yaml | 43 +- unittest/formats/test_atom_styles.cpp | 288 ++++++----- 99 files changed, 13271 insertions(+), 13772 deletions(-) delete mode 100644 examples/micelle/log.25Mar24.micelle-rigid.g++.1 delete mode 100644 examples/micelle/log.25Mar24.micelle-rigid.g++.4 delete mode 100644 examples/micelle/log.25Mar24.micelle.g++.1 delete mode 100644 examples/micelle/log.25Mar24.micelle.g++.4 create mode 100644 examples/micelle/log.29Mar2019.micelle-rigid.g++.1 create mode 100644 examples/micelle/log.29Mar2019.micelle-rigid.g++.4 create mode 100644 examples/micelle/log.29Mar2019.micelle.g++.1 create mode 100644 examples/micelle/log.29Mar2019.micelle.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.infile.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.infile.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.molecule.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.molecule.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.poems.g++.1 create mode 100644 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examples/rigid/log.27Nov18.rigid.nve.early.g++.4 create mode 100644 examples/rigid/log.27Nov18.rigid.nve.g++.1 create mode 100644 examples/rigid/log.27Nov18.rigid.nve.g++.4 create mode 100644 examples/rigid/log.27Nov18.rigid.property.g++.1 create mode 100644 examples/rigid/log.27Nov18.rigid.property.g++.4 create mode 100644 examples/rigid/log.27Nov18.rigid.tnr.g++.1 create mode 100644 examples/rigid/log.27Nov18.rigid.tnr.g++.4 diff --git a/examples/micelle/in.micelle b/examples/micelle/in.micelle index 1626d09993..34bc9ad359 100644 --- a/examples/micelle/in.micelle +++ b/examples/micelle/in.micelle @@ -1,72 +1,72 @@ # 2d micelle simulation -dimension 2 +dimension 2 -neighbor 0.33 bin -neigh_modify delay 5 +neighbor 0.3 bin +neigh_modify delay 5 -atom_style bond +atom_style bond # Soft potential push-off -read_data data.micelle -special_bonds fene +read_data data.micelle +special_bonds fene -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 -bond_style harmonic -bond_coeff 1 50.0 0.75 +bond_style harmonic +bond_coeff 1 50.0 0.75 -velocity all create 0.45 2349852 +velocity all create 0.45 2349852 -variable prefactor equal ramp(1.0,20.0) +variable prefactor equal ramp(1.0,20.0) -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d -thermo 50 -run 1000 +thermo 50 +run 1000 -unfix 3 +unfix 3 # Main run -pair_style lj/cut 2.5 +pair_style lj/cut 2.5 # solvent/head - full-size and long-range -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 # tail/tail - size-averaged and long-range -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 # solvent/tail - full-size and repulsive -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 # head/tail - size-averaged and repulsive -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 -thermo 50 +thermo 50 -#dump 1 all atom 2000 dump.micelle +#dump 1 all atom 2000 dump.micelle -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 -reset_timestep 0 -run 1000 +reset_timestep 0 +run 1000 diff --git a/examples/micelle/in.micelle-rigid b/examples/micelle/in.micelle-rigid index 21a9cb8a58..93cb2655f8 100644 --- a/examples/micelle/in.micelle-rigid +++ b/examples/micelle/in.micelle-rigid @@ -1,87 +1,87 @@ # 2d micelle simulation -dimension 2 +dimension 2 -neighbor 0.33 bin -neigh_modify delay 5 +neighbor 0.3 bin +neigh_modify delay 5 -atom_style bond +atom_style bond # Soft potential push-off -read_data data.micelle -special_bonds fene +read_data data.micelle +special_bonds fene -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 -bond_style harmonic -bond_coeff 1 50.0 0.75 +bond_style harmonic +bond_coeff 1 50.0 0.75 -velocity all create 0.45 2349852 +velocity all create 0.45 2349852 -variable prefactor equal ramp(1.0,20.0) +variable prefactor equal ramp(1.0,20.0) -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d -thermo 50 -run 500 +thermo 50 +run 500 -unfix 3 +unfix 3 # Main run -pair_style lj/cut 2.5 +pair_style lj/cut 2.5 # solvent/head - full-size and long-range -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 # tail/tail - size-averaged and long-range -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 # solvent/tail - full-size and repulsive -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 # head/tail - size-averaged and repulsive -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 -thermo 50 +thermo 50 -#dump 1 all atom 2000 dump.micelle +#dump 1 all atom 2000 dump.micelle -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 -reset_timestep 0 +reset_timestep 0 group solvent molecule 0 group solute subtract all solvent unfix 1 unfix 2 unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -fix 4 all enforce2d -run 500 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +fix 4 all enforce2d +run 500 unfix 2 unfix 4 unfix 5 -fix 5 solute rigid/small molecule -fix 4 all enforce2d -run 500 +fix 5 solute rigid/small molecule +fix 4 all enforce2d +run 500 diff --git a/examples/micelle/log.25Mar24.micelle-rigid.g++.1 b/examples/micelle/log.25Mar24.micelle-rigid.g++.1 deleted file mode 100644 index 8008630d76..0000000000 --- a/examples/micelle/log.25Mar24.micelle-rigid.g++.1 +++ /dev/null @@ -1,272 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.33 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle -Reading data file ... - orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.004 seconds -special_bonds fene -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000 seconds - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 500 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) -Neighbor list info ... - update: every = 1 steps, delay = 5 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.45246 - ghost atom cutoff = 1.45246 - binsize = 0.72623, bins = 50 50 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d - bin: standard -WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) -Per MPI rank memory allocation (min/avg/max) = 4.148 | 4.148 | 4.148 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 - 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 - 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 - 200 0.45 1.01454 0.10663502 1.5708 4.7598476 - 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 - 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 - 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 - 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 - 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 - 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 -Loop time of 0.0683956 on 1 procs for 500 steps with 1200 atoms - -Performance: 3158095.858 tau/day, 7310.407 timesteps/s, 8.772 Matom-step/s -99.1% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.042818 | 0.042818 | 0.042818 | 0.0 | 62.60 -Bond | 0.0026205 | 0.0026205 | 0.0026205 | 0.0 | 3.83 -Neigh | 0.011794 | 0.011794 | 0.011794 | 0.0 | 17.24 -Comm | 0.0014012 | 0.0014012 | 0.0014012 | 0.0 | 2.05 -Output | 0.00012752 | 0.00012752 | 0.00012752 | 0.0 | 0.19 -Modify | 0.0078924 | 0.0078924 | 0.0078924 | 0.0 | 11.54 -Other | | 0.001743 | | | 2.55 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 198 ave 198 max 198 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3199 ave 3199 max 3199 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3199 -Ave neighs/atom = 2.6658333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 48 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 - 150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 500 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 5 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.83 - ghost atom cutoff = 2.83 - binsize = 1.415, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 - 50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109 - 100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772 - 150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796 - 200 0.49410558 -1.7945459 0.13695201 -1.2565449 3.7958258 - 250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445 - 300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851 - 350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818 - 400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566 - 450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611 - 500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738 -Loop time of 0.129419 on 1 procs for 500 steps with 1200 atoms - -Performance: 1668996.565 tau/day, 3863.418 timesteps/s, 4.636 Matom-step/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.059482 | 0.059482 | 0.059482 | 0.0 | 45.96 -Bond | 0.0027154 | 0.0027154 | 0.0027154 | 0.0 | 2.10 -Neigh | 0.017086 | 0.017086 | 0.017086 | 0.0 | 13.20 -Comm | 0.0019065 | 0.0019065 | 0.0019065 | 0.0 | 1.47 -Output | 0.00012035 | 0.00012035 | 0.00012035 | 0.0 | 0.09 -Modify | 0.046099 | 0.046099 | 0.046099 | 0.0 | 35.62 -Other | | 0.002009 | | | 1.55 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 413 ave 413 max 413 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8944 ave 8944 max 8944 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8944 -Ave neighs/atom = 7.4533333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 41 -Dangerous builds = 1 -unfix 2 -unfix 4 -unfix 5 -fix 5 solute rigid/small molecule - create bodies CPU = 0.000 seconds - 150 rigid bodies with 450 atoms - 1.3043524 = max distance from body owner to body atom -fix 4 all enforce2d -run 500 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 9.306 | 9.306 | 9.306 Mbytes - Step Temp E_pair E_mol TotEng Press - 500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752 - 550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662 - 600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379 - 650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789 - 700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082 - 750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147 - 800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481 - 850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703 - 900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388 - 950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786 - 1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987 -Loop time of 0.119542 on 1 procs for 500 steps with 1200 atoms - -Performance: 1806900.644 tau/day, 4182.640 timesteps/s, 5.019 Matom-step/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.058715 | 0.058715 | 0.058715 | 0.0 | 49.12 -Bond | 0.0028428 | 0.0028428 | 0.0028428 | 0.0 | 2.38 -Neigh | 0.015212 | 0.015212 | 0.015212 | 0.0 | 12.73 -Comm | 0.0019242 | 0.0019242 | 0.0019242 | 0.0 | 1.61 -Output | 0.00018977 | 0.00018977 | 0.00018977 | 0.0 | 0.16 -Modify | 0.038399 | 0.038399 | 0.038399 | 0.0 | 32.12 -Other | | 0.002259 | | | 1.89 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 425 ave 425 max 425 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8846 ave 8846 max 8846 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8846 -Ave neighs/atom = 7.3716667 -Ave special neighs/atom = 0.5 -Neighbor list builds = 36 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.25Mar24.micelle-rigid.g++.4 b/examples/micelle/log.25Mar24.micelle-rigid.g++.4 deleted file mode 100644 index b5c53e9b05..0000000000 --- a/examples/micelle/log.25Mar24.micelle-rigid.g++.4 +++ /dev/null @@ -1,272 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.33 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle -Reading data file ... - orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.004 seconds -special_bonds fene -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000 seconds - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 500 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) -Neighbor list info ... - update: every = 1 steps, delay = 5 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.45246 - ghost atom cutoff = 1.45246 - binsize = 0.72623, bins = 50 50 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d - bin: standard -WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) -Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 - 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 - 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 - 200 0.45 1.01454 0.10663502 1.5708 4.7598476 - 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 - 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 - 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 - 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 - 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 - 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 -Loop time of 0.0217401 on 4 procs for 500 steps with 1200 atoms - -Performance: 9935551.276 tau/day, 22998.961 timesteps/s, 27.599 Matom-step/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0088539 | 0.0095602 | 0.010452 | 0.6 | 43.97 -Bond | 0.00058476 | 0.00062647 | 0.00070207 | 0.0 | 2.88 -Neigh | 0.0030965 | 0.0031112 | 0.0031222 | 0.0 | 14.31 -Comm | 0.0040493 | 0.0050374 | 0.0057508 | 0.9 | 23.17 -Output | 8.0051e-05 | 8.6079e-05 | 0.00010294 | 0.0 | 0.40 -Modify | 0.0024258 | 0.0025227 | 0.0026365 | 0.2 | 11.60 -Other | | 0.0007961 | | | 3.66 - -Nlocal: 300 ave 305 max 292 min -Histogram: 1 0 0 0 0 0 1 1 0 1 -Nghost: 105.25 ave 110 max 99 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Neighs: 799.75 ave 817 max 763 min -Histogram: 1 0 0 0 0 0 0 1 0 2 - -Total # of neighbors = 3199 -Ave neighs/atom = 2.6658333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 48 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 - 150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 500 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 5 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.83 - ghost atom cutoff = 2.83 - binsize = 1.415, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.375 | 5.375 | 5.375 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 - 50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109 - 100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772 - 150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796 - 200 0.49410558 -1.7945459 0.13695201 -1.2565449 3.7958258 - 250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445 - 300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851 - 350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818 - 400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566 - 450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611 - 500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738 -Loop time of 0.0560481 on 4 procs for 500 steps with 1200 atoms - -Performance: 3853834.547 tau/day, 8920.913 timesteps/s, 10.705 Matom-step/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.013556 | 0.013707 | 0.013803 | 0.1 | 24.46 -Bond | 0.00063884 | 0.00066997 | 0.0007103 | 0.0 | 1.20 -Neigh | 0.004707 | 0.0047121 | 0.0047151 | 0.0 | 8.41 -Comm | 0.0060936 | 0.0061963 | 0.006299 | 0.1 | 11.06 -Output | 9.3791e-05 | 0.00010703 | 0.00013426 | 0.0 | 0.19 -Modify | 0.029359 | 0.029467 | 0.029627 | 0.1 | 52.57 -Other | | 0.001189 | | | 2.12 - -Nlocal: 300 ave 303 max 296 min -Histogram: 1 0 0 0 1 0 0 0 1 1 -Nghost: 217.75 ave 220 max 215 min -Histogram: 1 0 0 0 0 0 2 0 0 1 -Neighs: 2236 ave 2264 max 2213 min -Histogram: 1 0 1 0 0 1 0 0 0 1 - -Total # of neighbors = 8944 -Ave neighs/atom = 7.4533333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 41 -Dangerous builds = 1 -unfix 2 -unfix 4 -unfix 5 -fix 5 solute rigid/small molecule - create bodies CPU = 0.000 seconds - 150 rigid bodies with 450 atoms - 1.3043524 = max distance from body owner to body atom -fix 4 all enforce2d -run 500 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 9.233 | 9.233 | 9.234 Mbytes - Step Temp E_pair E_mol TotEng Press - 500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752 - 550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662 - 600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379 - 650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789 - 700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082 - 750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147 - 800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481 - 850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703 - 900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388 - 950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786 - 1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987 -Loop time of 0.0401556 on 4 procs for 500 steps with 1200 atoms - -Performance: 5379078.679 tau/day, 12451.571 timesteps/s, 14.942 Matom-step/s -98.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.013239 | 0.013488 | 0.013882 | 0.2 | 33.59 -Bond | 0.00064766 | 0.00068403 | 0.00074631 | 0.0 | 1.70 -Neigh | 0.0040808 | 0.0040899 | 0.0041035 | 0.0 | 10.19 -Comm | 0.0056353 | 0.0060663 | 0.0063864 | 0.3 | 15.11 -Output | 0.0001049 | 0.0001153 | 0.00014195 | 0.0 | 0.29 -Modify | 0.014414 | 0.014559 | 0.014753 | 0.1 | 36.26 -Other | | 0.001153 | | | 2.87 - -Nlocal: 300 ave 305 max 295 min -Histogram: 1 0 0 0 1 0 1 0 0 1 -Nghost: 226 ave 231 max 220 min -Histogram: 1 0 0 0 1 0 0 1 0 1 -Neighs: 2211.5 ave 2313 max 2144 min -Histogram: 1 1 0 0 1 0 0 0 0 1 - -Total # of neighbors = 8846 -Ave neighs/atom = 7.3716667 -Ave special neighs/atom = 0.5 -Neighbor list builds = 36 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.25Mar24.micelle.g++.1 b/examples/micelle/log.25Mar24.micelle.g++.1 deleted file mode 100644 index 4b519e0ea7..0000000000 --- a/examples/micelle/log.25Mar24.micelle.g++.1 +++ /dev/null @@ -1,229 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.33 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle -Reading data file ... - orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.005 seconds -special_bonds fene -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000 seconds - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) -Neighbor list info ... - update: every = 1 steps, delay = 5 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.45246 - ghost atom cutoff = 1.45246 - binsize = 0.72623, bins = 50 50 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d - bin: standard -WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) -Per MPI rank memory allocation (min/avg/max) = 4.148 | 4.148 | 4.148 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.135036 on 1 procs for 1000 steps with 1200 atoms - -Performance: 3199144.549 tau/day, 7405.427 timesteps/s, 8.887 Matom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.086466 | 0.086466 | 0.086466 | 0.0 | 64.03 -Bond | 0.0052524 | 0.0052524 | 0.0052524 | 0.0 | 3.89 -Neigh | 0.020278 | 0.020278 | 0.020278 | 0.0 | 15.02 -Comm | 0.0026978 | 0.0026978 | 0.0026978 | 0.0 | 2.00 -Output | 0.00032119 | 0.00032119 | 0.00032119 | 0.0 | 0.24 -Modify | 0.016117 | 0.016117 | 0.016117 | 0.0 | 11.94 -Other | | 0.003904 | | | 2.89 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 200 ave 200 max 200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3220 ave 3220 max 3220 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3220 -Ave neighs/atom = 2.6833333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 84 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -run 1000 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 5 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.83 - ghost atom cutoff = 2.83 - binsize = 1.415, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.141 | 4.141 | 4.141 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 - 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 - 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 - 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 - 200 0.45 -1.8918673 0.082422107 -1.3598201 2.5629655 - 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 - 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 - 350 0.47650026 -1.9313687 0.072115118 -1.3831504 2.1987532 - 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 - 450 0.47220237 -1.9468502 0.065625625 -1.4094157 2.0984288 - 500 0.46846731 -1.9444333 0.076696281 -1.3996601 2.0528682 - 550 0.47683129 -1.958676 0.070589717 -1.4116523 2.0856022 - 600 0.46851244 -1.9338267 0.070605485 -1.3950992 2.2640498 - 650 0.46874143 -1.9462493 0.069134673 -1.4087638 2.1070264 - 700 0.46437375 -1.9309952 0.071977553 -1.3950309 2.2256927 - 750 0.47326219 -1.9484255 0.075435861 -1.4001218 2.0880257 - 800 0.45 -1.9646003 0.064159585 -1.4508158 2.0612708 - 850 0.46748293 -1.9705587 0.060384889 -1.4430805 1.9472917 - 900 0.46909505 -1.9537228 0.06246996 -1.4225487 2.0222946 - 950 0.45631552 -1.9387752 0.067536414 -1.4153035 2.0638412 - 1000 0.45 -1.9727636 0.058608205 -1.4645304 1.9982412 -Loop time of 0.172925 on 1 procs for 1000 steps with 1200 atoms - -Performance: 2498198.117 tau/day, 5782.866 timesteps/s, 6.939 Matom-step/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.11308 | 0.11308 | 0.11308 | 0.0 | 65.39 -Bond | 0.0054036 | 0.0054036 | 0.0054036 | 0.0 | 3.12 -Neigh | 0.032892 | 0.032892 | 0.032892 | 0.0 | 19.02 -Comm | 0.0038268 | 0.0038268 | 0.0038268 | 0.0 | 2.21 -Output | 0.00023892 | 0.00023892 | 0.00023892 | 0.0 | 0.14 -Modify | 0.013461 | 0.013461 | 0.013461 | 0.0 | 7.78 -Other | | 0.004027 | | | 2.33 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 421 ave 421 max 421 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8779 ave 8779 max 8779 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8779 -Ave neighs/atom = 7.3158333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 77 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.25Mar24.micelle.g++.4 b/examples/micelle/log.25Mar24.micelle.g++.4 deleted file mode 100644 index 174cab5f5e..0000000000 --- a/examples/micelle/log.25Mar24.micelle.g++.4 +++ /dev/null @@ -1,229 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.33 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle -Reading data file ... - orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.004 seconds -special_bonds fene -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000 seconds - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) -Neighbor list info ... - update: every = 1 steps, delay = 5 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.45246 - ghost atom cutoff = 1.45246 - binsize = 0.72623, bins = 50 50 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d - bin: standard -WARNING: Communication cutoff 1.45246 is shorter than a bond length based estimate of 1.455. This may lead to errors. (src/comm.cpp:730) -Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.0430044 on 4 procs for 1000 steps with 1200 atoms - -Performance: 10045485.178 tau/day, 23253.438 timesteps/s, 27.904 Matom-step/s -98.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.01855 | 0.019447 | 0.019916 | 0.4 | 45.22 -Bond | 0.0011939 | 0.0012689 | 0.0013518 | 0.2 | 2.95 -Neigh | 0.0054396 | 0.0054535 | 0.0054635 | 0.0 | 12.68 -Comm | 0.0093296 | 0.0097958 | 0.010731 | 0.6 | 22.78 -Output | 0.00016417 | 0.00018578 | 0.00024995 | 0.0 | 0.43 -Modify | 0.0049758 | 0.0050749 | 0.005268 | 0.2 | 11.80 -Other | | 0.001778 | | | 4.14 - -Nlocal: 300 ave 306 max 294 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 103 ave 110 max 98 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 805 ave 827 max 768 min -Histogram: 1 0 0 0 0 0 1 0 1 1 - -Total # of neighbors = 3220 -Ave neighs/atom = 2.6833333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 84 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -run 1000 -Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 5 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.83 - ghost atom cutoff = 2.83 - binsize = 1.415, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.125 | 4.125 | 4.125 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 - 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 - 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 - 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 - 200 0.45 -1.8918673 0.082422107 -1.3598201 2.5629655 - 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 - 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 - 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 - 400 0.45 -1.9554318 0.08160394 -1.4242028 2.0787066 - 450 0.47220237 -1.9468502 0.065625625 -1.4094157 2.0984288 - 500 0.46846732 -1.9444333 0.076696282 -1.3996601 2.0528682 - 550 0.47683129 -1.958676 0.070589715 -1.4116523 2.0856023 - 600 0.46851246 -1.9338267 0.070605474 -1.3950992 2.2640497 - 650 0.46874145 -1.9462493 0.069134673 -1.4087638 2.1070263 - 700 0.46437384 -1.9309953 0.071977538 -1.3950309 2.2256921 - 750 0.47326257 -1.9484258 0.075435782 -1.4001218 2.0880238 - 800 0.45 -1.9646002 0.064159564 -1.4508156 2.0612711 - 850 0.46748245 -1.9705585 0.060385282 -1.4430803 1.9472928 - 900 0.46909475 -1.953722 0.062469986 -1.4225482 2.0223017 - 950 0.45631666 -1.9387749 0.067535547 -1.415303 2.0638464 - 1000 0.45 -1.9727662 0.058608374 -1.4645328 1.9982544 -Loop time of 0.0580559 on 4 procs for 1000 steps with 1200 atoms - -Performance: 7441102.030 tau/day, 17224.773 timesteps/s, 20.670 Matom-step/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.025537 | 0.026849 | 0.0293 | 0.9 | 46.25 -Bond | 0.0012241 | 0.0013287 | 0.0015123 | 0.3 | 2.29 -Neigh | 0.0093194 | 0.0093648 | 0.0093978 | 0.0 | 16.13 -Comm | 0.011992 | 0.014606 | 0.015998 | 1.3 | 25.16 -Output | 0.00018318 | 0.0001963 | 0.0002352 | 0.0 | 0.34 -Modify | 0.003441 | 0.0035887 | 0.0037522 | 0.2 | 6.18 -Other | | 0.002122 | | | 3.66 - -Nlocal: 300 ave 305 max 294 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Nghost: 222.25 ave 231 max 215 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 2195 ave 2233 max 2150 min -Histogram: 1 0 0 0 0 2 0 0 0 1 - -Total # of neighbors = 8780 -Ave neighs/atom = 7.3166667 -Ave special neighs/atom = 0.5 -Neighbor list builds = 77 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 new file mode 100644 index 0000000000..f1001e6cea --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 @@ -0,0 +1,260 @@ +LAMMPS (29 Mar 2019) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000473022 secs + read_data CPU = 0.0024147 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.00022316 secs + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms + +Performance: 2093802.885 tau/day, 4846.766 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21 +Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11 +Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64 +Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86 +Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17 +Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37 +Other | | 0.002726 | | | 2.64 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 197 ave 197 max 197 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3094 ave 3094 max 3094 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.57833 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 + 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 + 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 + 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 + 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 + 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 + 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 + 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 + 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 +Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms + +Performance: 1208012.705 tau/day, 2796.326 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17 +Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38 +Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92 +Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45 +Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10 +Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34 +Other | | 0.00293 | | | 1.64 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 416 ave 416 max 416 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8769 ave 8769 max 8769 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8769 +Ave neighs/atom = 7.3075 +Ave special neighs/atom = 0.5 +Neighbor list builds = 47 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 0.00015378 secs +150 rigid bodies with 450 atoms + 1.30435 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes +Step Temp E_pair E_mol TotEng Press + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 + 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 + 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 + 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 + 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 + 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 + 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 + 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 + 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 + 950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332 + 1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141 +Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms + +Performance: 1297278.008 tau/day, 3002.958 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51 +Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56 +Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83 +Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44 +Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11 +Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66 +Other | | 0.003141 | | | 1.89 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 415 ave 415 max 415 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8743 ave 8743 max 8743 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8743 +Ave neighs/atom = 7.28583 +Ave special neighs/atom = 0.5 +Neighbor list builds = 40 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 new file mode 100644 index 0000000000..e65f67a527 --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 @@ -0,0 +1,260 @@ +LAMMPS (29 Mar 2019) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000422001 secs + read_data CPU = 0.00473404 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000183344 secs + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms + +Performance: 5066547.720 tau/day, 11728.120 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16 +Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95 +Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95 +Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78 +Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62 +Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28 +Other | | 0.002669 | | | 6.26 + +Nlocal: 300 ave 304 max 292 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Nghost: 103.5 ave 108 max 98 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 773.5 ave 792 max 735 min +Histogram: 1 0 0 0 0 0 0 0 2 1 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.57833 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 + 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 + 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 + 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 + 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 + 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 + 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 + 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 + 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 +Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms + +Performance: 2434100.210 tau/day, 5634.491 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74 +Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30 +Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32 +Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30 +Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29 +Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73 +Other | | 0.002938 | | | 3.31 + +Nlocal: 300 ave 309 max 291 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 218.75 ave 223 max 216 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Neighs: 2192.25 ave 2251 max 2113 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 8769 +Ave neighs/atom = 7.3075 +Ave special neighs/atom = 0.5 +Neighbor list builds = 47 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 7.70092e-05 secs +150 rigid bodies with 450 atoms + 1.30435 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes +Step Temp E_pair E_mol TotEng Press + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 + 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 + 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 + 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 + 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 + 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 + 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 + 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 + 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 + 950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332 + 1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141 +Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms + +Performance: 3671840.233 tau/day, 8499.630 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47 +Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93 +Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98 +Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29 +Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42 +Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11 +Other | | 0.00224 | | | 3.81 + +Nlocal: 300 ave 303 max 295 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 219 ave 224 max 215 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 2185.75 ave 2244 max 2143 min +Histogram: 1 1 0 0 0 1 0 0 0 1 + +Total # of neighbors = 8743 +Ave neighs/atom = 7.28583 +Ave special neighs/atom = 0.5 +Neighbor list builds = 40 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle.g++.1 b/examples/micelle/log.29Mar2019.micelle.g++.1 new file mode 100644 index 0000000000..d482d6c890 --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (29 Mar 2019) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.00037837 secs + read_data CPU = 0.00206876 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000177383 secs + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 + 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 + 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 + 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 + 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 + 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 + 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 + 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 + 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 + 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 + 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 + 600 0.45 0.58193041 0.088386617 1.119942 5.131481 + 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 + 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 + 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 + 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 + 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 + 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 + 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 + 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 +Loop time of 0.208895 on 1 procs for 1000 steps with 1200 atoms + +Performance: 2068027.282 tau/day, 4787.100 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14142 | 0.14142 | 0.14142 | 0.0 | 67.70 +Bond | 0.008441 | 0.008441 | 0.008441 | 0.0 | 4.04 +Neigh | 0.025716 | 0.025716 | 0.025716 | 0.0 | 12.31 +Comm | 0.0036864 | 0.0036864 | 0.0036864 | 0.0 | 1.76 +Output | 0.0003562 | 0.0003562 | 0.0003562 | 0.0 | 0.17 +Modify | 0.023699 | 0.023699 | 0.023699 | 0.0 | 11.35 +Other | | 0.00558 | | | 2.67 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 195 ave 195 max 195 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3136 ave 3136 max 3136 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3136 +Ave neighs/atom = 2.61333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 92 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 + 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 + 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 + 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 + 200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655 + 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 + 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 + 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 + 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 + 450 0.47220236 -1.9468502 0.065625624 -1.4094157 2.0984288 + 500 0.4684673 -1.9444333 0.076696283 -1.3996601 2.0528682 + 550 0.47683128 -1.958676 0.070589719 -1.4116523 2.0856022 + 600 0.46851243 -1.9338267 0.07060548 -1.3950992 2.26405 + 650 0.46874142 -1.9462493 0.069134685 -1.4087638 2.1070263 + 700 0.46437384 -1.9309953 0.071977522 -1.3950309 2.2256923 + 750 0.47326225 -1.9484255 0.075435845 -1.4001218 2.0880254 + 800 0.45 -1.9646005 0.064159585 -1.4508159 2.0612696 + 850 0.46748307 -1.970559 0.060384874 -1.4430806 1.9472879 + 900 0.46909484 -1.953723 0.062470295 -1.4225488 2.0222909 + 950 0.45631531 -1.9387753 0.067536568 -1.4153037 2.0638421 + 1000 0.45 -1.9727646 0.058607721 -1.4645318 1.9982315 +Loop time of 0.252254 on 1 procs for 1000 steps with 1200 atoms + +Performance: 1712557.882 tau/day, 3964.254 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17177 | 0.17177 | 0.17177 | 0.0 | 68.09 +Bond | 0.0084555 | 0.0084555 | 0.0084555 | 0.0 | 3.35 +Neigh | 0.03991 | 0.03991 | 0.03991 | 0.0 | 15.82 +Comm | 0.0049119 | 0.0049119 | 0.0049119 | 0.0 | 1.95 +Output | 0.00039077 | 0.00039077 | 0.00039077 | 0.0 | 0.15 +Modify | 0.021131 | 0.021131 | 0.021131 | 0.0 | 8.38 +Other | | 0.005685 | | | 2.25 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 415 ave 415 max 415 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8586 ave 8586 max 8586 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8586 +Ave neighs/atom = 7.155 +Ave special neighs/atom = 0.5 +Neighbor list builds = 86 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle.g++.4 b/examples/micelle/log.29Mar2019.micelle.g++.4 new file mode 100644 index 0000000000..f3a54970cf --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (29 Mar 2019) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000413656 secs + read_data CPU = 0.00487924 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000178576 secs + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 + 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 + 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 + 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 + 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 + 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 + 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 + 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 + 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 + 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 + 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 + 600 0.45 0.58193041 0.088386617 1.119942 5.131481 + 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 + 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 + 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 + 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 + 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 + 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 + 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 + 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 +Loop time of 0.0906248 on 4 procs for 1000 steps with 1200 atoms + +Performance: 4766906.584 tau/day, 11034.506 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.036572 | 0.039266 | 0.041216 | 1.0 | 43.33 +Bond | 0.0023205 | 0.0024512 | 0.0025697 | 0.2 | 2.70 +Neigh | 0.0088909 | 0.0089301 | 0.0089679 | 0.0 | 9.85 +Comm | 0.022308 | 0.024047 | 0.027175 | 1.3 | 26.53 +Output | 0.00057411 | 0.00061274 | 0.00071025 | 0.0 | 0.68 +Modify | 0.0083182 | 0.0092374 | 0.0098341 | 0.6 | 10.19 +Other | | 0.006081 | | | 6.71 + +Nlocal: 300 ave 305 max 292 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 100.25 ave 108 max 93 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 784 ave 815 max 739 min +Histogram: 1 0 0 0 0 0 1 1 0 1 + +Total # of neighbors = 3136 +Ave neighs/atom = 2.61333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 92 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 + 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 + 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 + 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 + 200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655 + 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 + 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 + 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 + 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 + 450 0.47220236 -1.9468502 0.065625625 -1.4094157 2.0984288 + 500 0.4684673 -1.9444333 0.076696285 -1.3996601 2.0528682 + 550 0.47683128 -1.958676 0.070589721 -1.4116523 2.0856023 + 600 0.46851245 -1.9338267 0.070605469 -1.3950992 2.26405 + 650 0.46874143 -1.9462493 0.069134686 -1.4087638 2.1070262 + 700 0.4643739 -1.9309953 0.071977511 -1.3950309 2.225692 + 750 0.47326259 -1.9484258 0.075435808 -1.4001218 2.0880235 + 800 0.45 -1.9646003 0.06415956 -1.4508158 2.0612703 + 850 0.46748278 -1.9705588 0.06038513 -1.4430804 1.9472884 + 900 0.46909438 -1.9537221 0.062470305 -1.4225483 2.0223008 + 950 0.45631508 -1.9387742 0.067536066 -1.4153033 2.063854 + 1000 0.45 -1.9727651 0.058608085 -1.464532 1.9982447 +Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms + +Performance: 4917357.613 tau/day, 11382.772 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.043517 | 0.044455 | 0.046903 | 0.7 | 50.60 +Bond | 0.0020199 | 0.0022303 | 0.0024347 | 0.4 | 2.54 +Neigh | 0.012207 | 0.012335 | 0.012512 | 0.1 | 14.04 +Comm | 0.014938 | 0.018265 | 0.020068 | 1.5 | 20.79 +Output | 0.00061369 | 0.00064814 | 0.00073504 | 0.0 | 0.74 +Modify | 0.0052264 | 0.0053691 | 0.0055039 | 0.2 | 6.11 +Other | | 0.00455 | | | 5.18 + +Nlocal: 300 ave 305 max 296 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 219.5 ave 228 max 214 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 2146.5 ave 2201 max 2114 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 8586 +Ave neighs/atom = 7.155 +Ave special neighs/atom = 0.5 +Neighbor list builds = 86 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.infile.g++.1 b/examples/rigid/log.20Mar22.rigid.infile.g++.1 new file mode 100644 index 0000000000..7c554d2778 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.infile.g++.1 @@ -0,0 +1,312 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat + 9 rigid bodies with 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Reading rigid body data for 4 bodies from file bodyinfo.dat +Reading rigid body data for 4 bodies from file bodyinfo.dat +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722793e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06941 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 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16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532812 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652435 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156167 0 5269.5203 12.011611 + 9600 16738.549 -0.02681437 0 5269.5163 12.011415 + 9650 16738.765 -0.10191524 0 5269.5092 12.011013 + 9700 16735.041 1.0589895 0 5269.4979 12.062708 + 9750 16738.013 0.13550156 0 5269.5101 11.407246 + 9800 16738.512 -0.011620325 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270436 0 5269.5237 11.395099 + 9900 16738.489 -0.0002498452 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395077 + 10000 16738.49 0 0 5269.5246 11.395076 +Loop time of 0.0882903 on 1 procs for 10000 steps with 81 atoms + +Performance: 978589.581 tau/day, 113262.683 timesteps/s +97.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0064583 | 0.0064583 | 0.0064583 | 0.0 | 7.31 +Neigh | 0.027186 | 0.027186 | 0.027186 | 0.0 | 30.79 +Comm | 0.0057041 | 0.0057041 | 0.0057041 | 0.0 | 6.46 +Output | 0.0020628 | 0.0020628 | 0.0020628 | 0.0 | 2.34 +Modify | 0.042816 | 0.042816 | 0.042816 | 0.0 | 48.49 +Other | | 0.004063 | | | 4.60 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.infile.g++.4 b/examples/rigid/log.20Mar22.rigid.infile.g++.4 new file mode 100644 index 0000000000..2e0535a69a --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.infile.g++.4 @@ -0,0 +1,312 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat + 9 rigid bodies with 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Reading rigid body data for 4 bodies from file bodyinfo.dat +Reading rigid body data for 4 bodies from file bodyinfo.dat +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 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16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 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16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.004530741 0 5269.5178 12.01162 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156168 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191524 0 5269.5092 12.011013 + 9700 16735.041 1.0589899 0 5269.4979 12.062708 + 9750 16738.013 0.13550149 0 5269.5101 11.407246 + 9800 16738.512 -0.011620325 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270428 0 5269.5237 11.395099 + 9900 16738.489 -0.0002498452 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395077 + 10000 16738.49 0 0 5269.5246 11.395076 +Loop time of 0.100422 on 4 procs for 10000 steps with 81 atoms + +Performance: 860368.209 tau/day, 99579.654 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0014853 | 0.0020649 | 0.0026245 | 0.9 | 2.06 +Neigh | 0.0075956 | 0.0080256 | 0.0091971 | 0.8 | 7.99 +Comm | 0.037221 | 0.041059 | 0.043195 | 1.2 | 40.89 +Output | 0.0020995 | 0.0023594 | 0.003073 | 0.8 | 2.35 +Modify | 0.041318 | 0.042855 | 0.044215 | 0.5 | 42.67 +Other | | 0.004059 | | | 4.04 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.molecule.g++.1 b/examples/rigid/log.20Mar22.rigid.molecule.g++.1 new file mode 100644 index 0000000000..b4a4b28d92 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.molecule.g++.1 @@ -0,0 +1,349 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid molecule + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.233 | 5.233 | 5.233 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.97228e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06941 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156166 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191524 0 5269.5092 12.011013 + 9700 16735.041 1.0589897 0 5269.4979 12.062708 + 9750 16738.013 0.1355014 0 5269.5101 11.407246 + 9800 16738.512 -0.011620325 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270449 0 5269.5237 11.395099 + 9900 16738.489 -0.00024984529 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395077 + 10000 16738.49 0 0 5269.5246 11.395076 +Loop time of 0.0974108 on 1 procs for 10000 steps with 81 atoms + +Performance: 886965.415 tau/day, 102658.034 timesteps/s +96.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0068054 | 0.0068054 | 0.0068054 | 0.0 | 6.99 +Bond | 0.00034618 | 0.00034618 | 0.00034618 | 0.0 | 0.36 +Neigh | 0.033076 | 0.033076 | 0.033076 | 0.0 | 33.96 +Comm | 0.0067938 | 0.0067938 | 0.0067938 | 0.0 | 6.97 +Output | 0.0022905 | 0.0022905 | 0.0022905 | 0.0 | 2.35 +Modify | 0.044027 | 0.044027 | 0.044027 | 0.0 | 45.20 +Other | | 0.004071 | | | 4.18 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.molecule.g++.4 b/examples/rigid/log.20Mar22.rigid.molecule.g++.4 new file mode 100644 index 0000000000..63835843a0 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.molecule.g++.4 @@ -0,0 +1,349 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid molecule + 9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.08 | 5.112 | 5.206 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722775e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3750 16737.731 0.20706556 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06941 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690662 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8550 16738.483 -0.004530741 0 5269.5178 12.01162 + 8600 16738.474 -0.00076532815 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652439 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156171 0 5269.5203 12.011611 + 9600 16738.549 -0.026814373 0 5269.5163 12.011415 + 9650 16738.765 -0.10191525 0 5269.5092 12.011013 + 9700 16735.041 1.0589908 0 5269.4979 12.062708 + 9750 16738.013 0.13550139 0 5269.5101 11.407247 + 9800 16738.512 -0.011620323 0 5269.5201 11.394975 + 9850 16738.489 -0.00067270407 0 5269.5237 11.395099 + 9900 16738.489 -0.00024984518 0 5269.5242 11.395086 + 9950 16738.49 0 0 5269.5245 11.395077 + 10000 16738.49 0 0 5269.5246 11.395076 +Loop time of 0.102079 on 4 procs for 10000 steps with 81 atoms + +Performance: 846406.333 tau/day, 97963.696 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0015357 | 0.0020418 | 0.0024561 | 0.7 | 2.00 +Bond | 0.00030031 | 0.00031957 | 0.00034464 | 0.0 | 0.31 +Neigh | 0.0091719 | 0.0094934 | 0.010243 | 0.4 | 9.30 +Comm | 0.038015 | 0.041242 | 0.043481 | 1.1 | 40.40 +Output | 0.002223 | 0.0024412 | 0.0030738 | 0.7 | 2.39 +Modify | 0.040725 | 0.042557 | 0.043982 | 0.7 | 41.69 +Other | | 0.003983 | | | 3.90 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.poems.g++.1 b/examples/rigid/log.20Mar22.rigid.poems.g++.1 new file mode 100644 index 0000000000..32edd0fd0c --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems.g++.1 @@ -0,0 +1,328 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045742 + 850 17821.483 711.53827 0 3681.7854 7.438428 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19374 0 3681.3037 11.787982 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184716 + 1150 20849.582 206.01696 0 3680.9472 -0.86699118 + 1200 21815.003 45.317409 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064083 + 1300 20780.781 217.36511 0 3680.8286 6.0538604 + 1350 20558.971 254.36489 0 3680.8601 -3.6773868 + 1400 21485.029 99.812844 0 3680.6511 -16.185479 + 1450 21771.107 52.159653 0 3680.6775 -2.4756655 + 1500 21520.949 93.503876 0 3680.3286 2.1023573 + 1550 21351.419 121.6813 0 3680.2511 5.5159876 + 1600 20778.804 216.92191 0 3680.0559 15.089203 + 1650 21477.636 100.21873 0 3679.8247 -1.1045277 + 1700 18501.33 596.4807 0 3680.0357 -15.6798 + 1750 18563.64 587.34824 0 3681.2882 33.532308 + 1800 19110.175 494.82517 0 3679.8543 18.024074 + 1850 21364.178 119.23765 0 3679.9339 2.5290144 + 1900 20146.588 322.15509 0 3679.9197 5.7317299 + 1950 20692.676 231.25264 0 3680.0319 4.297803 + 2000 20943.902 189.11251 0 3679.7629 -22.643824 + 2050 19667.823 401.86882 0 3679.8394 3.6241915 + 2100 20280.125 299.81485 0 3679.8357 7.4804047 + 2150 19181.201 483.6306 0 3680.4975 22.63342 + 2200 21301.144 130.54014 0 3680.7308 4.7074288 + 2250 20484.876 266.98315 0 3681.1291 -8.6578278 + 2300 18648.161 573.07329 0 3681.1001 -5.2550954 + 2350 21515.748 95.243054 0 3681.201 -9.386512 + 2400 21462.551 104.18267 0 3681.2745 -29.46442 + 2450 20107.732 330.99437 0 3682.2831 35.38497 + 2500 20771.509 220.47713 0 3682.3953 -12.324858 + 2550 20499.887 265.58494 0 3682.2327 -22.713874 + 2600 21462.182 105.24427 0 3682.2747 -10.175788 + 2650 21004.949 181.51383 0 3682.3387 4.949195 + 2700 18673.552 570.45017 0 3682.7089 21.201437 + 2750 21257.562 139.198 0 3682.1249 -7.5793039 + 2800 21559.645 88.844759 0 3682.119 -6.2360467 + 2850 20865.227 204.46262 0 3682.0004 0.39575069 + 2900 19428.614 443.93293 0 3682.0352 12.796676 + 2950 19630.1 410.18487 0 3681.8681 -0.50572623 + 3000 19663.218 404.06316 0 3681.2661 6.0827093 + 3050 19087.572 500.8452 0 3682.1073 -6.3526476 + 3100 18229.94 643.77681 0 3682.1001 11.453637 + 3150 18927.492 527.51919 0 3682.1011 -1.662863 + 3200 18320.514 628.55895 0 3681.978 21.176126 + 3250 18204.677 647.96462 0 3682.0775 11.331521 + 3300 19231.978 477.02117 0 3682.3509 3.8381593 + 3350 18153.44 656.70376 0 3682.2772 15.135615 + 3400 17476.768 770.0598 0 3682.8545 -3.394312 + 3450 21097.531 166.17241 0 3682.4276 3.74301 + 3500 17605.784 747.54808 0 3681.8454 3.3420627 + 3550 19238.34 476.00608 0 3682.3961 1.1413836 + 3600 18155.288 656.57434 0 3682.4557 3.4360446 + 3650 18735.622 559.2377 0 3681.8413 28.760363 + 3700 15310.261 1134.4215 0 3686.1317 44.207018 + 3750 15377.116 1123.4786 0 3686.3313 7.6773215 + 3800 18798.895 549.05928 0 3682.2084 -12.905825 + 3850 18322.563 628.87744 0 3682.6379 -16.067793 + 3900 19963.049 355.65441 0 3682.8292 3.4694064 + 3950 19925.48 361.2507 0 3682.1641 5.0058567 + 4000 19141.423 492.41081 0 3682.648 -12.782769 + 4050 20022.241 345.61655 0 3682.6568 -3.0149905 + 4100 21348.635 124.95646 0 3683.0624 -4.85779 + 4150 21011.812 181.1132 0 3683.0819 -3.9526196 + 4200 20222.276 312.63945 0 3683.0187 -23.63437 + 4250 20957.757 189.77152 0 3682.731 -1.3712469 + 4300 20070.215 337.5751 0 3682.611 -6.8816517 + 4350 21322.437 129.09228 0 3682.8318 -6.9442178 + 4400 19440.445 442.77531 0 3682.8495 -0.11606236 + 4450 20964.516 188.67174 0 3682.7577 4.8533525 + 4500 13530.08 1428.5497 0 3683.563 12.333187 + 4550 20461.637 272.58882 0 3682.8616 4.5111943 + 4600 17072.994 836.58228 0 3682.0812 5.7611617 + 4650 18860.748 539.82027 0 3683.2782 -2.5558958 + 4700 18373.927 621.04093 0 3683.3621 5.4020702 + 4750 20321.437 296.63662 0 3683.5428 8.9571617 + 4800 21083.122 169.84086 0 3683.6946 10.566368 + 4850 20499.669 267.7012 0 3684.3128 4.2924237 + 4900 20308.781 300.38168 0 3685.1785 -12.396923 + 4950 21043.303 178.56295 0 3685.7801 3.8923762 + 5000 20718.383 232.52208 0 3685.5859 -12.43234 + 5050 21005.749 184.4363 0 3685.3945 -7.6463487 + 5100 20714.133 233.27745 0 3685.6329 -1.6944135 + 5150 19577.452 422.73035 0 3685.639 -21.831219 + 5200 14044.647 1343.9545 0 3684.729 -6.8407194 + 5250 19089.805 504.0893 0 3685.7235 4.05641 + 5300 21094.745 169.94699 0 3685.7378 -0.66593212 + 5350 19907.559 366.77598 0 3684.7024 1.5248525 + 5400 20382.81 289.13263 0 3686.2676 -11.919321 + 5450 19593.693 420.70548 0 3686.3209 -1.1568628 + 5500 20906.08 202.09801 0 3686.4447 -2.4284971 + 5550 16315.465 965.56973 0 3684.8138 -33.178221 + 5600 19714.57 400.39687 0 3686.1586 19.950231 + 5650 20561.724 259.54797 0 3686.502 8.2074524 + 5700 19349.502 460.7789 0 3685.6959 16.252649 + 5750 21006.818 185.56805 0 3686.7044 -11.96089 + 5800 20268.2 307.97547 0 3686.0089 17.322311 + 5850 21018.322 184.16179 0 3687.2154 -14.379909 + 5900 19695.647 404.57094 0 3687.1787 -20.718904 + 5950 21021.687 183.66311 0 3687.2776 -15.206081 + 6000 18947.535 529.30554 0 3687.2281 17.863927 + 6050 15272.373 1141.012 0 3686.4075 -0.43375666 + 6100 17766.197 721.75792 0 3682.7908 11.378913 + 6150 18612.573 584.06688 0 3686.1623 17.543241 + 6200 19005.155 518.97146 0 3686.4973 -16.223107 + 6250 20997.507 187.55499 0 3687.1394 -11.613546 + 6300 19639.901 413.58048 0 3686.8974 14.407136 + 6350 19580.399 423.02818 0 3686.428 -5.5801796 + 6400 14134.119 1332.0662 0 3687.7527 84.864425 + 6450 21598.824 87.419966 0 3687.224 -5.8358352 + 6500 18208.216 649.29108 0 3683.9938 -8.1510884 + 6550 19364.586 459.59813 0 3687.0291 -12.053563 + 6600 20710.927 235.11914 0 3686.9403 -1.0470193 + 6650 21132.334 165.08091 0 3687.1366 1.0785471 + 6700 20217.285 317.589 0 3687.1365 0.055447462 + 6750 21232.279 148.57412 0 3687.2873 -2.4551657 + 6800 20292.683 304.76539 0 3686.8793 -0.42311295 + 6850 19056.291 510.49927 0 3686.5478 6.9533826 + 6900 20429.82 282.23764 0 3687.2076 -4.2360112 + 6950 21281.278 140.27361 0 3687.1533 -0.07475261 + 7000 17173.388 824.54446 0 3686.7758 10.753828 + 7050 18079.7 674.56274 0 3687.846 12.975804 + 7100 16433.233 950.73904 0 3689.6112 -10.5102 + 7150 19033.335 515.59672 0 3687.8193 0.29109447 + 7200 17286.428 809.02352 0 3690.0948 2.3015698 + 7250 16811.962 886.6645 0 3688.6582 -7.4787512 + 7300 15992.461 1023.4849 0 3688.895 -5.2354222 + 7350 19211.451 487.63129 0 3689.5398 8.4351737 + 7400 19065.682 511.95629 0 3689.57 -12.47448 + 7450 21369.265 128.10098 0 3689.6451 2.2930546 + 7500 16807.109 888.64602 0 3689.8308 14.761969 + 7550 18063.046 679.21873 0 3689.7264 3.8950434 + 7600 17794.987 724.55404 0 3690.3851 14.379016 + 7650 17904.751 706.14354 0 3690.2688 23.813776 + 7700 19670.09 411.3021 0 3689.6504 14.099245 + 7750 18082.562 675.23975 0 3689.0001 15.788521 + 7800 17776.135 726.91445 0 3689.6037 6.9780735 + 7850 17062.575 846.33412 0 3690.0966 -8.9289256 + 7900 19059.2 513.07737 0 3689.6107 16.992843 + 7950 16269.685 978.48914 0 3690.1033 11.180179 + 8000 20115.278 336.91405 0 3689.4604 -6.4882518 + 8050 21173.72 161.15229 0 3690.1056 -2.2164491 + 8100 19238.235 484.42784 0 3690.8004 23.412709 + 8150 18438.4 617.58743 0 3690.6542 0.89156316 + 8200 21438.764 117.12721 0 3690.2546 -1.7193227 + 8250 21195.806 157.66607 0 3690.3003 3.820447 + 8300 21177.549 161.13702 0 3690.7286 0.94938203 + 8350 21060.267 181.06887 0 3691.1135 2.8179025 + 8400 20087.113 343.46206 0 3691.3142 8.1484473 + 8450 19298.478 474.87133 0 3691.2843 -16.239664 + 8500 21654.353 82.083485 0 3691.1423 -8.1464138 + 8550 19920.544 371.34795 0 3691.4386 20.765144 + 8600 21692.293 75.655154 0 3691.0373 -13.316763 + 8650 21231.322 151.8989 0 3690.4526 -11.388238 + 8700 19530.647 434.89585 0 3690.0037 2.7433786 + 8750 19720.63 403.07773 0 3689.8493 -6.416414 + 8800 21321.378 136.04091 0 3689.604 1.3661635 + 8850 19811.906 387.80489 0 3689.7893 3.704143 + 8900 19734.167 400.92444 0 3689.9523 2.5685155 + 8950 21076.459 177.18119 0 3689.9244 -11.939513 + 9000 20967.246 195.42966 0 3689.9707 2.0092705 + 9050 21122.023 169.62103 0 3689.9582 2.3791301 + 9100 20169.346 328.27229 0 3689.8299 -3.5017988 + 9150 21418.641 119.84513 0 3689.6187 2.486073 + 9200 20876.042 210.26452 0 3689.6048 -5.3839897 + 9250 21572.38 93.74407 0 3689.1407 -8.3676952 + 9300 20944.78 197.98577 0 3688.7824 1.3278314 + 9350 20706.52 237.48767 0 3688.5744 4.6944204 + 9400 16412.314 953.47251 0 3688.8581 26.134976 + 9450 20461.68 277.76243 0 3688.0424 17.647445 + 9500 20893.994 205.64261 0 3687.9749 -10.642418 + 9550 20503.447 270.63504 0 3687.8761 -17.769897 + 9600 19677.799 408.05887 0 3687.692 -2.7938604 + 9650 17480.971 774.1855 0 3687.6806 0.59827043 + 9700 17799.126 721.50817 0 3688.0292 44.387928 + 9750 20443.384 280.16837 0 3687.399 3.0619324 + 9800 20545.255 263.40108 0 3687.6102 3.6229381 + 9850 20722.819 233.57142 0 3687.3745 0.86462694 + 9900 21128.462 165.09767 0 3686.508 -6.9636843 + 9950 21343.307 130.46714 0 3687.685 -9.7382705 + 10000 20623.887 250.37866 0 3687.6932 2.7529835 +Loop time of 2.27157 on 1 procs for 10000 steps with 81 atoms + +Performance: 38035.351 tau/day, 4402.240 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.092926 | 0.092926 | 0.092926 | 0.0 | 4.09 +Neigh | 0.076362 | 0.076362 | 0.076362 | 0.0 | 3.36 +Comm | 0.0069691 | 0.0069691 | 0.0069691 | 0.0 | 0.31 +Output | 0.0037444 | 0.0037444 | 0.0037444 | 0.0 | 0.16 +Modify | 2.0832 | 2.0832 | 2.0832 | 0.0 | 91.71 +Other | | 0.00841 | | | 0.37 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 62 ave 62 max 62 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 905 ave 905 max 905 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 905 +Ave neighs/atom = 11.17284 +Neighbor list builds = 991 +Dangerous builds = 927 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems.g++.4 b/examples/rigid/log.20Mar22.rigid.poems.g++.4 new file mode 100644 index 0000000000..7e651a7aaf --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems.g++.4 @@ -0,0 +1,328 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045742 + 850 17821.483 711.53827 0 3681.7854 7.4384281 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19374 0 3681.3037 11.787982 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184716 + 1150 20849.582 206.01696 0 3680.9472 -0.86699115 + 1200 21815.003 45.317409 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064083 + 1300 20780.781 217.36511 0 3680.8286 6.0538606 + 1350 20558.971 254.36489 0 3680.8601 -3.6773868 + 1400 21485.03 99.812843 0 3680.6511 -16.185479 + 1450 21771.107 52.159652 0 3680.6775 -2.4756656 + 1500 21520.949 93.503872 0 3680.3286 2.1023574 + 1550 21351.419 121.68131 0 3680.2511 5.5159875 + 1600 20778.804 216.92191 0 3680.0559 15.089203 + 1650 21477.636 100.21877 0 3679.8247 -1.104524 + 1700 18501.329 596.48084 0 3680.0357 -15.679806 + 1750 18563.639 587.34841 0 3681.2882 33.532316 + 1800 19110.174 494.82524 0 3679.8543 18.024079 + 1850 21364.178 119.23767 0 3679.9339 2.5290075 + 1900 20146.588 322.15506 0 3679.9197 5.7317368 + 1950 20692.674 231.25288 0 3680.0319 4.2977982 + 2000 20943.904 189.11229 0 3679.7629 -22.643749 + 2050 19667.815 401.87016 0 3679.8394 3.6240972 + 2100 20280.109 299.81759 0 3679.8357 7.4803647 + 2150 19181.146 483.63975 0 3680.4974 22.634167 + 2200 21301.194 130.53171 0 3680.7308 4.7072523 + 2250 20484.79 266.99736 0 3681.1291 -8.6583002 + 2300 18648.002 573.09962 0 3681.1 -5.2548835 + 2350 21515.851 95.225745 0 3681.2009 -9.3875216 + 2400 21462.37 104.21272 0 3681.2744 -29.459857 + 2450 20108.034 330.94394 0 3682.2829 35.37058 + 2500 20771.818 220.42545 0 3682.3951 -12.318936 + 2550 20502.815 265.09577 0 3682.2316 -22.726822 + 2600 21462.006 105.2733 0 3682.2744 -10.180394 + 2650 21009.656 180.72738 0 3682.3367 4.9580828 + 2700 18680.012 569.37179 0 3682.7071 21.114114 + 2750 21256.19 139.42201 0 3682.1203 -7.4744399 + 2800 21552.267 90.071446 0 3682.1159 -6.2906304 + 2850 20879.958 202.00905 0 3682.0021 0.57990903 + 2900 19018.645 512.35214 0 3682.1262 13.883084 + 2950 19819.365 378.55747 0 3681.785 -0.7348943 + 3000 20269.229 303.35149 0 3681.5563 6.3088075 + 3050 19236.727 475.99457 0 3682.1158 -10.703575 + 3100 18391.55 616.96976 0 3682.2281 9.850079 + 3150 20258.563 305.82076 0 3682.248 7.1951283 + 3200 20716.384 229.15502 0 3681.8856 2.9042294 + 3250 18662.237 572.0784 0 3682.4512 9.2108597 + 3300 19162.278 488.60646 0 3682.3195 3.3306562 + 3350 21235.679 142.98279 0 3682.2626 0.29397483 + 3400 17677.053 736.09247 0 3682.2679 32.75269 + 3450 20852.392 206.65618 0 3682.0548 -4.8319056 + 3500 21182.918 151.46754 0 3681.9539 -5.6330382 + 3550 20589.85 250.40724 0 3682.049 12.582133 + 3600 20973.659 186.28043 0 3681.8903 10.935266 + 3650 17838.632 707.92145 0 3681.0268 -17.200926 + 3700 21538.002 92.744409 0 3682.4114 -0.72124229 + 3750 21390.294 117.90865 0 3682.9576 -7.8431786 + 3800 17921.046 696.50311 0 3683.344 -9.4641531 + 3850 20356.471 290.22624 0 3682.9715 2.4593463 + 3900 20374.077 287.10249 0 3682.782 -1.9519082 + 3950 20563.915 255.29993 0 3682.619 -6.124649 + 4000 20991.467 184.76183 0 3683.3397 1.8954961 + 4050 17805.623 716.24698 0 3683.8509 -20.454944 + 4100 19916.389 363.86301 0 3683.2611 -0.27912557 + 4150 19221.623 480.01232 0 3683.6161 -11.562492 + 4200 20526.82 261.78571 0 3682.9224 -3.9522917 + 4250 20922.813 196.1799 0 3683.3154 0.11947446 + 4300 19956.66 357.78133 0 3683.8914 19.156093 + 4350 19735.73 394.45981 0 3683.7482 14.865775 + 4400 21702.656 67.099805 0 3684.2092 -13.502538 + 4450 18163.055 656.97231 0 3684.1482 -0.6243111 + 4500 17477.718 771.25976 0 3684.2127 -0.4664004 + 4550 20676.507 238.19814 0 3684.2827 -19.444969 + 4600 17322.922 796.77058 0 3683.9242 27.003966 + 4650 11905.158 1704.9151 0 3689.1082 15.574169 + 4700 18689.079 569.80982 0 3684.6563 -14.67311 + 4750 19821.745 381.01914 0 3684.6433 5.0436795 + 4800 20621.335 247.96269 0 3684.8518 -16.407263 + 4850 21923.814 30.965964 0 3684.935 -13.418244 + 4900 18840.555 544.41538 0 3684.5079 11.005357 + 4950 15366.601 1124.2481 0 3685.3482 17.412375 + 5000 18274.314 639.01311 0 3684.732 5.3261109 + 5050 21173.687 155.83673 0 3684.7845 5.4056809 + 5100 21738.219 61.75201 0 3684.7885 -2.631945 + 5150 16597.949 918.84841 0 3685.1732 -10.124101 + 5200 20752.758 225.95919 0 3684.7522 -5.2441372 + 5250 17652.088 741.2645 0 3683.2793 2.0080739 + 5300 19907.523 366.53115 0 3684.4516 8.4266792 + 5350 20104.189 334.14522 0 3684.8433 17.21925 + 5400 21499.848 101.71631 0 3685.0243 -6.1103541 + 5450 21203.533 151.14574 0 3685.068 -5.9468503 + 5500 21076.513 172.45652 0 3685.2088 5.1418181 + 5550 20158.398 325.56609 0 3685.2992 -1.6486034 + 5600 20787.836 221.19563 0 3685.835 -10.66805 + 5650 19687.154 404.77204 0 3685.9644 -23.49128 + 5700 20419.311 282.58328 0 3685.8017 -0.52808211 + 5750 19738.522 395.95893 0 3685.7126 1.3889817 + 5800 18300.025 635.66905 0 3685.6732 23.490447 + 5850 20585.004 255.02032 0 3685.8543 -0.20699939 + 5900 20373.839 290.15881 0 3685.7987 -7.9712187 + 5950 18163.832 659.91192 0 3687.2173 5.4494586 + 6000 21049.247 177.43029 0 3685.6382 2.9138342 + 6050 21239.803 145.77613 0 3685.7433 -1.4927769 + 6100 20686.361 237.86454 0 3685.5913 -0.95516297 + 6150 20461.754 275.31546 0 3685.6079 -3.4166412 + 6200 19264.208 474.73017 0 3685.4316 11.750757 + 6250 21180.813 155.31746 0 3685.4529 2.8188219 + 6300 21047.543 177.4394 0 3685.3632 1.8641486 + 6350 20232.576 313.17716 0 3685.2731 2.8150209 + 6400 20185.616 321.33454 0 3685.6038 -3.8697311 + 6450 18969.632 523.95865 0 3685.5639 0.6725512 + 6500 17592.574 753.49959 0 3685.5952 -1.2557393 + 6550 21279.049 138.42524 0 3684.9335 -1.208945 + 6600 21408.457 116.4143 0 3684.4904 -1.5332953 + 6650 19758.218 391.17316 0 3684.2096 1.8511312 + 6700 20766.943 223.44631 0 3684.6036 -2.3672623 + 6750 20399.631 284.09914 0 3684.0377 -5.4089876 + 6800 21296.628 135.14662 0 3684.5847 -3.8442549 + 6850 20641.481 244.4451 0 3684.692 1.4020639 + 6900 20852.81 209.23009 0 3684.6984 1.8512104 + 6950 20940.555 194.66882 0 3684.7614 -6.554676 + 7000 19496.988 435.28199 0 3684.78 -15.120269 + 7050 19796.829 385.04227 0 3684.5138 -4.1068804 + 7100 19945.264 360.42431 0 3684.635 -4.0629042 + 7150 19431.123 446.12911 0 3684.6497 -6.8321751 + 7200 16864.851 873.80043 0 3684.6089 14.309069 + 7250 20438.75 277.85982 0 3684.3181 -11.41223 + 7300 17688.684 734.01576 0 3682.1298 35.938373 + 7350 21573.419 88.63421 0 3684.204 -3.9032749 + 7400 21198.486 150.72249 0 3683.8034 -7.1477117 + 7450 20586.708 252.93928 0 3684.0572 -7.6634645 + 7500 21815.377 48.180377 0 3684.0765 0.97457507 + 7550 17791.352 718.87564 0 3684.101 28.248235 + 7600 21828.874 45.928597 0 3684.0742 -0.25814944 + 7650 20827.961 212.35674 0 3683.6835 -3.4083384 + 7700 21319.176 130.43547 0 3683.6315 -12.434856 + 7750 20127.904 328.69643 0 3683.3471 -16.975711 + 7800 21741.772 59.679206 0 3683.3078 3.6261863 + 7850 19612.334 414.37418 0 3683.0964 1.3763274 + 7900 20071.318 337.74624 0 3682.9658 -0.40982763 + 7950 17925.664 695.29582 0 3682.9065 17.104439 + 8000 19125.978 492.76383 0 3680.4268 10.807662 + 8050 20233.848 310.42681 0 3682.7347 13.386237 + 8100 20551.619 257.86699 0 3683.1368 -13.97515 + 8150 21578.323 86.88362 0 3683.2708 -9.6811587 + 8200 21154.833 157.72897 0 3683.5344 0.62312375 + 8250 21321.143 129.83967 0 3683.3636 1.9536438 + 8300 21041.696 176.04177 0 3682.9911 4.7475567 + 8350 19883.39 369.32649 0 3683.2247 -7.0959328 + 8400 21626.067 79.062992 0 3683.4075 -14.919059 + 8450 21375.201 120.86836 0 3683.4019 -5.3461514 + 8500 20281.059 303.10304 0 3683.2796 3.7975093 + 8550 21170.533 154.48432 0 3682.9065 -1.1568561 + 8600 17754.931 724.00158 0 3683.1568 14.15254 + 8650 20685.478 235.65879 0 3683.2385 -5.2694179 + 8700 21489.165 101.90509 0 3683.4326 -4.2510612 + 8750 21106.682 165.41638 0 3683.1968 -3.9186708 + 8800 19149.516 491.5843 0 3683.1702 -11.419849 + 8850 21451.865 108.1814 0 3683.4923 -7.8256219 + 8900 19567.4 421.81206 0 3683.0454 -0.71997056 + 8950 20934.097 194.48033 0 3683.4965 -7.0106879 + 9000 18531.559 595.25957 0 3683.8528 3.7449399 + 9050 18868.821 537.22549 0 3682.029 9.9926092 + 9100 19972.527 354.73119 0 3683.4858 -0.30871263 + 9150 19641.651 409.18618 0 3682.7947 -1.3036238 + 9200 20019.08 346.19657 0 3682.7099 6.7425386 + 9250 19259.286 473.04973 0 3682.9308 -24.120659 + 9300 21597.757 82.971857 0 3682.598 -13.748483 + 9350 19348.379 457.23576 0 3681.9656 3.1571402 + 9400 19129.588 493.35235 0 3681.617 8.6293783 + 9450 20337.025 291.20959 0 3680.7138 6.8590795 + 9500 20581.788 249.65891 0 3679.9569 -18.892836 + 9550 19482.069 433.0077 0 3680.0192 23.029778 + 9600 19182.794 482.96871 0 3680.101 -11.081731 + 9650 20086.771 332.5311 0 3680.3263 -18.939681 + 9700 20274.046 300.98818 0 3679.9959 6.7538762 + 9750 18743.595 555.08045 0 3679.0129 8.2757138 + 9800 19464.311 435.66288 0 3679.7148 7.0528759 + 9850 21249.848 138.27382 0 3679.9152 -10.847402 + 9900 21156.214 153.84621 0 3679.8819 -7.8359674 + 9950 21643.134 72.547515 0 3679.7365 -10.507744 + 10000 19587.948 414.64942 0 3679.3075 6.1173553 +Loop time of 2.36879 on 4 procs for 10000 steps with 81 atoms + +Performance: 36474.344 tau/day, 4221.568 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.005348 | 0.024925 | 0.056071 | 12.2 | 1.05 +Neigh | 0.0075012 | 0.022046 | 0.043933 | 9.3 | 0.93 +Comm | 0.13135 | 0.16461 | 0.1917 | 5.9 | 6.95 +Output | 0.0036298 | 0.004271 | 0.0056384 | 1.2 | 0.18 +Modify | 2.1147 | 2.1322 | 2.1418 | 0.7 | 90.01 +Other | | 0.02072 | | | 0.87 + +Nlocal: 20.25 ave 81 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 41 ave 78 max 11 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 193.5 ave 774 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 774 +Ave neighs/atom = 9.5555556 +Neighbor list builds = 989 +Dangerous builds = 915 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems2.g++.1 b/examples/rigid/log.20Mar22.rigid.poems2.g++.1 new file mode 100644 index 0000000000..57f2040a67 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems2.g++.1 @@ -0,0 +1,330 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7382 0 3904.4344 18.086359 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173524 + 200 20705.978 69.977442 0 3904.4178 9.0928158 + 250 19552.211 283.50525 0 3904.285 15.670465 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47231 0 3902.9213 0.6921524 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05177 0 3902.1317 4.6838621 + 850 19932.48 210.71175 0 3901.9118 3.4716043 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61915 0 3902.4586 -2.272315 + 1050 20859.506 39.696993 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.874422 + 1200 20767.681 56.717094 0 3902.5839 -34.817444 + 1250 20625.583 82.586399 0 3902.1388 11.697329 + 1300 20690.013 71.006478 0 3902.4903 -29.292777 + 1350 20936.019 26.022786 0 3903.0634 1.0316025 + 1400 19753.559 244.81785 0 3902.8844 6.7138514 + 1450 15690.149 998.342 0 3903.9252 48.124557 + 1500 20234.455 155.92516 0 3903.0465 13.17221 + 1550 20779.631 55.063009 0 3903.1428 -2.639045 + 1600 20642.753 80.233905 0 3902.9659 -2.4688467 + 1650 18785.696 423.90402 0 3902.7365 -5.6466663 + 1700 20965.076 20.760444 0 3903.182 -0.45364296 + 1750 18935.406 396.96067 0 3903.5173 25.913302 + 1800 20581.559 91.756972 0 3903.1567 3.8217234 + 1850 20616.946 85.184849 0 3903.1378 4.1907972 + 1900 16602.053 828.40949 0 3902.8637 -0.49505122 + 1950 20175.526 166.53362 0 3902.7421 5.603825 + 2000 20261.924 150.39322 0 3902.6014 -1.196958 + 2050 20170.339 167.40504 0 3902.6531 -0.80849882 + 2100 19820.132 231.26755 0 3901.6624 3.1476607 + 2150 20666.19 75.838461 0 3902.9106 0.53899287 + 2200 19873.51 222.53286 0 3902.8124 7.9310276 + 2250 18548.063 467.69698 0 3902.5235 16.905356 + 2300 20616.61 84.762399 0 3902.6531 -6.7872951 + 2350 18167.738 538.13635 0 3902.5322 -11.458285 + 2400 20120.227 177.01954 0 3902.9875 -1.2593018 + 2450 20436.599 118.32469 0 3902.8801 -6.5989174 + 2500 18919.923 400.26361 0 3903.9531 32.37476 + 2550 19675.809 259.77151 0 3903.4398 19.437327 + 2600 19739.842 247.86388 0 3903.3901 -7.519784 + 2650 20557.026 96.530313 0 3903.387 0.60211646 + 2700 20666.602 76.099892 0 3903.2484 0.16825503 + 2750 20924.585 28.453883 0 3903.3771 2.4227171 + 2800 20360.659 132.8596 0 3903.352 4.1440877 + 2850 20783.475 54.518625 0 3903.3102 -0.57312067 + 2900 20456.181 115.03745 0 3903.2191 -20.118887 + 2950 20779.493 55.321394 0 3903.3756 -0.26783079 + 3000 20011.867 197.30216 0 3903.2035 -1.4704201 + 3050 20741.875 62.208723 0 3903.2966 -7.5432815 + 3100 21001.754 14.148298 0 3903.362 2.9676438 + 3150 20244.086 154.44639 0 3903.3512 -1.9071213 + 3200 20639.615 81.136426 0 3903.2873 1.4826467 + 3250 20735.244 63.529571 0 3903.3895 2.1127055 + 3300 20142.891 173.22282 0 3903.3878 4.7739415 + 3350 19963.765 206.21899 0 3903.2126 5.5410771 + 3400 16628.667 824.13627 0 3903.519 36.087673 + 3450 19228.218 342.81569 0 3903.5968 3.1057274 + 3500 19759.293 244.57876 0 3903.707 2.2339557 + 3550 19853.21 227.06362 0 3903.584 -1.0882119 + 3600 19673.516 260.64854 0 3903.8923 -10.63775 + 3650 19619.238 270.5393 0 3903.7316 -6.3746003 + 3700 20756.865 59.790243 0 3903.6542 -8.3015766 + 3750 20265.025 150.47347 0 3903.2559 -5.7284695 + 3800 20944.683 24.669276 0 3903.3142 -0.070552298 + 3850 19344.831 320.59492 0 3902.971 13.040749 + 3900 19978.209 203.00247 0 3902.6708 0.15638133 + 3950 19864.118 224.19359 0 3902.734 0.453229 + 4000 17606.216 642.71493 0 3903.1252 -12.656002 + 4050 18017.895 566.54102 0 3903.1883 12.133906 + 4100 20092.963 182.17593 0 3903.095 7.7445947 + 4150 20555.337 96.395074 0 3902.939 -6.5429752 + 4200 20709.781 67.869199 0 3903.0138 -2.8653003 + 4250 18956.203 392.20748 0 3902.6155 -1.6249728 + 4300 17816.204 603.72704 0 3903.0241 23.089239 + 4350 18979.742 388.04678 0 3902.8138 3.2511108 + 4400 20272.085 148.82367 0 3902.9135 1.9518268 + 4450 18820.003 417.74789 0 3902.9337 6.3979299 + 4500 19991.936 200.50131 0 3902.7117 3.5118553 + 4550 20915.092 29.663898 0 3902.8291 -2.3174641 + 4600 20690.37 71.125087 0 3902.6752 -12.008575 + 4650 18893.76 404.50849 0 3903.3529 15.006184 + 4700 18611.123 456.1263 0 3902.6306 -5.3574892 + 4750 20497.821 106.5856 0 3902.4784 0.85039837 + 4800 20803.214 50.120522 0 3902.5675 3.8610873 + 4850 18849.598 411.72635 0 3902.3927 9.2029058 + 4900 18121.714 546.68042 0 3902.5533 9.4522272 + 4950 20377.499 128.99323 0 3902.6041 5.3825395 + 5000 20686.114 72.039749 0 3902.8016 -5.706271 + 5050 20180.449 165.51368 0 3902.634 -16.418461 + 5100 20274.947 148.36657 0 3902.9864 -5.6668309 + 5150 18042.324 560.74137 0 3901.9125 3.6791541 + 5200 20794.666 52.204446 0 3903.0685 -1.4517721 + 5250 19073.55 371.18834 0 3903.3272 -13.457439 + 5300 20821.412 47.364313 0 3903.1813 2.258098 + 5350 20583.073 91.271191 0 3902.9513 5.4323985 + 5400 20490.967 108.41184 0 3903.0353 4.122905 + 5450 18141.79 543.66874 0 3903.2594 -0.19951075 + 5500 20274.012 148.55528 0 3903.002 5.0489974 + 5550 17806.237 605.43454 0 3902.8858 43.80619 + 5600 20999.825 14.341937 0 3903.1983 1.0879933 + 5650 20930.929 27.025347 0 3903.1234 -7.0860209 + 5700 20677.725 73.853093 0 3903.0614 2.6864775 + 5750 20521.264 102.87509 0 3903.1092 2.6940548 + 5800 20792.571 52.596021 0 3903.0721 1.2910217 + 5850 20518.674 103.26595 0 3903.0204 -9.2547271 + 5900 18417.885 491.66696 0 3902.3865 -12.049357 + 5950 17243.837 709.37858 0 3902.6817 -6.2357188 + 6000 20262.525 149.56918 0 3901.8885 -0.28964823 + 6050 19883.554 219.14043 0 3901.2801 2.3071707 + 6100 16548.178 838.47869 0 3902.956 -11.715644 + 6150 19601.177 272.14674 0 3901.9944 -0.9008056 + 6200 20499.796 106.2363 0 3902.4949 0.79071424 + 6250 19601.106 272.50139 0 3902.3359 -1.9306693 + 6300 17210.685 712.70535 0 3899.8692 4.8890923 + 6350 19911.896 214.91041 0 3902.2985 12.691129 + 6400 18834.642 411.87123 0 3899.7678 -1.9447856 + 6450 20216.311 158.39781 0 3902.1591 2.6009109 + 6500 20452.025 114.97122 0 3902.3832 0.14644416 + 6550 19142.589 357.34097 0 3902.2649 2.8968485 + 6600 20412.915 122.08784 0 3902.2573 3.1343105 + 6650 17317.867 699.39994 0 3906.4123 42.25563 + 6700 20479.771 109.8036 0 3902.3537 1.3520625 + 6750 20306.902 142.12484 0 3902.6623 2.2032106 + 6800 20755.367 58.994834 0 3902.5814 -0.90518094 + 6850 20471.259 111.7197 0 3902.6936 1.5799331 + 6900 20702.025 69.15032 0 3902.8586 9.3910371 + 6950 20477.695 110.34414 0 3902.5099 1.8181164 + 7000 20560.727 95.057704 0 3902.5998 -15.686006 + 7050 20336.675 136.39386 0 3902.4448 1.3704327 + 7100 20757.399 58.950153 0 3902.913 -6.4250981 + 7150 20870.958 38.095649 0 3903.088 -4.1962169 + 7200 20706.869 68.489134 0 3903.0944 2.8322659 + 7250 20386.713 127.7432 0 3903.0604 6.0287391 + 7300 18391.773 497.21001 0 3903.0939 19.202343 + 7350 20178.898 166.4993 0 3903.3322 1.5682417 + 7400 16858.704 781.78682 0 3903.7691 21.317514 + 7450 17509.513 660.71963 0 3903.2221 -5.9456143 + 7500 19974.601 204.20412 0 3903.2043 -0.69202711 + 7550 20917.053 29.73415 0 3903.2626 -3.9962577 + 7600 20923.518 28.482703 0 3903.2083 -1.9016251 + 7650 20549.528 97.630612 0 3903.0987 3.5512257 + 7700 20861.441 39.903885 0 3903.1337 2.4426264 + 7750 18843.349 413.64461 0 3903.1537 2.677739 + 7800 20616.054 85.214364 0 3903.0021 3.9639004 + 7850 16478.851 851.93376 0 3903.5728 7.3763128 + 7900 20312.115 141.35103 0 3902.8539 4.6707271 + 7950 20389.623 127.16589 0 3903.0219 3.4414001 + 8000 20452.117 115.30715 0 3902.7362 -1.0162528 + 8050 20857.093 40.791886 0 3903.2164 -15.150068 + 8100 19817.543 233.4997 0 3903.415 0.89346046 + 8150 18649.521 449.9112 0 3903.5262 -0.40053588 + 8200 19619.276 270.37616 0 3903.5754 5.5161492 + 8250 20393.176 127.01336 0 3903.5275 2.122613 + 8300 19145.912 358.00424 0 3903.5435 3.863924 + 8350 19636.311 267.17226 0 3903.5262 -7.1496084 + 8400 19086.332 368.86693 0 3903.3729 7.0968952 + 8450 19494.416 292.89527 0 3902.9723 3.1750935 + 8500 20041.919 191.77756 0 3903.244 0.95215503 + 8550 20357.561 133.15478 0 3903.0736 -0.14020152 + 8600 16998.797 756.07003 0 3903.9954 -16.724408 + 8650 20853.26 41.386996 0 3903.1017 -3.2612965 + 8700 20767.768 57.360884 0 3903.2438 1.1157649 + 8750 20752.546 60.106518 0 3903.1705 0.39130547 + 8800 20574.407 92.99798 0 3903.0734 0.61728166 + 8850 20326.99 138.94203 0 3903.1995 -1.9434522 + 8900 17408.108 679.53222 0 3903.2559 21.935371 + 8950 20471.21 112.2721 0 3903.2368 1.8142747 + 9000 19129.591 360.35257 0 3902.8694 4.5786395 + 9050 20439.668 117.89541 0 3903.0191 2.5585685 + 9100 20780.375 54.788664 0 3903.0062 3.8312459 + 9150 19904.559 216.61504 0 3902.6445 12.150414 + 9200 20961.295 21.52065 0 3903.2419 -0.2120699 + 9250 19315.252 326.44175 0 3903.3402 -19.740867 + 9300 20653.002 78.77764 0 3903.4076 -7.8068233 + 9350 18961.572 391.20947 0 3902.6117 -12.660843 + 9400 16262.179 892.67633 0 3904.191 22.2435 + 9450 17064.394 743.33301 0 3903.406 36.139436 + 9500 18075.588 555.06436 0 3902.3954 24.598176 + 9550 20487.738 109.06287 0 3903.0884 2.6320759 + 9600 20358.609 133.36993 0 3903.4828 0.76449113 + 9650 19849.022 228.46312 0 3904.208 9.5547064 + 9700 20448.112 116.8757 0 3903.5632 -1.0845697 + 9750 20472.78 112.51661 0 3903.7722 -0.30676738 + 9800 19491.99 293.35361 0 3902.9814 -20.10857 + 9850 19895.603 218.42479 0 3902.7957 -0.18235641 + 9900 19704.336 254.55068 0 3903.5019 14.553184 + 9950 17689.462 627.9788 0 3903.805 4.9918088 + 10000 20184.205 165.29396 0 3903.1097 2.9472364 +Loop time of 2.2898 on 1 procs for 10000 steps with 81 atoms + +Performance: 37732.583 tau/day, 4367.197 timesteps/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.053341 | 0.053341 | 0.053341 | 0.0 | 2.33 +Neigh | 0.056174 | 0.056174 | 0.056174 | 0.0 | 2.45 +Comm | 0.0087028 | 0.0087028 | 0.0087028 | 0.0 | 0.38 +Output | 0.0036774 | 0.0036774 | 0.0036774 | 0.0 | 0.16 +Modify | 2.1598 | 2.1598 | 2.1598 | 0.0 | 94.32 +Other | | 0.008128 | | | 0.35 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 113 ave 113 max 113 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 582 ave 582 max 582 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 582 +Ave neighs/atom = 7.1851852 +Neighbor list builds = 993 +Dangerous builds = 950 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems2.g++.4 b/examples/rigid/log.20Mar22.rigid.poems2.g++.4 new file mode 100644 index 0000000000..89585cd109 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems2.g++.4 @@ -0,0 +1,330 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7382 0 3904.4344 18.086358 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173524 + 200 20705.978 69.977039 0 3904.4174 9.0928122 + 250 19552.211 283.50525 0 3904.285 15.670466 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47271 0 3902.9217 0.69215592 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05197 0 3902.1319 4.6838632 + 850 19932.48 210.71175 0 3901.9118 3.4716031 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61915 0 3902.4586 -2.272315 + 1050 20859.506 39.696993 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.8744219 + 1200 20767.681 56.717095 0 3902.5839 -34.817444 + 1250 20625.583 82.586198 0 3902.1386 11.697328 + 1300 20690.013 71.006478 0 3902.4903 -29.29278 + 1350 20936.019 26.022786 0 3903.0634 1.0316025 + 1400 19753.56 244.81784 0 3902.8844 6.7138497 + 1450 15690.149 998.34213 0 3903.9252 48.124569 + 1500 20234.455 155.92516 0 3903.0465 13.172207 + 1550 20779.631 55.063019 0 3903.1428 -2.6390455 + 1600 20642.753 80.233821 0 3902.9659 -2.4688431 + 1650 18785.698 423.90364 0 3902.7365 -5.6466892 + 1700 20965.076 20.760451 0 3903.182 -0.45366172 + 1750 18935.412 396.95958 0 3903.5173 25.913174 + 1800 20581.554 91.757912 0 3903.1567 3.8218442 + 1850 20616.949 85.184789 0 3903.1382 4.1907933 + 1900 16601.896 828.43849 0 3902.8638 -0.49468175 + 1950 20175.564 166.52646 0 3902.7421 5.6035728 + 2000 20262.525 150.28224 0 3902.6017 -1.1967705 + 2050 20168.994 167.65314 0 3902.6521 -0.80723928 + 2100 19810.955 232.96524 0 3901.6605 3.1936531 + 2150 20667.232 75.645145 0 3902.9103 0.54812734 + 2200 19863.772 224.34646 0 3902.8228 7.9294465 + 2250 18808.943 419.2084 0 3902.3461 14.344526 + 2300 20573.665 92.761842 0 3902.6999 -6.7671703 + 2350 19075.104 369.95414 0 3902.3809 -9.5353568 + 2400 20273.873 148.53775 0 3902.9586 -1.93796 + 2450 20087.769 182.30216 0 3902.2593 2.131796 + 2500 20711.602 67.530554 0 3903.0124 2.6280244 + 2550 19971.224 204.75926 0 3903.134 3.1760522 + 2600 20620.084 85.027145 0 3903.5612 -0.92888063 + 2650 19737.546 248.65474 0 3903.7559 -3.3218688 + 2700 20650.724 79.522243 0 3903.7303 -7.5918025 + 2750 19863.245 225.2505 0 3903.6292 9.2140221 + 2800 18992.457 386.73547 0 3903.8572 2.6244537 + 2850 18703.899 440.48356 0 3904.1685 14.561348 + 2900 17939.805 581.74599 0 3903.932 -8.0863089 + 2950 20867.516 39.38186 0 3903.7367 3.0985423 + 3000 19767.994 242.8847 0 3903.6243 1.5943109 + 3050 20397.448 126.31591 0 3903.6212 -0.14982775 + 3100 20978.114 19.126395 0 3903.9623 -9.6797253 + 3150 18303.556 513.8514 0 3903.3989 4.5940322 + 3200 19156.505 356.46608 0 3903.9671 10.071308 + 3250 17484.205 666.52199 0 3904.3377 -4.1641768 + 3300 18069.94 557.75947 0 3904.0447 11.868707 + 3350 20855.645 41.964632 0 3904.1212 5.4186293 + 3400 18011.986 568.76255 0 3904.3155 25.262783 + 3450 18669.69 446.92755 0 3904.2776 -4.194499 + 3500 20248.799 154.22147 0 3903.9991 3.9211572 + 3550 20226.024 158.64726 0 3904.2072 1.5299114 + 3600 20267.02 151.25631 0 3904.4082 -8.9821729 + 3650 20522.946 103.65382 0 3904.1994 -14.433796 + 3700 20892.319 35.294614 0 3904.2426 -21.264596 + 3750 19942.202 211.02993 0 3904.0304 -1.6428817 + 3800 20421.678 122.08118 0 3903.8734 1.7137935 + 3850 17899.53 588.82593 0 3903.5536 -24.450276 + 3900 20721.119 66.486999 0 3903.7312 -7.1772088 + 3950 20946.484 24.799445 0 3903.778 -0.4028037 + 4000 20985.362 17.608355 0 3903.7865 4.7522266 + 4050 19969.779 205.46466 0 3903.5719 18.941639 + 4100 20479.578 110.56561 0 3903.08 2.3715952 + 4150 18110.701 549.53348 0 3903.367 1.133321 + 4200 19321.098 325.58216 0 3903.5634 -3.7574942 + 4250 20734.436 63.87616 0 3903.5865 0.48350623 + 4300 19446.823 302.1727 0 3903.4362 4.0462392 + 4350 20494.669 108.1918 0 3903.501 2.9789077 + 4400 20379.244 129.61413 0 3903.5482 4.0881089 + 4450 19710.564 253.4251 0 3903.5295 5.3334683 + 4500 20744.753 61.785082 0 3903.406 4.0015409 + 4550 19948.024 208.76984 0 3902.8484 2.705423 + 4600 18367.368 502.69569 0 3904.0602 21.476471 + 4650 20559.367 96.133242 0 3903.4234 2.2549454 + 4700 20940.135 25.547808 0 3903.3505 -8.9042666 + 4750 20128.703 175.82088 0 3903.3584 -8.1450176 + 4800 20632.27 82.543887 0 3903.3347 -0.55649542 + 4850 19864.539 224.63792 0 3903.2563 7.1553461 + 4900 19332.037 323.15561 0 3903.1625 17.020214 + 4950 19055.575 373.68069 0 3902.4908 10.149457 + 5000 20219.484 159.21383 0 3903.5627 3.1806346 + 5050 17557.761 652.32864 0 3903.7659 10.733736 + 5100 20615.337 85.795304 0 3903.4503 -3.6035636 + 5150 20759.853 59.155843 0 3903.573 2.0152286 + 5200 20082.007 184.39375 0 3903.2839 -5.3745109 + 5250 18689.521 442.59842 0 3903.6208 -9.8911164 + 5300 20038.496 192.34221 0 3903.1749 -2.1437039 + 5350 19897.455 218.70142 0 3903.4154 0.64582116 + 5400 18732.385 434.21543 0 3903.1755 12.98676 + 5450 19831.487 230.79099 0 3903.2886 11.439958 + 5500 20079.89 184.6953 0 3903.1935 4.0906279 + 5550 20453.497 115.47128 0 3903.1559 7.8844436 + 5600 16673.041 815.52661 0 3903.1267 -20.17797 + 5650 19691.378 256.6412 0 3903.1928 3.7103317 + 5700 20345.743 135.29997 0 3903.0302 5.6373816 + 5750 20769.613 56.906603 0 3903.1312 -17.564762 + 5800 20713.369 67.38314 0 3903.1922 -5.340631 + 5850 20799.947 51.348865 0 3903.1909 -2.7827653 + 5900 19581.933 273.51588 0 3899.7997 12.347375 + 5950 20444.438 116.909 0 3902.9161 -0.74896654 + 6000 18970.948 389.99664 0 3903.1352 26.642912 + 6050 19414.753 307.13217 0 3902.4568 25.86316 + 6100 20780.042 54.586474 0 3902.7424 1.5387425 + 6150 20885.872 35.091585 0 3902.8456 -8.251884 + 6200 19825.81 231.40943 0 3902.8558 6.7196589 + 6250 20578.278 92.255994 0 3903.0481 -5.9647091 + 6300 20093.43 181.8699 0 3902.8754 -9.9906069 + 6350 20605.294 87.180289 0 3902.9755 -3.5643876 + 6400 19737.257 247.84828 0 3902.8958 -4.2783347 + 6450 19884.717 220.81633 0 3903.1714 3.8758905 + 6500 18719.372 436.94802 0 3903.4984 1.7865904 + 6550 20096.883 181.63346 0 3903.2784 2.395512 + 6600 20888.673 35.003062 0 3903.2758 2.7728947 + 6650 20437.85 118.16373 0 3902.9507 8.1456757 + 6700 19241.051 339.73065 0 3902.8882 13.740454 + 6750 20407.542 123.94326 0 3903.1177 7.6285942 + 6800 20536.785 99.976706 0 3903.0851 8.3496632 + 6850 20625.328 83.579677 0 3903.0849 6.5074992 + 6900 20705.37 68.944625 0 3903.2724 3.1905177 + 6950 18872.424 408.67134 0 3903.5647 6.2638845 + 7000 20072.762 186.18051 0 3903.3586 -22.780407 + 7050 20461.879 114.07495 0 3903.3117 -11.495523 + 7100 19811.566 234.50237 0 3903.3108 1.1212695 + 7150 20742.918 61.884088 0 3903.1651 -3.7907508 + 7200 20911.192 30.599903 0 3903.0429 -7.0262304 + 7250 20879.755 36.30274 0 3902.9241 -5.8018787 + 7300 20682.32 72.703261 0 3902.7626 -3.3446789 + 7350 19401.046 309.70672 0 3902.493 3.4836528 + 7400 20220.542 157.83897 0 3902.3838 2.3400031 + 7450 17691.193 625.47764 0 3901.6244 25.239568 + 7500 19745.294 245.02566 0 3901.5615 5.3622843 + 7550 19685.719 256.70983 0 3902.2133 3.4560563 + 7600 18830.192 415.10021 0 3902.1727 -0.10282681 + 7650 19613.136 270.18979 0 3902.2521 8.2241536 + 7700 20989.015 15.636879 0 3902.4915 1.2955204 + 7750 20301.583 142.90625 0 3902.4586 0.12548373 + 7800 18360.147 502.50342 0 3902.5307 17.117272 + 7850 20796.478 51.032537 0 3902.2321 -3.0993883 + 7900 20284.267 145.64296 0 3901.9887 -1.2682383 + 7950 20280.983 146.13471 0 3901.8723 3.5999841 + 8000 20915.869 28.730821 0 3902.0399 2.4987291 + 8050 20745.162 60.19981 0 3901.8964 4.0643481 + 8100 20509.039 103.70462 0 3901.6748 1.0771863 + 8150 20212.97 158.64893 0 3901.7916 3.0000215 + 8200 20323.463 138.25912 0 3901.8634 -1.2802945 + 8250 19997.284 198.37183 0 3901.5727 -2.6431964 + 8300 20138.402 171.75824 0 3901.092 1.7669897 + 8350 20367.568 130.22531 0 3901.9972 -1.2153731 + 8400 19945.534 208.35675 0 3901.9741 1.6021151 + 8450 20112.534 177.18642 0 3901.7298 2.2413008 + 8500 20686.7 71.116816 0 3901.9873 2.2888545 + 8550 18081.94 553.83586 0 3902.3432 7.8257937 + 8600 18320.081 505.67086 0 3898.2784 16.554878 + 8650 20235.305 154.43021 0 3901.709 3.1740823 + 8700 20355.413 132.22512 0 3901.746 4.3436482 + 8750 20087.188 182.11349 0 3901.9631 10.422134 + 8800 20400.795 124.09819 0 3902.0232 2.1179177 + 8850 20678.731 72.825797 0 3902.2204 -3.4491441 + 8900 20372.643 129.5072 0 3902.2189 -8.2166415 + 8950 20851.731 40.899364 0 3902.331 -5.8382839 + 9000 20318.076 139.61775 0 3902.2243 -4.1960802 + 9050 16879.415 776.53739 0 3902.3549 -14.429475 + 9100 19135.149 358.68223 0 3902.2284 -15.50479 + 9150 20689.556 70.939656 0 3902.339 -2.9876179 + 9200 19949.801 207.54882 0 3901.9564 6.4259245 + 9250 20207.027 160.2813 0 3902.3233 1.7402195 + 9300 20030.005 192.99466 0 3902.2548 5.300728 + 9350 19795.291 236.24003 0 3902.0347 5.8677745 + 9400 18232.093 526.18752 0 3902.501 19.344893 + 9450 18789.641 422.30568 0 3901.8687 -7.5185247 + 9500 16332.599 874.10423 0 3898.6597 16.241378 + 9550 18572.572 462.19972 0 3901.5649 -10.777359 + 9600 19859.645 223.32209 0 3901.0341 0.89631957 + 9650 19092.741 365.35768 0 3901.0504 6.7830005 + 9700 18391.154 495.72792 0 3901.4972 6.0683847 + 9750 17790.092 608.60997 0 3903.0714 8.2090184 + 9800 17681.783 628.99951 0 3903.4038 14.231747 + 9850 17804.412 605.54067 0 3902.654 22.308453 + 9900 19134.472 359.37911 0 3902.7999 8.5633158 + 9950 20099.055 180.28604 0 3902.3332 4.7905855 + 10000 20035.447 192.30744 0 3902.5754 1.8299201 +Loop time of 2.31994 on 4 procs for 10000 steps with 81 atoms + +Performance: 37242.315 tau/day, 4310.453 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0052789 | 0.014781 | 0.038634 | 11.4 | 0.64 +Neigh | 0.0081228 | 0.016514 | 0.033404 | 7.7 | 0.71 +Comm | 0.12269 | 0.13668 | 0.14951 | 3.1 | 5.89 +Output | 0.0034489 | 0.0039413 | 0.0050811 | 1.1 | 0.17 +Modify | 2.1036 | 2.1312 | 2.1509 | 1.2 | 91.86 +Other | | 0.01685 | | | 0.73 + +Nlocal: 20.25 ave 36 max 0 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 35.25 ave 47 max 24 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 137.5 ave 252 max 0 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 550 +Ave neighs/atom = 6.7901235 +Neighbor list builds = 994 +Dangerous builds = 956 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems3.g++.1 b/examples/rigid/log.20Mar22.rigid.poems3.g++.1 new file mode 100644 index 0000000000..b565d9f79d --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems3.g++.1 @@ -0,0 +1,329 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all poems file unconnected-bodies.dat +WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035) +9 clusters, 9 bodies, 0 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.686 571.71596 0 5265.8207 32.006226 + 100 16298.5 136.65142 0 5267.6607 16.443791 + 150 16682.639 17.488068 0 5269.43 14.900278 + 200 16733.955 1.3724268 0 5269.4692 14.569123 + 250 16738.877 -0.15250573 0 5269.4939 14.496287 + 300 16738.611 -0.05516662 0 5269.5077 14.495909 + 350 16738.515 -0.01744351 0 5269.5152 14.496329 + 400 16738.488 -0.0060096677 0 5269.5178 14.496497 + 450 16738.479 -0.0012712918 0 5269.5199 14.496575 + 500 16738.479 -0.00081070354 0 5269.5203 14.49658 + 550 16738.479 -0.00083205205 0 5269.5203 14.496577 + 600 16738.479 -0.0005835658 0 5269.5206 14.49658 + 650 16738.479 -0.00047227225 0 5269.5206 14.496583 + 700 16738.479 0 0 5269.521 14.496593 + 750 16738.479 0 0 5269.5211 14.496595 + 800 16738.479 0 0 5269.5211 14.496596 + 850 16738.479 0 0 5269.5211 14.496595 + 900 16738.479 0 0 5269.5212 14.496593 + 950 16738.485 -0.003532391 0 5269.5196 14.496546 + 1000 16738.609 -0.051135033 0 5269.5109 14.496098 + 1050 16737.381 0.32991002 0 5269.5055 14.525627 + 1100 16737.915 0.16210932 0 5269.5058 14.531848 + 1150 16738.726 -0.089235332 0 5269.5098 14.509768 + 1200 16738.49 -0.0075446298 0 5269.5169 14.510489 + 1250 16738.48 0 0 5269.5214 14.510585 + 1300 16738.48 0 0 5269.5214 14.510587 + 1350 16738.48 0 0 5269.5215 14.510588 + 1400 16738.48 -0.00044742303 0 5269.5211 14.510581 + 1450 16738.481 -0.0010975104 0 5269.5207 14.51057 + 1500 16738.481 -0.00057925965 0 5269.5211 14.510575 + 1550 16738.48 0 0 5269.5216 14.510582 + 1600 16738.48 0 0 5269.5216 14.510581 + 1650 16738.481 0 0 5269.5216 14.510581 + 1700 16738.481 0 0 5269.5217 14.510582 + 1750 16738.481 0 0 5269.5217 14.510583 + 1800 16738.481 0 0 5269.5217 14.510585 + 1850 16738.481 0 0 5269.5218 14.510585 + 1900 16738.481 0 0 5269.5218 14.510585 + 1950 16738.487 -0.0031700155 0 5269.5206 14.510534 + 2000 16738.514 -0.013238802 0 5269.5188 14.510401 + 2050 16738.578 -0.03654435 0 5269.5158 14.510155 + 2100 16738.656 -0.063182323 0 5269.5137 14.510082 + 2150 16738.63 -0.056004395 0 5269.5127 14.510096 + 2200 16738.579 -0.038415873 0 5269.5143 14.510273 + 2250 16738.538 -0.023709094 0 5269.516 14.510414 + 2300 16738.512 -0.013252539 0 5269.5182 14.510501 + 2350 16738.491 -0.0045593284 0 5269.5203 14.510598 + 2400 16738.482 -0.00052242487 0 5269.5217 14.510655 + 2450 16738.486 -0.0023245722 0 5269.5211 14.510627 + 2500 16738.491 -0.005189304 0 5269.5197 14.510606 + 2550 16738.604 -0.044988104 0 5269.5155 14.510185 + 2600 16738.446 0.00096754005 0 5269.5117 14.510521 + 2650 16732.887 1.753125 0 5269.5138 14.598792 + 2700 16738.784 -0.10629556 0 5269.5107 14.499176 + 2750 16734.136 1.359459 0 5269.5135 14.594678 + 2800 16738.608 -0.047184149 0 5269.5147 14.510254 + 2850 16738.509 -0.012527238 0 5269.5181 14.509344 + 2900 16738.487 -0.0026065529 0 5269.521 14.509512 + 2950 16738.498 -0.0082248532 0 5269.519 14.509457 + 3000 16738.683 -0.071294028 0 5269.514 14.509005 + 3050 16717.444 6.5874862 0 5269.4864 14.834144 + 3100 16657.654 25.431253 0 5269.5074 14.467824 + 3150 16739.322 -0.28964062 0 5269.497 13.658821 + 3200 16733.615 1.4969789 0 5269.487 11.998304 + 3250 16737.289 0.35071214 0 5269.4974 11.918931 + 3300 16732.493 1.8663821 0 5269.503 12.109003 + 3350 16738.717 -0.087719164 0 5269.5085 11.979747 + 3400 16738.586 -0.045267897 0 5269.5095 11.97972 + 3450 16738.662 -0.071274216 0 5269.5076 11.979564 + 3500 16738.853 -0.13644992 0 5269.5026 11.979658 + 3550 16729.612 2.7475277 0 5269.4774 12.195939 + 3600 16728.659 3.0596069 0 5269.4893 12.241248 + 3650 16738.923 -0.15949792 0 5269.5014 11.991857 + 3700 16738.76 -0.10695054 0 5269.5028 11.992932 + 3750 16738.751 -0.10105954 0 5269.5057 11.993137 + 3800 16738.597 -0.048627545 0 5269.5097 11.993456 + 3850 16738.507 -0.016053927 0 5269.5138 11.992973 + 3900 16738.485 -0.0060825487 0 5269.5169 11.993052 + 3950 16738.475 -0.0014953722 0 5269.5183 11.993119 + 4000 16738.472 -0.00054315391 0 5269.5184 11.99315 + 4050 16738.472 -0.00023792127 0 5269.5187 11.993172 + 4100 16738.472 0 0 5269.5189 11.993188 + 4150 16738.472 0 0 5269.5189 11.993188 + 4200 16738.472 0 0 5269.519 11.993178 + 4250 16738.472 0 0 5269.519 11.993164 + 4300 16738.472 0 0 5269.5191 11.993152 + 4350 16738.473 0 0 5269.5191 11.993147 + 4400 16738.473 0 0 5269.5192 11.993149 + 4450 16738.473 0 0 5269.5192 11.993158 + 4500 16738.473 0 0 5269.5193 11.99317 + 4550 16738.473 0 0 5269.5193 11.993176 + 4600 16738.473 0 0 5269.5194 11.993174 + 4650 16738.473 0 0 5269.5194 11.993167 + 4700 16738.474 0 0 5269.5195 11.993162 + 4750 16738.474 0 0 5269.5195 11.99316 + 4800 16738.474 0 0 5269.5196 11.99316 + 4850 16738.474 0 0 5269.5196 11.993163 + 4900 16738.474 0 0 5269.5197 11.99317 + 4950 16738.474 0 0 5269.5197 11.993176 + 5000 16738.475 0 0 5269.5198 11.993174 + 5050 16738.475 0 0 5269.5198 11.993165 + 5100 16738.475 0 0 5269.5199 11.993155 + 5150 16738.475 0 0 5269.5199 11.99315 + 5200 16738.475 0 0 5269.52 11.993153 + 5250 16738.475 0 0 5269.52 11.993161 + 5300 16738.476 0 0 5269.5201 11.993173 + 5350 16738.476 0 0 5269.5201 11.993185 + 5400 16738.476 0 0 5269.5202 11.993189 + 5450 16738.476 0 0 5269.5202 11.993181 + 5500 16738.476 0 0 5269.5203 11.993165 + 5550 16738.483 -0.0030091905 0 5269.5195 11.993097 + 5600 16738.534 -0.020777802 0 5269.5177 11.992799 + 5650 16738.649 -0.059321662 0 5269.5153 11.993266 + 5700 16409.08 103.75288 0 5269.5745 23.626238 + 5750 16738.578 -0.036776519 0 5269.5155 11.910545 + 5800 16738.484 -0.0047306177 0 5269.518 11.911008 + 5850 16738.477 -0.00022082692 0 5269.5202 11.911078 + 5900 16738.477 -0.00033136078 0 5269.5203 11.91107 + 5950 16738.478 -0.00036902212 0 5269.5203 11.911052 + 6000 16738.477 0 0 5269.5206 11.911044 + 6050 16738.477 0 0 5269.5207 11.911034 + 6100 16738.478 0 0 5269.5207 11.911032 + 6150 16738.478 0 0 5269.5208 11.911037 + 6200 16738.478 0 0 5269.5208 11.911049 + 6250 16738.478 0 0 5269.5209 11.911062 + 6300 16738.478 0 0 5269.5209 11.911068 + 6350 16738.478 0 0 5269.521 11.911065 + 6400 16738.478 0 0 5269.521 11.911058 + 6450 16738.479 0 0 5269.5211 11.911052 + 6500 16738.479 0 0 5269.5211 11.911047 + 6550 16738.479 0 0 5269.5212 11.911046 + 6600 16738.479 0 0 5269.5212 11.911049 + 6650 16738.479 0 0 5269.5213 11.911056 + 6700 16738.479 0 0 5269.5213 11.911062 + 6750 16738.48 0 0 5269.5214 11.91106 + 6800 16738.48 0 0 5269.5214 11.911051 + 6850 16738.48 0 0 5269.5215 11.911044 + 6900 16738.48 0 0 5269.5215 11.911041 + 6950 16738.48 0 0 5269.5216 11.911045 + 7000 16738.48 0 0 5269.5216 11.911053 + 7050 16738.481 0 0 5269.5217 11.911063 + 7100 16738.481 0 0 5269.5217 11.911071 + 7150 16738.481 0 0 5269.5218 11.911072 + 7200 16738.481 0 0 5269.5218 11.911063 + 7250 16738.481 0 0 5269.5219 11.911048 + 7300 16738.481 0 0 5269.5219 11.911036 + 7350 16738.482 0 0 5269.522 11.911031 + 7400 16738.482 0 0 5269.522 11.911035 + 7450 16738.482 0 0 5269.5221 11.911046 + 7500 16738.482 0 0 5269.5221 11.911062 + 7550 16738.482 0 0 5269.5222 11.911077 + 7600 16738.482 0 0 5269.5222 11.911081 + 7650 16738.483 0 0 5269.5223 11.911071 + 7700 16738.483 0 0 5269.5223 11.911054 + 7750 16738.483 0 0 5269.5224 11.911039 + 7800 16738.483 0 0 5269.5224 11.911031 + 7850 16738.483 0 0 5269.5225 11.911031 + 7900 16738.483 0 0 5269.5226 11.911039 + 7950 16738.484 0 0 5269.5226 11.911052 + 8000 16738.484 0 0 5269.5227 11.911065 + 8050 16738.484 0 0 5269.5227 11.91107 + 8100 16738.484 0 0 5269.5228 11.911065 + 8150 16738.484 0 0 5269.5228 11.911056 + 8200 16738.484 0 0 5269.5229 11.911047 + 8250 16738.485 0 0 5269.5229 11.911042 + 8300 16738.485 0 0 5269.523 11.911041 + 8350 16738.485 0 0 5269.523 11.911046 + 8400 16738.485 0 0 5269.5231 11.911055 + 8450 16738.485 0 0 5269.5231 11.911062 + 8500 16738.485 0 0 5269.5232 11.91106 + 8550 16738.486 0 0 5269.5232 11.911053 + 8600 16738.487 -0.00084974054 0 5269.5227 11.911032 + 8650 16738.486 0 0 5269.5233 11.911046 + 8700 16738.486 0 0 5269.5234 11.91105 + 8750 16738.486 0 0 5269.5235 11.911056 + 8800 16738.486 0 0 5269.5235 11.911063 + 8850 16738.487 -0.000227631 0 5269.5234 11.911065 + 8900 16738.487 0 0 5269.5236 11.911068 + 8950 16738.487 0 0 5269.5237 11.911058 + 9000 16738.487 0 0 5269.5237 11.911045 + 9050 16738.487 0 0 5269.5238 11.911036 + 9100 16738.487 0 0 5269.5238 11.911034 + 9150 16738.488 0 0 5269.5239 11.91104 + 9200 16738.488 0 0 5269.5239 11.911052 + 9250 16738.488 0 0 5269.524 11.911068 + 9300 16738.488 0 0 5269.524 11.911079 + 9350 16738.488 0 0 5269.5241 11.911078 + 9400 16738.492 -0.0016306436 0 5269.5235 11.911038 + 9450 16738.492 -0.0032567429 0 5269.522 11.911005 + 9500 16738.495 -0.0036645351 0 5269.5224 11.910982 + 9550 16738.49 -0.0010673912 0 5269.5237 11.911012 + 9600 16738.489 0 0 5269.5244 11.911032 + 9650 16738.489 0 0 5269.5244 11.911043 + 9700 16738.49 0 0 5269.5245 11.911058 + 9750 16738.49 0 0 5269.5245 11.911071 + 9800 16738.49 0 0 5269.5246 11.911073 + 9850 16738.49 0 0 5269.5246 11.911065 + 9900 16738.49 0 0 5269.5247 11.911053 + 9950 16738.491 -0.00058544643 0 5269.5243 11.911032 + 10000 16738.493 -0.0015244931 0 5269.5242 11.911015 +Loop time of 2.30195 on 1 procs for 10000 steps with 81 atoms + +Performance: 37533.440 tau/day, 4344.148 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0076839 | 0.0076839 | 0.0076839 | 0.0 | 0.33 +Neigh | 0.029562 | 0.029562 | 0.029562 | 0.0 | 1.28 +Comm | 0.0084877 | 0.0084877 | 0.0084877 | 0.0 | 0.37 +Output | 0.0037958 | 0.0037958 | 0.0037958 | 0.0 | 0.16 +Modify | 2.2446 | 2.2446 | 2.2446 | 0.0 | 97.51 +Other | | 0.00785 | | | 0.34 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 69 ave 69 max 69 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4 +Ave neighs/atom = 0.049382716 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems3.g++.4 b/examples/rigid/log.20Mar22.rigid.poems3.g++.4 new file mode 100644 index 0000000000..39fd6245e0 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems3.g++.4 @@ -0,0 +1,329 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all poems file unconnected-bodies.dat +WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035) +9 clusters, 9 bodies, 0 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.686 571.71596 0 5265.8207 32.006226 + 100 16298.5 136.65142 0 5267.6607 16.443791 + 150 16682.639 17.488068 0 5269.43 14.900278 + 200 16733.955 1.3724268 0 5269.4692 14.569123 + 250 16738.877 -0.15250573 0 5269.4939 14.496287 + 300 16738.611 -0.05516662 0 5269.5077 14.495909 + 350 16738.515 -0.01744351 0 5269.5152 14.496329 + 400 16738.488 -0.0060096677 0 5269.5178 14.496497 + 450 16738.479 -0.0012712918 0 5269.5199 14.496575 + 500 16738.479 -0.00081070354 0 5269.5203 14.49658 + 550 16738.479 -0.00083205205 0 5269.5203 14.496577 + 600 16738.479 -0.0005835658 0 5269.5206 14.49658 + 650 16738.479 -0.00047227225 0 5269.5206 14.496583 + 700 16738.479 0 0 5269.521 14.496593 + 750 16738.479 0 0 5269.5211 14.496595 + 800 16738.479 0 0 5269.5211 14.496596 + 850 16738.479 0 0 5269.5211 14.496595 + 900 16738.479 0 0 5269.5212 14.496593 + 950 16738.485 -0.003532391 0 5269.5196 14.496546 + 1000 16738.609 -0.051135033 0 5269.5109 14.496098 + 1050 16737.381 0.32991002 0 5269.5055 14.525627 + 1100 16737.915 0.16210932 0 5269.5058 14.531848 + 1150 16738.726 -0.089235332 0 5269.5098 14.509768 + 1200 16738.49 -0.0075446298 0 5269.5169 14.510489 + 1250 16738.48 0 0 5269.5214 14.510585 + 1300 16738.48 0 0 5269.5214 14.510587 + 1350 16738.48 0 0 5269.5215 14.510588 + 1400 16738.48 -0.00044742303 0 5269.5211 14.510581 + 1450 16738.481 -0.0010975104 0 5269.5207 14.51057 + 1500 16738.481 -0.00057925965 0 5269.5211 14.510575 + 1550 16738.48 0 0 5269.5216 14.510582 + 1600 16738.48 0 0 5269.5216 14.510581 + 1650 16738.481 0 0 5269.5216 14.510581 + 1700 16738.481 0 0 5269.5217 14.510582 + 1750 16738.481 0 0 5269.5217 14.510583 + 1800 16738.481 0 0 5269.5217 14.510585 + 1850 16738.481 0 0 5269.5218 14.510585 + 1900 16738.481 0 0 5269.5218 14.510585 + 1950 16738.487 -0.0031700155 0 5269.5206 14.510534 + 2000 16738.514 -0.013238802 0 5269.5188 14.510401 + 2050 16738.578 -0.03654435 0 5269.5158 14.510155 + 2100 16738.656 -0.063182323 0 5269.5137 14.510082 + 2150 16738.63 -0.056004395 0 5269.5127 14.510096 + 2200 16738.579 -0.038415873 0 5269.5143 14.510273 + 2250 16738.538 -0.023709094 0 5269.516 14.510414 + 2300 16738.512 -0.013252539 0 5269.5182 14.510501 + 2350 16738.491 -0.0045593284 0 5269.5203 14.510598 + 2400 16738.482 -0.00052242487 0 5269.5217 14.510655 + 2450 16738.486 -0.0023245722 0 5269.5211 14.510627 + 2500 16738.491 -0.005189304 0 5269.5197 14.510606 + 2550 16738.604 -0.044988104 0 5269.5155 14.510185 + 2600 16738.446 0.0009675401 0 5269.5117 14.510521 + 2650 16732.887 1.753125 0 5269.5138 14.598792 + 2700 16738.784 -0.10629556 0 5269.5107 14.499176 + 2750 16734.136 1.359459 0 5269.5135 14.594678 + 2800 16738.608 -0.047184149 0 5269.5147 14.510254 + 2850 16738.509 -0.012527238 0 5269.5181 14.509344 + 2900 16738.487 -0.0026065529 0 5269.521 14.509512 + 2950 16738.498 -0.0082248532 0 5269.519 14.509457 + 3000 16738.683 -0.071294028 0 5269.514 14.509005 + 3050 16717.444 6.5874862 0 5269.4864 14.834144 + 3100 16657.654 25.431253 0 5269.5074 14.467824 + 3150 16739.322 -0.28964062 0 5269.497 13.658821 + 3200 16733.615 1.4969789 0 5269.487 11.998304 + 3250 16737.289 0.35071214 0 5269.4974 11.918931 + 3300 16732.493 1.8663821 0 5269.503 12.109003 + 3350 16738.717 -0.087719164 0 5269.5085 11.979747 + 3400 16738.586 -0.045267897 0 5269.5095 11.97972 + 3450 16738.662 -0.071274216 0 5269.5076 11.979564 + 3500 16738.853 -0.13644992 0 5269.5026 11.979658 + 3550 16729.612 2.7475277 0 5269.4774 12.195939 + 3600 16728.659 3.059607 0 5269.4893 12.241248 + 3650 16738.923 -0.15949792 0 5269.5014 11.991857 + 3700 16738.76 -0.10695054 0 5269.5028 11.992932 + 3750 16738.751 -0.10105954 0 5269.5057 11.993137 + 3800 16738.597 -0.048627545 0 5269.5097 11.993456 + 3850 16738.507 -0.016053927 0 5269.5138 11.992973 + 3900 16738.485 -0.0060825487 0 5269.5169 11.993052 + 3950 16738.475 -0.0014953722 0 5269.5183 11.993119 + 4000 16738.472 -0.00054315391 0 5269.5184 11.99315 + 4050 16738.472 -0.00023792126 0 5269.5187 11.993172 + 4100 16738.472 0 0 5269.5189 11.993188 + 4150 16738.472 0 0 5269.5189 11.993188 + 4200 16738.472 0 0 5269.519 11.993178 + 4250 16738.472 0 0 5269.519 11.993164 + 4300 16738.472 0 0 5269.5191 11.993152 + 4350 16738.473 0 0 5269.5191 11.993147 + 4400 16738.473 0 0 5269.5192 11.993149 + 4450 16738.473 0 0 5269.5192 11.993158 + 4500 16738.473 0 0 5269.5193 11.99317 + 4550 16738.473 0 0 5269.5193 11.993176 + 4600 16738.473 0 0 5269.5194 11.993174 + 4650 16738.473 0 0 5269.5194 11.993167 + 4700 16738.474 0 0 5269.5195 11.993162 + 4750 16738.474 0 0 5269.5195 11.99316 + 4800 16738.474 0 0 5269.5196 11.99316 + 4850 16738.474 0 0 5269.5196 11.993163 + 4900 16738.474 0 0 5269.5197 11.99317 + 4950 16738.474 0 0 5269.5197 11.993176 + 5000 16738.475 0 0 5269.5198 11.993174 + 5050 16738.475 0 0 5269.5198 11.993165 + 5100 16738.475 0 0 5269.5199 11.993155 + 5150 16738.475 0 0 5269.5199 11.99315 + 5200 16738.475 0 0 5269.52 11.993153 + 5250 16738.475 0 0 5269.52 11.993161 + 5300 16738.476 0 0 5269.5201 11.993173 + 5350 16738.476 0 0 5269.5201 11.993185 + 5400 16738.476 0 0 5269.5202 11.993189 + 5450 16738.476 0 0 5269.5202 11.993181 + 5500 16738.476 0 0 5269.5203 11.993165 + 5550 16738.483 -0.0030091905 0 5269.5195 11.993097 + 5600 16738.534 -0.020777802 0 5269.5177 11.992799 + 5650 16738.649 -0.059321662 0 5269.5153 11.993266 + 5700 16409.08 103.75288 0 5269.5745 23.626238 + 5750 16738.578 -0.036776519 0 5269.5155 11.910545 + 5800 16738.484 -0.0047306177 0 5269.518 11.911008 + 5850 16738.477 -0.00022082692 0 5269.5202 11.911078 + 5900 16738.477 -0.00033136078 0 5269.5203 11.91107 + 5950 16738.478 -0.00036902212 0 5269.5203 11.911052 + 6000 16738.477 0 0 5269.5206 11.911044 + 6050 16738.477 0 0 5269.5207 11.911034 + 6100 16738.478 0 0 5269.5207 11.911032 + 6150 16738.478 0 0 5269.5208 11.911037 + 6200 16738.478 0 0 5269.5208 11.911049 + 6250 16738.478 0 0 5269.5209 11.911062 + 6300 16738.478 0 0 5269.5209 11.911068 + 6350 16738.478 0 0 5269.521 11.911065 + 6400 16738.478 0 0 5269.521 11.911058 + 6450 16738.479 0 0 5269.5211 11.911052 + 6500 16738.479 0 0 5269.5211 11.911047 + 6550 16738.479 0 0 5269.5212 11.911046 + 6600 16738.479 0 0 5269.5212 11.911049 + 6650 16738.479 0 0 5269.5213 11.911056 + 6700 16738.479 0 0 5269.5213 11.911062 + 6750 16738.48 0 0 5269.5214 11.91106 + 6800 16738.48 0 0 5269.5214 11.911051 + 6850 16738.48 0 0 5269.5215 11.911044 + 6900 16738.48 0 0 5269.5215 11.911041 + 6950 16738.48 0 0 5269.5216 11.911045 + 7000 16738.48 0 0 5269.5216 11.911053 + 7050 16738.481 0 0 5269.5217 11.911063 + 7100 16738.481 0 0 5269.5217 11.911071 + 7150 16738.481 0 0 5269.5218 11.911072 + 7200 16738.481 0 0 5269.5218 11.911063 + 7250 16738.481 0 0 5269.5219 11.911048 + 7300 16738.481 0 0 5269.5219 11.911036 + 7350 16738.482 0 0 5269.522 11.911031 + 7400 16738.482 0 0 5269.522 11.911035 + 7450 16738.482 0 0 5269.5221 11.911046 + 7500 16738.482 0 0 5269.5221 11.911062 + 7550 16738.482 0 0 5269.5222 11.911077 + 7600 16738.482 0 0 5269.5222 11.911081 + 7650 16738.483 0 0 5269.5223 11.911071 + 7700 16738.483 0 0 5269.5223 11.911054 + 7750 16738.483 0 0 5269.5224 11.911039 + 7800 16738.483 0 0 5269.5224 11.911031 + 7850 16738.483 0 0 5269.5225 11.911031 + 7900 16738.483 0 0 5269.5226 11.911039 + 7950 16738.484 0 0 5269.5226 11.911052 + 8000 16738.484 0 0 5269.5227 11.911065 + 8050 16738.484 0 0 5269.5227 11.91107 + 8100 16738.484 0 0 5269.5228 11.911065 + 8150 16738.484 0 0 5269.5228 11.911056 + 8200 16738.484 0 0 5269.5229 11.911047 + 8250 16738.485 0 0 5269.5229 11.911042 + 8300 16738.485 0 0 5269.523 11.911041 + 8350 16738.485 0 0 5269.523 11.911046 + 8400 16738.485 0 0 5269.5231 11.911055 + 8450 16738.485 0 0 5269.5231 11.911062 + 8500 16738.485 0 0 5269.5232 11.91106 + 8550 16738.486 0 0 5269.5232 11.911053 + 8600 16738.487 -0.00084974055 0 5269.5227 11.911032 + 8650 16738.486 0 0 5269.5233 11.911046 + 8700 16738.486 0 0 5269.5234 11.91105 + 8750 16738.486 0 0 5269.5235 11.911056 + 8800 16738.486 0 0 5269.5235 11.911063 + 8850 16738.487 -0.000227631 0 5269.5234 11.911065 + 8900 16738.487 0 0 5269.5236 11.911068 + 8950 16738.487 0 0 5269.5237 11.911058 + 9000 16738.487 0 0 5269.5237 11.911045 + 9050 16738.487 0 0 5269.5238 11.911036 + 9100 16738.487 0 0 5269.5238 11.911034 + 9150 16738.488 0 0 5269.5239 11.91104 + 9200 16738.488 0 0 5269.5239 11.911052 + 9250 16738.488 0 0 5269.524 11.911068 + 9300 16738.488 0 0 5269.524 11.911079 + 9350 16738.488 0 0 5269.5241 11.911078 + 9400 16738.492 -0.0016306433 0 5269.5235 11.911038 + 9450 16738.492 -0.0032567425 0 5269.522 11.911005 + 9500 16738.495 -0.0036645345 0 5269.5224 11.910982 + 9550 16738.49 -0.001067391 0 5269.5237 11.911012 + 9600 16738.489 0 0 5269.5244 11.911032 + 9650 16738.489 0 0 5269.5244 11.911043 + 9700 16738.49 0 0 5269.5245 11.911058 + 9750 16738.49 0 0 5269.5245 11.911071 + 9800 16738.49 0 0 5269.5246 11.911073 + 9850 16738.49 0 0 5269.5246 11.911065 + 9900 16738.49 0 0 5269.5247 11.911053 + 9950 16738.491 -0.00058544648 0 5269.5243 11.911032 + 10000 16738.493 -0.0015244933 0 5269.5242 11.911015 +Loop time of 2.36483 on 4 procs for 10000 steps with 81 atoms + +Performance: 36535.358 tau/day, 4228.629 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0030635 | 0.0035263 | 0.0040903 | 0.7 | 0.15 +Neigh | 0.0093439 | 0.01002 | 0.010976 | 0.6 | 0.42 +Comm | 0.11912 | 0.12509 | 0.13346 | 1.5 | 5.29 +Output | 0.003411 | 0.0038449 | 0.0050123 | 1.1 | 0.16 +Modify | 2.1961 | 2.2052 | 2.2137 | 0.5 | 93.25 +Other | | 0.01717 | | | 0.73 + +Nlocal: 20.25 ave 27 max 9 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 31.5 ave 51 max 15 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 1 ave 4 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 4 +Ave neighs/atom = 0.049382716 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems4.g++.1 b/examples/rigid/log.20Mar22.rigid.poems4.g++.1 new file mode 100644 index 0000000000..e2febc5ed9 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems4.g++.1 @@ -0,0 +1,328 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies.dat +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045742 + 850 17821.483 711.53827 0 3681.7854 7.438428 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19374 0 3681.3037 11.787982 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184716 + 1150 20849.582 206.01696 0 3680.9472 -0.86699118 + 1200 21815.003 45.317409 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064083 + 1300 20780.781 217.36511 0 3680.8286 6.0538604 + 1350 20558.971 254.36489 0 3680.8601 -3.6773868 + 1400 21485.029 99.812844 0 3680.6511 -16.185479 + 1450 21771.107 52.159653 0 3680.6775 -2.4756655 + 1500 21520.949 93.503876 0 3680.3286 2.1023573 + 1550 21351.419 121.6813 0 3680.2511 5.5159876 + 1600 20778.804 216.92191 0 3680.0559 15.089203 + 1650 21477.636 100.21873 0 3679.8247 -1.1045277 + 1700 18501.33 596.4807 0 3680.0357 -15.6798 + 1750 18563.64 587.34824 0 3681.2882 33.532308 + 1800 19110.175 494.82517 0 3679.8543 18.024074 + 1850 21364.178 119.23765 0 3679.9339 2.5290144 + 1900 20146.588 322.15509 0 3679.9197 5.7317299 + 1950 20692.676 231.25264 0 3680.0319 4.297803 + 2000 20943.902 189.11251 0 3679.7629 -22.643824 + 2050 19667.823 401.86882 0 3679.8394 3.6241915 + 2100 20280.125 299.81485 0 3679.8357 7.4804047 + 2150 19181.201 483.6306 0 3680.4975 22.63342 + 2200 21301.144 130.54014 0 3680.7308 4.7074288 + 2250 20484.876 266.98315 0 3681.1291 -8.6578278 + 2300 18648.161 573.07329 0 3681.1001 -5.2550954 + 2350 21515.748 95.243054 0 3681.201 -9.386512 + 2400 21462.551 104.18267 0 3681.2745 -29.46442 + 2450 20107.732 330.99437 0 3682.2831 35.38497 + 2500 20771.509 220.47713 0 3682.3953 -12.324858 + 2550 20499.887 265.58494 0 3682.2327 -22.713874 + 2600 21462.182 105.24427 0 3682.2747 -10.175788 + 2650 21004.949 181.51383 0 3682.3387 4.949195 + 2700 18673.552 570.45017 0 3682.7089 21.201437 + 2750 21257.562 139.198 0 3682.1249 -7.5793039 + 2800 21559.645 88.844759 0 3682.119 -6.2360467 + 2850 20865.227 204.46262 0 3682.0004 0.39575069 + 2900 19428.614 443.93293 0 3682.0352 12.796676 + 2950 19630.1 410.18487 0 3681.8681 -0.50572623 + 3000 19663.218 404.06316 0 3681.2661 6.0827093 + 3050 19087.572 500.8452 0 3682.1073 -6.3526476 + 3100 18229.94 643.77681 0 3682.1001 11.453637 + 3150 18927.492 527.51919 0 3682.1011 -1.662863 + 3200 18320.514 628.55895 0 3681.978 21.176126 + 3250 18204.677 647.96462 0 3682.0775 11.331521 + 3300 19231.978 477.02117 0 3682.3509 3.8381593 + 3350 18153.44 656.70376 0 3682.2772 15.135615 + 3400 17476.768 770.0598 0 3682.8545 -3.394312 + 3450 21097.531 166.17241 0 3682.4276 3.74301 + 3500 17605.784 747.54808 0 3681.8454 3.3420627 + 3550 19238.34 476.00608 0 3682.3961 1.1413836 + 3600 18155.288 656.57434 0 3682.4557 3.4360446 + 3650 18735.622 559.2377 0 3681.8413 28.760363 + 3700 15310.261 1134.4215 0 3686.1317 44.207018 + 3750 15377.116 1123.4786 0 3686.3313 7.6773215 + 3800 18798.895 549.05928 0 3682.2084 -12.905825 + 3850 18322.563 628.87744 0 3682.6379 -16.067793 + 3900 19963.049 355.65441 0 3682.8292 3.4694064 + 3950 19925.48 361.2507 0 3682.1641 5.0058567 + 4000 19141.423 492.41081 0 3682.648 -12.782769 + 4050 20022.241 345.61655 0 3682.6568 -3.0149905 + 4100 21348.635 124.95646 0 3683.0624 -4.85779 + 4150 21011.812 181.1132 0 3683.0819 -3.9526196 + 4200 20222.276 312.63945 0 3683.0187 -23.63437 + 4250 20957.757 189.77152 0 3682.731 -1.3712469 + 4300 20070.215 337.5751 0 3682.611 -6.8816517 + 4350 21322.437 129.09228 0 3682.8318 -6.9442178 + 4400 19440.445 442.77531 0 3682.8495 -0.11606236 + 4450 20964.516 188.67174 0 3682.7577 4.8533525 + 4500 13530.08 1428.5497 0 3683.563 12.333187 + 4550 20461.637 272.58882 0 3682.8616 4.5111943 + 4600 17072.994 836.58228 0 3682.0812 5.7611617 + 4650 18860.748 539.82027 0 3683.2782 -2.5558958 + 4700 18373.927 621.04093 0 3683.3621 5.4020702 + 4750 20321.437 296.63662 0 3683.5428 8.9571617 + 4800 21083.122 169.84086 0 3683.6946 10.566368 + 4850 20499.669 267.7012 0 3684.3128 4.2924237 + 4900 20308.781 300.38168 0 3685.1785 -12.396923 + 4950 21043.303 178.56295 0 3685.7801 3.8923762 + 5000 20718.383 232.52208 0 3685.5859 -12.43234 + 5050 21005.749 184.4363 0 3685.3945 -7.6463487 + 5100 20714.133 233.27745 0 3685.6329 -1.6944135 + 5150 19577.452 422.73035 0 3685.639 -21.831219 + 5200 14044.647 1343.9545 0 3684.729 -6.8407194 + 5250 19089.805 504.0893 0 3685.7235 4.05641 + 5300 21094.745 169.94699 0 3685.7378 -0.66593212 + 5350 19907.559 366.77598 0 3684.7024 1.5248525 + 5400 20382.81 289.13263 0 3686.2676 -11.919321 + 5450 19593.693 420.70548 0 3686.3209 -1.1568628 + 5500 20906.08 202.09801 0 3686.4447 -2.4284971 + 5550 16315.465 965.56973 0 3684.8138 -33.178221 + 5600 19714.57 400.39687 0 3686.1586 19.950231 + 5650 20561.724 259.54797 0 3686.502 8.2074524 + 5700 19349.502 460.7789 0 3685.6959 16.252649 + 5750 21006.818 185.56805 0 3686.7044 -11.96089 + 5800 20268.2 307.97547 0 3686.0089 17.322311 + 5850 21018.322 184.16179 0 3687.2154 -14.379909 + 5900 19695.647 404.57094 0 3687.1787 -20.718904 + 5950 21021.687 183.66311 0 3687.2776 -15.206081 + 6000 18947.535 529.30554 0 3687.2281 17.863927 + 6050 15272.373 1141.012 0 3686.4075 -0.43375666 + 6100 17766.197 721.75792 0 3682.7908 11.378913 + 6150 18612.573 584.06688 0 3686.1623 17.543241 + 6200 19005.155 518.97146 0 3686.4973 -16.223107 + 6250 20997.507 187.55499 0 3687.1394 -11.613546 + 6300 19639.901 413.58048 0 3686.8974 14.407136 + 6350 19580.399 423.02818 0 3686.428 -5.5801796 + 6400 14134.119 1332.0662 0 3687.7527 84.864425 + 6450 21598.824 87.419966 0 3687.224 -5.8358352 + 6500 18208.216 649.29108 0 3683.9938 -8.1510884 + 6550 19364.586 459.59813 0 3687.0291 -12.053563 + 6600 20710.927 235.11914 0 3686.9403 -1.0470193 + 6650 21132.334 165.08091 0 3687.1366 1.0785471 + 6700 20217.285 317.589 0 3687.1365 0.055447462 + 6750 21232.279 148.57412 0 3687.2873 -2.4551657 + 6800 20292.683 304.76539 0 3686.8793 -0.42311295 + 6850 19056.291 510.49927 0 3686.5478 6.9533826 + 6900 20429.82 282.23764 0 3687.2076 -4.2360112 + 6950 21281.278 140.27361 0 3687.1533 -0.07475261 + 7000 17173.388 824.54446 0 3686.7758 10.753828 + 7050 18079.7 674.56274 0 3687.846 12.975804 + 7100 16433.233 950.73904 0 3689.6112 -10.5102 + 7150 19033.335 515.59672 0 3687.8193 0.29109447 + 7200 17286.428 809.02352 0 3690.0948 2.3015698 + 7250 16811.962 886.6645 0 3688.6582 -7.4787512 + 7300 15992.461 1023.4849 0 3688.895 -5.2354222 + 7350 19211.451 487.63129 0 3689.5398 8.4351737 + 7400 19065.682 511.95629 0 3689.57 -12.47448 + 7450 21369.265 128.10098 0 3689.6451 2.2930546 + 7500 16807.109 888.64602 0 3689.8308 14.761969 + 7550 18063.046 679.21873 0 3689.7264 3.8950434 + 7600 17794.987 724.55404 0 3690.3851 14.379016 + 7650 17904.751 706.14354 0 3690.2688 23.813776 + 7700 19670.09 411.3021 0 3689.6504 14.099245 + 7750 18082.562 675.23975 0 3689.0001 15.788521 + 7800 17776.135 726.91445 0 3689.6037 6.9780735 + 7850 17062.575 846.33412 0 3690.0966 -8.9289256 + 7900 19059.2 513.07737 0 3689.6107 16.992843 + 7950 16269.685 978.48914 0 3690.1033 11.180179 + 8000 20115.278 336.91405 0 3689.4604 -6.4882518 + 8050 21173.72 161.15229 0 3690.1056 -2.2164491 + 8100 19238.235 484.42784 0 3690.8004 23.412709 + 8150 18438.4 617.58743 0 3690.6542 0.89156316 + 8200 21438.764 117.12721 0 3690.2546 -1.7193227 + 8250 21195.806 157.66607 0 3690.3003 3.820447 + 8300 21177.549 161.13702 0 3690.7286 0.94938203 + 8350 21060.267 181.06887 0 3691.1135 2.8179025 + 8400 20087.113 343.46206 0 3691.3142 8.1484473 + 8450 19298.478 474.87133 0 3691.2843 -16.239664 + 8500 21654.353 82.083485 0 3691.1423 -8.1464138 + 8550 19920.544 371.34795 0 3691.4386 20.765144 + 8600 21692.293 75.655154 0 3691.0373 -13.316763 + 8650 21231.322 151.8989 0 3690.4526 -11.388238 + 8700 19530.647 434.89585 0 3690.0037 2.7433786 + 8750 19720.63 403.07773 0 3689.8493 -6.416414 + 8800 21321.378 136.04091 0 3689.604 1.3661635 + 8850 19811.906 387.80489 0 3689.7893 3.704143 + 8900 19734.167 400.92444 0 3689.9523 2.5685155 + 8950 21076.459 177.18119 0 3689.9244 -11.939513 + 9000 20967.246 195.42966 0 3689.9707 2.0092705 + 9050 21122.023 169.62103 0 3689.9582 2.3791301 + 9100 20169.346 328.27229 0 3689.8299 -3.5017988 + 9150 21418.641 119.84513 0 3689.6187 2.486073 + 9200 20876.042 210.26452 0 3689.6048 -5.3839897 + 9250 21572.38 93.74407 0 3689.1407 -8.3676952 + 9300 20944.78 197.98577 0 3688.7824 1.3278314 + 9350 20706.52 237.48767 0 3688.5744 4.6944204 + 9400 16412.314 953.47251 0 3688.8581 26.134976 + 9450 20461.68 277.76243 0 3688.0424 17.647445 + 9500 20893.994 205.64261 0 3687.9749 -10.642418 + 9550 20503.447 270.63504 0 3687.8761 -17.769897 + 9600 19677.799 408.05887 0 3687.692 -2.7938604 + 9650 17480.971 774.1855 0 3687.6806 0.59827043 + 9700 17799.126 721.50817 0 3688.0292 44.387928 + 9750 20443.384 280.16837 0 3687.399 3.0619324 + 9800 20545.255 263.40108 0 3687.6102 3.6229381 + 9850 20722.819 233.57142 0 3687.3745 0.86462694 + 9900 21128.462 165.09767 0 3686.508 -6.9636843 + 9950 21343.307 130.46714 0 3687.685 -9.7382705 + 10000 20623.887 250.37866 0 3687.6932 2.7529835 +Loop time of 2.28812 on 1 procs for 10000 steps with 81 atoms + +Performance: 37760.318 tau/day, 4370.407 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.094122 | 0.094122 | 0.094122 | 0.0 | 4.11 +Neigh | 0.076427 | 0.076427 | 0.076427 | 0.0 | 3.34 +Comm | 0.0066867 | 0.0066867 | 0.0066867 | 0.0 | 0.29 +Output | 0.003606 | 0.003606 | 0.003606 | 0.0 | 0.16 +Modify | 2.0986 | 2.0986 | 2.0986 | 0.0 | 91.72 +Other | | 0.008698 | | | 0.38 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 62 ave 62 max 62 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 905 ave 905 max 905 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 905 +Ave neighs/atom = 11.17284 +Neighbor list builds = 991 +Dangerous builds = 927 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems4.g++.4 b/examples/rigid/log.20Mar22.rigid.poems4.g++.4 new file mode 100644 index 0000000000..6240237758 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems4.g++.4 @@ -0,0 +1,328 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies.dat +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045742 + 850 17821.483 711.53827 0 3681.7854 7.4384281 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19374 0 3681.3037 11.787982 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184716 + 1150 20849.582 206.01696 0 3680.9472 -0.86699115 + 1200 21815.003 45.317409 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064083 + 1300 20780.781 217.36511 0 3680.8286 6.0538606 + 1350 20558.971 254.36489 0 3680.8601 -3.6773868 + 1400 21485.03 99.812843 0 3680.6511 -16.185479 + 1450 21771.107 52.159652 0 3680.6775 -2.4756656 + 1500 21520.949 93.503872 0 3680.3286 2.1023574 + 1550 21351.419 121.68131 0 3680.2511 5.5159875 + 1600 20778.804 216.92191 0 3680.0559 15.089203 + 1650 21477.636 100.21877 0 3679.8247 -1.104524 + 1700 18501.329 596.48084 0 3680.0357 -15.679806 + 1750 18563.639 587.34841 0 3681.2882 33.532316 + 1800 19110.174 494.82524 0 3679.8543 18.024079 + 1850 21364.178 119.23767 0 3679.9339 2.5290075 + 1900 20146.588 322.15506 0 3679.9197 5.7317368 + 1950 20692.674 231.25288 0 3680.0319 4.2977982 + 2000 20943.904 189.11229 0 3679.7629 -22.643749 + 2050 19667.815 401.87016 0 3679.8394 3.6240972 + 2100 20280.109 299.81759 0 3679.8357 7.4803647 + 2150 19181.146 483.63975 0 3680.4974 22.634167 + 2200 21301.194 130.53171 0 3680.7308 4.7072523 + 2250 20484.79 266.99736 0 3681.1291 -8.6583002 + 2300 18648.002 573.09962 0 3681.1 -5.2548835 + 2350 21515.851 95.225745 0 3681.2009 -9.3875216 + 2400 21462.37 104.21272 0 3681.2744 -29.459857 + 2450 20108.034 330.94394 0 3682.2829 35.37058 + 2500 20771.818 220.42545 0 3682.3951 -12.318936 + 2550 20502.815 265.09577 0 3682.2316 -22.726822 + 2600 21462.006 105.2733 0 3682.2744 -10.180394 + 2650 21009.656 180.72738 0 3682.3367 4.9580828 + 2700 18680.012 569.37179 0 3682.7071 21.114114 + 2750 21256.19 139.42201 0 3682.1203 -7.4744399 + 2800 21552.267 90.071446 0 3682.1159 -6.2906304 + 2850 20879.958 202.00905 0 3682.0021 0.57990903 + 2900 19018.645 512.35214 0 3682.1262 13.883084 + 2950 19819.365 378.55747 0 3681.785 -0.7348943 + 3000 20269.229 303.35149 0 3681.5563 6.3088075 + 3050 19236.727 475.99457 0 3682.1158 -10.703575 + 3100 18391.55 616.96976 0 3682.2281 9.850079 + 3150 20258.563 305.82076 0 3682.248 7.1951283 + 3200 20716.384 229.15502 0 3681.8856 2.9042294 + 3250 18662.237 572.0784 0 3682.4512 9.2108597 + 3300 19162.278 488.60646 0 3682.3195 3.3306562 + 3350 21235.679 142.98279 0 3682.2626 0.29397483 + 3400 17677.053 736.09247 0 3682.2679 32.75269 + 3450 20852.392 206.65618 0 3682.0548 -4.8319056 + 3500 21182.918 151.46754 0 3681.9539 -5.6330382 + 3550 20589.85 250.40724 0 3682.049 12.582133 + 3600 20973.659 186.28043 0 3681.8903 10.935266 + 3650 17838.632 707.92145 0 3681.0268 -17.200926 + 3700 21538.002 92.744409 0 3682.4114 -0.72124229 + 3750 21390.294 117.90865 0 3682.9576 -7.8431786 + 3800 17921.046 696.50311 0 3683.344 -9.4641531 + 3850 20356.471 290.22624 0 3682.9715 2.4593463 + 3900 20374.077 287.10249 0 3682.782 -1.9519082 + 3950 20563.915 255.29993 0 3682.619 -6.124649 + 4000 20991.467 184.76183 0 3683.3397 1.8954961 + 4050 17805.623 716.24698 0 3683.8509 -20.454944 + 4100 19916.389 363.86301 0 3683.2611 -0.27912557 + 4150 19221.623 480.01232 0 3683.6161 -11.562492 + 4200 20526.82 261.78571 0 3682.9224 -3.9522917 + 4250 20922.813 196.1799 0 3683.3154 0.11947446 + 4300 19956.66 357.78133 0 3683.8914 19.156093 + 4350 19735.73 394.45981 0 3683.7482 14.865775 + 4400 21702.656 67.099805 0 3684.2092 -13.502538 + 4450 18163.055 656.97231 0 3684.1482 -0.6243111 + 4500 17477.718 771.25976 0 3684.2127 -0.4664004 + 4550 20676.507 238.19814 0 3684.2827 -19.444969 + 4600 17322.922 796.77058 0 3683.9242 27.003966 + 4650 11905.158 1704.9151 0 3689.1082 15.574169 + 4700 18689.079 569.80982 0 3684.6563 -14.67311 + 4750 19821.745 381.01914 0 3684.6433 5.0436795 + 4800 20621.335 247.96269 0 3684.8518 -16.407263 + 4850 21923.814 30.965964 0 3684.935 -13.418244 + 4900 18840.555 544.41538 0 3684.5079 11.005357 + 4950 15366.601 1124.2481 0 3685.3482 17.412375 + 5000 18274.314 639.01311 0 3684.732 5.3261109 + 5050 21173.687 155.83673 0 3684.7845 5.4056809 + 5100 21738.219 61.75201 0 3684.7885 -2.631945 + 5150 16597.949 918.84841 0 3685.1732 -10.124101 + 5200 20752.758 225.95919 0 3684.7522 -5.2441372 + 5250 17652.088 741.2645 0 3683.2793 2.0080739 + 5300 19907.523 366.53115 0 3684.4516 8.4266792 + 5350 20104.189 334.14522 0 3684.8433 17.21925 + 5400 21499.848 101.71631 0 3685.0243 -6.1103541 + 5450 21203.533 151.14574 0 3685.068 -5.9468503 + 5500 21076.513 172.45652 0 3685.2088 5.1418181 + 5550 20158.398 325.56609 0 3685.2992 -1.6486034 + 5600 20787.836 221.19563 0 3685.835 -10.66805 + 5650 19687.154 404.77204 0 3685.9644 -23.49128 + 5700 20419.311 282.58328 0 3685.8017 -0.52808211 + 5750 19738.522 395.95893 0 3685.7126 1.3889817 + 5800 18300.025 635.66905 0 3685.6732 23.490447 + 5850 20585.004 255.02032 0 3685.8543 -0.20699939 + 5900 20373.839 290.15881 0 3685.7987 -7.9712187 + 5950 18163.832 659.91192 0 3687.2173 5.4494586 + 6000 21049.247 177.43029 0 3685.6382 2.9138342 + 6050 21239.803 145.77613 0 3685.7433 -1.4927769 + 6100 20686.361 237.86454 0 3685.5913 -0.95516297 + 6150 20461.754 275.31546 0 3685.6079 -3.4166412 + 6200 19264.208 474.73017 0 3685.4316 11.750757 + 6250 21180.813 155.31746 0 3685.4529 2.8188219 + 6300 21047.543 177.4394 0 3685.3632 1.8641486 + 6350 20232.576 313.17716 0 3685.2731 2.8150209 + 6400 20185.616 321.33454 0 3685.6038 -3.8697311 + 6450 18969.632 523.95865 0 3685.5639 0.6725512 + 6500 17592.574 753.49959 0 3685.5952 -1.2557393 + 6550 21279.049 138.42524 0 3684.9335 -1.208945 + 6600 21408.457 116.4143 0 3684.4904 -1.5332953 + 6650 19758.218 391.17316 0 3684.2096 1.8511312 + 6700 20766.943 223.44631 0 3684.6036 -2.3672623 + 6750 20399.631 284.09914 0 3684.0377 -5.4089876 + 6800 21296.628 135.14662 0 3684.5847 -3.8442549 + 6850 20641.481 244.4451 0 3684.692 1.4020639 + 6900 20852.81 209.23009 0 3684.6984 1.8512104 + 6950 20940.555 194.66882 0 3684.7614 -6.554676 + 7000 19496.988 435.28199 0 3684.78 -15.120269 + 7050 19796.829 385.04227 0 3684.5138 -4.1068804 + 7100 19945.264 360.42431 0 3684.635 -4.0629042 + 7150 19431.123 446.12911 0 3684.6497 -6.8321751 + 7200 16864.851 873.80043 0 3684.6089 14.309069 + 7250 20438.75 277.85982 0 3684.3181 -11.41223 + 7300 17688.684 734.01576 0 3682.1298 35.938373 + 7350 21573.419 88.63421 0 3684.204 -3.9032749 + 7400 21198.486 150.72249 0 3683.8034 -7.1477117 + 7450 20586.708 252.93928 0 3684.0572 -7.6634645 + 7500 21815.377 48.180377 0 3684.0765 0.97457507 + 7550 17791.352 718.87564 0 3684.101 28.248235 + 7600 21828.874 45.928597 0 3684.0742 -0.25814944 + 7650 20827.961 212.35674 0 3683.6835 -3.4083384 + 7700 21319.176 130.43547 0 3683.6315 -12.434856 + 7750 20127.904 328.69643 0 3683.3471 -16.975711 + 7800 21741.772 59.679206 0 3683.3078 3.6261863 + 7850 19612.334 414.37418 0 3683.0964 1.3763274 + 7900 20071.318 337.74624 0 3682.9658 -0.40982763 + 7950 17925.664 695.29582 0 3682.9065 17.104439 + 8000 19125.978 492.76383 0 3680.4268 10.807662 + 8050 20233.848 310.42681 0 3682.7347 13.386237 + 8100 20551.619 257.86699 0 3683.1368 -13.97515 + 8150 21578.323 86.88362 0 3683.2708 -9.6811587 + 8200 21154.833 157.72897 0 3683.5344 0.62312375 + 8250 21321.143 129.83967 0 3683.3636 1.9536438 + 8300 21041.696 176.04177 0 3682.9911 4.7475567 + 8350 19883.39 369.32649 0 3683.2247 -7.0959328 + 8400 21626.067 79.062992 0 3683.4075 -14.919059 + 8450 21375.201 120.86836 0 3683.4019 -5.3461514 + 8500 20281.059 303.10304 0 3683.2796 3.7975093 + 8550 21170.533 154.48432 0 3682.9065 -1.1568561 + 8600 17754.931 724.00158 0 3683.1568 14.15254 + 8650 20685.478 235.65879 0 3683.2385 -5.2694179 + 8700 21489.165 101.90509 0 3683.4326 -4.2510612 + 8750 21106.682 165.41638 0 3683.1968 -3.9186708 + 8800 19149.516 491.5843 0 3683.1702 -11.419849 + 8850 21451.865 108.1814 0 3683.4923 -7.8256219 + 8900 19567.4 421.81206 0 3683.0454 -0.71997056 + 8950 20934.097 194.48033 0 3683.4965 -7.0106879 + 9000 18531.559 595.25957 0 3683.8528 3.7449399 + 9050 18868.821 537.22549 0 3682.029 9.9926092 + 9100 19972.527 354.73119 0 3683.4858 -0.30871263 + 9150 19641.651 409.18618 0 3682.7947 -1.3036238 + 9200 20019.08 346.19657 0 3682.7099 6.7425386 + 9250 19259.286 473.04973 0 3682.9308 -24.120659 + 9300 21597.757 82.971857 0 3682.598 -13.748483 + 9350 19348.379 457.23576 0 3681.9656 3.1571402 + 9400 19129.588 493.35235 0 3681.617 8.6293783 + 9450 20337.025 291.20959 0 3680.7138 6.8590795 + 9500 20581.788 249.65891 0 3679.9569 -18.892836 + 9550 19482.069 433.0077 0 3680.0192 23.029778 + 9600 19182.794 482.96871 0 3680.101 -11.081731 + 9650 20086.771 332.5311 0 3680.3263 -18.939681 + 9700 20274.046 300.98818 0 3679.9959 6.7538762 + 9750 18743.595 555.08045 0 3679.0129 8.2757138 + 9800 19464.311 435.66288 0 3679.7148 7.0528759 + 9850 21249.848 138.27382 0 3679.9152 -10.847402 + 9900 21156.214 153.84621 0 3679.8819 -7.8359674 + 9950 21643.134 72.547515 0 3679.7365 -10.507744 + 10000 19587.948 414.64942 0 3679.3075 6.1173553 +Loop time of 2.35562 on 4 procs for 10000 steps with 81 atoms + +Performance: 36678.236 tau/day, 4245.166 timesteps/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0055581 | 0.024882 | 0.055326 | 12.0 | 1.06 +Neigh | 0.0073809 | 0.022107 | 0.043683 | 9.2 | 0.94 +Comm | 0.12484 | 0.14528 | 0.1833 | 6.2 | 6.17 +Output | 0.0035526 | 0.0041048 | 0.0055462 | 1.3 | 0.17 +Modify | 2.1078 | 2.1414 | 2.162 | 1.5 | 90.91 +Other | | 0.0178 | | | 0.76 + +Nlocal: 20.25 ave 81 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 41 ave 78 max 11 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 193.5 ave 774 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 774 +Ave neighs/atom = 9.5555556 +Neighbor list builds = 989 +Dangerous builds = 915 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems5.g++.1 b/examples/rigid/log.20Mar22.rigid.poems5.g++.1 new file mode 100644 index 0000000000..5a18042516 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems5.g++.1 @@ -0,0 +1,329 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies2.dat +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7382 0 3904.4344 18.086359 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173524 + 200 20705.978 69.977442 0 3904.4178 9.0928158 + 250 19552.211 283.50525 0 3904.285 15.670465 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47231 0 3902.9213 0.6921524 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05177 0 3902.1317 4.6838621 + 850 19932.48 210.71175 0 3901.9118 3.4716043 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61915 0 3902.4586 -2.272315 + 1050 20859.506 39.696993 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.874422 + 1200 20767.681 56.717094 0 3902.5839 -34.817444 + 1250 20625.583 82.586399 0 3902.1388 11.697329 + 1300 20690.013 71.006478 0 3902.4903 -29.292777 + 1350 20936.019 26.022786 0 3903.0634 1.0316025 + 1400 19753.559 244.81785 0 3902.8844 6.7138514 + 1450 15690.149 998.342 0 3903.9252 48.124557 + 1500 20234.455 155.92516 0 3903.0465 13.17221 + 1550 20779.631 55.063009 0 3903.1428 -2.639045 + 1600 20642.753 80.233905 0 3902.9659 -2.4688467 + 1650 18785.696 423.90402 0 3902.7365 -5.6466663 + 1700 20965.076 20.760444 0 3903.182 -0.45364296 + 1750 18935.406 396.96067 0 3903.5173 25.913302 + 1800 20581.559 91.756972 0 3903.1567 3.8217234 + 1850 20616.946 85.184849 0 3903.1378 4.1907972 + 1900 16602.053 828.40949 0 3902.8637 -0.49505122 + 1950 20175.526 166.53362 0 3902.7421 5.603825 + 2000 20261.924 150.39322 0 3902.6014 -1.196958 + 2050 20170.339 167.40504 0 3902.6531 -0.80849882 + 2100 19820.132 231.26755 0 3901.6624 3.1476607 + 2150 20666.19 75.838461 0 3902.9106 0.53899287 + 2200 19873.51 222.53286 0 3902.8124 7.9310276 + 2250 18548.063 467.69698 0 3902.5235 16.905356 + 2300 20616.61 84.762399 0 3902.6531 -6.7872951 + 2350 18167.738 538.13635 0 3902.5322 -11.458285 + 2400 20120.227 177.01954 0 3902.9875 -1.2593018 + 2450 20436.599 118.32469 0 3902.8801 -6.5989174 + 2500 18919.923 400.26361 0 3903.9531 32.37476 + 2550 19675.809 259.77151 0 3903.4398 19.437327 + 2600 19739.842 247.86388 0 3903.3901 -7.519784 + 2650 20557.026 96.530313 0 3903.387 0.60211646 + 2700 20666.602 76.099892 0 3903.2484 0.16825503 + 2750 20924.585 28.453883 0 3903.3771 2.4227171 + 2800 20360.659 132.8596 0 3903.352 4.1440877 + 2850 20783.475 54.518625 0 3903.3102 -0.57312067 + 2900 20456.181 115.03745 0 3903.2191 -20.118887 + 2950 20779.493 55.321394 0 3903.3756 -0.26783079 + 3000 20011.867 197.30216 0 3903.2035 -1.4704201 + 3050 20741.875 62.208723 0 3903.2966 -7.5432815 + 3100 21001.754 14.148298 0 3903.362 2.9676438 + 3150 20244.086 154.44639 0 3903.3512 -1.9071213 + 3200 20639.615 81.136426 0 3903.2873 1.4826467 + 3250 20735.244 63.529571 0 3903.3895 2.1127055 + 3300 20142.891 173.22282 0 3903.3878 4.7739415 + 3350 19963.765 206.21899 0 3903.2126 5.5410771 + 3400 16628.667 824.13627 0 3903.519 36.087673 + 3450 19228.218 342.81569 0 3903.5968 3.1057274 + 3500 19759.293 244.57876 0 3903.707 2.2339557 + 3550 19853.21 227.06362 0 3903.584 -1.0882119 + 3600 19673.516 260.64854 0 3903.8923 -10.63775 + 3650 19619.238 270.5393 0 3903.7316 -6.3746003 + 3700 20756.865 59.790243 0 3903.6542 -8.3015766 + 3750 20265.025 150.47347 0 3903.2559 -5.7284695 + 3800 20944.683 24.669276 0 3903.3142 -0.070552298 + 3850 19344.831 320.59492 0 3902.971 13.040749 + 3900 19978.209 203.00247 0 3902.6708 0.15638133 + 3950 19864.118 224.19359 0 3902.734 0.453229 + 4000 17606.216 642.71493 0 3903.1252 -12.656002 + 4050 18017.895 566.54102 0 3903.1883 12.133906 + 4100 20092.963 182.17593 0 3903.095 7.7445947 + 4150 20555.337 96.395074 0 3902.939 -6.5429752 + 4200 20709.781 67.869199 0 3903.0138 -2.8653003 + 4250 18956.203 392.20748 0 3902.6155 -1.6249728 + 4300 17816.204 603.72704 0 3903.0241 23.089239 + 4350 18979.742 388.04678 0 3902.8138 3.2511108 + 4400 20272.085 148.82367 0 3902.9135 1.9518268 + 4450 18820.003 417.74789 0 3902.9337 6.3979299 + 4500 19991.936 200.50131 0 3902.7117 3.5118553 + 4550 20915.092 29.663898 0 3902.8291 -2.3174641 + 4600 20690.37 71.125087 0 3902.6752 -12.008575 + 4650 18893.76 404.50849 0 3903.3529 15.006184 + 4700 18611.123 456.1263 0 3902.6306 -5.3574892 + 4750 20497.821 106.5856 0 3902.4784 0.85039837 + 4800 20803.214 50.120522 0 3902.5675 3.8610873 + 4850 18849.598 411.72635 0 3902.3927 9.2029058 + 4900 18121.714 546.68042 0 3902.5533 9.4522272 + 4950 20377.499 128.99323 0 3902.6041 5.3825395 + 5000 20686.114 72.039749 0 3902.8016 -5.706271 + 5050 20180.449 165.51368 0 3902.634 -16.418461 + 5100 20274.947 148.36657 0 3902.9864 -5.6668309 + 5150 18042.324 560.74137 0 3901.9125 3.6791541 + 5200 20794.666 52.204446 0 3903.0685 -1.4517721 + 5250 19073.55 371.18834 0 3903.3272 -13.457439 + 5300 20821.412 47.364313 0 3903.1813 2.258098 + 5350 20583.073 91.271191 0 3902.9513 5.4323985 + 5400 20490.967 108.41184 0 3903.0353 4.122905 + 5450 18141.79 543.66874 0 3903.2594 -0.19951075 + 5500 20274.012 148.55528 0 3903.002 5.0489974 + 5550 17806.237 605.43454 0 3902.8858 43.80619 + 5600 20999.825 14.341937 0 3903.1983 1.0879933 + 5650 20930.929 27.025347 0 3903.1234 -7.0860209 + 5700 20677.725 73.853093 0 3903.0614 2.6864775 + 5750 20521.264 102.87509 0 3903.1092 2.6940548 + 5800 20792.571 52.596021 0 3903.0721 1.2910217 + 5850 20518.674 103.26595 0 3903.0204 -9.2547271 + 5900 18417.885 491.66696 0 3902.3865 -12.049357 + 5950 17243.837 709.37858 0 3902.6817 -6.2357188 + 6000 20262.525 149.56918 0 3901.8885 -0.28964823 + 6050 19883.554 219.14043 0 3901.2801 2.3071707 + 6100 16548.178 838.47869 0 3902.956 -11.715644 + 6150 19601.177 272.14674 0 3901.9944 -0.9008056 + 6200 20499.796 106.2363 0 3902.4949 0.79071424 + 6250 19601.106 272.50139 0 3902.3359 -1.9306693 + 6300 17210.685 712.70535 0 3899.8692 4.8890923 + 6350 19911.896 214.91041 0 3902.2985 12.691129 + 6400 18834.642 411.87123 0 3899.7678 -1.9447856 + 6450 20216.311 158.39781 0 3902.1591 2.6009109 + 6500 20452.025 114.97122 0 3902.3832 0.14644416 + 6550 19142.589 357.34097 0 3902.2649 2.8968485 + 6600 20412.915 122.08784 0 3902.2573 3.1343105 + 6650 17317.867 699.39994 0 3906.4123 42.25563 + 6700 20479.771 109.8036 0 3902.3537 1.3520625 + 6750 20306.902 142.12484 0 3902.6623 2.2032106 + 6800 20755.367 58.994834 0 3902.5814 -0.90518094 + 6850 20471.259 111.7197 0 3902.6936 1.5799331 + 6900 20702.025 69.15032 0 3902.8586 9.3910371 + 6950 20477.695 110.34414 0 3902.5099 1.8181164 + 7000 20560.727 95.057704 0 3902.5998 -15.686006 + 7050 20336.675 136.39386 0 3902.4448 1.3704327 + 7100 20757.399 58.950153 0 3902.913 -6.4250981 + 7150 20870.958 38.095649 0 3903.088 -4.1962169 + 7200 20706.869 68.489134 0 3903.0944 2.8322659 + 7250 20386.713 127.7432 0 3903.0604 6.0287391 + 7300 18391.773 497.21001 0 3903.0939 19.202343 + 7350 20178.898 166.4993 0 3903.3322 1.5682417 + 7400 16858.704 781.78682 0 3903.7691 21.317514 + 7450 17509.513 660.71963 0 3903.2221 -5.9456143 + 7500 19974.601 204.20412 0 3903.2043 -0.69202711 + 7550 20917.053 29.73415 0 3903.2626 -3.9962577 + 7600 20923.518 28.482703 0 3903.2083 -1.9016251 + 7650 20549.528 97.630612 0 3903.0987 3.5512257 + 7700 20861.441 39.903885 0 3903.1337 2.4426264 + 7750 18843.349 413.64461 0 3903.1537 2.677739 + 7800 20616.054 85.214364 0 3903.0021 3.9639004 + 7850 16478.851 851.93376 0 3903.5728 7.3763128 + 7900 20312.115 141.35103 0 3902.8539 4.6707271 + 7950 20389.623 127.16589 0 3903.0219 3.4414001 + 8000 20452.117 115.30715 0 3902.7362 -1.0162528 + 8050 20857.093 40.791886 0 3903.2164 -15.150068 + 8100 19817.543 233.4997 0 3903.415 0.89346046 + 8150 18649.521 449.9112 0 3903.5262 -0.40053588 + 8200 19619.276 270.37616 0 3903.5754 5.5161492 + 8250 20393.176 127.01336 0 3903.5275 2.122613 + 8300 19145.912 358.00424 0 3903.5435 3.863924 + 8350 19636.311 267.17226 0 3903.5262 -7.1496084 + 8400 19086.332 368.86693 0 3903.3729 7.0968952 + 8450 19494.416 292.89527 0 3902.9723 3.1750935 + 8500 20041.919 191.77756 0 3903.244 0.95215503 + 8550 20357.561 133.15478 0 3903.0736 -0.14020152 + 8600 16998.797 756.07003 0 3903.9954 -16.724408 + 8650 20853.26 41.386996 0 3903.1017 -3.2612965 + 8700 20767.768 57.360884 0 3903.2438 1.1157649 + 8750 20752.546 60.106518 0 3903.1705 0.39130547 + 8800 20574.407 92.99798 0 3903.0734 0.61728166 + 8850 20326.99 138.94203 0 3903.1995 -1.9434522 + 8900 17408.108 679.53222 0 3903.2559 21.935371 + 8950 20471.21 112.2721 0 3903.2368 1.8142747 + 9000 19129.591 360.35257 0 3902.8694 4.5786395 + 9050 20439.668 117.89541 0 3903.0191 2.5585685 + 9100 20780.375 54.788664 0 3903.0062 3.8312459 + 9150 19904.559 216.61504 0 3902.6445 12.150414 + 9200 20961.295 21.52065 0 3903.2419 -0.2120699 + 9250 19315.252 326.44175 0 3903.3402 -19.740867 + 9300 20653.002 78.77764 0 3903.4076 -7.8068233 + 9350 18961.572 391.20947 0 3902.6117 -12.660843 + 9400 16262.179 892.67633 0 3904.191 22.2435 + 9450 17064.394 743.33301 0 3903.406 36.139436 + 9500 18075.588 555.06436 0 3902.3954 24.598176 + 9550 20487.738 109.06287 0 3903.0884 2.6320759 + 9600 20358.609 133.36993 0 3903.4828 0.76449113 + 9650 19849.022 228.46312 0 3904.208 9.5547064 + 9700 20448.112 116.8757 0 3903.5632 -1.0845697 + 9750 20472.78 112.51661 0 3903.7722 -0.30676738 + 9800 19491.99 293.35361 0 3902.9814 -20.10857 + 9850 19895.603 218.42479 0 3902.7957 -0.18235641 + 9900 19704.336 254.55068 0 3903.5019 14.553184 + 9950 17689.462 627.9788 0 3903.805 4.9918088 + 10000 20184.205 165.29396 0 3903.1097 2.9472364 +Loop time of 2.28393 on 1 procs for 10000 steps with 81 atoms + +Performance: 37829.498 tau/day, 4378.414 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.052911 | 0.052911 | 0.052911 | 0.0 | 2.32 +Neigh | 0.056658 | 0.056658 | 0.056658 | 0.0 | 2.48 +Comm | 0.0087389 | 0.0087389 | 0.0087389 | 0.0 | 0.38 +Output | 0.0037996 | 0.0037996 | 0.0037996 | 0.0 | 0.17 +Modify | 2.1537 | 2.1537 | 2.1537 | 0.0 | 94.30 +Other | | 0.008147 | | | 0.36 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 113 ave 113 max 113 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 582 ave 582 max 582 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 582 +Ave neighs/atom = 7.1851852 +Neighbor list builds = 993 +Dangerous builds = 950 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems5.g++.4 b/examples/rigid/log.20Mar22.rigid.poems5.g++.4 new file mode 100644 index 0000000000..cbf8b05490 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems5.g++.4 @@ -0,0 +1,329 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies2.dat +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7382 0 3904.4344 18.086358 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173524 + 200 20705.978 69.977039 0 3904.4174 9.0928122 + 250 19552.211 283.50525 0 3904.285 15.670466 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47271 0 3902.9217 0.69215592 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05197 0 3902.1319 4.6838632 + 850 19932.48 210.71175 0 3901.9118 3.4716031 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61915 0 3902.4586 -2.272315 + 1050 20859.506 39.696993 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.8744219 + 1200 20767.681 56.717095 0 3902.5839 -34.817444 + 1250 20625.583 82.586198 0 3902.1386 11.697328 + 1300 20690.013 71.006478 0 3902.4903 -29.29278 + 1350 20936.019 26.022786 0 3903.0634 1.0316025 + 1400 19753.56 244.81784 0 3902.8844 6.7138497 + 1450 15690.149 998.34213 0 3903.9252 48.124569 + 1500 20234.455 155.92516 0 3903.0465 13.172207 + 1550 20779.631 55.063019 0 3903.1428 -2.6390455 + 1600 20642.753 80.233821 0 3902.9659 -2.4688431 + 1650 18785.698 423.90364 0 3902.7365 -5.6466892 + 1700 20965.076 20.760451 0 3903.182 -0.45366172 + 1750 18935.412 396.95958 0 3903.5173 25.913174 + 1800 20581.554 91.757912 0 3903.1567 3.8218442 + 1850 20616.949 85.184789 0 3903.1382 4.1907933 + 1900 16601.896 828.43849 0 3902.8638 -0.49468175 + 1950 20175.564 166.52646 0 3902.7421 5.6035728 + 2000 20262.525 150.28224 0 3902.6017 -1.1967705 + 2050 20168.994 167.65314 0 3902.6521 -0.80723928 + 2100 19810.955 232.96524 0 3901.6605 3.1936531 + 2150 20667.232 75.645145 0 3902.9103 0.54812734 + 2200 19863.772 224.34646 0 3902.8228 7.9294465 + 2250 18808.943 419.2084 0 3902.3461 14.344526 + 2300 20573.665 92.761842 0 3902.6999 -6.7671703 + 2350 19075.104 369.95414 0 3902.3809 -9.5353568 + 2400 20273.873 148.53775 0 3902.9586 -1.93796 + 2450 20087.769 182.30216 0 3902.2593 2.131796 + 2500 20711.602 67.530554 0 3903.0124 2.6280244 + 2550 19971.224 204.75926 0 3903.134 3.1760522 + 2600 20620.084 85.027145 0 3903.5612 -0.92888063 + 2650 19737.546 248.65474 0 3903.7559 -3.3218688 + 2700 20650.724 79.522243 0 3903.7303 -7.5918025 + 2750 19863.245 225.2505 0 3903.6292 9.2140221 + 2800 18992.457 386.73547 0 3903.8572 2.6244537 + 2850 18703.899 440.48356 0 3904.1685 14.561348 + 2900 17939.805 581.74599 0 3903.932 -8.0863089 + 2950 20867.516 39.38186 0 3903.7367 3.0985423 + 3000 19767.994 242.8847 0 3903.6243 1.5943109 + 3050 20397.448 126.31591 0 3903.6212 -0.14982775 + 3100 20978.114 19.126395 0 3903.9623 -9.6797253 + 3150 18303.556 513.8514 0 3903.3989 4.5940322 + 3200 19156.505 356.46608 0 3903.9671 10.071308 + 3250 17484.205 666.52199 0 3904.3377 -4.1641768 + 3300 18069.94 557.75947 0 3904.0447 11.868707 + 3350 20855.645 41.964632 0 3904.1212 5.4186293 + 3400 18011.986 568.76255 0 3904.3155 25.262783 + 3450 18669.69 446.92755 0 3904.2776 -4.194499 + 3500 20248.799 154.22147 0 3903.9991 3.9211572 + 3550 20226.024 158.64726 0 3904.2072 1.5299114 + 3600 20267.02 151.25631 0 3904.4082 -8.9821729 + 3650 20522.946 103.65382 0 3904.1994 -14.433796 + 3700 20892.319 35.294614 0 3904.2426 -21.264596 + 3750 19942.202 211.02993 0 3904.0304 -1.6428817 + 3800 20421.678 122.08118 0 3903.8734 1.7137935 + 3850 17899.53 588.82593 0 3903.5536 -24.450276 + 3900 20721.119 66.486999 0 3903.7312 -7.1772088 + 3950 20946.484 24.799445 0 3903.778 -0.4028037 + 4000 20985.362 17.608355 0 3903.7865 4.7522266 + 4050 19969.779 205.46466 0 3903.5719 18.941639 + 4100 20479.578 110.56561 0 3903.08 2.3715952 + 4150 18110.701 549.53348 0 3903.367 1.133321 + 4200 19321.098 325.58216 0 3903.5634 -3.7574942 + 4250 20734.436 63.87616 0 3903.5865 0.48350623 + 4300 19446.823 302.1727 0 3903.4362 4.0462392 + 4350 20494.669 108.1918 0 3903.501 2.9789077 + 4400 20379.244 129.61413 0 3903.5482 4.0881089 + 4450 19710.564 253.4251 0 3903.5295 5.3334683 + 4500 20744.753 61.785082 0 3903.406 4.0015409 + 4550 19948.024 208.76984 0 3902.8484 2.705423 + 4600 18367.368 502.69569 0 3904.0602 21.476471 + 4650 20559.367 96.133242 0 3903.4234 2.2549454 + 4700 20940.135 25.547808 0 3903.3505 -8.9042666 + 4750 20128.703 175.82088 0 3903.3584 -8.1450176 + 4800 20632.27 82.543887 0 3903.3347 -0.55649542 + 4850 19864.539 224.63792 0 3903.2563 7.1553461 + 4900 19332.037 323.15561 0 3903.1625 17.020214 + 4950 19055.575 373.68069 0 3902.4908 10.149457 + 5000 20219.484 159.21383 0 3903.5627 3.1806346 + 5050 17557.761 652.32864 0 3903.7659 10.733736 + 5100 20615.337 85.795304 0 3903.4503 -3.6035636 + 5150 20759.853 59.155843 0 3903.573 2.0152286 + 5200 20082.007 184.39375 0 3903.2839 -5.3745109 + 5250 18689.521 442.59842 0 3903.6208 -9.8911164 + 5300 20038.496 192.34221 0 3903.1749 -2.1437039 + 5350 19897.455 218.70142 0 3903.4154 0.64582116 + 5400 18732.385 434.21543 0 3903.1755 12.98676 + 5450 19831.487 230.79099 0 3903.2886 11.439958 + 5500 20079.89 184.6953 0 3903.1935 4.0906279 + 5550 20453.497 115.47128 0 3903.1559 7.8844436 + 5600 16673.041 815.52661 0 3903.1267 -20.17797 + 5650 19691.378 256.6412 0 3903.1928 3.7103317 + 5700 20345.743 135.29997 0 3903.0302 5.6373816 + 5750 20769.613 56.906603 0 3903.1312 -17.564762 + 5800 20713.369 67.38314 0 3903.1922 -5.340631 + 5850 20799.947 51.348865 0 3903.1909 -2.7827653 + 5900 19581.933 273.51588 0 3899.7997 12.347375 + 5950 20444.438 116.909 0 3902.9161 -0.74896654 + 6000 18970.948 389.99664 0 3903.1352 26.642912 + 6050 19414.753 307.13217 0 3902.4568 25.86316 + 6100 20780.042 54.586474 0 3902.7424 1.5387425 + 6150 20885.872 35.091585 0 3902.8456 -8.251884 + 6200 19825.81 231.40943 0 3902.8558 6.7196589 + 6250 20578.278 92.255994 0 3903.0481 -5.9647091 + 6300 20093.43 181.8699 0 3902.8754 -9.9906069 + 6350 20605.294 87.180289 0 3902.9755 -3.5643876 + 6400 19737.257 247.84828 0 3902.8958 -4.2783347 + 6450 19884.717 220.81633 0 3903.1714 3.8758905 + 6500 18719.372 436.94802 0 3903.4984 1.7865904 + 6550 20096.883 181.63346 0 3903.2784 2.395512 + 6600 20888.673 35.003062 0 3903.2758 2.7728947 + 6650 20437.85 118.16373 0 3902.9507 8.1456757 + 6700 19241.051 339.73065 0 3902.8882 13.740454 + 6750 20407.542 123.94326 0 3903.1177 7.6285942 + 6800 20536.785 99.976706 0 3903.0851 8.3496632 + 6850 20625.328 83.579677 0 3903.0849 6.5074992 + 6900 20705.37 68.944625 0 3903.2724 3.1905177 + 6950 18872.424 408.67134 0 3903.5647 6.2638845 + 7000 20072.762 186.18051 0 3903.3586 -22.780407 + 7050 20461.879 114.07495 0 3903.3117 -11.495523 + 7100 19811.566 234.50237 0 3903.3108 1.1212695 + 7150 20742.918 61.884088 0 3903.1651 -3.7907508 + 7200 20911.192 30.599903 0 3903.0429 -7.0262304 + 7250 20879.755 36.30274 0 3902.9241 -5.8018787 + 7300 20682.32 72.703261 0 3902.7626 -3.3446789 + 7350 19401.046 309.70672 0 3902.493 3.4836528 + 7400 20220.542 157.83897 0 3902.3838 2.3400031 + 7450 17691.193 625.47764 0 3901.6244 25.239568 + 7500 19745.294 245.02566 0 3901.5615 5.3622843 + 7550 19685.719 256.70983 0 3902.2133 3.4560563 + 7600 18830.192 415.10021 0 3902.1727 -0.10282681 + 7650 19613.136 270.18979 0 3902.2521 8.2241536 + 7700 20989.015 15.636879 0 3902.4915 1.2955204 + 7750 20301.583 142.90625 0 3902.4586 0.12548373 + 7800 18360.147 502.50342 0 3902.5307 17.117272 + 7850 20796.478 51.032537 0 3902.2321 -3.0993883 + 7900 20284.267 145.64296 0 3901.9887 -1.2682383 + 7950 20280.983 146.13471 0 3901.8723 3.5999841 + 8000 20915.869 28.730821 0 3902.0399 2.4987291 + 8050 20745.162 60.19981 0 3901.8964 4.0643481 + 8100 20509.039 103.70462 0 3901.6748 1.0771863 + 8150 20212.97 158.64893 0 3901.7916 3.0000215 + 8200 20323.463 138.25912 0 3901.8634 -1.2802945 + 8250 19997.284 198.37183 0 3901.5727 -2.6431964 + 8300 20138.402 171.75824 0 3901.092 1.7669897 + 8350 20367.568 130.22531 0 3901.9972 -1.2153731 + 8400 19945.534 208.35675 0 3901.9741 1.6021151 + 8450 20112.534 177.18642 0 3901.7298 2.2413008 + 8500 20686.7 71.116816 0 3901.9873 2.2888545 + 8550 18081.94 553.83586 0 3902.3432 7.8257937 + 8600 18320.081 505.67086 0 3898.2784 16.554878 + 8650 20235.305 154.43021 0 3901.709 3.1740823 + 8700 20355.413 132.22512 0 3901.746 4.3436482 + 8750 20087.188 182.11349 0 3901.9631 10.422134 + 8800 20400.795 124.09819 0 3902.0232 2.1179177 + 8850 20678.731 72.825797 0 3902.2204 -3.4491441 + 8900 20372.643 129.5072 0 3902.2189 -8.2166415 + 8950 20851.731 40.899364 0 3902.331 -5.8382839 + 9000 20318.076 139.61775 0 3902.2243 -4.1960802 + 9050 16879.415 776.53739 0 3902.3549 -14.429475 + 9100 19135.149 358.68223 0 3902.2284 -15.50479 + 9150 20689.556 70.939656 0 3902.339 -2.9876179 + 9200 19949.801 207.54882 0 3901.9564 6.4259245 + 9250 20207.027 160.2813 0 3902.3233 1.7402195 + 9300 20030.005 192.99466 0 3902.2548 5.300728 + 9350 19795.291 236.24003 0 3902.0347 5.8677745 + 9400 18232.093 526.18752 0 3902.501 19.344893 + 9450 18789.641 422.30568 0 3901.8687 -7.5185247 + 9500 16332.599 874.10423 0 3898.6597 16.241378 + 9550 18572.572 462.19972 0 3901.5649 -10.777359 + 9600 19859.645 223.32209 0 3901.0341 0.89631957 + 9650 19092.741 365.35768 0 3901.0504 6.7830005 + 9700 18391.154 495.72792 0 3901.4972 6.0683847 + 9750 17790.092 608.60997 0 3903.0714 8.2090184 + 9800 17681.783 628.99951 0 3903.4038 14.231747 + 9850 17804.412 605.54067 0 3902.654 22.308453 + 9900 19134.472 359.37911 0 3902.7999 8.5633158 + 9950 20099.055 180.28604 0 3902.3332 4.7905855 + 10000 20035.447 192.30744 0 3902.5754 1.8299201 +Loop time of 2.34062 on 4 procs for 10000 steps with 81 atoms + +Performance: 36913.309 tau/day, 4272.374 timesteps/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0052865 | 0.014915 | 0.039366 | 11.6 | 0.64 +Neigh | 0.0080708 | 0.016504 | 0.03345 | 7.7 | 0.71 +Comm | 0.1357 | 0.14237 | 0.15111 | 1.5 | 6.08 +Output | 0.0033429 | 0.0037922 | 0.0050931 | 1.2 | 0.16 +Modify | 2.1033 | 2.1433 | 2.1609 | 1.6 | 91.57 +Other | | 0.01973 | | | 0.84 + +Nlocal: 20.25 ave 36 max 0 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 35.25 ave 47 max 24 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 137.5 ave 252 max 0 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 550 +Ave neighs/atom = 6.7901235 +Neighbor list builds = 994 +Dangerous builds = 956 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.1 b/examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.1 new file mode 100644 index 0000000000..e69de29bb2 diff --git a/examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.4 b/examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.4 new file mode 100644 index 0000000000..e69de29bb2 diff --git a/examples/rigid/log.20Mar22.rigid.small.g++.1 b/examples/rigid/log.20Mar22.rigid.small.g++.1 new file mode 100644 index 0000000000..e34bdad80d --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.small.g++.1 @@ -0,0 +1,322 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/small molecule + create bodies CPU = 0.000 seconds + 9 rigid bodies with 81 atoms + 1.2247449 = max distance from body owner to body atom + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722826e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.255443 0 5269.4841 11.963561 + 3300 16732.156 1.9585966 0 5269.4893 12.234024 + 3350 16738.655 -0.079693235 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.05932751 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.092031 + 3550 16713.405 7.8460623 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663192 0 5269.4882 12.027009 + 3700 16738.602 -0.070934371 0 5269.4889 12.025288 + 3750 16737.731 0.20706562 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690678 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646809 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307407 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532803 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.0003765242 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156153 0 5269.5203 12.011611 + 9600 16738.549 -0.026814361 0 5269.5163 12.011415 + 9650 16738.765 -0.1019152 0 5269.5092 12.011013 + 9700 16735.041 1.0589855 0 5269.4979 12.062708 + 9750 16738.013 0.13550223 0 5269.5101 11.407246 + 9800 16738.512 -0.01162033 0 5269.5201 11.394974 + 9850 16738.489 -0.000672705 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984511 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395077 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.097001 on 1 procs for 10000 steps with 81 atoms + +Performance: 890712.494 tau/day, 103091.724 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0064264 | 0.0064264 | 0.0064264 | 0.0 | 6.63 +Bond | 0.0003385 | 0.0003385 | 0.0003385 | 0.0 | 0.35 +Neigh | 0.030894 | 0.030894 | 0.030894 | 0.0 | 31.85 +Comm | 0.0065732 | 0.0065732 | 0.0065732 | 0.0 | 6.78 +Output | 0.0021773 | 0.0021773 | 0.0021773 | 0.0 | 2.24 +Modify | 0.046477 | 0.046477 | 0.046477 | 0.0 | 47.91 +Other | | 0.004115 | | | 4.24 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.small.g++.4 b/examples/rigid/log.20Mar22.rigid.small.g++.4 new file mode 100644 index 0000000000..03bb7a39c0 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.small.g++.4 @@ -0,0 +1,322 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/small molecule + create bodies CPU = 0.000 seconds + 9 rigid bodies with 81 atoms + 1.2247449 = max distance from body owner to body atom + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.972281e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532812 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652435 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156165 0 5269.5203 12.011611 + 9600 16738.549 -0.02681437 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589893 0 5269.4979 12.062708 + 9750 16738.013 0.1355014 0 5269.5101 11.407246 + 9800 16738.512 -0.011620326 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270465 0 5269.5237 11.395099 + 9900 16738.489 -0.00024984533 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395077 + 10000 16738.49 0 0 5269.5246 11.395076 +Loop time of 0.115632 on 4 procs for 10000 steps with 81 atoms + +Performance: 747196.558 tau/day, 86481.083 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0014528 | 0.0020376 | 0.0024938 | 0.9 | 1.76 +Bond | 0.00030255 | 0.00030731 | 0.00031718 | 0.0 | 0.27 +Neigh | 0.0089963 | 0.0094964 | 0.010494 | 0.6 | 8.21 +Comm | 0.035947 | 0.038848 | 0.040951 | 1.0 | 33.60 +Output | 0.0022924 | 0.002542 | 0.0032643 | 0.8 | 2.20 +Modify | 0.056743 | 0.058255 | 0.059447 | 0.4 | 50.38 +Other | | 0.004146 | | | 3.59 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.small.infile.g++.1 b/examples/rigid/log.20Mar22.rigid.small.infile.g++.1 new file mode 100644 index 0000000000..7c5f672309 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.small.infile.g++.1 @@ -0,0 +1,323 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/small molecule infile bodyinfo.dat + create bodies CPU = 0.000 seconds + 9 rigid bodies with 81 atoms + 1.2247449 = max distance from body owner to body atom + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Reading rigid body data for 4 bodies from file bodyinfo.dat +Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722817e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.05932751 0 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12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690668 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646805 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652432 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589884 0 5269.4979 12.062708 + 9750 16738.013 0.13550153 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270481 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984532 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395077 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.0973982 on 1 procs for 10000 steps with 81 atoms + +Performance: 887079.894 tau/day, 102671.284 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0065928 | 0.0065928 | 0.0065928 | 0.0 | 6.77 +Bond | 0.00033457 | 0.00033457 | 0.00033457 | 0.0 | 0.34 +Neigh | 0.031245 | 0.031245 | 0.031245 | 0.0 | 32.08 +Comm | 0.0065444 | 0.0065444 | 0.0065444 | 0.0 | 6.72 +Output | 0.0024004 | 0.0024004 | 0.0024004 | 0.0 | 2.46 +Modify | 0.045966 | 0.045966 | 0.045966 | 0.0 | 47.19 +Other | | 0.004315 | | | 4.43 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Mar22.rigid.small.infile.g++.4 b/examples/rigid/log.20Mar22.rigid.small.infile.g++.4 new file mode 100644 index 0000000000..aad4e878dc --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.small.infile.g++.4 @@ -0,0 +1,323 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style bond + +pair_style lj/cut 2.5 + +read_data data.rigid.small +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/small molecule infile bodyinfo.dat + create bodies CPU = 0.000 seconds + 9 rigid bodies with 81 atoms + 1.2247449 = max distance from body owner to body atom + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Reading rigid body data for 4 bodies from file bodyinfo.dat +Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722791e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585966 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.05932751 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460622 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663193 0 5269.4882 12.027009 + 3700 16738.602 -0.070934369 0 5269.4889 12.025288 + 3750 16737.731 0.20706559 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690669 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646806 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532809 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.0003765243 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156164 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589884 0 5269.4979 12.062708 + 9750 16738.013 0.13550185 0 5269.5101 11.407246 + 9800 16738.512 -0.011620326 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270434 0 5269.5237 11.395099 + 9900 16738.489 -0.00024984508 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395077 + 10000 16738.49 0 0 5269.5246 11.395076 +Loop time of 0.135757 on 4 procs for 10000 steps with 81 atoms + +Performance: 636433.251 tau/day, 73661.256 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0020781 | 0.0024716 | 0.0032187 | 0.9 | 1.82 +Bond | 0.00029013 | 0.000332 | 0.00037076 | 0.0 | 0.24 +Neigh | 0.0087772 | 0.011705 | 0.014134 | 2.3 | 8.62 +Comm | 0.042702 | 0.045012 | 0.048023 | 1.1 | 33.16 +Output | 0.0027373 | 0.0030292 | 0.0036178 | 0.6 | 2.23 +Modify | 0.067437 | 0.068617 | 0.069634 | 0.3 | 50.54 +Other | | 0.004589 | | | 3.38 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.atomfile.g++.1 b/examples/rigid/log.25Mar24.rigid.atomfile.g++.1 deleted file mode 100644 index 4f76779be7..0000000000 --- a/examples/rigid/log.25Mar24.rigid.atomfile.g++.1 +++ /dev/null @@ -1,341 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -variable bodies atomfile bodies.txt -fix 1 all rigid custom v_bodies - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.483 | 4.483 | 4.483 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589881 0 5269.4979 12.062708 - 9750 16738.013 0.13550093 0 5269.5101 11.407245 - 9800 16738.512 -0.01162033 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 - 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.119912 on 1 procs for 10000 steps with 81 atoms - -Performance: 720528.892 tau/day, 83394.548 timesteps/s, 6.755 Matom-step/s -98.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.007138 | 0.007138 | 0.007138 | 0.0 | 5.95 -Neigh | 0.04331 | 0.04331 | 0.04331 | 0.0 | 36.12 -Comm | 0.0080707 | 0.0080707 | 0.0080707 | 0.0 | 6.73 -Output | 0.001757 | 0.001757 | 0.001757 | 0.0 | 1.47 -Modify | 0.052965 | 0.052965 | 0.052965 | 0.0 | 44.17 -Other | | 0.006671 | | | 5.56 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.atomfile.g++.4 b/examples/rigid/log.25Mar24.rigid.atomfile.g++.4 deleted file mode 100644 index 071a4de5d0..0000000000 --- a/examples/rigid/log.25Mar24.rigid.atomfile.g++.4 +++ /dev/null @@ -1,341 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -variable bodies atomfile bodies.txt -fix 1 all rigid custom v_bodies - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.33 | 4.362 | 4.456 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589886 0 5269.4979 12.062708 - 9750 16738.013 0.13550089 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.135195 on 4 procs for 10000 steps with 81 atoms - -Performance: 639077.466 tau/day, 73967.299 timesteps/s, 5.991 Matom-step/s -97.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0016842 | 0.0023498 | 0.0027328 | 0.8 | 1.74 -Neigh | 0.012614 | 0.013371 | 0.014361 | 0.5 | 9.89 -Comm | 0.062345 | 0.06407 | 0.065902 | 0.6 | 47.39 -Output | 0.0018312 | 0.0019801 | 0.0024023 | 0.5 | 1.46 -Modify | 0.038532 | 0.039713 | 0.041474 | 0.6 | 29.37 -Other | | 0.01371 | | | 10.14 - -Nlocal: 20.25 ave 37 max 3 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.atomvar.g++.1 b/examples/rigid/log.25Mar24.rigid.atomvar.g++.1 deleted file mode 100644 index 7510d35ec1..0000000000 --- a/examples/rigid/log.25Mar24.rigid.atomvar.g++.1 +++ /dev/null @@ -1,341 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) -fix 1 all rigid custom v_bodies - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.358 | 4.358 | 4.358 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589881 0 5269.4979 12.062708 - 9750 16738.013 0.13550093 0 5269.5101 11.407245 - 9800 16738.512 -0.01162033 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 - 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.131374 on 1 procs for 10000 steps with 81 atoms - -Performance: 657662.971 tau/day, 76118.399 timesteps/s, 6.166 Matom-step/s -99.1% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0075531 | 0.0075531 | 0.0075531 | 0.0 | 5.75 -Neigh | 0.047177 | 0.047177 | 0.047177 | 0.0 | 35.91 -Comm | 0.0090961 | 0.0090961 | 0.0090961 | 0.0 | 6.92 -Output | 0.0018917 | 0.0018917 | 0.0018917 | 0.0 | 1.44 -Modify | 0.058064 | 0.058064 | 0.058064 | 0.0 | 44.20 -Other | | 0.007593 | | | 5.78 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.atomvar.g++.4 b/examples/rigid/log.25Mar24.rigid.atomvar.g++.4 deleted file mode 100644 index b7adcacb14..0000000000 --- a/examples/rigid/log.25Mar24.rigid.atomvar.g++.4 +++ /dev/null @@ -1,341 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) -fix 1 all rigid custom v_bodies - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.205 | 4.237 | 4.331 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589886 0 5269.4979 12.062708 - 9750 16738.013 0.13550089 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.135534 on 4 procs for 10000 steps with 81 atoms - -Performance: 637479.927 tau/day, 73782.399 timesteps/s, 5.976 Matom-step/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0016589 | 0.0022805 | 0.0027973 | 0.9 | 1.68 -Neigh | 0.012838 | 0.013347 | 0.014456 | 0.6 | 9.85 -Comm | 0.062667 | 0.064428 | 0.066142 | 0.6 | 47.54 -Output | 0.0018075 | 0.001966 | 0.0024125 | 0.6 | 1.45 -Modify | 0.038219 | 0.039639 | 0.041101 | 0.6 | 29.25 -Other | | 0.01387 | | | 10.24 - -Nlocal: 20.25 ave 37 max 3 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.early.g++.1 b/examples/rigid/log.25Mar24.rigid.early.g++.1 deleted file mode 100644 index 9f5d86312e..0000000000 --- a/examples/rigid/log.25Mar24.rigid.early.g++.1 +++ /dev/null @@ -1,340 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 - 9 rigid bodies with 81 atoms - -fix_modify 1 bodyforces early - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589881 0 5269.4979 12.062708 - 9750 16738.013 0.13550093 0 5269.5101 11.407245 - 9800 16738.512 -0.01162033 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 - 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.127115 on 1 procs for 10000 steps with 81 atoms - -Performance: 679698.303 tau/day, 78668.785 timesteps/s, 6.372 Matom-step/s -99.2% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0074904 | 0.0074904 | 0.0074904 | 0.0 | 5.89 -Neigh | 0.044675 | 0.044675 | 0.044675 | 0.0 | 35.15 -Comm | 0.0079194 | 0.0079194 | 0.0079194 | 0.0 | 6.23 -Output | 0.0018129 | 0.0018129 | 0.0018129 | 0.0 | 1.43 -Modify | 0.057845 | 0.057845 | 0.057845 | 0.0 | 45.51 -Other | | 0.007372 | | | 5.80 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.early.g++.4 b/examples/rigid/log.25Mar24.rigid.early.g++.4 deleted file mode 100644 index e0b182d9fc..0000000000 --- a/examples/rigid/log.25Mar24.rigid.early.g++.4 +++ /dev/null @@ -1,340 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 - 9 rigid bodies with 81 atoms - -fix_modify 1 bodyforces early - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589886 0 5269.4979 12.062708 - 9750 16738.013 0.13550089 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.133679 on 4 procs for 10000 steps with 81 atoms - -Performance: 646325.439 tau/day, 74806.185 timesteps/s, 6.059 Matom-step/s -98.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0016629 | 0.0023406 | 0.0028762 | 0.9 | 1.75 -Neigh | 0.012558 | 0.013331 | 0.015279 | 1.0 | 9.97 -Comm | 0.060677 | 0.062779 | 0.0646 | 0.7 | 46.96 -Output | 0.0017495 | 0.001914 | 0.0023526 | 0.6 | 1.43 -Modify | 0.037566 | 0.039361 | 0.040514 | 0.6 | 29.44 -Other | | 0.01395 | | | 10.44 - -Nlocal: 20.25 ave 37 max 3 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.g++.1 b/examples/rigid/log.25Mar24.rigid.g++.1 deleted file mode 100644 index 6b27146c6b..0000000000 --- a/examples/rigid/log.25Mar24.rigid.g++.1 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.002 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589881 0 5269.4979 12.062708 - 9750 16738.013 0.13550093 0 5269.5101 11.407245 - 9800 16738.512 -0.01162033 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 - 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.136528 on 1 procs for 10000 steps with 81 atoms - -Performance: 632835.120 tau/day, 73244.806 timesteps/s, 5.933 Matom-step/s -98.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0091674 | 0.0091674 | 0.0091674 | 0.0 | 6.71 -Neigh | 0.046854 | 0.046854 | 0.046854 | 0.0 | 34.32 -Comm | 0.0076933 | 0.0076933 | 0.0076933 | 0.0 | 5.63 -Output | 0.001779 | 0.001779 | 0.001779 | 0.0 | 1.30 -Modify | 0.063842 | 0.063842 | 0.063842 | 0.0 | 46.76 -Other | | 0.007193 | | | 5.27 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.g++.4 b/examples/rigid/log.25Mar24.rigid.g++.4 deleted file mode 100644 index c2f691b7ec..0000000000 --- a/examples/rigid/log.25Mar24.rigid.g++.4 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589886 0 5269.4979 12.062708 - 9750 16738.013 0.13550089 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.134503 on 4 procs for 10000 steps with 81 atoms - -Performance: 642365.322 tau/day, 74347.838 timesteps/s, 6.022 Matom-step/s -96.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0016076 | 0.0023247 | 0.002836 | 0.9 | 1.73 -Neigh | 0.012491 | 0.013229 | 0.0145 | 0.7 | 9.84 -Comm | 0.062105 | 0.063666 | 0.06514 | 0.5 | 47.33 -Output | 0.0017602 | 0.0019318 | 0.0024227 | 0.6 | 1.44 -Modify | 0.038132 | 0.039518 | 0.040852 | 0.5 | 29.38 -Other | | 0.01383 | | | 10.29 - -Nlocal: 20.25 ave 37 max 3 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.gravity.g++.1 b/examples/rigid/log.25Mar24.rigid.gravity.g++.1 deleted file mode 100644 index 87b814dfab..0000000000 --- a/examples/rigid/log.25Mar24.rigid.gravity.g++.1 +++ /dev/null @@ -1,228 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -#Pour composite granular particles on flat wall - -newton on -atom_style sphere -atom_modify map array sort 0 0 - -thermo_modify flush yes -units si - -variable minrad equal 0.5 -variable maxrad equal 1.4 - -variable skin equal 0.3*${maxrad} -variable skin equal 0.3*1.4 - -boundary p p f -region reg block 0 20 0 20 0 200 units box -create_box 1 reg -Created orthogonal box = (0 0 0) to (20 20 200) - 1 by 1 by 1 MPI processor grid - -fix prop all property/atom mol ghost yes - -variable dumpfreq equal 1000 -variable logfreq equal 1000 - -pair_style gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0 -pair_coeff * * - -timestep 0.0001 - -group particles type 1 -0 atoms in group particles -atom_modify first particles - -neighbor ${skin} bin -neighbor 0.42 bin -group rigid type 1 -0 atoms in group rigid -neigh_modify every 1 delay 0 check yes exclude molecule/intra all - -thermo ${logfreq} -thermo 1000 -thermo_style custom step cpu atoms ke -WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904) -thermo_modify flush yes lost warn - -comm_modify vel yes cutoff 3 - -molecule mymol molecule.data -Read molecule template mymol: -LAMMPS data file created for rigid body molecule template - 1 molecules - 0 fragments - 5 atoms with max type 1 - 0 bonds with max type 0 - 0 angles with max type 0 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -region pourreg block 5 15 5 15 80 100 side in units box - -#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity -# and the 'gravity' keyword to fix rigid/small were not available. -# These settings produce undesirable behavior, where gravity can induce -# torque on rigid bodies. -#fix gravfix all gravity 9.8 vector 0 0 -1 #disable -#fix rigidfix all rigid/small molecule mol mymol #gravity gravfix - -#The correct behavior is recovered with the following settings: -fix gravfix all gravity 9.8 vector 0 0 -1 disable -fix rigidfix all rigid/small molecule mol mymol gravity gravfix - create bodies CPU = 0.000 seconds - 0 rigid bodies with 0 atoms - 1.2 = max distance from body owner to body atom - -fix pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix -Particle insertion: 15 every 20203 steps, 5 by step 1 - -fix zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL - -#dump 1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz - -run 100000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.62 - ghost atom cutoff = 3 - binsize = 0.81, bins = 25 25 247 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair gran/hooke/history, perpetual - attributes: half, newton on, size, history - pair build: half/size/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.893 | 6.893 | 6.893 Mbytes - Step CPU Atoms KinEng - 0 0 0 -0 - 1000 0.005385611 25 -0 - 2000 0.01106897 25 -0 - 3000 0.01569532 25 -0 - 4000 0.020782538 25 -0 - 5000 0.02656256 25 -0 - 6000 0.03132421 25 -0 - 7000 0.035996621 25 -0 - 8000 0.040816339 25 -0 - 9000 0.045911912 25 -0 - 10000 0.051486339 25 -0 - 11000 0.058049641 25 -0 - 12000 0.063206805 25 -0 - 13000 0.068374138 25 -0 - 14000 0.073423818 25 -0 - 15000 0.078890587 25 -0 - 16000 0.086372246 25 -0 - 17000 0.091912312 25 -0 - 18000 0.097317178 25 -0 - 19000 0.10284163 25 -0 - 20000 0.10836857 25 -0 - 21000 0.11476057 25 -0 - 22000 0.12201322 25 -0 - 23000 0.127963 25 -0 - 24000 0.13386968 25 -0 - 25000 0.1397396 25 -0 - 26000 0.14672759 25 -0 - 27000 0.15447534 25 -0 - 28000 0.16103509 25 -0 - 29000 0.16703686 25 -0 - 30000 0.17306375 25 -0 - 31000 0.18150464 25 -0 - 32000 0.1874536 25 -0 - 33000 0.19372953 25 -0 - 34000 0.19997087 25 -0 - 35000 0.20643521 25 -0 - 36000 0.21499446 25 -0 - 37000 0.22129475 25 -0 - 38000 0.2278159 25 -0 - 39000 0.23262556 25 -0 - 40000 0.23679 25 -0 - 41000 0.2428383 25 -0 - 42000 0.24757287 25 -0 - 43000 0.25190701 25 -0 - 44000 0.25617771 25 -0 - 45000 0.26057242 25 -0 - 46000 0.26469065 25 -0 - 47000 0.26921214 25 -0 - 48000 0.27502337 25 -0 - 49000 0.27911905 25 -0 - 50000 0.28338379 25 -0 - 51000 0.28736617 25 -0 - 52000 0.29127304 25 -0 - 53000 0.29504445 25 -0 - 54000 0.29898933 25 -0 - 55000 0.30479176 25 -0 - 56000 0.30893347 25 -0 - 57000 0.31277358 25 -0 - 58000 0.31658797 25 -0 - 59000 0.32024112 25 -0 - 60000 0.32373109 25 -0 - 61000 0.32753442 25 -0 - 62000 0.33123815 25 -0 - 63000 0.33643285 25 -0 - 64000 0.34036569 25 -0 - 65000 0.34399532 25 -0 - 66000 0.3475875 25 -0 - 67000 0.35124833 25 -0 - 68000 0.35503825 25 -0 - 69000 0.35870471 25 -0 - 70000 0.3624294 25 -0 - 71000 0.36714884 25 -0 - 72000 0.37082887 25 -0 - 73000 0.37459885 25 -0 - 74000 0.37835449 25 -0 - 75000 0.38245549 25 -0 - 76000 0.38681838 25 -0 - 77000 0.39069919 25 -0 - 78000 0.39460729 25 -0 - 79000 0.39908672 25 -0 - 80000 0.40266481 25 -0 - 81000 0.40645032 25 -0 - 82000 0.41005038 25 -0 - 83000 0.41355864 25 -0 - 84000 0.41741638 25 -0 - 85000 0.42182475 25 -0 - 86000 0.42614449 25 -0 - 87000 0.43024819 25 -0 - 88000 0.43389722 25 -0 - 89000 0.4372946 25 -0 - 90000 0.44097963 25 -0 - 91000 0.44451596 25 -0 - 92000 0.44800886 25 -0 - 93000 0.45171482 25 -0 - 94000 0.45568312 25 -0 - 95000 0.46068385 25 -0 - 96000 0.46423783 25 -0 - 97000 0.46783791 25 -0 - 98000 0.47132532 25 -0 - 99000 0.47462675 25 -0 - 100000 0.47811781 25 -0 -Loop time of 0.478128 on 1 procs for 100000 steps with 25 atoms - -99.3% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.016638 | 0.016638 | 0.016638 | 0.0 | 3.48 -Neigh | 0.12338 | 0.12338 | 0.12338 | 0.0 | 25.81 -Comm | 0.026212 | 0.026212 | 0.026212 | 0.0 | 5.48 -Output | 0.0015672 | 0.0015672 | 0.0015672 | 0.0 | 0.33 -Modify | 0.28303 | 0.28303 | 0.28303 | 0.0 | 59.20 -Other | | 0.0273 | | | 5.71 - -Nlocal: 25 ave 25 max 25 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1 ave 1 max 1 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 703 -Dangerous builds = 0 - -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.gravity.g++.4 b/examples/rigid/log.25Mar24.rigid.gravity.g++.4 deleted file mode 100644 index ddf76fb4d6..0000000000 --- a/examples/rigid/log.25Mar24.rigid.gravity.g++.4 +++ /dev/null @@ -1,228 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -#Pour composite granular particles on flat wall - -newton on -atom_style sphere -atom_modify map array sort 0 0 - -thermo_modify flush yes -units si - -variable minrad equal 0.5 -variable maxrad equal 1.4 - -variable skin equal 0.3*${maxrad} -variable skin equal 0.3*1.4 - -boundary p p f -region reg block 0 20 0 20 0 200 units box -create_box 1 reg -Created orthogonal box = (0 0 0) to (20 20 200) - 1 by 1 by 4 MPI processor grid - -fix prop all property/atom mol ghost yes - -variable dumpfreq equal 1000 -variable logfreq equal 1000 - -pair_style gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0 -pair_coeff * * - -timestep 0.0001 - -group particles type 1 -0 atoms in group particles -atom_modify first particles - -neighbor ${skin} bin -neighbor 0.42 bin -group rigid type 1 -0 atoms in group rigid -neigh_modify every 1 delay 0 check yes exclude molecule/intra all - -thermo ${logfreq} -thermo 1000 -thermo_style custom step cpu atoms ke -WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904) -thermo_modify flush yes lost warn - -comm_modify vel yes cutoff 3 - -molecule mymol molecule.data -Read molecule template mymol: -LAMMPS data file created for rigid body molecule template - 1 molecules - 0 fragments - 5 atoms with max type 1 - 0 bonds with max type 0 - 0 angles with max type 0 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -region pourreg block 5 15 5 15 80 100 side in units box - -#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity -# and the 'gravity' keyword to fix rigid/small were not available. -# These settings produce undesirable behavior, where gravity can induce -# torque on rigid bodies. -#fix gravfix all gravity 9.8 vector 0 0 -1 #disable -#fix rigidfix all rigid/small molecule mol mymol #gravity gravfix - -#The correct behavior is recovered with the following settings: -fix gravfix all gravity 9.8 vector 0 0 -1 disable -fix rigidfix all rigid/small molecule mol mymol gravity gravfix - create bodies CPU = 0.000 seconds - 0 rigid bodies with 0 atoms - 1.2 = max distance from body owner to body atom - -fix pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix -Particle insertion: 15 every 20203 steps, 5 by step 1 - -fix zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL - -#dump 1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz - -run 100000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.62 - ghost atom cutoff = 3 - binsize = 0.81, bins = 25 25 247 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair gran/hooke/history, perpetual - attributes: half, newton on, size, history - pair build: half/size/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.09 | 6.09 | 6.09 Mbytes - Step CPU Atoms KinEng - 0 0 0 -0 - 1000 0.007155423 25 -0 - 2000 0.013621411 25 -0 - 3000 0.018069993 25 -0 - 4000 0.022375597 25 -0 - 5000 0.027610001 25 -0 - 6000 0.032700728 25 -0 - 7000 0.036781214 25 -0 - 8000 0.041026343 25 -0 - 9000 0.045133974 25 -0 - 10000 0.049302504 25 -0 - 11000 0.053475155 25 -0 - 12000 0.058101552 25 -0 - 13000 0.063617332 25 -0 - 14000 0.070220865 25 -0 - 15000 0.079467476 25 -0 - 16000 0.085128592 25 -0 - 17000 0.088670803 25 -0 - 18000 0.093576466 25 -0 - 19000 0.096967506 25 -0 - 20000 0.10032704 25 -0 - 21000 0.1037381 25 -0 - 22000 0.10714647 25 -0 - 23000 0.11062389 25 -0 - 24000 0.11408744 25 -0 - 25000 0.12017243 25 -0 - 26000 0.12858759 25 -0 - 27000 0.13356253 25 -0 - 28000 0.13819667 25 -0 - 29000 0.14299332 25 -0 - 30000 0.14766723 25 -0 - 31000 0.15258071 25 -0 - 32000 0.15836989 25 -0 - 33000 0.16306841 25 -0 - 34000 0.16769723 25 -0 - 35000 0.172317 25 -0 - 36000 0.17698336 25 -0 - 37000 0.18173594 25 -0 - 38000 0.1879449 25 -0 - 39000 0.19236501 25 -0 - 40000 0.1964458 25 -0 - 41000 0.20045733 25 -0 - 42000 0.20454794 25 -0 - 43000 0.20872097 25 -0 - 44000 0.21291348 25 -0 - 45000 0.21780319 25 -0 - 46000 0.22260816 25 -0 - 47000 0.22686931 25 -0 - 48000 0.23117793 25 -0 - 49000 0.23535185 25 -0 - 50000 0.24054306 25 -0 - 51000 0.24463963 25 -0 - 52000 0.24938311 25 -0 - 53000 0.25348209 25 -0 - 54000 0.25745703 25 -0 - 55000 0.26145377 25 -0 - 56000 0.26534485 25 -0 - 57000 0.26928518 25 -0 - 58000 0.27321574 25 -0 - 59000 0.27791991 25 -0 - 60000 0.28284558 25 -0 - 61000 0.28673327 25 -0 - 62000 0.29055931 25 -0 - 63000 0.2945131 25 -0 - 64000 0.29846467 25 -0 - 65000 0.30238139 25 -0 - 66000 0.3062491 25 -0 - 67000 0.31026454 25 -0 - 68000 0.31498685 25 -0 - 69000 0.31887771 25 -0 - 70000 0.32278066 25 -0 - 71000 0.32658541 25 -0 - 72000 0.33047871 25 -0 - 73000 0.33441507 25 -0 - 74000 0.33830186 25 -0 - 75000 0.34298503 25 -0 - 76000 0.3470502 25 -0 - 77000 0.35093166 25 -0 - 78000 0.35472767 25 -0 - 79000 0.35858626 25 -0 - 80000 0.36236101 25 -0 - 81000 0.36621078 25 -0 - 82000 0.36998141 25 -0 - 83000 0.37417451 25 -0 - 84000 0.37850331 25 -0 - 85000 0.38230344 25 -0 - 86000 0.38621429 25 -0 - 87000 0.38998154 25 -0 - 88000 0.39378687 25 -0 - 89000 0.397529 25 -0 - 90000 0.40133202 25 -0 - 91000 0.40575097 25 -0 - 92000 0.41012392 25 -0 - 93000 0.41397633 25 -0 - 94000 0.41791732 25 -0 - 95000 0.42174915 25 -0 - 96000 0.42570384 25 -0 - 97000 0.4295687 25 -0 - 98000 0.43339555 25 -0 - 99000 0.43810319 25 -0 - 100000 0.44205356 25 -0 -Loop time of 0.442071 on 4 procs for 100000 steps with 25 atoms - -99.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0043596 | 0.0077919 | 0.015026 | 4.9 | 1.76 -Neigh | 0.03639 | 0.037869 | 0.038842 | 0.5 | 8.57 -Comm | 0.029189 | 0.034805 | 0.038937 | 2.3 | 7.87 -Output | 0.00094691 | 0.0012173 | 0.0019545 | 1.2 | 0.28 -Modify | 0.031085 | 0.10076 | 0.24754 | 27.5 | 22.79 -Other | | 0.2596 | | | 58.73 - -Nlocal: 6.25 ave 25 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 0.25 ave 1 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 703 -Dangerous builds = 0 - -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.infile.g++.1 b/examples/rigid/log.25Mar24.rigid.infile.g++.1 deleted file mode 100644 index a8d6f550aa..0000000000 --- a/examples/rigid/log.25Mar24.rigid.infile.g++.1 +++ /dev/null @@ -1,310 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat - 9 rigid bodies with 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Reading rigid body data for 4 bodies from file bodyinfo.dat -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722859e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.05932751 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663193 0 5269.4882 12.027009 - 3700 16738.602 -0.070934369 0 5269.4889 12.025288 - 3750 16737.731 0.20706559 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690669 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646805 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532807 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.0003765243 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156155 0 5269.5203 12.011611 - 9600 16738.549 -0.026814365 0 5269.5163 12.011415 - 9650 16738.765 -0.10191521 0 5269.5092 12.011013 - 9700 16735.041 1.0589871 0 5269.4979 12.062708 - 9750 16738.013 0.13550136 0 5269.5101 11.407245 - 9800 16738.512 -0.01162033 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270559 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984558 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.134486 on 1 procs for 10000 steps with 81 atoms - -Performance: 642445.705 tau/day, 74357.142 timesteps/s, 6.023 Matom-step/s -99.0% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0076798 | 0.0076798 | 0.0076798 | 0.0 | 5.71 -Neigh | 0.048776 | 0.048776 | 0.048776 | 0.0 | 36.27 -Comm | 0.0085249 | 0.0085249 | 0.0085249 | 0.0 | 6.34 -Output | 0.0021846 | 0.0021846 | 0.0021846 | 0.0 | 1.62 -Modify | 0.059372 | 0.059372 | 0.059372 | 0.0 | 44.15 -Other | | 0.007949 | | | 5.91 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.infile.g++.4 b/examples/rigid/log.25Mar24.rigid.infile.g++.4 deleted file mode 100644 index 0e4f37b698..0000000000 --- a/examples/rigid/log.25Mar24.rigid.infile.g++.4 +++ /dev/null @@ -1,310 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 infile bodyinfo.dat - 9 rigid bodies with 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Reading rigid body data for 4 bodies from file bodyinfo.dat -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722861e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706559 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690667 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532809 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652433 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 - 9600 16738.549 -0.026814367 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589878 0 5269.4979 12.062708 - 9750 16738.013 0.13550114 0 5269.5101 11.407245 - 9800 16738.512 -0.01162033 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270564 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984568 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.135118 on 4 procs for 10000 steps with 81 atoms - -Performance: 639441.862 tau/day, 74009.475 timesteps/s, 5.995 Matom-step/s -97.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0015919 | 0.0022753 | 0.0028384 | 0.9 | 1.68 -Neigh | 0.012494 | 0.013468 | 0.015484 | 1.0 | 9.97 -Comm | 0.061357 | 0.0636 | 0.06555 | 0.7 | 47.07 -Output | 0.0017441 | 0.0018894 | 0.0023095 | 0.6 | 1.40 -Modify | 0.037856 | 0.039816 | 0.041217 | 0.6 | 29.47 -Other | | 0.01407 | | | 10.41 - -Nlocal: 20.25 ave 37 max 3 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.molecule.g++.1 b/examples/rigid/log.25Mar24.rigid.molecule.g++.1 deleted file mode 100644 index 75d05c3d07..0000000000 --- a/examples/rigid/log.25Mar24.rigid.molecule.g++.1 +++ /dev/null @@ -1,319 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid molecule - 9 rigid bodies with 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.233 | 5.233 | 5.233 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589881 0 5269.4979 12.062708 - 9750 16738.013 0.13550093 0 5269.5101 11.407245 - 9800 16738.512 -0.01162033 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 - 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.130618 on 1 procs for 10000 steps with 81 atoms - -Performance: 661470.393 tau/day, 76559.073 timesteps/s, 6.201 Matom-step/s -99.2% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0069622 | 0.0069622 | 0.0069622 | 0.0 | 5.33 -Bond | 0.00033246 | 0.00033246 | 0.00033246 | 0.0 | 0.25 -Neigh | 0.053402 | 0.053402 | 0.053402 | 0.0 | 40.88 -Comm | 0.008192 | 0.008192 | 0.008192 | 0.0 | 6.27 -Output | 0.0015884 | 0.0015884 | 0.0015884 | 0.0 | 1.22 -Modify | 0.053219 | 0.053219 | 0.053219 | 0.0 | 40.74 -Other | | 0.006922 | | | 5.30 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.molecule.g++.4 b/examples/rigid/log.25Mar24.rigid.molecule.g++.4 deleted file mode 100644 index 6cbb88d471..0000000000 --- a/examples/rigid/log.25Mar24.rigid.molecule.g++.4 +++ /dev/null @@ -1,319 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid molecule - 9 rigid bodies with 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.08 | 5.112 | 5.206 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589886 0 5269.4979 12.062708 - 9750 16738.013 0.13550089 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.139893 on 4 procs for 10000 steps with 81 atoms - -Performance: 617616.025 tau/day, 71483.336 timesteps/s, 5.790 Matom-step/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0015795 | 0.0022375 | 0.0027109 | 0.9 | 1.60 -Bond | 0.00031772 | 0.00032314 | 0.00032894 | 0.0 | 0.23 -Neigh | 0.015169 | 0.016101 | 0.017803 | 0.8 | 11.51 -Comm | 0.063065 | 0.06514 | 0.06737 | 0.7 | 46.56 -Output | 0.001945 | 0.0020985 | 0.0025044 | 0.5 | 1.50 -Modify | 0.03865 | 0.039853 | 0.041246 | 0.6 | 28.49 -Other | | 0.01414 | | | 10.11 - -Nlocal: 20.25 ave 37 max 3 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.nve.early.g++.1 b/examples/rigid/log.25Mar24.rigid.nve.early.g++.1 deleted file mode 100644 index d9fbe7ee28..0000000000 --- a/examples/rigid/log.25Mar24.rigid.nve.early.g++.1 +++ /dev/null @@ -1,340 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 - 9 rigid bodies with 81 atoms - -fix_modify 1 bodyforces early - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.688 571.72044 0 5265.826 32.006558 - 100 16298.426 136.669 0 5267.6551 16.445373 - 150 16682.627 17.489692 0 5269.4277 14.900277 - 200 16733.935 1.3740602 0 5269.4647 14.569704 - 250 16738.854 -0.15258528 0 5269.4868 14.496759 - 300 16738.584 -0.055187603 0 5269.4992 14.496371 - 350 16738.492 -0.017449036 0 5269.5078 14.496801 - 400 16738.472 -0.006012316 0 5269.513 14.496991 - 450 16738.469 -0.0012715314 0 5269.5169 14.497085 - 500 16738.471 -0.00081065611 0 5269.5177 14.497095 - 550 16738.47 -0.00083201064 0 5269.5175 14.497091 - 600 16738.469 -0.00058353965 0 5269.5174 14.497091 - 650 16738.467 -0.0004722653 0 5269.5169 14.497088 - 700 16738.462 0 0 5269.5158 14.497085 - 750 16738.454 0 0 5269.5134 14.497066 - 800 16738.449 0 0 5269.5116 14.497052 - 850 16738.451 0 0 5269.5123 14.497057 - 900 16738.46 0 0 5269.5151 14.497079 - 950 16738.475 -0.0035324469 0 5269.5163 14.497056 - 1000 16738.603 -0.05113463 0 5269.509 14.496621 - 1050 16737.376 0.32970882 0 5269.5037 14.526144 - 1100 16737.909 0.16215423 0 5269.5038 14.53237 - 1150 16738.719 -0.089236594 0 5269.5074 14.510282 - 1200 16738.477 -0.0075446521 0 5269.513 14.51099 - 1250 16738.458 0 0 5269.5146 14.511061 - 1300 16738.448 0 0 5269.5114 14.511036 - 1350 16738.444 0 0 5269.5102 14.511026 - 1400 16738.449 -0.00044714105 0 5269.5113 14.511031 - 1450 16738.458 -0.0010956657 0 5269.5136 14.511043 - 1500 16738.464 -0.00057735083 0 5269.516 14.511066 - 1550 16738.467 0 0 5269.5173 14.511083 - 1600 16738.469 0 0 5269.5179 14.511087 - 1650 16738.47 0 0 5269.5183 14.511091 - 1700 16738.469 0 0 5269.5181 14.511089 - 1750 16738.464 0 0 5269.5164 14.511076 - 1800 16738.455 0 0 5269.5137 14.511055 - 1850 16738.45 0 0 5269.5121 14.511042 - 1900 16738.453 0 0 5269.513 14.511049 - 1950 16738.468 -0.0031854173 0 5269.5144 14.51102 - 2000 16738.501 -0.01331726 0 5269.5148 14.510906 - 2050 16738.568 -0.036719673 0 5269.5126 14.510668 - 2100 16738.646 -0.063312431 0 5269.5103 14.510597 - 2150 16738.619 -0.05606591 0 5269.5091 14.510608 - 2200 16738.566 -0.038448437 0 5269.5101 14.510779 - 2250 16738.52 -0.023712465 0 5269.5103 14.510906 - 2300 16738.485 -0.01323561 0 5269.5099 14.510971 - 2350 16738.457 -0.0045452995 0 5269.5097 14.511049 - 2400 16738.449 -0.00052013007 0 5269.5113 14.511107 - 2450 16738.461 -0.002321933 0 5269.5132 14.511099 - 2500 16738.474 -0.0051804641 0 5269.5145 14.511103 - 2550 16738.592 -0.04492566 0 5269.5117 14.510696 - 2600 16738.45 -0.0038193536 0 5269.5082 14.510939 - 2650 16733.621 1.5177478 0 5269.5097 14.586333 - 2700 16738.772 -0.1064304 0 5269.5069 14.500913 - 2750 16733.165 1.6598389 0 5269.5082 14.616957 - 2800 16738.577 -0.04523598 0 5269.5068 14.51458 - 2850 16738.475 -0.01269037 0 5269.5073 14.513396 - 2900 16738.449 -0.002688737 0 5269.5089 14.513555 - 2950 16738.465 -0.0082345477 0 5269.5084 14.513515 - 3000 16738.657 -0.071197475 0 5269.5061 14.513024 - 3050 16706.71 9.9435728 0 5269.4634 15.021496 - 3100 16643.257 29.968327 0 5269.5123 14.548247 - 3150 16739.45 -0.33134743 0 5269.4956 13.595814 - 3200 16731.445 2.1723572 0 5269.4792 12.100834 - 3250 16612.686 39.57457 0 5269.4942 13.879807 - 3300 16738.601 -0.059713795 0 5269.4997 12.666612 - 3350 16738.587 -0.044640809 0 5269.5106 12.663574 - 3400 16737.995 0.14468663 0 5269.5136 12.680161 - 3450 16738.607 -0.050706049 0 5269.5107 12.665118 - 3500 16738.819 -0.12122411 0 5269.5069 12.665394 - 3550 16738.498 -0.021940182 0 5269.5052 12.676141 - 3600 16673.205 20.482364 0 5269.4544 13.525704 - 3650 16738.648 -0.074052044 0 5269.5003 12.817014 - 3700 16738.632 -0.07184695 0 5269.4975 12.810978 - 3750 16738.621 -0.07013081 0 5269.4958 12.811663 - 3800 16738.552 -0.044378799 0 5269.4998 12.811871 - 3850 16738.492 -0.015384402 0 5269.5099 12.811397 - 3900 16738.487 -0.0058199162 0 5269.518 12.811514 - 3950 16738.482 -0.0012032457 0 5269.521 12.811589 - 4000 16738.478 -0.00020707654 0 5269.5208 12.811606 - 4050 16738.477 0 0 5269.5207 12.811608 - 4100 16738.477 0 0 5269.5206 12.811607 - 4150 16738.475 0 0 5269.5199 12.811602 - 4200 16738.464 0 0 5269.5165 12.811576 - 4250 16738.446 0 0 5269.5109 12.811532 - 4300 16738.44 0 0 5269.5089 12.811516 - 4350 16738.454 0 0 5269.5131 12.811549 - 4400 16738.468 0 0 5269.5177 12.811585 - 4450 16738.47 0 0 5269.5184 12.811591 - 4500 16738.466 0 0 5269.517 12.811579 - 4550 16738.463 0 0 5269.5162 12.811573 - 4600 16738.466 0 0 5269.517 12.81158 - 4650 16738.471 0 0 5269.5186 12.811592 - 4700 16738.47 0 0 5269.5182 12.811589 - 4750 16738.456 0 0 5269.5139 12.811556 - 4800 16738.441 0 0 5269.5091 12.811518 - 4850 16738.444 0 0 5269.5102 12.811526 - 4900 16738.462 0 0 5269.5159 12.81157 - 4950 16738.475 0 0 5269.5201 12.811603 - 5000 16738.479 0 0 5269.5212 12.811612 - 5050 16738.479 0 0 5269.5212 12.811612 - 5100 16738.479 0 0 5269.5212 12.811612 - 5150 16738.478 0 0 5269.5209 12.81161 - 5200 16738.472 0 0 5269.519 12.811595 - 5250 16738.456 0 0 5269.5138 12.811555 - 5300 16738.432 0 0 5269.5064 12.811497 - 5350 16738.422 0 0 5269.5033 12.811472 - 5400 16738.438 0 0 5269.5082 12.81151 - 5450 16738.46 0 0 5269.515 12.811564 - 5500 16738.471 -0.0002100851 0 5269.5183 12.811588 - 5550 16738.481 -0.003484166 0 5269.5185 12.811534 - 5600 16738.542 -0.024500002 0 5269.5164 12.81122 - 5650 16738.641 -0.058023282 0 5269.5142 12.812225 - 5700 16384.935 111.24508 0 5269.4653 26.09278 - 5750 16738.555 -0.030778873 0 5269.5142 13.052328 - 5800 16738.462 -0.0034050629 0 5269.5125 13.052653 - 5850 16738.441 -0.00034406845 0 5269.5089 13.052656 - 5900 16738.443 0 0 5269.5098 13.052667 - 5950 16738.459 0 0 5269.5149 13.052707 - 6000 16738.468 0 0 5269.5177 13.052729 - 6050 16738.466 0 0 5269.5172 13.052725 - 6100 16738.462 0 0 5269.516 13.052715 - 6150 16738.463 0 0 5269.5162 13.052717 - 6200 16738.468 0 0 5269.5178 13.052729 - 6250 16738.472 0 0 5269.5189 13.052738 - 6300 16738.465 0 0 5269.5169 13.052723 - 6350 16738.448 0 0 5269.5115 13.052681 - 6400 16738.439 0 0 5269.5086 13.052658 - 6450 16738.451 0 0 5269.5124 13.052687 - 6500 16738.469 0 0 5269.5181 13.052732 - 6550 16738.478 0 0 5269.5209 13.052754 - 6600 16738.48 0 0 5269.5214 13.052758 - 6650 16738.479 0 0 5269.5213 13.052757 - 6700 16738.48 -0.00057913194 0 5269.521 13.052744 - 6750 16738.483 -0.0025329373 0 5269.5198 13.0527 - 6800 16738.482 -0.0065110045 0 5269.5156 13.052612 - 6850 16738.465 -0.0072245165 0 5269.5095 13.052574 - 6900 16738.436 -0.0036561206 0 5269.5039 13.052609 - 6950 16738.433 -0.0010530752 0 5269.5056 13.052661 - 7000 16738.455 -0.00056878712 0 5269.5132 13.052723 - 7050 16738.475 -0.0011717775 0 5269.5187 13.052755 - 7100 16738.48 -0.00047531448 0 5269.5209 13.052781 - 7150 16738.479 0 0 5269.5211 13.052788 - 7200 16738.478 0 0 5269.5207 13.052785 - 7250 16738.477 0 0 5269.5207 13.052785 - 7300 16738.476 0 0 5269.5201 13.052781 - 7350 16738.466 0 0 5269.5172 13.052758 - 7400 16738.448 0 0 5269.5115 13.052714 - 7450 16738.438 0 0 5269.5083 13.052688 - 7500 16738.448 0 0 5269.5115 13.052713 - 7550 16738.464 -0.00053504438 0 5269.5158 13.052742 - 7600 16738.483 -0.010043243 0 5269.5123 13.052657 - 7650 16738.674 -0.077543712 0 5269.5051 13.052041 - 7700 16736.839 0.49724664 0 5269.502 13.085872 - 7750 16731.931 2.0427463 0 5269.5024 13.190769 - 7800 16738.762 -0.10404434 0 5269.5061 13.082626 - 7850 16738.525 -0.024994384 0 5269.5108 13.082681 - 7900 16738.479 -0.008372534 0 5269.5129 13.082885 - 7950 16738.449 -0.0038549468 0 5269.5079 13.082917 - 8000 16738.441 -0.0016367618 0 5269.5074 13.082937 - 8050 16738.455 -0.0014865651 0 5269.5123 13.082971 - 8100 16738.47 -0.00072796093 0 5269.5175 13.083021 - 8150 16738.476 0 0 5269.5202 13.08305 - 8200 16738.477 0 0 5269.5204 13.083051 - 8250 16738.476 0 0 5269.5201 13.083049 - 8300 16738.474 0 0 5269.5197 13.083046 - 8350 16738.47 0 0 5269.5185 13.083036 - 8400 16738.462 -0.0017116105 0 5269.5142 13.082984 - 8450 16738.447 -0.003289664 0 5269.5078 13.082915 - 8500 16738.429 -0.00098100125 0 5269.5043 13.082918 - 8550 16738.435 0 0 5269.5075 13.082953 - 8600 16738.458 0 0 5269.5146 13.083009 - 8650 16738.474 0 0 5269.5195 13.083048 - 8700 16738.478 0 0 5269.5208 13.083058 - 8750 16738.477 0 0 5269.5206 13.083056 - 8800 16738.476 0 0 5269.5203 13.083054 - 8850 16738.477 0 0 5269.5206 13.083056 - 8900 16738.476 0 0 5269.5203 13.083054 - 8950 16738.468 0 0 5269.5177 13.083034 - 9000 16738.451 0 0 5269.5122 13.082991 - 9050 16738.44 0 0 5269.5089 13.082965 - 9100 16738.448 0 0 5269.5113 13.082984 - 9150 16738.46 0 0 5269.5153 13.083014 - 9200 16738.464 0 0 5269.5163 13.083023 - 9250 16738.462 0 0 5269.5158 13.083019 - 9300 16738.462 0 0 5269.5159 13.08302 - 9350 16738.467 0 0 5269.5174 13.083031 - 9400 16738.472 -0.00023657901 0 5269.5188 13.083039 - 9450 16738.472 0 0 5269.519 13.083044 - 9500 16738.46 0 0 5269.5153 13.083016 - 9550 16738.443 0 0 5269.5099 13.082974 - 9600 16738.441 0 0 5269.5092 13.082967 - 9650 16738.458 -0.00038368065 0 5269.5142 13.083 - 9700 16738.475 -0.00099963025 0 5269.519 13.083029 - 9750 16738.492 -0.0049852397 0 5269.5203 13.082953 - 9800 16738.483 -0.0018715252 0 5269.5204 13.083034 - 9850 16738.477 0 0 5269.5205 13.083063 - 9900 16738.477 -0.0018402419 0 5269.5186 13.083025 - 9950 16738.482 -0.005648013 0 5269.5164 13.082936 - 10000 16738.467 -0.0045058746 0 5269.5129 13.082944 -Loop time of 0.13715 on 1 procs for 10000 steps with 81 atoms - -Performance: 629968.103 tau/day, 72912.975 timesteps/s, 5.906 Matom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0074777 | 0.0074777 | 0.0074777 | 0.0 | 5.45 -Neigh | 0.043608 | 0.043608 | 0.043608 | 0.0 | 31.80 -Comm | 0.0078838 | 0.0078838 | 0.0078838 | 0.0 | 5.75 -Output | 0.002002 | 0.002002 | 0.002002 | 0.0 | 1.46 -Modify | 0.06884 | 0.06884 | 0.06884 | 0.0 | 50.19 -Other | | 0.007339 | | | 5.35 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 63 ave 63 max 63 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 19 ave 19 max 19 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 19 -Ave neighs/atom = 0.2345679 -Neighbor list builds = 1481 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.nve.early.g++.4 b/examples/rigid/log.25Mar24.rigid.nve.early.g++.4 deleted file mode 100644 index 077e7976b9..0000000000 --- a/examples/rigid/log.25Mar24.rigid.nve.early.g++.4 +++ /dev/null @@ -1,340 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 - 9 rigid bodies with 81 atoms - -fix_modify 1 bodyforces early - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.688 571.72044 0 5265.826 32.006558 - 100 16298.426 136.669 0 5267.6551 16.445373 - 150 16682.627 17.489692 0 5269.4277 14.900277 - 200 16733.935 1.3740602 0 5269.4647 14.569704 - 250 16738.854 -0.15258528 0 5269.4868 14.496759 - 300 16738.584 -0.055187603 0 5269.4992 14.496371 - 350 16738.492 -0.017449036 0 5269.5078 14.496801 - 400 16738.472 -0.006012316 0 5269.513 14.496991 - 450 16738.469 -0.0012715314 0 5269.5169 14.497085 - 500 16738.471 -0.00081065611 0 5269.5177 14.497095 - 550 16738.47 -0.00083201064 0 5269.5175 14.497091 - 600 16738.469 -0.00058353965 0 5269.5174 14.497091 - 650 16738.467 -0.0004722653 0 5269.5169 14.497088 - 700 16738.462 0 0 5269.5158 14.497085 - 750 16738.454 0 0 5269.5134 14.497066 - 800 16738.449 0 0 5269.5116 14.497052 - 850 16738.451 0 0 5269.5123 14.497057 - 900 16738.46 0 0 5269.5151 14.497079 - 950 16738.475 -0.0035324469 0 5269.5163 14.497056 - 1000 16738.603 -0.05113463 0 5269.509 14.496621 - 1050 16737.376 0.32970882 0 5269.5037 14.526144 - 1100 16737.909 0.16215423 0 5269.5038 14.53237 - 1150 16738.719 -0.089236594 0 5269.5074 14.510282 - 1200 16738.477 -0.0075446521 0 5269.513 14.51099 - 1250 16738.458 0 0 5269.5146 14.511061 - 1300 16738.448 0 0 5269.5114 14.511036 - 1350 16738.444 0 0 5269.5102 14.511026 - 1400 16738.449 -0.00044714105 0 5269.5113 14.511031 - 1450 16738.458 -0.0010956657 0 5269.5136 14.511043 - 1500 16738.464 -0.00057735083 0 5269.516 14.511066 - 1550 16738.467 0 0 5269.5173 14.511083 - 1600 16738.469 0 0 5269.5179 14.511087 - 1650 16738.47 0 0 5269.5183 14.511091 - 1700 16738.469 0 0 5269.5181 14.511089 - 1750 16738.464 0 0 5269.5164 14.511076 - 1800 16738.455 0 0 5269.5137 14.511055 - 1850 16738.45 0 0 5269.5121 14.511042 - 1900 16738.453 0 0 5269.513 14.511049 - 1950 16738.468 -0.0031854173 0 5269.5144 14.51102 - 2000 16738.501 -0.01331726 0 5269.5148 14.510906 - 2050 16738.568 -0.036719673 0 5269.5126 14.510668 - 2100 16738.646 -0.063312431 0 5269.5103 14.510597 - 2150 16738.619 -0.05606591 0 5269.5091 14.510608 - 2200 16738.566 -0.038448437 0 5269.5101 14.510779 - 2250 16738.52 -0.023712465 0 5269.5103 14.510906 - 2300 16738.485 -0.01323561 0 5269.5099 14.510971 - 2350 16738.457 -0.0045452995 0 5269.5097 14.511049 - 2400 16738.449 -0.00052013007 0 5269.5113 14.511107 - 2450 16738.461 -0.002321933 0 5269.5132 14.511099 - 2500 16738.474 -0.0051804641 0 5269.5145 14.511103 - 2550 16738.592 -0.04492566 0 5269.5117 14.510696 - 2600 16738.45 -0.0038193536 0 5269.5082 14.510939 - 2650 16733.621 1.5177478 0 5269.5097 14.586333 - 2700 16738.772 -0.1064304 0 5269.5069 14.500913 - 2750 16733.165 1.6598389 0 5269.5082 14.616957 - 2800 16738.577 -0.04523598 0 5269.5068 14.51458 - 2850 16738.475 -0.01269037 0 5269.5073 14.513396 - 2900 16738.449 -0.002688737 0 5269.5089 14.513555 - 2950 16738.465 -0.0082345477 0 5269.5084 14.513515 - 3000 16738.657 -0.071197475 0 5269.5061 14.513024 - 3050 16706.71 9.9435728 0 5269.4634 15.021496 - 3100 16643.257 29.968327 0 5269.5123 14.548247 - 3150 16739.45 -0.33134743 0 5269.4956 13.595814 - 3200 16731.445 2.1723572 0 5269.4792 12.100834 - 3250 16612.686 39.57457 0 5269.4942 13.879807 - 3300 16738.601 -0.059713795 0 5269.4997 12.666612 - 3350 16738.587 -0.044640809 0 5269.5106 12.663574 - 3400 16737.995 0.14468663 0 5269.5136 12.680161 - 3450 16738.607 -0.050706049 0 5269.5107 12.665118 - 3500 16738.819 -0.12122411 0 5269.5069 12.665394 - 3550 16738.498 -0.021940181 0 5269.5052 12.676141 - 3600 16673.205 20.482364 0 5269.4544 13.525704 - 3650 16738.648 -0.074052045 0 5269.5003 12.817014 - 3700 16738.632 -0.07184695 0 5269.4975 12.810978 - 3750 16738.621 -0.07013081 0 5269.4958 12.811663 - 3800 16738.552 -0.044378799 0 5269.4998 12.811871 - 3850 16738.492 -0.015384402 0 5269.5099 12.811397 - 3900 16738.487 -0.0058199162 0 5269.518 12.811514 - 3950 16738.482 -0.0012032457 0 5269.521 12.811589 - 4000 16738.478 -0.00020707654 0 5269.5208 12.811606 - 4050 16738.477 0 0 5269.5207 12.811608 - 4100 16738.477 0 0 5269.5206 12.811607 - 4150 16738.475 0 0 5269.5199 12.811602 - 4200 16738.464 0 0 5269.5165 12.811576 - 4250 16738.446 0 0 5269.5109 12.811532 - 4300 16738.44 0 0 5269.5089 12.811516 - 4350 16738.454 0 0 5269.5131 12.811549 - 4400 16738.468 0 0 5269.5177 12.811585 - 4450 16738.47 0 0 5269.5184 12.811591 - 4500 16738.466 0 0 5269.517 12.811579 - 4550 16738.463 0 0 5269.5162 12.811573 - 4600 16738.466 0 0 5269.517 12.81158 - 4650 16738.471 0 0 5269.5186 12.811592 - 4700 16738.47 0 0 5269.5182 12.811589 - 4750 16738.456 0 0 5269.5139 12.811556 - 4800 16738.441 0 0 5269.5091 12.811518 - 4850 16738.444 0 0 5269.5102 12.811526 - 4900 16738.462 0 0 5269.5159 12.81157 - 4950 16738.475 0 0 5269.5201 12.811603 - 5000 16738.479 0 0 5269.5212 12.811612 - 5050 16738.479 0 0 5269.5212 12.811612 - 5100 16738.479 0 0 5269.5212 12.811612 - 5150 16738.478 0 0 5269.5209 12.81161 - 5200 16738.472 0 0 5269.519 12.811595 - 5250 16738.456 0 0 5269.5138 12.811555 - 5300 16738.432 0 0 5269.5064 12.811497 - 5350 16738.422 0 0 5269.5033 12.811472 - 5400 16738.438 0 0 5269.5082 12.81151 - 5450 16738.46 0 0 5269.515 12.811564 - 5500 16738.471 -0.0002100851 0 5269.5183 12.811588 - 5550 16738.481 -0.003484166 0 5269.5185 12.811534 - 5600 16738.542 -0.024500002 0 5269.5164 12.81122 - 5650 16738.641 -0.058023282 0 5269.5142 12.812225 - 5700 16384.935 111.24508 0 5269.4653 26.09278 - 5750 16738.555 -0.030778873 0 5269.5142 13.052328 - 5800 16738.462 -0.0034050628 0 5269.5125 13.052653 - 5850 16738.441 -0.00034406845 0 5269.5089 13.052656 - 5900 16738.443 0 0 5269.5098 13.052667 - 5950 16738.459 0 0 5269.5149 13.052707 - 6000 16738.468 0 0 5269.5177 13.052729 - 6050 16738.466 0 0 5269.5172 13.052725 - 6100 16738.462 0 0 5269.516 13.052715 - 6150 16738.463 0 0 5269.5162 13.052717 - 6200 16738.468 0 0 5269.5178 13.052729 - 6250 16738.472 0 0 5269.5189 13.052738 - 6300 16738.465 0 0 5269.5169 13.052723 - 6350 16738.448 0 0 5269.5115 13.052681 - 6400 16738.439 0 0 5269.5086 13.052658 - 6450 16738.451 0 0 5269.5124 13.052687 - 6500 16738.469 0 0 5269.5181 13.052732 - 6550 16738.478 0 0 5269.5209 13.052754 - 6600 16738.48 0 0 5269.5214 13.052758 - 6650 16738.479 0 0 5269.5213 13.052757 - 6700 16738.48 -0.00057913195 0 5269.521 13.052744 - 6750 16738.483 -0.0025329373 0 5269.5198 13.0527 - 6800 16738.482 -0.0065110047 0 5269.5156 13.052612 - 6850 16738.465 -0.0072245166 0 5269.5095 13.052574 - 6900 16738.436 -0.0036561206 0 5269.5039 13.052609 - 6950 16738.433 -0.0010530752 0 5269.5056 13.052661 - 7000 16738.455 -0.00056878712 0 5269.5132 13.052723 - 7050 16738.475 -0.0011717775 0 5269.5187 13.052755 - 7100 16738.48 -0.00047531448 0 5269.5209 13.052781 - 7150 16738.479 0 0 5269.5211 13.052788 - 7200 16738.478 0 0 5269.5207 13.052785 - 7250 16738.477 0 0 5269.5207 13.052785 - 7300 16738.476 0 0 5269.5201 13.052781 - 7350 16738.466 0 0 5269.5172 13.052758 - 7400 16738.448 0 0 5269.5115 13.052714 - 7450 16738.438 0 0 5269.5083 13.052688 - 7500 16738.448 0 0 5269.5115 13.052713 - 7550 16738.464 -0.00053504439 0 5269.5158 13.052742 - 7600 16738.483 -0.010043243 0 5269.5123 13.052657 - 7650 16738.674 -0.077543714 0 5269.5051 13.052041 - 7700 16736.839 0.49724671 0 5269.502 13.085872 - 7750 16731.931 2.0427465 0 5269.5024 13.190769 - 7800 16738.762 -0.10404434 0 5269.5061 13.082626 - 7850 16738.525 -0.024994385 0 5269.5108 13.082681 - 7900 16738.479 -0.008372534 0 5269.5129 13.082885 - 7950 16738.449 -0.0038549468 0 5269.5079 13.082917 - 8000 16738.441 -0.0016367617 0 5269.5074 13.082937 - 8050 16738.455 -0.0014865651 0 5269.5123 13.082971 - 8100 16738.47 -0.00072796092 0 5269.5175 13.083021 - 8150 16738.476 0 0 5269.5202 13.08305 - 8200 16738.477 0 0 5269.5204 13.083051 - 8250 16738.476 0 0 5269.5201 13.083049 - 8300 16738.474 0 0 5269.5197 13.083046 - 8350 16738.47 0 0 5269.5185 13.083036 - 8400 16738.462 -0.0017116105 0 5269.5142 13.082984 - 8450 16738.447 -0.003289664 0 5269.5078 13.082915 - 8500 16738.429 -0.00098100125 0 5269.5043 13.082918 - 8550 16738.435 0 0 5269.5075 13.082953 - 8600 16738.458 0 0 5269.5146 13.083009 - 8650 16738.474 0 0 5269.5195 13.083048 - 8700 16738.478 0 0 5269.5208 13.083058 - 8750 16738.477 0 0 5269.5206 13.083056 - 8800 16738.476 0 0 5269.5203 13.083054 - 8850 16738.477 0 0 5269.5206 13.083056 - 8900 16738.476 0 0 5269.5203 13.083054 - 8950 16738.468 0 0 5269.5177 13.083034 - 9000 16738.451 0 0 5269.5122 13.082991 - 9050 16738.44 0 0 5269.5089 13.082965 - 9100 16738.448 0 0 5269.5113 13.082984 - 9150 16738.46 0 0 5269.5153 13.083014 - 9200 16738.464 0 0 5269.5163 13.083023 - 9250 16738.462 0 0 5269.5158 13.083019 - 9300 16738.462 0 0 5269.5159 13.08302 - 9350 16738.467 0 0 5269.5174 13.083031 - 9400 16738.472 -0.00023657902 0 5269.5188 13.083039 - 9450 16738.472 0 0 5269.519 13.083044 - 9500 16738.46 0 0 5269.5153 13.083016 - 9550 16738.443 0 0 5269.5099 13.082974 - 9600 16738.441 0 0 5269.5092 13.082967 - 9650 16738.458 -0.00038368067 0 5269.5142 13.083 - 9700 16738.475 -0.00099963027 0 5269.519 13.083029 - 9750 16738.492 -0.00498524 0 5269.5203 13.082953 - 9800 16738.483 -0.0018715253 0 5269.5204 13.083034 - 9850 16738.477 0 0 5269.5205 13.083063 - 9900 16738.477 -0.0018402419 0 5269.5186 13.083025 - 9950 16738.482 -0.0056480132 0 5269.5164 13.082936 - 10000 16738.467 -0.0045058747 0 5269.5129 13.082944 -Loop time of 0.14818 on 4 procs for 10000 steps with 81 atoms - -Performance: 583075.499 tau/day, 67485.590 timesteps/s, 5.466 Matom-step/s -99.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0018099 | 0.0023754 | 0.0030445 | 1.0 | 1.60 -Neigh | 0.011989 | 0.012986 | 0.01555 | 1.3 | 8.76 -Comm | 0.062426 | 0.065066 | 0.066364 | 0.6 | 43.91 -Output | 0.0017674 | 0.0019257 | 0.002368 | 0.6 | 1.30 -Modify | 0.050371 | 0.051161 | 0.052809 | 0.4 | 34.53 -Other | | 0.01467 | | | 9.90 - -Nlocal: 20.25 ave 35 max 0 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Nghost: 41 ave 52 max 30 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 4.75 ave 19 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 19 -Ave neighs/atom = 0.2345679 -Neighbor list builds = 1481 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.nve.g++.1 b/examples/rigid/log.25Mar24.rigid.nve.g++.1 deleted file mode 100644 index 45bfc9f8d4..0000000000 --- a/examples/rigid/log.25Mar24.rigid.nve.g++.1 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.688 571.72044 0 5265.826 32.006558 - 100 16298.426 136.669 0 5267.6551 16.445373 - 150 16682.627 17.489692 0 5269.4277 14.900277 - 200 16733.935 1.3740602 0 5269.4647 14.569704 - 250 16738.854 -0.15258528 0 5269.4868 14.496759 - 300 16738.584 -0.055187603 0 5269.4992 14.496371 - 350 16738.492 -0.017449036 0 5269.5078 14.496801 - 400 16738.472 -0.006012316 0 5269.513 14.496991 - 450 16738.469 -0.0012715314 0 5269.5169 14.497085 - 500 16738.471 -0.00081065611 0 5269.5177 14.497095 - 550 16738.47 -0.00083201064 0 5269.5175 14.497091 - 600 16738.469 -0.00058353965 0 5269.5174 14.497091 - 650 16738.467 -0.0004722653 0 5269.5169 14.497088 - 700 16738.462 0 0 5269.5158 14.497085 - 750 16738.454 0 0 5269.5134 14.497066 - 800 16738.449 0 0 5269.5116 14.497052 - 850 16738.451 0 0 5269.5123 14.497057 - 900 16738.46 0 0 5269.5151 14.497079 - 950 16738.475 -0.0035324469 0 5269.5163 14.497056 - 1000 16738.603 -0.05113463 0 5269.509 14.496621 - 1050 16737.376 0.32970882 0 5269.5037 14.526144 - 1100 16737.909 0.16215423 0 5269.5038 14.53237 - 1150 16738.719 -0.089236594 0 5269.5074 14.510282 - 1200 16738.477 -0.0075446521 0 5269.513 14.51099 - 1250 16738.458 0 0 5269.5146 14.511061 - 1300 16738.448 0 0 5269.5114 14.511036 - 1350 16738.444 0 0 5269.5102 14.511026 - 1400 16738.449 -0.00044714105 0 5269.5113 14.511031 - 1450 16738.458 -0.0010956657 0 5269.5136 14.511043 - 1500 16738.464 -0.00057735083 0 5269.516 14.511066 - 1550 16738.467 0 0 5269.5173 14.511083 - 1600 16738.469 0 0 5269.5179 14.511087 - 1650 16738.47 0 0 5269.5183 14.511091 - 1700 16738.469 0 0 5269.5181 14.511089 - 1750 16738.464 0 0 5269.5164 14.511076 - 1800 16738.455 0 0 5269.5137 14.511055 - 1850 16738.45 0 0 5269.5121 14.511042 - 1900 16738.453 0 0 5269.513 14.511049 - 1950 16738.468 -0.0031854173 0 5269.5144 14.51102 - 2000 16738.501 -0.01331726 0 5269.5148 14.510906 - 2050 16738.568 -0.036719673 0 5269.5126 14.510668 - 2100 16738.646 -0.063312431 0 5269.5103 14.510597 - 2150 16738.619 -0.05606591 0 5269.5091 14.510608 - 2200 16738.566 -0.038448437 0 5269.5101 14.510779 - 2250 16738.52 -0.023712465 0 5269.5103 14.510906 - 2300 16738.485 -0.01323561 0 5269.5099 14.510971 - 2350 16738.457 -0.0045452995 0 5269.5097 14.511049 - 2400 16738.449 -0.00052013007 0 5269.5113 14.511107 - 2450 16738.461 -0.002321933 0 5269.5132 14.511099 - 2500 16738.474 -0.0051804641 0 5269.5145 14.511103 - 2550 16738.592 -0.04492566 0 5269.5117 14.510696 - 2600 16738.45 -0.0038193536 0 5269.5082 14.510939 - 2650 16733.621 1.5177478 0 5269.5097 14.586333 - 2700 16738.772 -0.1064304 0 5269.5069 14.500913 - 2750 16733.165 1.6598389 0 5269.5082 14.616957 - 2800 16738.577 -0.04523598 0 5269.5068 14.51458 - 2850 16738.475 -0.01269037 0 5269.5073 14.513396 - 2900 16738.449 -0.002688737 0 5269.5089 14.513555 - 2950 16738.465 -0.0082345477 0 5269.5084 14.513515 - 3000 16738.657 -0.071197475 0 5269.5061 14.513024 - 3050 16706.71 9.9435728 0 5269.4634 15.021496 - 3100 16643.257 29.968327 0 5269.5123 14.548247 - 3150 16739.45 -0.33134743 0 5269.4956 13.595814 - 3200 16731.445 2.1723572 0 5269.4792 12.100834 - 3250 16612.686 39.57457 0 5269.4942 13.879807 - 3300 16738.601 -0.059713795 0 5269.4997 12.666612 - 3350 16738.587 -0.044640809 0 5269.5106 12.663574 - 3400 16737.995 0.14468663 0 5269.5136 12.680161 - 3450 16738.607 -0.050706049 0 5269.5107 12.665118 - 3500 16738.819 -0.12122411 0 5269.5069 12.665394 - 3550 16738.498 -0.021940182 0 5269.5052 12.676141 - 3600 16673.205 20.482364 0 5269.4544 13.525704 - 3650 16738.648 -0.074052044 0 5269.5003 12.817014 - 3700 16738.632 -0.07184695 0 5269.4975 12.810978 - 3750 16738.621 -0.07013081 0 5269.4958 12.811663 - 3800 16738.552 -0.044378799 0 5269.4998 12.811871 - 3850 16738.492 -0.015384402 0 5269.5099 12.811397 - 3900 16738.487 -0.0058199162 0 5269.518 12.811514 - 3950 16738.482 -0.0012032457 0 5269.521 12.811589 - 4000 16738.478 -0.00020707654 0 5269.5208 12.811606 - 4050 16738.477 0 0 5269.5207 12.811608 - 4100 16738.477 0 0 5269.5206 12.811607 - 4150 16738.475 0 0 5269.5199 12.811602 - 4200 16738.464 0 0 5269.5165 12.811576 - 4250 16738.446 0 0 5269.5109 12.811532 - 4300 16738.44 0 0 5269.5089 12.811516 - 4350 16738.454 0 0 5269.5131 12.811549 - 4400 16738.468 0 0 5269.5177 12.811585 - 4450 16738.47 0 0 5269.5184 12.811591 - 4500 16738.466 0 0 5269.517 12.811579 - 4550 16738.463 0 0 5269.5162 12.811573 - 4600 16738.466 0 0 5269.517 12.81158 - 4650 16738.471 0 0 5269.5186 12.811592 - 4700 16738.47 0 0 5269.5182 12.811589 - 4750 16738.456 0 0 5269.5139 12.811556 - 4800 16738.441 0 0 5269.5091 12.811518 - 4850 16738.444 0 0 5269.5102 12.811526 - 4900 16738.462 0 0 5269.5159 12.81157 - 4950 16738.475 0 0 5269.5201 12.811603 - 5000 16738.479 0 0 5269.5212 12.811612 - 5050 16738.479 0 0 5269.5212 12.811612 - 5100 16738.479 0 0 5269.5212 12.811612 - 5150 16738.478 0 0 5269.5209 12.81161 - 5200 16738.472 0 0 5269.519 12.811595 - 5250 16738.456 0 0 5269.5138 12.811555 - 5300 16738.432 0 0 5269.5064 12.811497 - 5350 16738.422 0 0 5269.5033 12.811472 - 5400 16738.438 0 0 5269.5082 12.81151 - 5450 16738.46 0 0 5269.515 12.811564 - 5500 16738.471 -0.0002100851 0 5269.5183 12.811588 - 5550 16738.481 -0.003484166 0 5269.5185 12.811534 - 5600 16738.542 -0.024500002 0 5269.5164 12.81122 - 5650 16738.641 -0.058023282 0 5269.5142 12.812225 - 5700 16384.935 111.24508 0 5269.4653 26.09278 - 5750 16738.555 -0.030778873 0 5269.5142 13.052328 - 5800 16738.462 -0.0034050629 0 5269.5125 13.052653 - 5850 16738.441 -0.00034406845 0 5269.5089 13.052656 - 5900 16738.443 0 0 5269.5098 13.052667 - 5950 16738.459 0 0 5269.5149 13.052707 - 6000 16738.468 0 0 5269.5177 13.052729 - 6050 16738.466 0 0 5269.5172 13.052725 - 6100 16738.462 0 0 5269.516 13.052715 - 6150 16738.463 0 0 5269.5162 13.052717 - 6200 16738.468 0 0 5269.5178 13.052729 - 6250 16738.472 0 0 5269.5189 13.052738 - 6300 16738.465 0 0 5269.5169 13.052723 - 6350 16738.448 0 0 5269.5115 13.052681 - 6400 16738.439 0 0 5269.5086 13.052658 - 6450 16738.451 0 0 5269.5124 13.052687 - 6500 16738.469 0 0 5269.5181 13.052732 - 6550 16738.478 0 0 5269.5209 13.052754 - 6600 16738.48 0 0 5269.5214 13.052758 - 6650 16738.479 0 0 5269.5213 13.052757 - 6700 16738.48 -0.00057913194 0 5269.521 13.052744 - 6750 16738.483 -0.0025329373 0 5269.5198 13.0527 - 6800 16738.482 -0.0065110045 0 5269.5156 13.052612 - 6850 16738.465 -0.0072245165 0 5269.5095 13.052574 - 6900 16738.436 -0.0036561206 0 5269.5039 13.052609 - 6950 16738.433 -0.0010530752 0 5269.5056 13.052661 - 7000 16738.455 -0.00056878712 0 5269.5132 13.052723 - 7050 16738.475 -0.0011717775 0 5269.5187 13.052755 - 7100 16738.48 -0.00047531448 0 5269.5209 13.052781 - 7150 16738.479 0 0 5269.5211 13.052788 - 7200 16738.478 0 0 5269.5207 13.052785 - 7250 16738.477 0 0 5269.5207 13.052785 - 7300 16738.476 0 0 5269.5201 13.052781 - 7350 16738.466 0 0 5269.5172 13.052758 - 7400 16738.448 0 0 5269.5115 13.052714 - 7450 16738.438 0 0 5269.5083 13.052688 - 7500 16738.448 0 0 5269.5115 13.052713 - 7550 16738.464 -0.00053504438 0 5269.5158 13.052742 - 7600 16738.483 -0.010043243 0 5269.5123 13.052657 - 7650 16738.674 -0.077543712 0 5269.5051 13.052041 - 7700 16736.839 0.49724664 0 5269.502 13.085872 - 7750 16731.931 2.0427463 0 5269.5024 13.190769 - 7800 16738.762 -0.10404434 0 5269.5061 13.082626 - 7850 16738.525 -0.024994384 0 5269.5108 13.082681 - 7900 16738.479 -0.008372534 0 5269.5129 13.082885 - 7950 16738.449 -0.0038549468 0 5269.5079 13.082917 - 8000 16738.441 -0.0016367618 0 5269.5074 13.082937 - 8050 16738.455 -0.0014865651 0 5269.5123 13.082971 - 8100 16738.47 -0.00072796093 0 5269.5175 13.083021 - 8150 16738.476 0 0 5269.5202 13.08305 - 8200 16738.477 0 0 5269.5204 13.083051 - 8250 16738.476 0 0 5269.5201 13.083049 - 8300 16738.474 0 0 5269.5197 13.083046 - 8350 16738.47 0 0 5269.5185 13.083036 - 8400 16738.462 -0.0017116105 0 5269.5142 13.082984 - 8450 16738.447 -0.003289664 0 5269.5078 13.082915 - 8500 16738.429 -0.00098100125 0 5269.5043 13.082918 - 8550 16738.435 0 0 5269.5075 13.082953 - 8600 16738.458 0 0 5269.5146 13.083009 - 8650 16738.474 0 0 5269.5195 13.083048 - 8700 16738.478 0 0 5269.5208 13.083058 - 8750 16738.477 0 0 5269.5206 13.083056 - 8800 16738.476 0 0 5269.5203 13.083054 - 8850 16738.477 0 0 5269.5206 13.083056 - 8900 16738.476 0 0 5269.5203 13.083054 - 8950 16738.468 0 0 5269.5177 13.083034 - 9000 16738.451 0 0 5269.5122 13.082991 - 9050 16738.44 0 0 5269.5089 13.082965 - 9100 16738.448 0 0 5269.5113 13.082984 - 9150 16738.46 0 0 5269.5153 13.083014 - 9200 16738.464 0 0 5269.5163 13.083023 - 9250 16738.462 0 0 5269.5158 13.083019 - 9300 16738.462 0 0 5269.5159 13.08302 - 9350 16738.467 0 0 5269.5174 13.083031 - 9400 16738.472 -0.00023657901 0 5269.5188 13.083039 - 9450 16738.472 0 0 5269.519 13.083044 - 9500 16738.46 0 0 5269.5153 13.083016 - 9550 16738.443 0 0 5269.5099 13.082974 - 9600 16738.441 0 0 5269.5092 13.082967 - 9650 16738.458 -0.00038368065 0 5269.5142 13.083 - 9700 16738.475 -0.00099963025 0 5269.519 13.083029 - 9750 16738.492 -0.0049852397 0 5269.5203 13.082953 - 9800 16738.483 -0.0018715252 0 5269.5204 13.083034 - 9850 16738.477 0 0 5269.5205 13.083063 - 9900 16738.477 -0.0018402419 0 5269.5186 13.083025 - 9950 16738.482 -0.005648013 0 5269.5164 13.082936 - 10000 16738.467 -0.0045058746 0 5269.5129 13.082944 -Loop time of 0.139287 on 1 procs for 10000 steps with 81 atoms - -Performance: 620300.751 tau/day, 71794.068 timesteps/s, 5.815 Matom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0074128 | 0.0074128 | 0.0074128 | 0.0 | 5.32 -Neigh | 0.045566 | 0.045566 | 0.045566 | 0.0 | 32.71 -Comm | 0.007912 | 0.007912 | 0.007912 | 0.0 | 5.68 -Output | 0.0015912 | 0.0015912 | 0.0015912 | 0.0 | 1.14 -Modify | 0.06951 | 0.06951 | 0.06951 | 0.0 | 49.90 -Other | | 0.007295 | | | 5.24 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 63 ave 63 max 63 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 19 ave 19 max 19 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 19 -Ave neighs/atom = 0.2345679 -Neighbor list builds = 1481 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.nve.g++.4 b/examples/rigid/log.25Mar24.rigid.nve.g++.4 deleted file mode 100644 index af3c1c6489..0000000000 --- a/examples/rigid/log.25Mar24.rigid.nve.g++.4 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.201 | 4.233 | 4.327 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.688 571.72044 0 5265.826 32.006558 - 100 16298.426 136.669 0 5267.6551 16.445373 - 150 16682.627 17.489692 0 5269.4277 14.900277 - 200 16733.935 1.3740602 0 5269.4647 14.569704 - 250 16738.854 -0.15258528 0 5269.4868 14.496759 - 300 16738.584 -0.055187603 0 5269.4992 14.496371 - 350 16738.492 -0.017449036 0 5269.5078 14.496801 - 400 16738.472 -0.006012316 0 5269.513 14.496991 - 450 16738.469 -0.0012715314 0 5269.5169 14.497085 - 500 16738.471 -0.00081065611 0 5269.5177 14.497095 - 550 16738.47 -0.00083201064 0 5269.5175 14.497091 - 600 16738.469 -0.00058353965 0 5269.5174 14.497091 - 650 16738.467 -0.0004722653 0 5269.5169 14.497088 - 700 16738.462 0 0 5269.5158 14.497085 - 750 16738.454 0 0 5269.5134 14.497066 - 800 16738.449 0 0 5269.5116 14.497052 - 850 16738.451 0 0 5269.5123 14.497057 - 900 16738.46 0 0 5269.5151 14.497079 - 950 16738.475 -0.0035324469 0 5269.5163 14.497056 - 1000 16738.603 -0.05113463 0 5269.509 14.496621 - 1050 16737.376 0.32970882 0 5269.5037 14.526144 - 1100 16737.909 0.16215423 0 5269.5038 14.53237 - 1150 16738.719 -0.089236594 0 5269.5074 14.510282 - 1200 16738.477 -0.0075446521 0 5269.513 14.51099 - 1250 16738.458 0 0 5269.5146 14.511061 - 1300 16738.448 0 0 5269.5114 14.511036 - 1350 16738.444 0 0 5269.5102 14.511026 - 1400 16738.449 -0.00044714105 0 5269.5113 14.511031 - 1450 16738.458 -0.0010956657 0 5269.5136 14.511043 - 1500 16738.464 -0.00057735083 0 5269.516 14.511066 - 1550 16738.467 0 0 5269.5173 14.511083 - 1600 16738.469 0 0 5269.5179 14.511087 - 1650 16738.47 0 0 5269.5183 14.511091 - 1700 16738.469 0 0 5269.5181 14.511089 - 1750 16738.464 0 0 5269.5164 14.511076 - 1800 16738.455 0 0 5269.5137 14.511055 - 1850 16738.45 0 0 5269.5121 14.511042 - 1900 16738.453 0 0 5269.513 14.511049 - 1950 16738.468 -0.0031854173 0 5269.5144 14.51102 - 2000 16738.501 -0.01331726 0 5269.5148 14.510906 - 2050 16738.568 -0.036719673 0 5269.5126 14.510668 - 2100 16738.646 -0.063312431 0 5269.5103 14.510597 - 2150 16738.619 -0.05606591 0 5269.5091 14.510608 - 2200 16738.566 -0.038448437 0 5269.5101 14.510779 - 2250 16738.52 -0.023712465 0 5269.5103 14.510906 - 2300 16738.485 -0.01323561 0 5269.5099 14.510971 - 2350 16738.457 -0.0045452995 0 5269.5097 14.511049 - 2400 16738.449 -0.00052013007 0 5269.5113 14.511107 - 2450 16738.461 -0.002321933 0 5269.5132 14.511099 - 2500 16738.474 -0.0051804641 0 5269.5145 14.511103 - 2550 16738.592 -0.04492566 0 5269.5117 14.510696 - 2600 16738.45 -0.0038193536 0 5269.5082 14.510939 - 2650 16733.621 1.5177478 0 5269.5097 14.586333 - 2700 16738.772 -0.1064304 0 5269.5069 14.500913 - 2750 16733.165 1.6598389 0 5269.5082 14.616957 - 2800 16738.577 -0.04523598 0 5269.5068 14.51458 - 2850 16738.475 -0.01269037 0 5269.5073 14.513396 - 2900 16738.449 -0.002688737 0 5269.5089 14.513555 - 2950 16738.465 -0.0082345477 0 5269.5084 14.513515 - 3000 16738.657 -0.071197475 0 5269.5061 14.513024 - 3050 16706.71 9.9435728 0 5269.4634 15.021496 - 3100 16643.257 29.968327 0 5269.5123 14.548247 - 3150 16739.45 -0.33134743 0 5269.4956 13.595814 - 3200 16731.445 2.1723572 0 5269.4792 12.100834 - 3250 16612.686 39.57457 0 5269.4942 13.879807 - 3300 16738.601 -0.059713795 0 5269.4997 12.666612 - 3350 16738.587 -0.044640809 0 5269.5106 12.663574 - 3400 16737.995 0.14468663 0 5269.5136 12.680161 - 3450 16738.607 -0.050706049 0 5269.5107 12.665118 - 3500 16738.819 -0.12122411 0 5269.5069 12.665394 - 3550 16738.498 -0.021940181 0 5269.5052 12.676141 - 3600 16673.205 20.482364 0 5269.4544 13.525704 - 3650 16738.648 -0.074052045 0 5269.5003 12.817014 - 3700 16738.632 -0.07184695 0 5269.4975 12.810978 - 3750 16738.621 -0.07013081 0 5269.4958 12.811663 - 3800 16738.552 -0.044378799 0 5269.4998 12.811871 - 3850 16738.492 -0.015384402 0 5269.5099 12.811397 - 3900 16738.487 -0.0058199162 0 5269.518 12.811514 - 3950 16738.482 -0.0012032457 0 5269.521 12.811589 - 4000 16738.478 -0.00020707654 0 5269.5208 12.811606 - 4050 16738.477 0 0 5269.5207 12.811608 - 4100 16738.477 0 0 5269.5206 12.811607 - 4150 16738.475 0 0 5269.5199 12.811602 - 4200 16738.464 0 0 5269.5165 12.811576 - 4250 16738.446 0 0 5269.5109 12.811532 - 4300 16738.44 0 0 5269.5089 12.811516 - 4350 16738.454 0 0 5269.5131 12.811549 - 4400 16738.468 0 0 5269.5177 12.811585 - 4450 16738.47 0 0 5269.5184 12.811591 - 4500 16738.466 0 0 5269.517 12.811579 - 4550 16738.463 0 0 5269.5162 12.811573 - 4600 16738.466 0 0 5269.517 12.81158 - 4650 16738.471 0 0 5269.5186 12.811592 - 4700 16738.47 0 0 5269.5182 12.811589 - 4750 16738.456 0 0 5269.5139 12.811556 - 4800 16738.441 0 0 5269.5091 12.811518 - 4850 16738.444 0 0 5269.5102 12.811526 - 4900 16738.462 0 0 5269.5159 12.81157 - 4950 16738.475 0 0 5269.5201 12.811603 - 5000 16738.479 0 0 5269.5212 12.811612 - 5050 16738.479 0 0 5269.5212 12.811612 - 5100 16738.479 0 0 5269.5212 12.811612 - 5150 16738.478 0 0 5269.5209 12.81161 - 5200 16738.472 0 0 5269.519 12.811595 - 5250 16738.456 0 0 5269.5138 12.811555 - 5300 16738.432 0 0 5269.5064 12.811497 - 5350 16738.422 0 0 5269.5033 12.811472 - 5400 16738.438 0 0 5269.5082 12.81151 - 5450 16738.46 0 0 5269.515 12.811564 - 5500 16738.471 -0.0002100851 0 5269.5183 12.811588 - 5550 16738.481 -0.003484166 0 5269.5185 12.811534 - 5600 16738.542 -0.024500002 0 5269.5164 12.81122 - 5650 16738.641 -0.058023282 0 5269.5142 12.812225 - 5700 16384.935 111.24508 0 5269.4653 26.09278 - 5750 16738.555 -0.030778873 0 5269.5142 13.052328 - 5800 16738.462 -0.0034050628 0 5269.5125 13.052653 - 5850 16738.441 -0.00034406845 0 5269.5089 13.052656 - 5900 16738.443 0 0 5269.5098 13.052667 - 5950 16738.459 0 0 5269.5149 13.052707 - 6000 16738.468 0 0 5269.5177 13.052729 - 6050 16738.466 0 0 5269.5172 13.052725 - 6100 16738.462 0 0 5269.516 13.052715 - 6150 16738.463 0 0 5269.5162 13.052717 - 6200 16738.468 0 0 5269.5178 13.052729 - 6250 16738.472 0 0 5269.5189 13.052738 - 6300 16738.465 0 0 5269.5169 13.052723 - 6350 16738.448 0 0 5269.5115 13.052681 - 6400 16738.439 0 0 5269.5086 13.052658 - 6450 16738.451 0 0 5269.5124 13.052687 - 6500 16738.469 0 0 5269.5181 13.052732 - 6550 16738.478 0 0 5269.5209 13.052754 - 6600 16738.48 0 0 5269.5214 13.052758 - 6650 16738.479 0 0 5269.5213 13.052757 - 6700 16738.48 -0.00057913195 0 5269.521 13.052744 - 6750 16738.483 -0.0025329373 0 5269.5198 13.0527 - 6800 16738.482 -0.0065110047 0 5269.5156 13.052612 - 6850 16738.465 -0.0072245166 0 5269.5095 13.052574 - 6900 16738.436 -0.0036561206 0 5269.5039 13.052609 - 6950 16738.433 -0.0010530752 0 5269.5056 13.052661 - 7000 16738.455 -0.00056878712 0 5269.5132 13.052723 - 7050 16738.475 -0.0011717775 0 5269.5187 13.052755 - 7100 16738.48 -0.00047531448 0 5269.5209 13.052781 - 7150 16738.479 0 0 5269.5211 13.052788 - 7200 16738.478 0 0 5269.5207 13.052785 - 7250 16738.477 0 0 5269.5207 13.052785 - 7300 16738.476 0 0 5269.5201 13.052781 - 7350 16738.466 0 0 5269.5172 13.052758 - 7400 16738.448 0 0 5269.5115 13.052714 - 7450 16738.438 0 0 5269.5083 13.052688 - 7500 16738.448 0 0 5269.5115 13.052713 - 7550 16738.464 -0.00053504439 0 5269.5158 13.052742 - 7600 16738.483 -0.010043243 0 5269.5123 13.052657 - 7650 16738.674 -0.077543714 0 5269.5051 13.052041 - 7700 16736.839 0.49724671 0 5269.502 13.085872 - 7750 16731.931 2.0427465 0 5269.5024 13.190769 - 7800 16738.762 -0.10404434 0 5269.5061 13.082626 - 7850 16738.525 -0.024994385 0 5269.5108 13.082681 - 7900 16738.479 -0.008372534 0 5269.5129 13.082885 - 7950 16738.449 -0.0038549468 0 5269.5079 13.082917 - 8000 16738.441 -0.0016367617 0 5269.5074 13.082937 - 8050 16738.455 -0.0014865651 0 5269.5123 13.082971 - 8100 16738.47 -0.00072796092 0 5269.5175 13.083021 - 8150 16738.476 0 0 5269.5202 13.08305 - 8200 16738.477 0 0 5269.5204 13.083051 - 8250 16738.476 0 0 5269.5201 13.083049 - 8300 16738.474 0 0 5269.5197 13.083046 - 8350 16738.47 0 0 5269.5185 13.083036 - 8400 16738.462 -0.0017116105 0 5269.5142 13.082984 - 8450 16738.447 -0.003289664 0 5269.5078 13.082915 - 8500 16738.429 -0.00098100125 0 5269.5043 13.082918 - 8550 16738.435 0 0 5269.5075 13.082953 - 8600 16738.458 0 0 5269.5146 13.083009 - 8650 16738.474 0 0 5269.5195 13.083048 - 8700 16738.478 0 0 5269.5208 13.083058 - 8750 16738.477 0 0 5269.5206 13.083056 - 8800 16738.476 0 0 5269.5203 13.083054 - 8850 16738.477 0 0 5269.5206 13.083056 - 8900 16738.476 0 0 5269.5203 13.083054 - 8950 16738.468 0 0 5269.5177 13.083034 - 9000 16738.451 0 0 5269.5122 13.082991 - 9050 16738.44 0 0 5269.5089 13.082965 - 9100 16738.448 0 0 5269.5113 13.082984 - 9150 16738.46 0 0 5269.5153 13.083014 - 9200 16738.464 0 0 5269.5163 13.083023 - 9250 16738.462 0 0 5269.5158 13.083019 - 9300 16738.462 0 0 5269.5159 13.08302 - 9350 16738.467 0 0 5269.5174 13.083031 - 9400 16738.472 -0.00023657902 0 5269.5188 13.083039 - 9450 16738.472 0 0 5269.519 13.083044 - 9500 16738.46 0 0 5269.5153 13.083016 - 9550 16738.443 0 0 5269.5099 13.082974 - 9600 16738.441 0 0 5269.5092 13.082967 - 9650 16738.458 -0.00038368067 0 5269.5142 13.083 - 9700 16738.475 -0.00099963027 0 5269.519 13.083029 - 9750 16738.492 -0.00498524 0 5269.5203 13.082953 - 9800 16738.483 -0.0018715253 0 5269.5204 13.083034 - 9850 16738.477 0 0 5269.5205 13.083063 - 9900 16738.477 -0.0018402419 0 5269.5186 13.083025 - 9950 16738.482 -0.0056480132 0 5269.5164 13.082936 - 10000 16738.467 -0.0045058747 0 5269.5129 13.082944 -Loop time of 0.147071 on 4 procs for 10000 steps with 81 atoms - -Performance: 587469.667 tau/day, 67994.174 timesteps/s, 5.508 Matom-step/s -98.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0016588 | 0.0023518 | 0.0030017 | 1.0 | 1.60 -Neigh | 0.011581 | 0.012949 | 0.014883 | 1.1 | 8.80 -Comm | 0.063654 | 0.065097 | 0.066501 | 0.4 | 44.26 -Output | 0.0017378 | 0.0018782 | 0.0022756 | 0.5 | 1.28 -Modify | 0.049872 | 0.050432 | 0.051195 | 0.2 | 34.29 -Other | | 0.01436 | | | 9.77 - -Nlocal: 20.25 ave 35 max 0 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Nghost: 41 ave 52 max 30 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 4.75 ave 19 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 19 -Ave neighs/atom = 0.2345679 -Neighbor list builds = 1481 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.poems.g++.1 b/examples/rigid/log.25Mar24.rigid.poems.g++.1 deleted file mode 100644 index 0e69724dda..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems.g++.1 +++ /dev/null @@ -1,328 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384279 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184717 - 1150 20849.582 206.01695 0 3680.9472 -0.86699135 - 1200 21815.003 45.317412 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.06408 - 1300 20780.781 217.36509 0 3680.8286 6.0538614 - 1350 20558.971 254.36485 0 3680.8601 -3.6773923 - 1400 21485.029 99.812891 0 3680.6511 -16.185475 - 1450 21771.107 52.159624 0 3680.6775 -2.4756668 - 1500 21520.948 93.503905 0 3680.3286 2.1023577 - 1550 21351.418 121.68136 0 3680.2511 5.5159922 - 1600 20778.805 216.92182 0 3680.0559 15.089193 - 1650 21477.637 100.21853 0 3679.8247 -1.1045536 - 1700 18501.335 596.47986 0 3680.0357 -15.679729 - 1750 18563.64 587.34819 0 3681.2882 33.532254 - 1800 19110.181 494.82407 0 3679.8543 18.02406 - 1850 21364.186 119.23625 0 3679.9339 2.5290683 - 1900 20146.613 322.15086 0 3679.9197 5.7314718 - 1950 20692.671 231.25334 0 3680.0319 4.2977791 - 2000 20943.905 189.11211 0 3679.7629 -22.644575 - 2050 19667.965 401.84519 0 3679.8394 3.6247265 - 2100 20280.309 299.78396 0 3679.8355 7.4806221 - 2150 19181.565 483.57073 0 3680.4982 22.62593 - 2200 21300.569 130.63684 0 3680.7316 4.7090558 - 2250 20486.112 266.77753 0 3681.1296 -8.6505201 - 2300 18651.193 572.56862 0 3681.1008 -5.2604682 - 2350 21514.435 95.462414 0 3681.2016 -9.3718933 - 2400 21464.75 103.81741 0 3681.2757 -29.521964 - 2450 20103.185 331.7557 0 3682.2865 35.600257 - 2500 20767.309 221.18002 0 3682.3981 -12.41075 - 2550 20461.88 271.93545 0 3682.2488 -22.542329 - 2600 21463.807 104.97703 0 3682.2782 -10.118749 - 2650 20902.135 198.66716 0 3682.3564 5.0103958 - 2700 18582.384 585.6465 0 3682.7106 22.212808 - 2750 21079.961 168.86261 0 3682.1894 -8.8401109 - 2800 21425.876 111.18035 0 3682.1598 -6.7933883 - 2850 17414.605 780.0645 0 3682.4987 28.180022 - 2900 19978.961 352.1845 0 3682.0113 8.4280816 - 2950 21189.046 150.47808 0 3681.9858 2.8898793 - 3000 19271.367 469.54947 0 3681.4439 -7.1530396 - 3050 21470.889 103.45294 0 3681.9344 -1.4975516 - 3100 21574.513 85.87604 0 3681.6282 7.0301554 - 3150 21649.42 73.506656 0 3681.7434 1.6649326 - 3200 20857.44 205.3704 0 3681.6104 2.9318184 - 3250 18573.575 585.73328 0 3681.3292 5.9394399 - 3300 17938.353 691.67199 0 3681.3975 9.7205454 - 3350 18668.795 570.23722 0 3681.7031 3.6442733 - 3400 16834.721 876.36804 0 3682.1548 21.869594 - 3450 20148.848 323.06988 0 3681.2112 3.8120475 - 3500 21039.942 175.06064 0 3681.7177 1.4965105 - 3550 21439.472 108.66655 0 3681.9119 4.192594 - 3600 21457.784 105.54883 0 3681.8461 -2.932673 - 3650 21409.999 113.49591 0 3681.829 -15.09817 - 3700 21380.023 118.56895 0 3681.9061 -15.461367 - 3750 20422.085 277.28852 0 3680.9694 19.331799 - 3800 18275.038 635.75951 0 3681.5992 22.413362 - 3850 20906.341 197.06897 0 3681.4592 2.5691289 - 3900 20041.032 341.11847 0 3681.2905 1.8089245 - 3950 18917.084 528.44677 0 3681.2941 -10.656627 - 4000 20425.89 276.98688 0 3681.3018 7.5960674 - 4050 18289.157 633.13575 0 3681.3286 6.5695895 - 4100 19601.884 414.64621 0 3681.6269 8.6144847 - 4150 20790.308 216.9575 0 3682.0088 1.6300255 - 4200 21043.169 174.98738 0 3682.1822 3.8942459 - 4250 19073.45 503.63057 0 3682.5389 -10.975988 - 4300 21251.971 140.63454 0 3682.6298 -7.7937426 - 4350 20844.867 208.08653 0 3682.2311 -10.295096 - 4400 20869.781 203.57469 0 3681.8716 -8.7176985 - 4450 20384.41 284.19751 0 3681.5992 3.9044821 - 4500 20002.241 346.95848 0 3680.6654 12.100678 - 4550 21410.259 112.40994 0 3680.7864 -6.6653767 - 4600 18230.418 641.88921 0 3680.2922 22.502391 - 4650 21319.778 127.76737 0 3681.0638 -0.50309316 - 4700 19429.05 441.85455 0 3680.0296 20.851722 - 4750 20395.967 281.13332 0 3680.4611 12.635024 - 4800 19405.371 446.47714 0 3680.7056 -3.0340076 - 4850 19935.979 358.4478 0 3681.1109 -7.9390554 - 4900 18822.801 543.80607 0 3680.9396 -3.1086099 - 4950 20569.881 252.87963 0 3681.1932 11.807076 - 5000 20311.182 296.63458 0 3681.8315 -4.2409472 - 5050 20187.672 316.83663 0 3681.4486 1.8723981 - 5100 17439.679 775.35516 0 3681.9684 -5.7037267 - 5150 20394.4 282.56755 0 3681.6342 4.3399253 - 5200 20294.84 299.10095 0 3681.5742 -9.9868412 - 5250 20396.122 282.31614 0 3681.6698 -4.9932521 - 5300 20617.465 245.11679 0 3681.3609 0.97429493 - 5350 21651.191 72.878802 0 3681.4106 2.0913693 - 5400 19097.721 498.69617 0 3681.6496 21.808511 - 5450 21856.73 38.930299 0 3681.7186 -4.0225451 - 5500 20087.477 334.09405 0 3682.0069 5.7109498 - 5550 17734.477 726.10594 0 3681.8522 16.277738 - 5600 21183.231 151.714 0 3682.2525 -2.1080998 - 5650 20832.185 210.14251 0 3682.1733 -8.0602581 - 5700 18879.226 535.50935 0 3682.0471 -14.351666 - 5750 18931.81 529.67506 0 3684.9768 4.8675164 - 5800 21674.979 70.259619 0 3682.7561 -14.990544 - 5850 21395.905 116.47471 0 3682.4588 -0.94334402 - 5900 18532.955 593.27143 0 3682.0973 26.072477 - 5950 20767.534 220.78554 0 3682.0413 -1.6468662 - 6000 21546.127 91.167146 0 3682.1882 -5.4664857 - 6050 20085.534 334.40872 0 3681.9977 -0.34825498 - 6100 21218.156 145.88926 0 3682.2486 2.2871905 - 6150 20902.857 198.59424 0 3682.4038 6.0082154 - 6200 21726.547 61.195607 0 3682.2868 -2.2981656 - 6250 17507.589 764.20763 0 3682.1392 9.4977327 - 6300 21687.283 67.283821 0 3681.831 -8.694756 - 6350 19806.474 380.24632 0 3681.3254 -0.94067379 - 6400 21128.461 160.65399 0 3682.0641 -4.8435757 - 6450 19747.214 390.89694 0 3682.0992 1.9108969 - 6500 20460.408 272.79545 0 3682.8634 -4.1094877 - 6550 16740.095 892.11547 0 3682.1313 13.20551 - 6600 18326.164 628.80415 0 3683.1648 -19.884336 - 6650 18469.284 605.36384 0 3683.5778 10.345658 - 6700 21086.876 168.61821 0 3683.0976 -0.036118094 - 6750 19924.801 361.46485 0 3682.2649 -2.1144953 - 6800 19812.028 380.5919 0 3682.5966 11.119936 - 6850 19118.501 496.38857 0 3682.8054 0.53906703 - 6900 19221.04 478.31879 0 3681.8255 11.13851 - 6950 20482.79 269.03445 0 3682.8328 2.6705981 - 7000 16350.403 957.96283 0 3683.03 -2.9783385 - 7050 20789.906 218.36242 0 3683.3467 4.2465754 - 7100 17718.126 730.09011 0 3683.111 15.271811 - 7150 19020.414 513.34591 0 3683.4149 -8.3035633 - 7200 21165.007 156.24494 0 3683.7461 -7.3085107 - 7250 20520.422 264.35574 0 3684.4261 -6.7803072 - 7300 19078.795 505.10953 0 3684.9087 -11.147107 - 7350 20529.173 263.85389 0 3685.3827 0.59881989 - 7400 20548.068 261.27337 0 3685.9513 -5.0067382 - 7450 20849.172 211.46852 0 3686.3306 -0.80175538 - 7500 20869.894 207.95335 0 3686.2689 0.44541197 - 7550 18490.583 605.63557 0 3687.3993 -11.744631 - 7600 19185.381 488.52218 0 3686.0857 3.0881652 - 7650 20520.848 265.65037 0 3685.7917 -0.28165722 - 7700 20599.631 251.69265 0 3684.9645 0.19835423 - 7750 18428.55 614.11446 0 3685.5395 5.8092563 - 7800 19660.337 408.61674 0 3685.3396 4.9902979 - 7850 19409.663 450.30454 0 3685.2483 8.8641567 - 7900 21307.628 133.95865 0 3685.23 -1.8297128 - 7950 17828.245 713.05722 0 3684.4314 5.9673166 - 8000 15894.788 1036.4896 0 3685.621 57.567209 - 8050 18588.022 587.45738 0 3685.4611 1.5643233 - 8100 20664.194 241.59965 0 3685.632 -4.9298687 - 8150 17745.538 728.43249 0 3686.0221 6.121885 - 8200 18433.239 612.84747 0 3685.0539 17.078623 - 8250 19162.628 492.52511 0 3686.2965 12.204945 - 8300 18507.768 602.21188 0 3686.8399 -14.003487 - 8350 21010.715 184.80032 0 3686.5861 -0.93351338 - 8400 20888.233 205.24214 0 3686.6143 -5.3433619 - 8450 20920.621 199.6941 0 3686.4643 -30.437742 - 8500 17085.22 840.80474 0 3688.3414 3.9123878 - 8550 20900.377 203.87077 0 3687.267 -6.7525851 - 8600 19771.517 392.67499 0 3687.9278 13.762684 - 8650 19541.099 431.09497 0 3687.9448 2.0785077 - 8700 21056.327 178.88314 0 3688.2709 -13.663758 - 8750 20109.075 336.93228 0 3688.4447 -1.0445182 - 8800 21821.77 51.337654 0 3688.2993 -10.263971 - 8850 17653.401 740.45074 0 3682.6842 49.147758 - 8900 20311.01 302.92663 0 3688.095 -8.1910583 - 8950 19745.488 396.38557 0 3687.3003 -16.948557 - 9000 20248.989 311.52221 0 3686.3537 -2.4158415 - 9050 17850.649 710.17969 0 3685.2878 25.692377 - 9100 19370.284 456.73812 0 3685.1187 -21.201413 - 9150 20452.896 276.95741 0 3685.7735 2.0316457 - 9200 19174.266 488.9925 0 3684.7035 10.317202 - 9250 20174.171 323.4614 0 3685.8232 -2.1072552 - 9300 21442.761 111.68542 0 3685.479 -12.303658 - 9350 19697.287 402.21503 0 3685.0963 8.4697153 - 9400 21553.763 93.03581 0 3685.3297 -6.7286485 - 9450 18946.935 527.04498 0 3684.8674 -6.6174191 - 9500 21162.915 158.64321 0 3685.7957 -3.2085936 - 9550 20704.844 235.41227 0 3686.2196 10.847095 - 9600 20664.074 242.09733 0 3686.1096 3.7301969 - 9650 20829.655 214.20146 0 3685.8107 7.2197609 - 9700 17336.625 797.22781 0 3686.6654 14.775351 - 9750 19978.15 356.51126 0 3686.2029 -1.1978838 - 9800 21150.487 162.1616 0 3687.2427 -15.596643 - 9850 20849.962 213.10316 0 3688.0968 -5.5443282 - 9900 18407.158 620.93592 0 3688.7956 10.177471 - 9950 20459.637 278.24203 0 3688.1815 0.0020687238 - 10000 21667.112 78.10938 0 3689.2948 -12.660594 -Loop time of 3.06048 on 1 procs for 10000 steps with 81 atoms - -Performance: 28230.843 tau/day, 3267.459 timesteps/s, 264.664 katom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.11571 | 0.11571 | 0.11571 | 0.0 | 3.78 -Neigh | 0.094982 | 0.094982 | 0.094982 | 0.0 | 3.10 -Comm | 0.0098585 | 0.0098585 | 0.0098585 | 0.0 | 0.32 -Output | 0.003355 | 0.003355 | 0.003355 | 0.0 | 0.11 -Modify | 2.8226 | 2.8226 | 2.8226 | 0.0 | 92.23 -Other | | 0.01395 | | | 0.46 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 115 ave 115 max 115 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 808 ave 808 max 808 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 808 -Ave neighs/atom = 9.9753086 -Neighbor list builds = 1162 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems.g++.4 b/examples/rigid/log.25Mar24.rigid.poems.g++.4 deleted file mode 100644 index b75701792d..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems.g++.4 +++ /dev/null @@ -1,328 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384277 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184718 - 1150 20849.582 206.01695 0 3680.9472 -0.86699156 - 1200 21815.003 45.317416 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064076 - 1300 20780.781 217.36505 0 3680.8286 6.0538619 - 1350 20558.972 254.36481 0 3680.8601 -3.6773978 - 1400 21485.029 99.812941 0 3680.6511 -16.185471 - 1450 21771.108 52.159596 0 3680.6775 -2.4756679 - 1500 21520.948 93.503942 0 3680.3286 2.1023578 - 1550 21351.418 121.6814 0 3680.2511 5.5159969 - 1600 20778.805 216.92173 0 3680.0559 15.089183 - 1650 21477.639 100.21825 0 3679.8247 -1.1045878 - 1700 18501.342 596.47873 0 3680.0357 -15.679646 - 1750 18563.643 587.34777 0 3681.2882 33.532181 - 1800 19110.189 494.82286 0 3679.8543 18.024038 - 1850 21364.195 119.2348 0 3679.9339 2.5291365 - 1900 20146.638 322.1467 0 3679.9197 5.7312008 - 1950 20692.67 231.25355 0 3680.0319 4.297766 - 2000 20943.904 189.1122 0 3679.7629 -22.645478 - 2050 19668.123 401.81885 0 3679.8394 3.6254541 - 2100 20280.531 299.74669 0 3679.8352 7.4808896 - 2150 19182.034 483.49332 0 3680.4991 22.616956 - 2200 21299.885 130.75166 0 3680.7326 4.7110487 - 2250 20487.525 266.54254 0 3681.1301 -8.6422018 - 2300 18654.522 572.01515 0 3681.1021 -5.2661499 - 2350 21512.897 95.719565 0 3681.2024 -9.3553511 - 2400 21467.306 103.39279 0 3681.2771 -29.588234 - 2450 20097.914 332.63812 0 3682.2904 35.845886 - 2500 20762.362 222.00787 0 3682.4016 -12.509872 - 2550 20417.692 279.31982 0 3682.2685 -22.320693 - 2600 21468.738 104.15905 0 3682.2821 -10.050868 - 2650 20742.305 225.31121 0 3682.362 5.2887043 - 2700 18575.367 586.68141 0 3682.5759 21.990986 - 2750 20577.766 252.52411 0 3682.1518 -5.8697894 - 2800 20683.69 234.89244 0 3682.1741 -6.7464964 - 2850 16088.831 1001.1454 0 3682.6172 27.686908 - 2900 20715.565 229.46407 0 3682.0583 6.5207552 - 2950 19969.143 353.98595 0 3682.1765 5.3891903 - 3000 20429.639 277.11063 0 3682.0505 -10.302229 - 3050 19840.965 375.78339 0 3682.611 -6.1970263 - 3100 19149.859 490.69976 0 3682.3429 22.372557 - 3150 20421.772 278.3256 0 3681.9543 8.7381033 - 3200 19492.899 433.22833 0 3682.0448 4.3431162 - 3250 20231.034 310.12852 0 3681.9675 -3.2734265 - 3300 19420.155 445.8855 0 3682.578 14.157316 - 3350 21386.445 117.85565 0 3682.2631 1.9590216 - 3400 20372.28 286.91596 0 3682.296 8.2472357 - 3450 20870.351 203.91619 0 3682.308 7.9601676 - 3500 21469.401 104.14434 0 3682.3778 2.5067348 - 3550 21630.799 77.317219 0 3682.4504 -6.5148709 - 3600 21291.513 133.97558 0 3682.5611 -8.8761801 - 3650 19138.211 493.09199 0 3682.7937 25.075733 - 3700 21282.953 135.36631 0 3682.5252 -8.1163312 - 3750 20660.876 239.15863 0 3682.638 -24.806983 - 3800 20161.169 322.26065 0 3682.4555 13.204808 - 3850 19477.477 435.56421 0 3681.8105 31.065794 - 3900 21108.425 164.35492 0 3682.4258 0.37839399 - 3950 21195.124 150.68497 0 3683.2056 -10.098889 - 4000 21477.025 103.95273 0 3683.4568 -4.139886 - 4050 20603.58 249.35497 0 3683.2849 1.3114756 - 4100 19724.656 396.37166 0 3683.8144 -6.6159163 - 4150 20768.839 221.21034 0 3682.6835 -3.4649381 - 4200 19675.942 404.01538 0 3683.339 17.586922 - 4250 21022.927 179.12036 0 3682.9415 0.59436606 - 4300 20511.134 264.68208 0 3683.2044 8.8380269 - 4350 21038.204 177.05256 0 3683.42 -1.3698914 - 4400 18866.857 539.5082 0 3683.9844 10.461602 - 4450 21607.322 83.184316 0 3684.4046 -1.5071605 - 4500 20895.628 201.9445 0 3684.5492 5.7578991 - 4550 20210.744 316.5044 0 3684.9617 5.6678493 - 4600 20416.269 282.24539 0 3684.9569 -3.0067543 - 4650 18811.283 549.46791 0 3684.6817 7.5182454 - 4700 20899.462 201.92249 0 3685.1661 2.6998262 - 4750 20771.285 223.44307 0 3685.3239 12.165622 - 4800 21834.653 46.231798 0 3685.3407 2.021615 - 4850 21282.348 138.2858 0 3685.3437 4.2174481 - 4900 21892.433 36.607993 0 3685.3468 -10.208769 - 4950 21731.003 63.442124 0 3685.2759 -26.918841 - 5000 21476.967 105.69026 0 3685.1848 -10.007088 - 5050 20485.84 270.81814 0 3685.1248 0.65119013 - 5100 21485.763 104.28837 0 3685.2488 -5.3826149 - 5150 21485.096 104.44183 0 3685.2912 -1.274141 - 5200 21388.175 120.61165 0 3685.3074 -7.7953815 - 5250 20656.672 242.51472 0 3685.2934 -4.4067447 - 5300 20132.262 330.10916 0 3685.4862 -11.466755 - 5350 19080.054 505.63228 0 3685.6413 4.6356684 - 5400 21683.337 71.886529 0 3685.7761 -8.4520633 - 5450 20632.669 246.77173 0 3685.5499 5.5429152 - 5500 20896.92 202.76984 0 3685.5898 3.9762924 - 5550 21172.409 156.92085 0 3685.6557 2.6573146 - 5600 20695.91 236.255 0 3685.5733 -18.109158 - 5650 21741.679 61.956471 0 3685.5697 -3.7520994 - 5700 21164.94 157.60813 0 3685.098 2.4020734 - 5750 21075.393 172.84386 0 3685.4093 7.646915 - 5800 20638.831 245.82076 0 3685.6259 8.3009859 - 5850 20262.966 308.37489 0 3685.5359 7.5861941 - 5900 21730.418 63.97074 0 3685.7071 -6.2813552 - 5950 21820.659 48.990687 0 3685.7673 -5.6400713 - 6000 21027.051 181.2853 0 3685.7937 1.213872 - 6050 14422.66 1284.4174 0 3688.194 57.908667 - 6100 19852.685 377.0743 0 3685.8552 -5.1418207 - 6150 20678.783 239.10987 0 3685.5737 -11.982018 - 6200 19788.097 387.62127 0 3685.6375 -2.684571 - 6250 21611.523 83.575418 0 3685.496 1.7544019 - 6300 19214.109 482.45067 0 3684.8021 24.711965 - 6350 18800.074 553.07966 0 3686.4254 11.125791 - 6400 19771.53 390.40388 0 3685.659 -6.1254643 - 6450 20192.282 319.53713 0 3684.9175 13.959536 - 6500 20360.332 292.28682 0 3685.6755 4.4265274 - 6550 21778.739 56.056362 0 3685.8462 -4.6705452 - 6600 16612.689 917.96646 0 3686.748 -32.617733 - 6650 21068.368 174.38501 0 3685.7797 -0.84207954 - 6700 20749.675 227.41249 0 3685.6916 2.9235268 - 6750 20594.96 253.47665 0 3685.9699 -12.440843 - 6800 19974.133 357.05242 0 3686.0745 34.064247 - 6850 21802.523 52.05173 0 3685.8055 -1.4073818 - 6900 18644.747 577.97031 0 3685.4282 19.759245 - 6950 20463.441 274.90799 0 3685.4815 1.2230553 - 7000 20213.292 316.50714 0 3685.3892 23.9288 - 7050 21571.525 90.089593 0 3685.3437 -26.539261 - 7100 20480.036 271.77541 0 3685.1147 -0.13969301 - 7150 21064.842 174.4144 0 3685.2214 3.5451037 - 7200 21179.296 154.8514 0 3684.7341 -5.007319 - 7250 20714.182 232.84783 0 3685.2115 10.601943 - 7300 19341.561 461.91524 0 3685.5087 18.89547 - 7350 21011.016 183.55321 0 3685.3893 1.6481821 - 7400 21206.598 151.07364 0 3685.5066 1.5040526 - 7450 19999.404 352.83129 0 3686.0652 -18.58587 - 7500 21581.952 88.519362 0 3685.5114 -4.0009441 - 7550 21652.618 76.962392 0 3685.7321 -5.758242 - 7600 21207.411 150.86712 0 3685.4355 -0.023727123 - 7650 21756.168 59.804311 0 3685.8323 0.76768563 - 7700 21825.037 48.380795 0 3685.8869 -0.11098207 - 7750 21581.665 89.078228 0 3686.0223 -0.50220667 - 7800 21714.856 66.946216 0 3686.0889 4.637364 - 7850 21319.774 132.905 0 3686.2007 3.4663558 - 7900 21730.647 64.263898 0 3686.0384 1.0898763 - 7950 21597.663 86.255996 0 3685.8664 3.2847476 - 8000 21724.118 65.137632 0 3685.8239 3.7318614 - 8050 19672.702 406.56191 0 3685.3456 -0.37960768 - 8100 21696.026 69.71367 0 3685.7179 -6.2273451 - 8150 18869.648 540.09908 0 3685.0403 22.915669 - 8200 21717.002 66.01922 0 3685.5196 -4.8553801 - 8250 20292.502 303.3445 0 3685.4282 -13.203008 - 8300 21314.341 133.18215 0 3685.5724 -10.023288 - 8350 20992.272 186.87998 0 3685.592 -4.5538872 - 8400 21726.088 64.55825 0 3685.573 -5.1228188 - 8450 21188.98 153.93449 0 3685.4311 -6.8622554 - 8500 21113.87 166.54678 0 3685.5251 2.6009221 - 8550 20620.735 248.66776 0 3685.4569 -8.0047984 - 8600 19715.276 399.79648 0 3685.6758 -10.980391 - 8650 18898.94 535.95488 0 3685.7782 22.513752 - 8700 21692.841 70.067726 0 3685.5413 -3.3917479 - 8750 20242.909 311.87115 0 3685.6893 17.996012 - 8800 19253.702 476.69077 0 3685.6411 3.7170165 - 8850 17625.913 748.07802 0 3685.7302 11.095548 - 8900 21554.709 92.817998 0 3685.2696 0.30720376 - 8950 21585.337 87.685891 0 3685.2421 -0.22047593 - 9000 17454.847 776.14227 0 3685.2834 22.631913 - 9050 20023.106 347.35041 0 3684.5348 4.0008899 - 9100 21100.691 168.07199 0 3684.8539 2.9016681 - 9150 20307.206 299.45669 0 3683.991 2.1630277 - 9200 21747.579 60.245542 0 3684.8421 -15.419887 - 9250 21525.571 97.26157 0 3684.8567 -7.0449498 - 9300 15084.149 1170.5925 0 3684.6173 43.259279 - 9350 21198.648 151.70957 0 3684.8176 3.0716881 - 9400 17771.533 724.65805 0 3686.5802 -18.320033 - 9450 20029.819 346.23988 0 3684.543 -4.0976705 - 9500 19913.342 365.57743 0 3684.4677 2.4909741 - 9550 20594.619 252.35578 0 3684.7923 -4.4263632 - 9600 21013.668 182.33425 0 3684.6122 -1.9371919 - 9650 16915.052 865.78051 0 3684.9559 1.8697619 - 9700 18789.78 553.48818 0 3685.1181 15.642074 - 9750 21236.716 145.75801 0 3685.2107 -3.6730702 - 9800 20972.957 189.72849 0 3685.2214 0.85691231 - 9850 19658.721 408.29826 0 3684.7517 14.8446 - 9900 21624.401 81.484234 0 3685.5511 3.4507557 - 9950 21883.535 38.474607 0 3685.7304 0.3038348 - 10000 21355.31 126.72088 0 3685.9392 -5.5872974 -Loop time of 3.32742 on 4 procs for 10000 steps with 81 atoms - -Performance: 25966.084 tau/day, 3005.334 timesteps/s, 243.432 katom-step/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0073125 | 0.031081 | 0.067049 | 13.5 | 0.93 -Neigh | 0.010912 | 0.030444 | 0.058202 | 10.8 | 0.91 -Comm | 0.084952 | 0.12347 | 0.18323 | 10.9 | 3.71 -Output | 0.0033463 | 0.0038996 | 0.0047508 | 0.9 | 0.12 -Modify | 2.8501 | 2.9361 | 3.0072 | 3.5 | 88.24 -Other | | 0.2024 | | | 6.08 - -Nlocal: 20.25 ave 81 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 33.5 ave 66 max 2 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 212.5 ave 850 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 850 -Ave neighs/atom = 10.493827 -Neighbor list builds = 1246 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems2.g++.1 b/examples/rigid/log.25Mar24.rigid.poems2.g++.1 deleted file mode 100644 index 4a8cb1298a..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems2.g++.1 +++ /dev/null @@ -1,330 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -2 clusters, 9 bodies, 7 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12774.759 1538.7378 0 3904.434 18.086356 - 100 19803.641 237.21132 0 3904.5523 -3.1528278 - 150 20259.6 152.62072 0 3904.3985 -4.6173512 - 200 20705.978 69.977442 0 3904.4178 9.0928146 - 250 19552.211 283.50505 0 3904.2848 15.670464 - 300 19266.324 333.5788 0 3901.4165 7.2119173 - 350 20738.325 63.738945 0 3904.1694 -23.039989 - 400 20616.682 86.082444 0 3903.9864 -13.783584 - 450 19831.326 230.13818 0 3902.6059 0.42074126 - 500 20365.825 131.47231 0 3902.9213 0.69215475 - 550 20794.102 52.163238 0 3902.9229 4.5895354 - 600 20853.873 40.899172 0 3902.7275 2.3593042 - 650 19255.802 336.29509 0 3902.1844 10.341742 - 700 18526.969 471.02462 0 3901.9448 -0.61898691 - 750 18960.662 391.26028 0 3902.494 12.047308 - 800 20142.432 172.05197 0 3902.1319 4.6838632 - 850 19932.48 210.71155 0 3901.9116 3.471602 - 900 20243.528 153.13972 0 3901.9411 3.6490762 - 950 20388.132 126.88722 0 3902.4671 -4.4518463 - 1000 20076.333 184.61916 0 3902.4586 -2.2723139 - 1050 20859.506 39.696992 0 3902.5684 6.45166 - 1100 15284.661 1072.1908 0 3902.6836 21.194042 - 1150 19658.317 261.99809 0 3902.4272 -2.8744219 - 1200 20767.681 56.717093 0 3902.5839 -34.817443 - 1250 20625.583 82.586395 0 3902.1388 11.697328 - 1300 20690.013 71.006479 0 3902.4903 -29.292783 - 1350 20936.019 26.022787 0 3903.0634 1.0316033 - 1400 19753.56 244.81774 0 3902.8844 6.7138457 - 1450 15690.143 998.34271 0 3903.9248 48.124667 - 1500 20234.455 155.92517 0 3903.0465 13.172173 - 1550 20779.63 55.062895 0 3903.1426 -2.6390424 - 1600 20642.757 80.232879 0 3902.9657 -2.4687934 - 1650 18785.716 423.90031 0 3902.7365 -5.6468747 - 1700 20965.076 20.760295 0 3903.1818 -0.45382233 - 1750 18935.466 396.94949 0 3903.5173 25.912008 - 1800 20581.509 91.766145 0 3903.1567 3.8229018 - 1850 20616.968 85.18122 0 3903.1382 4.1907646 - 1900 16600.676 828.66496 0 3902.8643 -0.49197745 - 1950 20175.677 166.50513 0 3902.7416 5.6027746 - 2000 20268.078 149.2566 0 3902.6044 -1.1951453 - 2050 20155.388 170.16328 0 3902.6425 -0.79473147 - 2100 19715.497 250.63403 0 3901.652 3.6719022 - 2150 20677.205 73.792009 0 3902.9041 0.64246071 - 2200 20041.156 191.58407 0 3902.9093 7.4438342 - 2250 19924.453 213.0259 0 3902.7394 2.3652069 - 2300 20432.764 119.13103 0 3902.9763 -11.527566 - 2350 18265.828 520.75569 0 3903.3165 -8.9634198 - 2400 19574.981 277.7963 0 3902.7927 1.8085002 - 2450 20655.975 77.958119 0 3903.1387 3.4001031 - 2500 19783.143 239.3546 0 3902.8995 24.872182 - 2550 16660.113 818.36907 0 3903.5752 -11.766765 - 2600 19789.524 238.61817 0 3903.3448 3.3910931 - 2650 18532.96 471.8684 0 3903.898 -4.812577 - 2700 19081.457 369.81185 0 3903.4151 -0.49159968 - 2750 20370.042 131.6764 0 3903.9064 -3.3818893 - 2800 20727.087 65.499688 0 3903.8491 4.3537941 - 2850 18252.657 523.061 0 3903.1827 11.774986 - 2900 20780.391 55.586541 0 3903.8071 5.4415831 - 2950 20361.047 132.98647 0 3903.5508 -2.4847656 - 3000 19528.633 284.87405 0 3901.2876 14.23453 - 3050 20385.56 127.80448 0 3902.9081 -0.51079949 - 3100 19040.7 376.96613 0 3903.0216 -8.9425331 - 3150 20053.417 189.7312 0 3903.327 4.6695643 - 3200 20862.681 40.219985 0 3903.6795 1.2220199 - 3250 20692.32 71.660474 0 3903.5716 2.118694 - 3300 20560.104 95.905282 0 3903.332 5.9856809 - 3350 20693.236 71.35789 0 3903.4387 3.9315564 - 3400 19045.135 376.64379 0 3903.5206 3.9692419 - 3450 20354.826 134.28157 0 3903.6938 7.6208552 - 3500 20528.053 102.12643 0 3903.6178 7.2863414 - 3550 20525.13 103.01612 0 3903.9661 8.4807852 - 3600 19782.42 240.28031 0 3903.6914 1.0181878 - 3650 20519.52 104.05243 0 3903.9636 -2.36641 - 3700 20024.307 195.68587 0 3903.8908 -6.261818 - 3750 20239.643 155.72722 0 3903.8092 -20.781566 - 3800 20601.2 88.794605 0 3903.8317 -11.491217 - 3850 20973.346 19.675436 0 3903.6283 -9.0554155 - 3900 16212.846 902.10241 0 3904.4813 -19.773976 - 3950 19645.576 264.59477 0 3902.6643 16.065663 - 4000 17439.655 673.47397 0 3903.0398 -3.7357722 - 4050 19305.077 328.50056 0 3903.5148 10.43441 - 4100 18634.36 451.24343 0 3902.0508 3.4327844 - 4150 20249.11 153.64108 0 3903.4763 -2.5190604 - 4200 19177.928 351.81896 0 3903.2871 -5.5110274 - 4250 20754.898 60.189732 0 3903.6893 -3.3019026 - 4300 19693.307 256.31591 0 3903.2245 5.8795929 - 4350 18411.713 494.6957 0 3904.2722 4.2513782 - 4400 18499.707 474.35141 0 3900.2231 10.120914 - 4450 18620.543 449.98137 0 3898.2301 0.74648702 - 4500 18930.676 398.47668 0 3904.1573 -3.3953153 - 4550 18708.382 438.70363 0 3903.2188 8.478793 - 4600 19937.049 211.7655 0 3903.8117 4.8300368 - 4650 19919.169 214.98435 0 3903.7194 -1.0166319 - 4700 19345.329 321.18127 0 3903.6496 -23.032019 - 4750 18391.67 498.629 0 3904.4939 -15.40779 - 4800 18597.103 459.20983 0 3903.1179 9.3900723 - 4850 19857.892 226.27908 0 3903.6665 4.1998427 - 4900 20428.515 120.59483 0 3903.6532 -1.8636046 - 4950 18457.127 485.79992 0 3903.7864 -7.2380409 - 5000 20543.123 99.480661 0 3903.7627 -0.39555479 - 5050 18716.671 436.46735 0 3902.5175 29.395654 - 5100 20048.411 191.03727 0 3903.706 -0.91178091 - 5150 19647.675 265.24989 0 3903.7083 3.8658742 - 5200 20787.465 54.078505 0 3903.6091 -3.3582221 - 5250 20630.096 83.165593 0 3903.5538 -11.86045 - 5300 16598.926 830.02918 0 3903.9043 -1.8793568 - 5350 19114.667 363.424 0 3903.1772 11.894383 - 5400 19563.654 280.22257 0 3903.1215 8.8285523 - 5450 20012.628 197.27325 0 3903.3154 2.1981092 - 5500 17845.428 599.4114 0 3904.1202 20.091131 - 5550 20630.423 82.857857 0 3903.3065 0.93827014 - 5600 19675.125 259.89939 0 3903.4411 -2.4034875 - 5650 19932.349 212.22024 0 3903.3961 2.0064698 - 5700 20499.192 107.17918 0 3903.3259 2.5440649 - 5750 19522.335 287.94941 0 3903.1966 -0.7615272 - 5800 18010.242 568.31554 0 3903.5455 -6.3433889 - 5850 20177.497 166.64243 0 3903.2159 -0.95012013 - 5900 17919.358 584.40694 0 3902.8065 10.49282 - 5950 18390.453 498.29164 0 3903.9311 10.026285 - 6000 18040.232 562.71939 0 3903.5032 0.22172862 - 6050 19777.355 240.88597 0 3903.3592 -3.1899015 - 6100 19132.014 360.58765 0 3903.5531 1.6644736 - 6150 19780.214 240.31985 0 3903.3224 4.2403325 - 6200 18883.45 406.45503 0 3903.3902 -3.5422327 - 6250 19875.924 222.49729 0 3903.2239 3.0535292 - 6300 19882.454 221.4928 0 3903.4287 5.7371152 - 6350 19040.565 377.18193 0 3903.2124 -0.26454332 - 6400 19137.008 359.7025 0 3903.5929 9.5375531 - 6450 19655.205 263.59789 0 3903.4507 -1.8592763 - 6500 18385.045 499.5436 0 3904.1816 -7.8549266 - 6550 18823.423 417.69964 0 3903.5187 -2.8268518 - 6600 19414.118 308.11966 0 3903.3268 4.6627243 - 6650 20533.065 100.75047 0 3903.1698 3.3716972 - 6700 20206.283 161.18079 0 3903.085 5.6368472 - 6750 19517.622 288.72511 0 3903.0995 0.3337076 - 6800 18152.278 541.45525 0 3902.9883 -7.2734044 - 6850 18910.032 401.19322 0 3903.0511 6.2653128 - 6900 18580.612 462.26403 0 3903.1182 15.681586 - 6950 20459.012 114.44928 0 3903.1552 -0.82985388 - 7000 20866.868 38.822988 0 3903.0578 -6.2182429 - 7050 20460.074 114.11492 0 3903.0175 -2.1465384 - 7100 20553.533 96.636153 0 3902.846 -5.105486 - 7150 20447.915 116.30898 0 3902.9599 8.2035464 - 7200 20703.396 69.030336 0 3902.9926 9.1221166 - 7250 19652.215 263.63438 0 3902.9335 17.675447 - 7300 20691.205 71.094727 0 3902.7994 -1.7423404 - 7350 18845.785 412.74313 0 3902.7033 -2.0276584 - 7400 18462.131 483.73088 0 3902.6441 -0.22424322 - 7450 20458.641 113.96173 0 3902.599 -4.9286236 - 7500 17681.258 628.1576 0 3902.4647 -16.803813 - 7550 19149.34 356.35773 0 3902.5318 -5.3481685 - 7600 19723.907 249.45462 0 3902.03 7.2597963 - 7650 19317.18 325.01536 0 3902.271 -0.16642424 - 7700 19620.248 269.22043 0 3902.5996 -4.6771277 - 7750 17751.083 615.46827 0 3902.7058 7.3637076 - 7800 20724.904 64.633157 0 3902.5784 5.2079592 - 7850 19966.924 204.60327 0 3902.1817 6.4943932 - 7900 19730.339 248.88701 0 3902.6536 8.4392109 - 7950 19907.748 216.06587 0 3902.6859 -5.1989259 - 8000 18217.971 528.46486 0 3902.1632 -15.394144 - 8050 17868.898 592.98294 0 3902.0381 9.1139508 - 8100 19370.601 315.22753 0 3902.3759 7.9651368 - 8150 18199.01 532.43818 0 3902.6252 10.07163 - 8200 20646.337 79.222148 0 3902.6179 0.17396159 - 8250 20811.938 48.374613 0 3902.4372 -14.594973 - 8300 20906.571 30.626024 0 3902.2132 -12.34909 - 8350 19873.431 221.86861 0 3902.1335 7.1435615 - 8400 20374.979 127.96219 0 3901.1064 10.527044 - 8450 20701.502 68.073078 0 3901.6846 2.5071154 - 8500 20452.423 113.98399 0 3901.4698 4.2164058 - 8550 19695.059 253.87834 0 3901.1115 8.0656507 - 8600 19447.531 299.45597 0 3900.8505 -0.71982287 - 8650 17202.668 714.55842 0 3900.2378 -16.743518 - 8700 18579.153 459.20676 0 3899.7906 3.4494692 - 8750 20247.204 150.39086 0 3899.8731 -0.1022032 - 8800 18520.797 469.57224 0 3899.3494 5.7412252 - 8850 16011.411 934.80107 0 3899.8772 34.500452 - 8900 19045.914 372.92529 0 3899.9464 10.001612 - 8950 19798.369 233.70991 0 3900.0746 9.3270865 - 9000 17141.02 725.70858 0 3899.9716 -6.7470927 - 9050 17722.847 617.81927 0 3899.828 -10.909071 - 9100 20811.604 45.701413 0 3899.7021 -12.300065 - 9150 18066.034 554.62654 0 3900.1884 -5.7606837 - 9200 19259.884 332.49612 0 3899.1412 -40.231609 - 9250 19116.782 359.42396 0 3899.5689 0.68271469 - 9300 18785.022 421.1178 0 3899.8256 -20.433345 - 9350 19018.32 377.90289 0 3899.814 3.2963902 - 9400 17321.798 691.93839 0 3899.6788 24.552549 - 9450 18318.437 507.12661 0 3899.4297 6.1367468 - 9500 16431.681 857.32722 0 3900.2311 25.431389 - 9550 17920.939 581.45381 0 3900.1462 9.1734747 - 9600 16603.394 825.79291 0 3900.4954 -5.9643183 - 9650 17753.931 607.15019 0 3894.9151 2.2302338 - 9700 17452.305 668.30613 0 3900.2145 2.4635322 - 9750 15955.164 945.80159 0 3900.4617 20.290857 - 9800 17958.495 574.7055 0 3900.3526 12.218625 - 9850 18759.766 423.66965 0 3897.7005 -4.8999337 - 9900 19798.529 232.2507 0 3898.6449 0.10312101 - 9950 18260.87 517.50071 0 3899.1432 5.7261992 - 10000 19116.279 359.58291 0 3899.6345 3.2110764 -Loop time of 3.11933 on 1 procs for 10000 steps with 81 atoms - -Performance: 27698.233 tau/day, 3205.814 timesteps/s, 259.671 katom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.063297 | 0.063297 | 0.063297 | 0.0 | 2.03 -Neigh | 0.072119 | 0.072119 | 0.072119 | 0.0 | 2.31 -Comm | 0.012058 | 0.012058 | 0.012058 | 0.0 | 0.39 -Output | 0.0036722 | 0.0036722 | 0.0036722 | 0.0 | 0.12 -Modify | 2.953 | 2.953 | 2.953 | 0.0 | 94.67 -Other | | 0.01515 | | | 0.49 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 105 ave 105 max 105 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 498 ave 498 max 498 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 498 -Ave neighs/atom = 6.1481481 -Neighbor list builds = 1202 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems2.g++.4 b/examples/rigid/log.25Mar24.rigid.poems2.g++.4 deleted file mode 100644 index bc26f32538..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems2.g++.4 +++ /dev/null @@ -1,330 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -2 clusters, 9 bodies, 7 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12774.759 1538.7378 0 3904.434 18.086356 - 100 19803.641 237.21132 0 3904.5523 -3.1528278 - 150 20259.6 152.62032 0 3904.3981 -4.6173548 - 200 20705.978 69.977442 0 3904.4178 9.0928146 - 250 19552.211 283.50525 0 3904.285 15.670465 - 300 19266.324 333.5792 0 3901.4169 7.2119197 - 350 20738.325 63.738945 0 3904.1694 -23.03999 - 400 20616.682 86.082444 0 3903.9864 -13.783584 - 450 19831.326 230.13858 0 3902.6063 0.42074361 - 500 20365.825 131.47271 0 3902.9217 0.69215592 - 550 20794.102 52.163238 0 3902.9229 4.5895354 - 600 20853.873 40.899172 0 3902.7275 2.3593042 - 650 19255.802 336.29509 0 3902.1844 10.341742 - 700 18526.969 471.02462 0 3901.9448 -0.61898691 - 750 18960.662 391.26068 0 3902.4944 12.04731 - 800 20142.432 172.05197 0 3902.1319 4.6838632 - 850 19932.48 210.71175 0 3901.9118 3.4716031 - 900 20243.528 153.13972 0 3901.9411 3.6490762 - 950 20388.132 126.88722 0 3902.4671 -4.4518463 - 1000 20076.333 184.61916 0 3902.4586 -2.272315 - 1050 20859.506 39.696992 0 3902.5684 6.45166 - 1100 15284.661 1072.1906 0 3902.6833 21.194041 - 1150 19658.317 261.99809 0 3902.4272 -2.8744196 - 1200 20767.681 56.717093 0 3902.5839 -34.817444 - 1250 20625.583 82.586396 0 3902.1388 11.697328 - 1300 20690.013 71.006479 0 3902.4903 -29.292783 - 1350 20936.019 26.022787 0 3903.0634 1.0316031 - 1400 19753.56 244.81777 0 3902.8844 6.713847 - 1450 15690.145 998.34279 0 3903.9252 48.124638 - 1500 20234.455 155.92476 0 3903.0461 13.17218 - 1550 20779.631 55.063072 0 3903.1428 -2.6390427 - 1600 20642.756 80.233303 0 3902.9659 -2.4688077 - 1650 18785.71 423.90132 0 3902.7365 -5.6468182 - 1700 20965.076 20.760481 0 3903.182 -0.45377448 - 1750 18935.45 396.95247 0 3903.5173 25.912353 - 1800 20581.523 91.763662 0 3903.1567 3.8225817 - 1850 20616.962 85.182351 0 3903.1382 4.1907744 - 1900 16601.061 828.59343 0 3902.8639 -0.49284971 - 1950 20175.618 166.51633 0 3902.7419 5.6031735 - 2000 20266.439 149.55931 0 3902.6036 -1.1956447 - 2050 20159.308 169.44017 0 3902.6453 -0.7983344 - 2100 19743.72 245.40822 0 3901.6527 3.5301052 - 2150 20674.556 74.284034 0 3902.9055 0.61532081 - 2200 19950.784 208.30189 0 3902.8915 7.6523945 - 2250 19817.161 232.7485 0 3902.5932 3.4492756 - 2300 20459.058 114.2307 0 3902.9451 -11.066393 - 2350 18359.21 503.25787 0 3903.1115 -9.0741539 - 2400 19952.914 207.84881 0 3902.8328 -0.53972874 - 2450 19661.352 259.78979 0 3900.781 7.8669927 - 2500 20917.293 29.699201 0 3903.2719 1.1433085 - 2550 20763.955 57.990256 0 3903.1671 -1.1088372 - 2600 20640.005 80.556339 0 3902.7795 9.6127007 - 2650 20823.227 47.292746 0 3903.446 2.2923503 - 2700 20401.43 125.53141 0 3903.5739 -8.0683618 - 2750 20689.918 72.242212 0 3903.7084 0.22078527 - 2800 20783.922 54.87309 0 3903.7476 2.0668249 - 2850 19258.563 336.84835 0 3903.2488 4.2704683 - 2900 20565.694 95.184831 0 3903.6468 -0.24799068 - 2950 20915.041 30.344751 0 3903.5004 -2.9900907 - 3000 19571.964 278.74004 0 3903.1778 12.195325 - 3050 20356.693 133.43974 0 3903.1976 0.11608195 - 3100 20047.888 190.69627 0 3903.268 -4.5895546 - 3150 19834.363 230.59072 0 3903.6209 -1.4352632 - 3200 20213.412 160.25129 0 3903.4757 3.7488266 - 3250 19286.774 332.04497 0 3903.6699 -5.0835358 - 3300 20952.226 23.774103 0 3903.816 0.10019546 - 3350 20407.952 124.62932 0 3903.8798 0.4403531 - 3400 19401.716 311.03567 0 3903.9461 1.8034568 - 3450 20880.78 37.20558 0 3904.0167 6.3948533 - 3500 19529.313 287.50301 0 3904.0425 12.311168 - 3550 20943.604 25.677677 0 3904.1228 5.1786098 - 3600 20272.725 149.91697 0 3904.1254 1.196909 - 3650 19781.047 240.95421 0 3904.1111 -8.5091671 - 3700 20613.433 86.53896 0 3903.8414 -9.1622102 - 3750 20567.605 95.294456 0 3904.1101 -0.11887825 - 3800 19891.98 220.32932 0 3904.0292 6.8801146 - 3850 20669.735 76.407858 0 3904.1365 -7.4310509 - 3900 20908.711 32.197181 0 3904.1807 -4.6573356 - 3950 20822.78 48.03134 0 3904.1018 0.086779759 - 4000 20199.055 163.66262 0 3904.2283 2.0027771 - 4050 20072.638 187.07041 0 3904.2256 4.4103784 - 4100 17724.651 619.7903 0 3902.1331 11.210006 - 4150 20760.201 60.001382 0 3904.4831 -3.8510009 - 4200 19159.102 356.30472 0 3904.2865 -2.3503308 - 4250 19403.974 311.3497 0 3904.6783 -1.2458384 - 4300 20858.687 42.000734 0 3904.7206 2.1750528 - 4350 20486.989 110.94383 0 3904.8306 5.017245 - 4400 20231.073 158.28825 0 3904.7832 7.4295979 - 4450 16369.689 873.39361 0 3904.8175 14.371454 - 4500 20745.196 63.11427 0 3904.8172 -7.855609 - 4550 18688.003 443.85636 0 3904.5977 9.8067426 - 4600 17755.672 616.68475 0 3904.7721 -3.9654703 - 4650 19843.131 230.34486 0 3904.9988 -0.13553926 - 4700 18873.202 409.99341 0 3905.0308 15.912724 - 4750 20605.355 89.223116 0 3905.0295 2.0847611 - 4800 20136.483 176.1278 0 3905.1062 -1.7091113 - 4850 19808.073 236.83278 0 3904.9945 5.0982271 - 4900 19142.083 359.55764 0 3904.3878 8.2072008 - 4950 20539.687 101.08198 0 3904.7277 8.0469319 - 5000 20840.809 45.759021 0 3905.168 4.771755 - 5050 20009.696 199.45528 0 3904.9546 6.1191423 - 5100 20882.034 38.247578 0 3905.2909 -6.3068822 - 5150 20329.869 140.47458 0 3905.2651 -21.720979 - 5200 17334.411 695.67098 0 3905.7471 -9.8243617 - 5250 19602.025 275.17282 0 3905.1775 -3.2371379 - 5300 20858.74 42.630642 0 3905.3603 0.38011789 - 5350 20828.619 48.188698 0 3905.3403 5.7187945 - 5400 20978.428 20.447148 0 3905.3413 6.1168011 - 5450 20115.374 179.9294 0 3904.9987 8.6440563 - 5500 20522.744 104.7733 0 3905.2815 -2.6561664 - 5550 20625.724 85.600795 0 3905.1792 -1.327206 - 5600 19559.638 282.68742 0 3904.8426 17.893028 - 5650 20552.224 98.978098 0 3904.9455 2.4489071 - 5700 19982.142 204.09989 0 3904.4966 9.9034011 - 5750 20408.825 125.30875 0 3904.7209 1.2515548 - 5800 19773.143 243.02134 0 3904.7144 -2.6729948 - 5850 20781.934 56.310486 0 3904.8168 -1.659054 - 5900 19807.668 236.54392 0 3904.6306 0.49776361 - 5950 20741.237 63.921667 0 3904.8916 4.2800039 - 6000 20322.7 140.98125 0 3904.4442 7.4978024 - 6050 20858.439 42.383629 0 3905.0575 -4.6872323 - 6100 20212.538 162.022 0 3905.0847 -7.0796165 - 6150 18513.957 476.7087 0 3905.2193 7.107138 - 6200 20802.734 52.621638 0 3904.9797 3.7242428 - 6250 20818.044 49.717458 0 3904.9109 -0.91041774 - 6300 19987.245 203.4635 0 3904.8052 -0.86714551 - 6350 20806.906 51.449749 0 3904.5806 -4.0699629 - 6400 20530.3 103.09809 0 3905.0055 1.660177 - 6450 20667.085 77.715553 0 3904.9535 0.99217521 - 6500 20515.816 105.81762 0 3905.0428 3.0994091 - 6550 20548.348 99.627131 0 3904.8769 -0.77417688 - 6600 19827.378 232.99889 0 3904.7355 3.295082 - 6650 19237.199 342.94808 0 3905.3923 -6.2226637 - 6700 19611.621 273.139 0 3904.9206 -3.5465535 - 6750 20874.805 39.1893 0 3904.8939 -0.051336814 - 6800 19433.717 305.99952 0 3904.8361 -19.858865 - 6850 20119.223 179.19987 0 3904.9818 4.6466283 - 6900 20467.389 114.77871 0 3905.0359 10.290214 - 6950 20334.202 139.43289 0 3905.0259 7.5448433 - 7000 20504.591 107.86929 0 3905.0158 -0.10092084 - 7050 17969.214 576.83722 0 3904.4694 10.852897 - 7100 19186.398 351.80467 0 3904.8414 0.24779979 - 7150 20261.23 152.54684 0 3904.6265 -7.0175844 - 7200 20696.821 71.985154 0 3904.7298 3.9649146 - 7250 18456.212 487.1819 0 3904.9989 5.8280225 - 7300 17705.1 625.95928 0 3904.6816 6.8298215 - 7350 17032.039 750.96958 0 3905.051 11.833303 - 7400 20557.431 97.599213 0 3904.5308 0.43747863 - 7450 20466.847 114.5693 0 3904.7261 1.9786538 - 7500 20416.862 123.31643 0 3904.2168 -2.9094738 - 7550 18433.95 487.50767 0 3901.2022 4.0921479 - 7600 19950.107 209.92208 0 3904.3863 3.9114888 - 7650 16037.844 934.94785 0 3904.9189 -1.2183461 - 7700 20145.239 173.99945 0 3904.5993 3.1185554 - 7750 18672.579 446.35236 0 3904.2373 4.1086445 - 7800 19740.616 249.10395 0 3904.7737 4.6048428 - 7850 20801.917 52.742096 0 3904.9489 1.5978265 - 7900 20305.348 144.57749 0 3904.8272 2.7348725 - 7950 20221.086 159.31958 0 3903.9652 7.1592496 - 8000 20826.907 47.953835 0 3904.7884 6.2728901 - 8050 18646.418 452.02126 0 3905.0617 5.9716218 - 8100 20653.653 80.183024 0 3904.9336 -1.8274783 - 8150 20843.275 45.172279 0 3905.0379 -6.9445524 - 8200 20364.78 133.45082 0 3904.7064 -12.094533 - 8250 18163.745 541.08818 0 3904.7447 -2.6103997 - 8300 20889.664 36.793018 0 3905.2494 -9.2650749 - 8350 20307.367 144.33088 0 3904.9543 -0.65999546 - 8400 20485.202 111.41317 0 3904.9691 -0.42802224 - 8450 20864.395 41.146879 0 3904.9238 7.7084978 - 8500 20901.899 34.291267 0 3905.0132 -5.2070823 - 8550 20211.78 162.02611 0 3904.9484 -5.8363409 - 8600 19639.538 268.05291 0 3905.0044 3.8180903 - 8650 19919.356 216.24885 0 3905.0185 0.17130921 - 8700 19499.449 293.97522 0 3904.9843 -4.897872 - 8750 20270.687 151.1571 0 3904.9879 0.28558082 - 8800 18804.137 422.61651 0 3904.864 15.351015 - 8850 20654.443 80.110976 0 3905.0078 4.1368065 - 8900 19953.725 209.81046 0 3904.9447 10.71743 - 8950 18195.013 536.67764 0 3906.1245 21.497802 - 9000 20478.531 112.78923 0 3905.1098 -13.053056 - 9050 20866.484 40.901611 0 3905.0653 -3.6134066 - 9100 20322.595 141.61419 0 3905.0577 15.459697 - 9150 20855.456 42.94311 0 3905.0646 4.9123213 - 9200 20208.201 162.79363 0 3905.0531 2.5454472 - 9250 18394.203 498.63686 0 3904.9707 0.041811692 - 9300 18776.997 427.7118 0 3904.9335 -7.652483 - 9350 18330.751 510.07857 0 3904.6621 8.3424059 - 9400 17538.366 657.08623 0 3904.9319 8.5478668 - 9450 20309.605 143.77142 0 3904.8093 6.6831447 - 9500 19982.331 203.81545 0 3904.2471 -7.6711411 - 9550 19410.612 310.1139 0 3904.6717 5.3983286 - 9600 19198.225 349.06634 0 3904.2932 -4.107658 - 9650 19388.043 314.31566 0 3904.6939 6.1198194 - 9700 18849.37 414.1045 0 3904.7286 5.4468861 - 9750 18263.312 523.38716 0 3905.4819 -0.56480349 - 9800 20421.858 122.53973 0 3904.3653 -15.641399 - 9850 17678.959 631.15683 0 3905.0381 -1.805446 - 9900 19421.046 306.67446 0 3903.1644 7.0287747 - 9950 18460.64 483.18902 0 3901.8261 3.658774 - 10000 19781.151 239.38136 0 3902.5575 6.3312911 -Loop time of 3.44431 on 4 procs for 10000 steps with 81 atoms - -Performance: 25084.833 tau/day, 2903.337 timesteps/s, 235.170 katom-step/s -98.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.007256 | 0.017426 | 0.044845 | 12.0 | 0.51 -Neigh | 0.010951 | 0.023139 | 0.043878 | 8.2 | 0.67 -Comm | 0.070404 | 0.096764 | 0.1104 | 5.0 | 2.81 -Output | 0.0039809 | 0.0074043 | 0.010167 | 2.6 | 0.21 -Modify | 3.0537 | 3.0735 | 3.1272 | 1.8 | 89.23 -Other | | 0.226 | | | 6.56 - -Nlocal: 20.25 ave 36 max 0 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Nghost: 38.25 ave 50 max 28 min -Histogram: 1 0 1 0 0 1 0 0 0 1 -Neighs: 126.5 ave 213 max 0 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 506 -Ave neighs/atom = 6.2469136 -Neighbor list builds = 1207 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems3.g++.1 b/examples/rigid/log.25Mar24.rigid.poems3.g++.1 deleted file mode 100644 index 2554c0f610..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems3.g++.1 +++ /dev/null @@ -1,329 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.000 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all poems file unconnected-bodies.dat -WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1038) -9 clusters, 9 bodies, 0 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.686 571.71596 0 5265.8207 32.006226 - 100 16298.5 136.65142 0 5267.6607 16.443791 - 150 16682.639 17.488068 0 5269.43 14.900278 - 200 16733.955 1.3724268 0 5269.4692 14.569123 - 250 16738.877 -0.15250573 0 5269.4939 14.496287 - 300 16738.611 -0.05516662 0 5269.5077 14.495909 - 350 16738.515 -0.01744351 0 5269.5152 14.496329 - 400 16738.488 -0.0060096677 0 5269.5178 14.496497 - 450 16738.479 -0.0012712918 0 5269.5199 14.496575 - 500 16738.479 -0.00081070354 0 5269.5203 14.49658 - 550 16738.479 -0.00083205205 0 5269.5203 14.496577 - 600 16738.479 -0.0005835658 0 5269.5206 14.49658 - 650 16738.479 -0.00047227225 0 5269.5206 14.496583 - 700 16738.479 0 0 5269.521 14.496593 - 750 16738.479 0 0 5269.5211 14.496595 - 800 16738.479 0 0 5269.5211 14.496596 - 850 16738.479 0 0 5269.5211 14.496595 - 900 16738.479 0 0 5269.5212 14.496593 - 950 16738.485 -0.003532391 0 5269.5196 14.496546 - 1000 16738.609 -0.051135033 0 5269.5109 14.496098 - 1050 16737.381 0.32991002 0 5269.5055 14.525627 - 1100 16737.915 0.16210932 0 5269.5058 14.531848 - 1150 16738.726 -0.089235332 0 5269.5098 14.509768 - 1200 16738.49 -0.0075446298 0 5269.5169 14.510489 - 1250 16738.48 0 0 5269.5214 14.510585 - 1300 16738.48 0 0 5269.5214 14.510587 - 1350 16738.48 0 0 5269.5215 14.510588 - 1400 16738.48 -0.00044742303 0 5269.5211 14.510581 - 1450 16738.481 -0.0010975104 0 5269.5207 14.51057 - 1500 16738.481 -0.00057925965 0 5269.5211 14.510575 - 1550 16738.48 0 0 5269.5216 14.510582 - 1600 16738.48 0 0 5269.5216 14.510581 - 1650 16738.481 0 0 5269.5216 14.510581 - 1700 16738.481 0 0 5269.5217 14.510582 - 1750 16738.481 0 0 5269.5217 14.510583 - 1800 16738.481 0 0 5269.5217 14.510585 - 1850 16738.481 0 0 5269.5218 14.510585 - 1900 16738.481 0 0 5269.5218 14.510585 - 1950 16738.487 -0.0031700155 0 5269.5206 14.510534 - 2000 16738.514 -0.013238802 0 5269.5188 14.510401 - 2050 16738.578 -0.03654435 0 5269.5158 14.510155 - 2100 16738.656 -0.063182323 0 5269.5137 14.510082 - 2150 16738.63 -0.056004395 0 5269.5127 14.510096 - 2200 16738.579 -0.038415873 0 5269.5143 14.510273 - 2250 16738.538 -0.023709094 0 5269.516 14.510414 - 2300 16738.512 -0.013252539 0 5269.5182 14.510501 - 2350 16738.491 -0.0045593284 0 5269.5203 14.510598 - 2400 16738.482 -0.00052242487 0 5269.5217 14.510655 - 2450 16738.486 -0.0023245722 0 5269.5211 14.510627 - 2500 16738.491 -0.005189304 0 5269.5197 14.510606 - 2550 16738.604 -0.044988104 0 5269.5155 14.510185 - 2600 16738.446 0.00096754004 0 5269.5117 14.510521 - 2650 16732.887 1.753125 0 5269.5138 14.598792 - 2700 16738.784 -0.10629556 0 5269.5107 14.499176 - 2750 16734.136 1.359459 0 5269.5135 14.594678 - 2800 16738.608 -0.047184149 0 5269.5147 14.510254 - 2850 16738.509 -0.012527238 0 5269.5181 14.509344 - 2900 16738.487 -0.0026065529 0 5269.521 14.509512 - 2950 16738.498 -0.0082248532 0 5269.519 14.509457 - 3000 16738.683 -0.071294028 0 5269.514 14.509005 - 3050 16717.444 6.5874862 0 5269.4864 14.834144 - 3100 16657.654 25.431253 0 5269.5074 14.467824 - 3150 16739.322 -0.28964062 0 5269.497 13.658821 - 3200 16733.615 1.4969789 0 5269.487 11.998304 - 3250 16737.289 0.35071213 0 5269.4974 11.918931 - 3300 16732.493 1.8663821 0 5269.503 12.109003 - 3350 16738.717 -0.087719164 0 5269.5085 11.979747 - 3400 16738.586 -0.045267897 0 5269.5095 11.97972 - 3450 16738.662 -0.071274216 0 5269.5076 11.979564 - 3500 16738.853 -0.13644992 0 5269.5026 11.979658 - 3550 16729.612 2.7475276 0 5269.4774 12.195939 - 3600 16728.659 3.059607 0 5269.4893 12.241248 - 3650 16738.923 -0.15949792 0 5269.5014 11.991857 - 3700 16738.76 -0.10695054 0 5269.5028 11.992932 - 3750 16738.751 -0.10105954 0 5269.5057 11.993137 - 3800 16738.597 -0.048627545 0 5269.5097 11.993456 - 3850 16738.507 -0.016053927 0 5269.5138 11.992973 - 3900 16738.485 -0.0060825487 0 5269.5169 11.993052 - 3950 16738.475 -0.0014953722 0 5269.5183 11.993119 - 4000 16738.472 -0.00054315391 0 5269.5184 11.99315 - 4050 16738.472 -0.00023792127 0 5269.5187 11.993172 - 4100 16738.472 0 0 5269.5189 11.993188 - 4150 16738.472 0 0 5269.5189 11.993188 - 4200 16738.472 0 0 5269.519 11.993178 - 4250 16738.472 0 0 5269.519 11.993164 - 4300 16738.472 0 0 5269.5191 11.993152 - 4350 16738.473 0 0 5269.5191 11.993147 - 4400 16738.473 0 0 5269.5192 11.993149 - 4450 16738.473 0 0 5269.5192 11.993158 - 4500 16738.473 0 0 5269.5193 11.99317 - 4550 16738.473 0 0 5269.5193 11.993176 - 4600 16738.473 0 0 5269.5194 11.993174 - 4650 16738.473 0 0 5269.5194 11.993167 - 4700 16738.474 0 0 5269.5195 11.993162 - 4750 16738.474 0 0 5269.5195 11.99316 - 4800 16738.474 0 0 5269.5196 11.99316 - 4850 16738.474 0 0 5269.5196 11.993163 - 4900 16738.474 0 0 5269.5197 11.99317 - 4950 16738.474 0 0 5269.5197 11.993176 - 5000 16738.475 0 0 5269.5198 11.993174 - 5050 16738.475 0 0 5269.5198 11.993165 - 5100 16738.475 0 0 5269.5199 11.993155 - 5150 16738.475 0 0 5269.5199 11.99315 - 5200 16738.475 0 0 5269.52 11.993153 - 5250 16738.475 0 0 5269.52 11.993161 - 5300 16738.476 0 0 5269.5201 11.993173 - 5350 16738.476 0 0 5269.5201 11.993185 - 5400 16738.476 0 0 5269.5202 11.993189 - 5450 16738.476 0 0 5269.5202 11.993181 - 5500 16738.476 0 0 5269.5203 11.993165 - 5550 16738.483 -0.0030091905 0 5269.5195 11.993097 - 5600 16738.534 -0.020777802 0 5269.5177 11.992799 - 5650 16738.649 -0.059321662 0 5269.5153 11.993266 - 5700 16409.08 103.75288 0 5269.5745 23.626238 - 5750 16738.578 -0.036776519 0 5269.5155 11.910545 - 5800 16738.484 -0.0047306177 0 5269.518 11.911008 - 5850 16738.477 -0.00022082692 0 5269.5202 11.911078 - 5900 16738.477 -0.00033136078 0 5269.5203 11.91107 - 5950 16738.478 -0.00036902212 0 5269.5203 11.911052 - 6000 16738.477 0 0 5269.5206 11.911044 - 6050 16738.477 0 0 5269.5207 11.911034 - 6100 16738.478 0 0 5269.5207 11.911032 - 6150 16738.478 0 0 5269.5208 11.911037 - 6200 16738.478 0 0 5269.5208 11.911049 - 6250 16738.478 0 0 5269.5209 11.911062 - 6300 16738.478 0 0 5269.5209 11.911068 - 6350 16738.478 0 0 5269.521 11.911065 - 6400 16738.478 0 0 5269.521 11.911058 - 6450 16738.479 0 0 5269.5211 11.911052 - 6500 16738.479 0 0 5269.5211 11.911047 - 6550 16738.479 0 0 5269.5212 11.911046 - 6600 16738.479 0 0 5269.5212 11.911049 - 6650 16738.479 0 0 5269.5213 11.911056 - 6700 16738.479 0 0 5269.5213 11.911062 - 6750 16738.48 0 0 5269.5214 11.91106 - 6800 16738.48 0 0 5269.5214 11.911051 - 6850 16738.48 0 0 5269.5215 11.911044 - 6900 16738.48 0 0 5269.5215 11.911041 - 6950 16738.48 0 0 5269.5216 11.911045 - 7000 16738.48 0 0 5269.5216 11.911053 - 7050 16738.481 0 0 5269.5217 11.911063 - 7100 16738.481 0 0 5269.5217 11.911071 - 7150 16738.481 0 0 5269.5218 11.911072 - 7200 16738.481 0 0 5269.5218 11.911063 - 7250 16738.481 0 0 5269.5219 11.911048 - 7300 16738.481 0 0 5269.5219 11.911036 - 7350 16738.482 0 0 5269.522 11.911031 - 7400 16738.482 0 0 5269.522 11.911035 - 7450 16738.482 0 0 5269.5221 11.911046 - 7500 16738.482 0 0 5269.5221 11.911062 - 7550 16738.482 0 0 5269.5222 11.911077 - 7600 16738.482 0 0 5269.5222 11.911081 - 7650 16738.483 0 0 5269.5223 11.911071 - 7700 16738.483 0 0 5269.5223 11.911054 - 7750 16738.483 0 0 5269.5224 11.911039 - 7800 16738.483 0 0 5269.5224 11.911031 - 7850 16738.483 0 0 5269.5225 11.911031 - 7900 16738.483 0 0 5269.5226 11.911039 - 7950 16738.484 0 0 5269.5226 11.911052 - 8000 16738.484 0 0 5269.5227 11.911065 - 8050 16738.484 0 0 5269.5227 11.91107 - 8100 16738.484 0 0 5269.5228 11.911065 - 8150 16738.484 0 0 5269.5228 11.911056 - 8200 16738.484 0 0 5269.5229 11.911047 - 8250 16738.485 0 0 5269.5229 11.911042 - 8300 16738.485 0 0 5269.523 11.911041 - 8350 16738.485 0 0 5269.523 11.911046 - 8400 16738.485 0 0 5269.5231 11.911055 - 8450 16738.485 0 0 5269.5231 11.911062 - 8500 16738.485 0 0 5269.5232 11.91106 - 8550 16738.486 0 0 5269.5232 11.911053 - 8600 16738.487 -0.00084974053 0 5269.5227 11.911032 - 8650 16738.486 0 0 5269.5233 11.911046 - 8700 16738.486 0 0 5269.5234 11.91105 - 8750 16738.486 0 0 5269.5235 11.911056 - 8800 16738.486 0 0 5269.5235 11.911063 - 8850 16738.487 -0.00022763101 0 5269.5234 11.911065 - 8900 16738.487 0 0 5269.5236 11.911068 - 8950 16738.487 0 0 5269.5237 11.911058 - 9000 16738.487 0 0 5269.5237 11.911045 - 9050 16738.487 0 0 5269.5238 11.911036 - 9100 16738.487 0 0 5269.5238 11.911034 - 9150 16738.488 0 0 5269.5239 11.91104 - 9200 16738.488 0 0 5269.5239 11.911052 - 9250 16738.488 0 0 5269.524 11.911068 - 9300 16738.488 0 0 5269.524 11.911079 - 9350 16738.488 0 0 5269.5241 11.911078 - 9400 16738.492 -0.0016306436 0 5269.5235 11.911038 - 9450 16738.492 -0.0032567427 0 5269.522 11.911005 - 9500 16738.495 -0.0036645346 0 5269.5224 11.910982 - 9550 16738.49 -0.001067391 0 5269.5237 11.911012 - 9600 16738.489 0 0 5269.5244 11.911032 - 9650 16738.489 0 0 5269.5244 11.911043 - 9700 16738.49 0 0 5269.5245 11.911058 - 9750 16738.49 0 0 5269.5245 11.911071 - 9800 16738.49 0 0 5269.5246 11.911073 - 9850 16738.49 0 0 5269.5246 11.911065 - 9900 16738.49 0 0 5269.5247 11.911053 - 9950 16738.491 -0.00058544655 0 5269.5243 11.911032 - 10000 16738.493 -0.0015244935 0 5269.5242 11.911015 -Loop time of 3.15773 on 1 procs for 10000 steps with 81 atoms - -Performance: 27361.390 tau/day, 3166.828 timesteps/s, 256.513 katom-step/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0090105 | 0.0090105 | 0.0090105 | 0.0 | 0.29 -Neigh | 0.047552 | 0.047552 | 0.047552 | 0.0 | 1.51 -Comm | 0.012213 | 0.012213 | 0.012213 | 0.0 | 0.39 -Output | 0.0028666 | 0.0028666 | 0.0028666 | 0.0 | 0.09 -Modify | 3.0714 | 3.0714 | 3.0714 | 0.0 | 97.27 -Other | | 0.01471 | | | 0.47 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 66 ave 66 max 66 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 4 ave 4 max 4 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4 -Ave neighs/atom = 0.049382716 -Neighbor list builds = 1576 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems3.g++.4 b/examples/rigid/log.25Mar24.rigid.poems3.g++.4 deleted file mode 100644 index 142b81ad80..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems3.g++.4 +++ /dev/null @@ -1,329 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all poems file unconnected-bodies.dat -WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1038) -9 clusters, 9 bodies, 0 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.686 571.71596 0 5265.8207 32.006226 - 100 16298.5 136.65142 0 5267.6607 16.443791 - 150 16682.639 17.488068 0 5269.43 14.900278 - 200 16733.955 1.3724268 0 5269.4692 14.569123 - 250 16738.877 -0.15250573 0 5269.4939 14.496287 - 300 16738.611 -0.05516662 0 5269.5077 14.495909 - 350 16738.515 -0.01744351 0 5269.5152 14.496329 - 400 16738.488 -0.0060096677 0 5269.5178 14.496497 - 450 16738.479 -0.0012712918 0 5269.5199 14.496575 - 500 16738.479 -0.00081070354 0 5269.5203 14.49658 - 550 16738.479 -0.00083205205 0 5269.5203 14.496577 - 600 16738.479 -0.0005835658 0 5269.5206 14.49658 - 650 16738.479 -0.00047227225 0 5269.5206 14.496583 - 700 16738.479 0 0 5269.521 14.496593 - 750 16738.479 0 0 5269.5211 14.496595 - 800 16738.479 0 0 5269.5211 14.496596 - 850 16738.479 0 0 5269.5211 14.496595 - 900 16738.479 0 0 5269.5212 14.496593 - 950 16738.485 -0.003532391 0 5269.5196 14.496546 - 1000 16738.609 -0.051135033 0 5269.5109 14.496098 - 1050 16737.381 0.32991002 0 5269.5055 14.525627 - 1100 16737.915 0.16210932 0 5269.5058 14.531848 - 1150 16738.726 -0.089235332 0 5269.5098 14.509768 - 1200 16738.49 -0.0075446298 0 5269.5169 14.510489 - 1250 16738.48 0 0 5269.5214 14.510585 - 1300 16738.48 0 0 5269.5214 14.510587 - 1350 16738.48 0 0 5269.5215 14.510588 - 1400 16738.48 -0.00044742303 0 5269.5211 14.510581 - 1450 16738.481 -0.0010975104 0 5269.5207 14.51057 - 1500 16738.481 -0.00057925965 0 5269.5211 14.510575 - 1550 16738.48 0 0 5269.5216 14.510582 - 1600 16738.48 0 0 5269.5216 14.510581 - 1650 16738.481 0 0 5269.5216 14.510581 - 1700 16738.481 0 0 5269.5217 14.510582 - 1750 16738.481 0 0 5269.5217 14.510583 - 1800 16738.481 0 0 5269.5217 14.510585 - 1850 16738.481 0 0 5269.5218 14.510585 - 1900 16738.481 0 0 5269.5218 14.510585 - 1950 16738.487 -0.0031700155 0 5269.5206 14.510534 - 2000 16738.514 -0.013238802 0 5269.5188 14.510401 - 2050 16738.578 -0.03654435 0 5269.5158 14.510155 - 2100 16738.656 -0.063182323 0 5269.5137 14.510082 - 2150 16738.63 -0.056004395 0 5269.5127 14.510096 - 2200 16738.579 -0.038415873 0 5269.5143 14.510273 - 2250 16738.538 -0.023709094 0 5269.516 14.510414 - 2300 16738.512 -0.013252539 0 5269.5182 14.510501 - 2350 16738.491 -0.0045593284 0 5269.5203 14.510598 - 2400 16738.482 -0.00052242487 0 5269.5217 14.510655 - 2450 16738.486 -0.0023245722 0 5269.5211 14.510627 - 2500 16738.491 -0.005189304 0 5269.5197 14.510606 - 2550 16738.604 -0.044988104 0 5269.5155 14.510185 - 2600 16738.446 0.00096754006 0 5269.5117 14.510521 - 2650 16732.887 1.753125 0 5269.5138 14.598792 - 2700 16738.784 -0.10629556 0 5269.5107 14.499176 - 2750 16734.136 1.359459 0 5269.5135 14.594678 - 2800 16738.608 -0.047184149 0 5269.5147 14.510254 - 2850 16738.509 -0.012527238 0 5269.5181 14.509344 - 2900 16738.487 -0.0026065529 0 5269.521 14.509512 - 2950 16738.498 -0.0082248532 0 5269.519 14.509457 - 3000 16738.683 -0.071294028 0 5269.514 14.509005 - 3050 16717.444 6.5874862 0 5269.4864 14.834144 - 3100 16657.654 25.431253 0 5269.5074 14.467824 - 3150 16739.322 -0.28964062 0 5269.497 13.658821 - 3200 16733.615 1.4969789 0 5269.487 11.998304 - 3250 16737.289 0.35071213 0 5269.4974 11.918931 - 3300 16732.493 1.866382 0 5269.503 12.109003 - 3350 16738.717 -0.087719164 0 5269.5085 11.979747 - 3400 16738.586 -0.045267897 0 5269.5095 11.97972 - 3450 16738.662 -0.071274216 0 5269.5076 11.979564 - 3500 16738.853 -0.13644992 0 5269.5026 11.979658 - 3550 16729.612 2.7475276 0 5269.4774 12.195939 - 3600 16728.659 3.059607 0 5269.4893 12.241248 - 3650 16738.923 -0.15949792 0 5269.5014 11.991857 - 3700 16738.76 -0.10695054 0 5269.5028 11.992932 - 3750 16738.751 -0.10105954 0 5269.5057 11.993137 - 3800 16738.597 -0.048627545 0 5269.5097 11.993456 - 3850 16738.507 -0.016053927 0 5269.5138 11.992973 - 3900 16738.485 -0.0060825487 0 5269.5169 11.993052 - 3950 16738.475 -0.0014953722 0 5269.5183 11.993119 - 4000 16738.472 -0.00054315391 0 5269.5184 11.99315 - 4050 16738.472 -0.00023792127 0 5269.5187 11.993172 - 4100 16738.472 0 0 5269.5189 11.993188 - 4150 16738.472 0 0 5269.5189 11.993188 - 4200 16738.472 0 0 5269.519 11.993178 - 4250 16738.472 0 0 5269.519 11.993164 - 4300 16738.472 0 0 5269.5191 11.993152 - 4350 16738.473 0 0 5269.5191 11.993147 - 4400 16738.473 0 0 5269.5192 11.993149 - 4450 16738.473 0 0 5269.5192 11.993158 - 4500 16738.473 0 0 5269.5193 11.99317 - 4550 16738.473 0 0 5269.5193 11.993176 - 4600 16738.473 0 0 5269.5194 11.993174 - 4650 16738.473 0 0 5269.5194 11.993167 - 4700 16738.474 0 0 5269.5195 11.993162 - 4750 16738.474 0 0 5269.5195 11.99316 - 4800 16738.474 0 0 5269.5196 11.99316 - 4850 16738.474 0 0 5269.5196 11.993163 - 4900 16738.474 0 0 5269.5197 11.99317 - 4950 16738.474 0 0 5269.5197 11.993176 - 5000 16738.475 0 0 5269.5198 11.993174 - 5050 16738.475 0 0 5269.5198 11.993165 - 5100 16738.475 0 0 5269.5199 11.993155 - 5150 16738.475 0 0 5269.5199 11.99315 - 5200 16738.475 0 0 5269.52 11.993153 - 5250 16738.475 0 0 5269.52 11.993161 - 5300 16738.476 0 0 5269.5201 11.993173 - 5350 16738.476 0 0 5269.5201 11.993185 - 5400 16738.476 0 0 5269.5202 11.993189 - 5450 16738.476 0 0 5269.5202 11.993181 - 5500 16738.476 0 0 5269.5203 11.993165 - 5550 16738.483 -0.0030091905 0 5269.5195 11.993097 - 5600 16738.534 -0.020777802 0 5269.5177 11.992799 - 5650 16738.649 -0.059321662 0 5269.5153 11.993266 - 5700 16409.08 103.75288 0 5269.5745 23.626238 - 5750 16738.578 -0.036776519 0 5269.5155 11.910545 - 5800 16738.484 -0.0047306177 0 5269.518 11.911008 - 5850 16738.477 -0.00022082692 0 5269.5202 11.911078 - 5900 16738.477 -0.00033136079 0 5269.5203 11.91107 - 5950 16738.478 -0.00036902212 0 5269.5203 11.911052 - 6000 16738.477 0 0 5269.5206 11.911044 - 6050 16738.477 0 0 5269.5207 11.911034 - 6100 16738.478 0 0 5269.5207 11.911032 - 6150 16738.478 0 0 5269.5208 11.911037 - 6200 16738.478 0 0 5269.5208 11.911049 - 6250 16738.478 0 0 5269.5209 11.911062 - 6300 16738.478 0 0 5269.5209 11.911068 - 6350 16738.478 0 0 5269.521 11.911065 - 6400 16738.478 0 0 5269.521 11.911058 - 6450 16738.479 0 0 5269.5211 11.911052 - 6500 16738.479 0 0 5269.5211 11.911047 - 6550 16738.479 0 0 5269.5212 11.911046 - 6600 16738.479 0 0 5269.5212 11.911049 - 6650 16738.479 0 0 5269.5213 11.911056 - 6700 16738.479 0 0 5269.5213 11.911062 - 6750 16738.48 0 0 5269.5214 11.91106 - 6800 16738.48 0 0 5269.5214 11.911051 - 6850 16738.48 0 0 5269.5215 11.911044 - 6900 16738.48 0 0 5269.5215 11.911041 - 6950 16738.48 0 0 5269.5216 11.911045 - 7000 16738.48 0 0 5269.5216 11.911053 - 7050 16738.481 0 0 5269.5217 11.911063 - 7100 16738.481 0 0 5269.5217 11.911071 - 7150 16738.481 0 0 5269.5218 11.911072 - 7200 16738.481 0 0 5269.5218 11.911063 - 7250 16738.481 0 0 5269.5219 11.911048 - 7300 16738.481 0 0 5269.5219 11.911036 - 7350 16738.482 0 0 5269.522 11.911031 - 7400 16738.482 0 0 5269.522 11.911035 - 7450 16738.482 0 0 5269.5221 11.911046 - 7500 16738.482 0 0 5269.5221 11.911062 - 7550 16738.482 0 0 5269.5222 11.911077 - 7600 16738.482 0 0 5269.5222 11.911081 - 7650 16738.483 0 0 5269.5223 11.911071 - 7700 16738.483 0 0 5269.5223 11.911054 - 7750 16738.483 0 0 5269.5224 11.911039 - 7800 16738.483 0 0 5269.5224 11.911031 - 7850 16738.483 0 0 5269.5225 11.911031 - 7900 16738.483 0 0 5269.5226 11.911039 - 7950 16738.484 0 0 5269.5226 11.911052 - 8000 16738.484 0 0 5269.5227 11.911065 - 8050 16738.484 0 0 5269.5227 11.91107 - 8100 16738.484 0 0 5269.5228 11.911065 - 8150 16738.484 0 0 5269.5228 11.911056 - 8200 16738.484 0 0 5269.5229 11.911047 - 8250 16738.485 0 0 5269.5229 11.911042 - 8300 16738.485 0 0 5269.523 11.911041 - 8350 16738.485 0 0 5269.523 11.911046 - 8400 16738.485 0 0 5269.5231 11.911055 - 8450 16738.485 0 0 5269.5231 11.911062 - 8500 16738.485 0 0 5269.5232 11.91106 - 8550 16738.486 0 0 5269.5232 11.911053 - 8600 16738.487 -0.00084974054 0 5269.5227 11.911032 - 8650 16738.486 0 0 5269.5233 11.911046 - 8700 16738.486 0 0 5269.5234 11.91105 - 8750 16738.486 0 0 5269.5235 11.911056 - 8800 16738.486 0 0 5269.5235 11.911063 - 8850 16738.487 -0.00022763102 0 5269.5234 11.911065 - 8900 16738.487 0 0 5269.5236 11.911068 - 8950 16738.487 0 0 5269.5237 11.911058 - 9000 16738.487 0 0 5269.5237 11.911045 - 9050 16738.487 0 0 5269.5238 11.911036 - 9100 16738.487 0 0 5269.5238 11.911034 - 9150 16738.488 0 0 5269.5239 11.91104 - 9200 16738.488 0 0 5269.5239 11.911052 - 9250 16738.488 0 0 5269.524 11.911068 - 9300 16738.488 0 0 5269.524 11.911079 - 9350 16738.488 0 0 5269.5241 11.911078 - 9400 16738.492 -0.0016306434 0 5269.5235 11.911038 - 9450 16738.492 -0.0032567424 0 5269.522 11.911005 - 9500 16738.495 -0.0036645342 0 5269.5224 11.910982 - 9550 16738.49 -0.0010673909 0 5269.5237 11.911012 - 9600 16738.489 0 0 5269.5244 11.911032 - 9650 16738.489 0 0 5269.5244 11.911043 - 9700 16738.49 0 0 5269.5245 11.911058 - 9750 16738.49 0 0 5269.5245 11.911071 - 9800 16738.49 0 0 5269.5246 11.911073 - 9850 16738.49 0 0 5269.5246 11.911065 - 9900 16738.49 0 0 5269.5247 11.911053 - 9950 16738.491 -0.0005854466 0 5269.5243 11.911032 - 10000 16738.493 -0.0015244937 0 5269.5242 11.911015 -Loop time of 3.27386 on 4 procs for 10000 steps with 81 atoms - -Performance: 26390.874 tau/day, 3054.499 timesteps/s, 247.414 katom-step/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.003643 | 0.0042095 | 0.0048106 | 0.7 | 0.13 -Neigh | 0.015047 | 0.01644 | 0.018121 | 0.9 | 0.50 -Comm | 0.08923 | 0.091442 | 0.093047 | 0.5 | 2.79 -Output | 0.0033998 | 0.0040485 | 0.0051625 | 1.0 | 0.12 -Modify | 2.9783 | 2.9943 | 3.0343 | 1.3 | 91.46 -Other | | 0.1635 | | | 4.99 - -Nlocal: 20.25 ave 27 max 9 min -Histogram: 1 0 0 0 0 1 0 0 0 2 -Nghost: 30.5 ave 50 max 14 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -Neighs: 1 ave 4 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 4 -Ave neighs/atom = 0.049382716 -Neighbor list builds = 1576 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems4.g++.1 b/examples/rigid/log.25Mar24.rigid.poems4.g++.1 deleted file mode 100644 index f754fba3b4..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems4.g++.1 +++ /dev/null @@ -1,328 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems file connected-bodies.dat -1 clusters, 9 bodies, 8 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384279 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184717 - 1150 20849.582 206.01695 0 3680.9472 -0.86699135 - 1200 21815.003 45.317412 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.06408 - 1300 20780.781 217.36509 0 3680.8286 6.0538614 - 1350 20558.971 254.36485 0 3680.8601 -3.6773923 - 1400 21485.029 99.812891 0 3680.6511 -16.185475 - 1450 21771.107 52.159624 0 3680.6775 -2.4756668 - 1500 21520.948 93.503905 0 3680.3286 2.1023577 - 1550 21351.418 121.68136 0 3680.2511 5.5159922 - 1600 20778.805 216.92182 0 3680.0559 15.089193 - 1650 21477.637 100.21853 0 3679.8247 -1.1045536 - 1700 18501.335 596.47986 0 3680.0357 -15.679729 - 1750 18563.64 587.34819 0 3681.2882 33.532254 - 1800 19110.181 494.82407 0 3679.8543 18.02406 - 1850 21364.186 119.23625 0 3679.9339 2.5290683 - 1900 20146.613 322.15086 0 3679.9197 5.7314718 - 1950 20692.671 231.25334 0 3680.0319 4.2977791 - 2000 20943.905 189.11211 0 3679.7629 -22.644575 - 2050 19667.965 401.84519 0 3679.8394 3.6247265 - 2100 20280.309 299.78396 0 3679.8355 7.4806221 - 2150 19181.565 483.57073 0 3680.4982 22.62593 - 2200 21300.569 130.63684 0 3680.7316 4.7090558 - 2250 20486.112 266.77753 0 3681.1296 -8.6505201 - 2300 18651.193 572.56862 0 3681.1008 -5.2604682 - 2350 21514.435 95.462414 0 3681.2016 -9.3718933 - 2400 21464.75 103.81741 0 3681.2757 -29.521964 - 2450 20103.185 331.7557 0 3682.2865 35.600257 - 2500 20767.309 221.18002 0 3682.3981 -12.41075 - 2550 20461.88 271.93545 0 3682.2488 -22.542329 - 2600 21463.807 104.97703 0 3682.2782 -10.118749 - 2650 20902.135 198.66716 0 3682.3564 5.0103958 - 2700 18582.384 585.6465 0 3682.7106 22.212808 - 2750 21079.961 168.86261 0 3682.1894 -8.8401109 - 2800 21425.876 111.18035 0 3682.1598 -6.7933883 - 2850 17414.605 780.0645 0 3682.4987 28.180022 - 2900 19978.961 352.1845 0 3682.0113 8.4280816 - 2950 21189.046 150.47808 0 3681.9858 2.8898793 - 3000 19271.367 469.54947 0 3681.4439 -7.1530396 - 3050 21470.889 103.45294 0 3681.9344 -1.4975516 - 3100 21574.513 85.87604 0 3681.6282 7.0301554 - 3150 21649.42 73.506656 0 3681.7434 1.6649326 - 3200 20857.44 205.3704 0 3681.6104 2.9318184 - 3250 18573.575 585.73328 0 3681.3292 5.9394399 - 3300 17938.353 691.67199 0 3681.3975 9.7205454 - 3350 18668.795 570.23722 0 3681.7031 3.6442733 - 3400 16834.721 876.36804 0 3682.1548 21.869594 - 3450 20148.848 323.06988 0 3681.2112 3.8120475 - 3500 21039.942 175.06064 0 3681.7177 1.4965105 - 3550 21439.472 108.66655 0 3681.9119 4.192594 - 3600 21457.784 105.54883 0 3681.8461 -2.932673 - 3650 21409.999 113.49591 0 3681.829 -15.09817 - 3700 21380.023 118.56895 0 3681.9061 -15.461367 - 3750 20422.085 277.28852 0 3680.9694 19.331799 - 3800 18275.038 635.75951 0 3681.5992 22.413362 - 3850 20906.341 197.06897 0 3681.4592 2.5691289 - 3900 20041.032 341.11847 0 3681.2905 1.8089245 - 3950 18917.084 528.44677 0 3681.2941 -10.656627 - 4000 20425.89 276.98688 0 3681.3018 7.5960674 - 4050 18289.157 633.13575 0 3681.3286 6.5695895 - 4100 19601.884 414.64621 0 3681.6269 8.6144847 - 4150 20790.308 216.9575 0 3682.0088 1.6300255 - 4200 21043.169 174.98738 0 3682.1822 3.8942459 - 4250 19073.45 503.63057 0 3682.5389 -10.975988 - 4300 21251.971 140.63454 0 3682.6298 -7.7937426 - 4350 20844.867 208.08653 0 3682.2311 -10.295096 - 4400 20869.781 203.57469 0 3681.8716 -8.7176985 - 4450 20384.41 284.19751 0 3681.5992 3.9044821 - 4500 20002.241 346.95848 0 3680.6654 12.100678 - 4550 21410.259 112.40994 0 3680.7864 -6.6653767 - 4600 18230.418 641.88921 0 3680.2922 22.502391 - 4650 21319.778 127.76737 0 3681.0638 -0.50309316 - 4700 19429.05 441.85455 0 3680.0296 20.851722 - 4750 20395.967 281.13332 0 3680.4611 12.635024 - 4800 19405.371 446.47714 0 3680.7056 -3.0340076 - 4850 19935.979 358.4478 0 3681.1109 -7.9390554 - 4900 18822.801 543.80607 0 3680.9396 -3.1086099 - 4950 20569.881 252.87963 0 3681.1932 11.807076 - 5000 20311.182 296.63458 0 3681.8315 -4.2409472 - 5050 20187.672 316.83663 0 3681.4486 1.8723981 - 5100 17439.679 775.35516 0 3681.9684 -5.7037267 - 5150 20394.4 282.56755 0 3681.6342 4.3399253 - 5200 20294.84 299.10095 0 3681.5742 -9.9868412 - 5250 20396.122 282.31614 0 3681.6698 -4.9932521 - 5300 20617.465 245.11679 0 3681.3609 0.97429493 - 5350 21651.191 72.878802 0 3681.4106 2.0913693 - 5400 19097.721 498.69617 0 3681.6496 21.808511 - 5450 21856.73 38.930299 0 3681.7186 -4.0225451 - 5500 20087.477 334.09405 0 3682.0069 5.7109498 - 5550 17734.477 726.10594 0 3681.8522 16.277738 - 5600 21183.231 151.714 0 3682.2525 -2.1080998 - 5650 20832.185 210.14251 0 3682.1733 -8.0602581 - 5700 18879.226 535.50935 0 3682.0471 -14.351666 - 5750 18931.81 529.67506 0 3684.9768 4.8675164 - 5800 21674.979 70.259619 0 3682.7561 -14.990544 - 5850 21395.905 116.47471 0 3682.4588 -0.94334402 - 5900 18532.955 593.27143 0 3682.0973 26.072477 - 5950 20767.534 220.78554 0 3682.0413 -1.6468662 - 6000 21546.127 91.167146 0 3682.1882 -5.4664857 - 6050 20085.534 334.40872 0 3681.9977 -0.34825498 - 6100 21218.156 145.88926 0 3682.2486 2.2871905 - 6150 20902.857 198.59424 0 3682.4038 6.0082154 - 6200 21726.547 61.195607 0 3682.2868 -2.2981656 - 6250 17507.589 764.20763 0 3682.1392 9.4977327 - 6300 21687.283 67.283821 0 3681.831 -8.694756 - 6350 19806.474 380.24632 0 3681.3254 -0.94067379 - 6400 21128.461 160.65399 0 3682.0641 -4.8435757 - 6450 19747.214 390.89694 0 3682.0992 1.9108969 - 6500 20460.408 272.79545 0 3682.8634 -4.1094877 - 6550 16740.095 892.11547 0 3682.1313 13.20551 - 6600 18326.164 628.80415 0 3683.1648 -19.884336 - 6650 18469.284 605.36384 0 3683.5778 10.345658 - 6700 21086.876 168.61821 0 3683.0976 -0.036118094 - 6750 19924.801 361.46485 0 3682.2649 -2.1144953 - 6800 19812.028 380.5919 0 3682.5966 11.119936 - 6850 19118.501 496.38857 0 3682.8054 0.53906703 - 6900 19221.04 478.31879 0 3681.8255 11.13851 - 6950 20482.79 269.03445 0 3682.8328 2.6705981 - 7000 16350.403 957.96283 0 3683.03 -2.9783385 - 7050 20789.906 218.36242 0 3683.3467 4.2465754 - 7100 17718.126 730.09011 0 3683.111 15.271811 - 7150 19020.414 513.34591 0 3683.4149 -8.3035633 - 7200 21165.007 156.24494 0 3683.7461 -7.3085107 - 7250 20520.422 264.35574 0 3684.4261 -6.7803072 - 7300 19078.795 505.10953 0 3684.9087 -11.147107 - 7350 20529.173 263.85389 0 3685.3827 0.59881989 - 7400 20548.068 261.27337 0 3685.9513 -5.0067382 - 7450 20849.172 211.46852 0 3686.3306 -0.80175538 - 7500 20869.894 207.95335 0 3686.2689 0.44541197 - 7550 18490.583 605.63557 0 3687.3993 -11.744631 - 7600 19185.381 488.52218 0 3686.0857 3.0881652 - 7650 20520.848 265.65037 0 3685.7917 -0.28165722 - 7700 20599.631 251.69265 0 3684.9645 0.19835423 - 7750 18428.55 614.11446 0 3685.5395 5.8092563 - 7800 19660.337 408.61674 0 3685.3396 4.9902979 - 7850 19409.663 450.30454 0 3685.2483 8.8641567 - 7900 21307.628 133.95865 0 3685.23 -1.8297128 - 7950 17828.245 713.05722 0 3684.4314 5.9673166 - 8000 15894.788 1036.4896 0 3685.621 57.567209 - 8050 18588.022 587.45738 0 3685.4611 1.5643233 - 8100 20664.194 241.59965 0 3685.632 -4.9298687 - 8150 17745.538 728.43249 0 3686.0221 6.121885 - 8200 18433.239 612.84747 0 3685.0539 17.078623 - 8250 19162.628 492.52511 0 3686.2965 12.204945 - 8300 18507.768 602.21188 0 3686.8399 -14.003487 - 8350 21010.715 184.80032 0 3686.5861 -0.93351338 - 8400 20888.233 205.24214 0 3686.6143 -5.3433619 - 8450 20920.621 199.6941 0 3686.4643 -30.437742 - 8500 17085.22 840.80474 0 3688.3414 3.9123878 - 8550 20900.377 203.87077 0 3687.267 -6.7525851 - 8600 19771.517 392.67499 0 3687.9278 13.762684 - 8650 19541.099 431.09497 0 3687.9448 2.0785077 - 8700 21056.327 178.88314 0 3688.2709 -13.663758 - 8750 20109.075 336.93228 0 3688.4447 -1.0445182 - 8800 21821.77 51.337654 0 3688.2993 -10.263971 - 8850 17653.401 740.45074 0 3682.6842 49.147758 - 8900 20311.01 302.92663 0 3688.095 -8.1910583 - 8950 19745.488 396.38557 0 3687.3003 -16.948557 - 9000 20248.989 311.52221 0 3686.3537 -2.4158415 - 9050 17850.649 710.17969 0 3685.2878 25.692377 - 9100 19370.284 456.73812 0 3685.1187 -21.201413 - 9150 20452.896 276.95741 0 3685.7735 2.0316457 - 9200 19174.266 488.9925 0 3684.7035 10.317202 - 9250 20174.171 323.4614 0 3685.8232 -2.1072552 - 9300 21442.761 111.68542 0 3685.479 -12.303658 - 9350 19697.287 402.21503 0 3685.0963 8.4697153 - 9400 21553.763 93.03581 0 3685.3297 -6.7286485 - 9450 18946.935 527.04498 0 3684.8674 -6.6174191 - 9500 21162.915 158.64321 0 3685.7957 -3.2085936 - 9550 20704.844 235.41227 0 3686.2196 10.847095 - 9600 20664.074 242.09733 0 3686.1096 3.7301969 - 9650 20829.655 214.20146 0 3685.8107 7.2197609 - 9700 17336.625 797.22781 0 3686.6654 14.775351 - 9750 19978.15 356.51126 0 3686.2029 -1.1978838 - 9800 21150.487 162.1616 0 3687.2427 -15.596643 - 9850 20849.962 213.10316 0 3688.0968 -5.5443282 - 9900 18407.158 620.93592 0 3688.7956 10.177471 - 9950 20459.637 278.24203 0 3688.1815 0.0020687238 - 10000 21667.112 78.10938 0 3689.2948 -12.660594 -Loop time of 3.40889 on 1 procs for 10000 steps with 81 atoms - -Performance: 25345.463 tau/day, 2933.503 timesteps/s, 237.614 katom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.12904 | 0.12904 | 0.12904 | 0.0 | 3.79 -Neigh | 0.10613 | 0.10613 | 0.10613 | 0.0 | 3.11 -Comm | 0.011135 | 0.011135 | 0.011135 | 0.0 | 0.33 -Output | 0.0042137 | 0.0042137 | 0.0042137 | 0.0 | 0.12 -Modify | 3.142 | 3.142 | 3.142 | 0.0 | 92.17 -Other | | 0.01636 | | | 0.48 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 115 ave 115 max 115 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 808 ave 808 max 808 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 808 -Ave neighs/atom = 9.9753086 -Neighbor list builds = 1162 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems4.g++.4 b/examples/rigid/log.25Mar24.rigid.poems4.g++.4 deleted file mode 100644 index e78a2e0f05..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems4.g++.4 +++ /dev/null @@ -1,328 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems file connected-bodies.dat -1 clusters, 9 bodies, 8 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384277 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184718 - 1150 20849.582 206.01695 0 3680.9472 -0.86699156 - 1200 21815.003 45.317416 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064076 - 1300 20780.781 217.36505 0 3680.8286 6.0538619 - 1350 20558.972 254.36481 0 3680.8601 -3.6773978 - 1400 21485.029 99.812941 0 3680.6511 -16.185471 - 1450 21771.108 52.159596 0 3680.6775 -2.4756679 - 1500 21520.948 93.503942 0 3680.3286 2.1023578 - 1550 21351.418 121.6814 0 3680.2511 5.5159969 - 1600 20778.805 216.92173 0 3680.0559 15.089183 - 1650 21477.639 100.21825 0 3679.8247 -1.1045878 - 1700 18501.342 596.47873 0 3680.0357 -15.679646 - 1750 18563.643 587.34777 0 3681.2882 33.532181 - 1800 19110.189 494.82286 0 3679.8543 18.024038 - 1850 21364.195 119.2348 0 3679.9339 2.5291365 - 1900 20146.638 322.1467 0 3679.9197 5.7312008 - 1950 20692.67 231.25355 0 3680.0319 4.297766 - 2000 20943.904 189.1122 0 3679.7629 -22.645478 - 2050 19668.123 401.81885 0 3679.8394 3.6254541 - 2100 20280.531 299.74669 0 3679.8352 7.4808896 - 2150 19182.034 483.49332 0 3680.4991 22.616956 - 2200 21299.885 130.75166 0 3680.7326 4.7110487 - 2250 20487.525 266.54254 0 3681.1301 -8.6422018 - 2300 18654.522 572.01515 0 3681.1021 -5.2661499 - 2350 21512.897 95.719565 0 3681.2024 -9.3553511 - 2400 21467.306 103.39279 0 3681.2771 -29.588234 - 2450 20097.914 332.63812 0 3682.2904 35.845886 - 2500 20762.362 222.00787 0 3682.4016 -12.509872 - 2550 20417.692 279.31982 0 3682.2685 -22.320693 - 2600 21468.738 104.15905 0 3682.2821 -10.050868 - 2650 20742.305 225.31121 0 3682.362 5.2887043 - 2700 18575.367 586.68141 0 3682.5759 21.990986 - 2750 20577.766 252.52411 0 3682.1518 -5.8697894 - 2800 20683.69 234.89244 0 3682.1741 -6.7464964 - 2850 16088.831 1001.1454 0 3682.6172 27.686908 - 2900 20715.565 229.46407 0 3682.0583 6.5207552 - 2950 19969.143 353.98595 0 3682.1765 5.3891903 - 3000 20429.639 277.11063 0 3682.0505 -10.302229 - 3050 19840.965 375.78339 0 3682.611 -6.1970263 - 3100 19149.859 490.69976 0 3682.3429 22.372557 - 3150 20421.772 278.3256 0 3681.9543 8.7381033 - 3200 19492.899 433.22833 0 3682.0448 4.3431162 - 3250 20231.034 310.12852 0 3681.9675 -3.2734265 - 3300 19420.155 445.8855 0 3682.578 14.157316 - 3350 21386.445 117.85565 0 3682.2631 1.9590216 - 3400 20372.28 286.91596 0 3682.296 8.2472357 - 3450 20870.351 203.91619 0 3682.308 7.9601676 - 3500 21469.401 104.14434 0 3682.3778 2.5067348 - 3550 21630.799 77.317219 0 3682.4504 -6.5148709 - 3600 21291.513 133.97558 0 3682.5611 -8.8761801 - 3650 19138.211 493.09199 0 3682.7937 25.075733 - 3700 21282.953 135.36631 0 3682.5252 -8.1163312 - 3750 20660.876 239.15863 0 3682.638 -24.806983 - 3800 20161.169 322.26065 0 3682.4555 13.204808 - 3850 19477.477 435.56421 0 3681.8105 31.065794 - 3900 21108.425 164.35492 0 3682.4258 0.37839399 - 3950 21195.124 150.68497 0 3683.2056 -10.098889 - 4000 21477.025 103.95273 0 3683.4568 -4.139886 - 4050 20603.58 249.35497 0 3683.2849 1.3114756 - 4100 19724.656 396.37166 0 3683.8144 -6.6159163 - 4150 20768.839 221.21034 0 3682.6835 -3.4649381 - 4200 19675.942 404.01538 0 3683.339 17.586922 - 4250 21022.927 179.12036 0 3682.9415 0.59436606 - 4300 20511.134 264.68208 0 3683.2044 8.8380269 - 4350 21038.204 177.05256 0 3683.42 -1.3698914 - 4400 18866.857 539.5082 0 3683.9844 10.461602 - 4450 21607.322 83.184316 0 3684.4046 -1.5071605 - 4500 20895.628 201.9445 0 3684.5492 5.7578991 - 4550 20210.744 316.5044 0 3684.9617 5.6678493 - 4600 20416.269 282.24539 0 3684.9569 -3.0067543 - 4650 18811.283 549.46791 0 3684.6817 7.5182454 - 4700 20899.462 201.92249 0 3685.1661 2.6998262 - 4750 20771.285 223.44307 0 3685.3239 12.165622 - 4800 21834.653 46.231798 0 3685.3407 2.021615 - 4850 21282.348 138.2858 0 3685.3437 4.2174481 - 4900 21892.433 36.607993 0 3685.3468 -10.208769 - 4950 21731.003 63.442124 0 3685.2759 -26.918841 - 5000 21476.967 105.69026 0 3685.1848 -10.007088 - 5050 20485.84 270.81814 0 3685.1248 0.65119013 - 5100 21485.763 104.28837 0 3685.2488 -5.3826149 - 5150 21485.096 104.44183 0 3685.2912 -1.274141 - 5200 21388.175 120.61165 0 3685.3074 -7.7953815 - 5250 20656.672 242.51472 0 3685.2934 -4.4067447 - 5300 20132.262 330.10916 0 3685.4862 -11.466755 - 5350 19080.054 505.63228 0 3685.6413 4.6356684 - 5400 21683.337 71.886529 0 3685.7761 -8.4520633 - 5450 20632.669 246.77173 0 3685.5499 5.5429152 - 5500 20896.92 202.76984 0 3685.5898 3.9762924 - 5550 21172.409 156.92085 0 3685.6557 2.6573146 - 5600 20695.91 236.255 0 3685.5733 -18.109158 - 5650 21741.679 61.956471 0 3685.5697 -3.7520994 - 5700 21164.94 157.60813 0 3685.098 2.4020734 - 5750 21075.393 172.84386 0 3685.4093 7.646915 - 5800 20638.831 245.82076 0 3685.6259 8.3009859 - 5850 20262.966 308.37489 0 3685.5359 7.5861941 - 5900 21730.418 63.97074 0 3685.7071 -6.2813552 - 5950 21820.659 48.990687 0 3685.7673 -5.6400713 - 6000 21027.051 181.2853 0 3685.7937 1.213872 - 6050 14422.66 1284.4174 0 3688.194 57.908667 - 6100 19852.685 377.0743 0 3685.8552 -5.1418207 - 6150 20678.783 239.10987 0 3685.5737 -11.982018 - 6200 19788.097 387.62127 0 3685.6375 -2.684571 - 6250 21611.523 83.575418 0 3685.496 1.7544019 - 6300 19214.109 482.45067 0 3684.8021 24.711965 - 6350 18800.074 553.07966 0 3686.4254 11.125791 - 6400 19771.53 390.40388 0 3685.659 -6.1254643 - 6450 20192.282 319.53713 0 3684.9175 13.959536 - 6500 20360.332 292.28682 0 3685.6755 4.4265274 - 6550 21778.739 56.056362 0 3685.8462 -4.6705452 - 6600 16612.689 917.96646 0 3686.748 -32.617733 - 6650 21068.368 174.38501 0 3685.7797 -0.84207954 - 6700 20749.675 227.41249 0 3685.6916 2.9235268 - 6750 20594.96 253.47665 0 3685.9699 -12.440843 - 6800 19974.133 357.05242 0 3686.0745 34.064247 - 6850 21802.523 52.05173 0 3685.8055 -1.4073818 - 6900 18644.747 577.97031 0 3685.4282 19.759245 - 6950 20463.441 274.90799 0 3685.4815 1.2230553 - 7000 20213.292 316.50714 0 3685.3892 23.9288 - 7050 21571.525 90.089593 0 3685.3437 -26.539261 - 7100 20480.036 271.77541 0 3685.1147 -0.13969301 - 7150 21064.842 174.4144 0 3685.2214 3.5451037 - 7200 21179.296 154.8514 0 3684.7341 -5.007319 - 7250 20714.182 232.84783 0 3685.2115 10.601943 - 7300 19341.561 461.91524 0 3685.5087 18.89547 - 7350 21011.016 183.55321 0 3685.3893 1.6481821 - 7400 21206.598 151.07364 0 3685.5066 1.5040526 - 7450 19999.404 352.83129 0 3686.0652 -18.58587 - 7500 21581.952 88.519362 0 3685.5114 -4.0009441 - 7550 21652.618 76.962392 0 3685.7321 -5.758242 - 7600 21207.411 150.86712 0 3685.4355 -0.023727123 - 7650 21756.168 59.804311 0 3685.8323 0.76768563 - 7700 21825.037 48.380795 0 3685.8869 -0.11098207 - 7750 21581.665 89.078228 0 3686.0223 -0.50220667 - 7800 21714.856 66.946216 0 3686.0889 4.637364 - 7850 21319.774 132.905 0 3686.2007 3.4663558 - 7900 21730.647 64.263898 0 3686.0384 1.0898763 - 7950 21597.663 86.255996 0 3685.8664 3.2847476 - 8000 21724.118 65.137632 0 3685.8239 3.7318614 - 8050 19672.702 406.56191 0 3685.3456 -0.37960768 - 8100 21696.026 69.71367 0 3685.7179 -6.2273451 - 8150 18869.648 540.09908 0 3685.0403 22.915669 - 8200 21717.002 66.01922 0 3685.5196 -4.8553801 - 8250 20292.502 303.3445 0 3685.4282 -13.203008 - 8300 21314.341 133.18215 0 3685.5724 -10.023288 - 8350 20992.272 186.87998 0 3685.592 -4.5538872 - 8400 21726.088 64.55825 0 3685.573 -5.1228188 - 8450 21188.98 153.93449 0 3685.4311 -6.8622554 - 8500 21113.87 166.54678 0 3685.5251 2.6009221 - 8550 20620.735 248.66776 0 3685.4569 -8.0047984 - 8600 19715.276 399.79648 0 3685.6758 -10.980391 - 8650 18898.94 535.95488 0 3685.7782 22.513752 - 8700 21692.841 70.067726 0 3685.5413 -3.3917479 - 8750 20242.909 311.87115 0 3685.6893 17.996012 - 8800 19253.702 476.69077 0 3685.6411 3.7170165 - 8850 17625.913 748.07802 0 3685.7302 11.095548 - 8900 21554.709 92.817998 0 3685.2696 0.30720376 - 8950 21585.337 87.685891 0 3685.2421 -0.22047593 - 9000 17454.847 776.14227 0 3685.2834 22.631913 - 9050 20023.106 347.35041 0 3684.5348 4.0008899 - 9100 21100.691 168.07199 0 3684.8539 2.9016681 - 9150 20307.206 299.45669 0 3683.991 2.1630277 - 9200 21747.579 60.245542 0 3684.8421 -15.419887 - 9250 21525.571 97.26157 0 3684.8567 -7.0449498 - 9300 15084.149 1170.5925 0 3684.6173 43.259279 - 9350 21198.648 151.70957 0 3684.8176 3.0716881 - 9400 17771.533 724.65805 0 3686.5802 -18.320033 - 9450 20029.819 346.23988 0 3684.543 -4.0976705 - 9500 19913.342 365.57743 0 3684.4677 2.4909741 - 9550 20594.619 252.35578 0 3684.7923 -4.4263632 - 9600 21013.668 182.33425 0 3684.6122 -1.9371919 - 9650 16915.052 865.78051 0 3684.9559 1.8697619 - 9700 18789.78 553.48818 0 3685.1181 15.642074 - 9750 21236.716 145.75801 0 3685.2107 -3.6730702 - 9800 20972.957 189.72849 0 3685.2214 0.85691231 - 9850 19658.721 408.29826 0 3684.7517 14.8446 - 9900 21624.401 81.484234 0 3685.5511 3.4507557 - 9950 21883.535 38.474607 0 3685.7304 0.3038348 - 10000 21355.31 126.72088 0 3685.9392 -5.5872974 -Loop time of 3.23589 on 4 procs for 10000 steps with 81 atoms - -Performance: 26700.576 tau/day, 3090.344 timesteps/s, 250.318 katom-step/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0072165 | 0.030554 | 0.065382 | 13.2 | 0.94 -Neigh | 0.010707 | 0.029677 | 0.056594 | 10.6 | 0.92 -Comm | 0.083225 | 0.12075 | 0.17828 | 10.6 | 3.73 -Output | 0.0034779 | 0.0040163 | 0.0050814 | 1.0 | 0.12 -Modify | 2.8247 | 2.8749 | 2.9245 | 2.6 | 88.85 -Other | | 0.176 | | | 5.44 - -Nlocal: 20.25 ave 81 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 33.5 ave 66 max 2 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 212.5 ave 850 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 850 -Ave neighs/atom = 10.493827 -Neighbor list builds = 1246 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems5.g++.1 b/examples/rigid/log.25Mar24.rigid.poems5.g++.1 deleted file mode 100644 index 03ca091c13..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems5.g++.1 +++ /dev/null @@ -1,329 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems file connected-bodies2.dat -2 clusters, 9 bodies, 7 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12774.759 1538.7378 0 3904.434 18.086356 - 100 19803.641 237.21132 0 3904.5523 -3.1528278 - 150 20259.6 152.62072 0 3904.3985 -4.6173512 - 200 20705.978 69.977442 0 3904.4178 9.0928146 - 250 19552.211 283.50505 0 3904.2848 15.670464 - 300 19266.324 333.5788 0 3901.4165 7.2119173 - 350 20738.325 63.738945 0 3904.1694 -23.039989 - 400 20616.682 86.082444 0 3903.9864 -13.783584 - 450 19831.326 230.13818 0 3902.6059 0.42074126 - 500 20365.825 131.47231 0 3902.9213 0.69215475 - 550 20794.102 52.163238 0 3902.9229 4.5895354 - 600 20853.873 40.899172 0 3902.7275 2.3593042 - 650 19255.802 336.29509 0 3902.1844 10.341742 - 700 18526.969 471.02462 0 3901.9448 -0.61898691 - 750 18960.662 391.26028 0 3902.494 12.047308 - 800 20142.432 172.05197 0 3902.1319 4.6838632 - 850 19932.48 210.71155 0 3901.9116 3.471602 - 900 20243.528 153.13972 0 3901.9411 3.6490762 - 950 20388.132 126.88722 0 3902.4671 -4.4518463 - 1000 20076.333 184.61916 0 3902.4586 -2.2723139 - 1050 20859.506 39.696992 0 3902.5684 6.45166 - 1100 15284.661 1072.1908 0 3902.6836 21.194042 - 1150 19658.317 261.99809 0 3902.4272 -2.8744219 - 1200 20767.681 56.717093 0 3902.5839 -34.817443 - 1250 20625.583 82.586395 0 3902.1388 11.697328 - 1300 20690.013 71.006479 0 3902.4903 -29.292783 - 1350 20936.019 26.022787 0 3903.0634 1.0316033 - 1400 19753.56 244.81774 0 3902.8844 6.7138457 - 1450 15690.143 998.34271 0 3903.9248 48.124667 - 1500 20234.455 155.92517 0 3903.0465 13.172173 - 1550 20779.63 55.062895 0 3903.1426 -2.6390424 - 1600 20642.757 80.232879 0 3902.9657 -2.4687934 - 1650 18785.716 423.90031 0 3902.7365 -5.6468747 - 1700 20965.076 20.760295 0 3903.1818 -0.45382233 - 1750 18935.466 396.94949 0 3903.5173 25.912008 - 1800 20581.509 91.766145 0 3903.1567 3.8229018 - 1850 20616.968 85.18122 0 3903.1382 4.1907646 - 1900 16600.676 828.66496 0 3902.8643 -0.49197745 - 1950 20175.677 166.50513 0 3902.7416 5.6027746 - 2000 20268.078 149.2566 0 3902.6044 -1.1951453 - 2050 20155.388 170.16328 0 3902.6425 -0.79473147 - 2100 19715.497 250.63403 0 3901.652 3.6719022 - 2150 20677.205 73.792009 0 3902.9041 0.64246071 - 2200 20041.156 191.58407 0 3902.9093 7.4438342 - 2250 19924.453 213.0259 0 3902.7394 2.3652069 - 2300 20432.764 119.13103 0 3902.9763 -11.527566 - 2350 18265.828 520.75569 0 3903.3165 -8.9634198 - 2400 19574.981 277.7963 0 3902.7927 1.8085002 - 2450 20655.975 77.958119 0 3903.1387 3.4001031 - 2500 19783.143 239.3546 0 3902.8995 24.872182 - 2550 16660.113 818.36907 0 3903.5752 -11.766765 - 2600 19789.524 238.61817 0 3903.3448 3.3910931 - 2650 18532.96 471.8684 0 3903.898 -4.812577 - 2700 19081.457 369.81185 0 3903.4151 -0.49159968 - 2750 20370.042 131.6764 0 3903.9064 -3.3818893 - 2800 20727.087 65.499688 0 3903.8491 4.3537941 - 2850 18252.657 523.061 0 3903.1827 11.774986 - 2900 20780.391 55.586541 0 3903.8071 5.4415831 - 2950 20361.047 132.98647 0 3903.5508 -2.4847656 - 3000 19528.633 284.87405 0 3901.2876 14.23453 - 3050 20385.56 127.80448 0 3902.9081 -0.51079949 - 3100 19040.7 376.96613 0 3903.0216 -8.9425331 - 3150 20053.417 189.7312 0 3903.327 4.6695643 - 3200 20862.681 40.219985 0 3903.6795 1.2220199 - 3250 20692.32 71.660474 0 3903.5716 2.118694 - 3300 20560.104 95.905282 0 3903.332 5.9856809 - 3350 20693.236 71.35789 0 3903.4387 3.9315564 - 3400 19045.135 376.64379 0 3903.5206 3.9692419 - 3450 20354.826 134.28157 0 3903.6938 7.6208552 - 3500 20528.053 102.12643 0 3903.6178 7.2863414 - 3550 20525.13 103.01612 0 3903.9661 8.4807852 - 3600 19782.42 240.28031 0 3903.6914 1.0181878 - 3650 20519.52 104.05243 0 3903.9636 -2.36641 - 3700 20024.307 195.68587 0 3903.8908 -6.261818 - 3750 20239.643 155.72722 0 3903.8092 -20.781566 - 3800 20601.2 88.794605 0 3903.8317 -11.491217 - 3850 20973.346 19.675436 0 3903.6283 -9.0554155 - 3900 16212.846 902.10241 0 3904.4813 -19.773976 - 3950 19645.576 264.59477 0 3902.6643 16.065663 - 4000 17439.655 673.47397 0 3903.0398 -3.7357722 - 4050 19305.077 328.50056 0 3903.5148 10.43441 - 4100 18634.36 451.24343 0 3902.0508 3.4327844 - 4150 20249.11 153.64108 0 3903.4763 -2.5190604 - 4200 19177.928 351.81896 0 3903.2871 -5.5110274 - 4250 20754.898 60.189732 0 3903.6893 -3.3019026 - 4300 19693.307 256.31591 0 3903.2245 5.8795929 - 4350 18411.713 494.6957 0 3904.2722 4.2513782 - 4400 18499.707 474.35141 0 3900.2231 10.120914 - 4450 18620.543 449.98137 0 3898.2301 0.74648702 - 4500 18930.676 398.47668 0 3904.1573 -3.3953153 - 4550 18708.382 438.70363 0 3903.2188 8.478793 - 4600 19937.049 211.7655 0 3903.8117 4.8300368 - 4650 19919.169 214.98435 0 3903.7194 -1.0166319 - 4700 19345.329 321.18127 0 3903.6496 -23.032019 - 4750 18391.67 498.629 0 3904.4939 -15.40779 - 4800 18597.103 459.20983 0 3903.1179 9.3900723 - 4850 19857.892 226.27908 0 3903.6665 4.1998427 - 4900 20428.515 120.59483 0 3903.6532 -1.8636046 - 4950 18457.127 485.79992 0 3903.7864 -7.2380409 - 5000 20543.123 99.480661 0 3903.7627 -0.39555479 - 5050 18716.671 436.46735 0 3902.5175 29.395654 - 5100 20048.411 191.03727 0 3903.706 -0.91178091 - 5150 19647.675 265.24989 0 3903.7083 3.8658742 - 5200 20787.465 54.078505 0 3903.6091 -3.3582221 - 5250 20630.096 83.165593 0 3903.5538 -11.86045 - 5300 16598.926 830.02918 0 3903.9043 -1.8793568 - 5350 19114.667 363.424 0 3903.1772 11.894383 - 5400 19563.654 280.22257 0 3903.1215 8.8285523 - 5450 20012.628 197.27325 0 3903.3154 2.1981092 - 5500 17845.428 599.4114 0 3904.1202 20.091131 - 5550 20630.423 82.857857 0 3903.3065 0.93827014 - 5600 19675.125 259.89939 0 3903.4411 -2.4034875 - 5650 19932.349 212.22024 0 3903.3961 2.0064698 - 5700 20499.192 107.17918 0 3903.3259 2.5440649 - 5750 19522.335 287.94941 0 3903.1966 -0.7615272 - 5800 18010.242 568.31554 0 3903.5455 -6.3433889 - 5850 20177.497 166.64243 0 3903.2159 -0.95012013 - 5900 17919.358 584.40694 0 3902.8065 10.49282 - 5950 18390.453 498.29164 0 3903.9311 10.026285 - 6000 18040.232 562.71939 0 3903.5032 0.22172862 - 6050 19777.355 240.88597 0 3903.3592 -3.1899015 - 6100 19132.014 360.58765 0 3903.5531 1.6644736 - 6150 19780.214 240.31985 0 3903.3224 4.2403325 - 6200 18883.45 406.45503 0 3903.3902 -3.5422327 - 6250 19875.924 222.49729 0 3903.2239 3.0535292 - 6300 19882.454 221.4928 0 3903.4287 5.7371152 - 6350 19040.565 377.18193 0 3903.2124 -0.26454332 - 6400 19137.008 359.7025 0 3903.5929 9.5375531 - 6450 19655.205 263.59789 0 3903.4507 -1.8592763 - 6500 18385.045 499.5436 0 3904.1816 -7.8549266 - 6550 18823.423 417.69964 0 3903.5187 -2.8268518 - 6600 19414.118 308.11966 0 3903.3268 4.6627243 - 6650 20533.065 100.75047 0 3903.1698 3.3716972 - 6700 20206.283 161.18079 0 3903.085 5.6368472 - 6750 19517.622 288.72511 0 3903.0995 0.3337076 - 6800 18152.278 541.45525 0 3902.9883 -7.2734044 - 6850 18910.032 401.19322 0 3903.0511 6.2653128 - 6900 18580.612 462.26403 0 3903.1182 15.681586 - 6950 20459.012 114.44928 0 3903.1552 -0.82985388 - 7000 20866.868 38.822988 0 3903.0578 -6.2182429 - 7050 20460.074 114.11492 0 3903.0175 -2.1465384 - 7100 20553.533 96.636153 0 3902.846 -5.105486 - 7150 20447.915 116.30898 0 3902.9599 8.2035464 - 7200 20703.396 69.030336 0 3902.9926 9.1221166 - 7250 19652.215 263.63438 0 3902.9335 17.675447 - 7300 20691.205 71.094727 0 3902.7994 -1.7423404 - 7350 18845.785 412.74313 0 3902.7033 -2.0276584 - 7400 18462.131 483.73088 0 3902.6441 -0.22424322 - 7450 20458.641 113.96173 0 3902.599 -4.9286236 - 7500 17681.258 628.1576 0 3902.4647 -16.803813 - 7550 19149.34 356.35773 0 3902.5318 -5.3481685 - 7600 19723.907 249.45462 0 3902.03 7.2597963 - 7650 19317.18 325.01536 0 3902.271 -0.16642424 - 7700 19620.248 269.22043 0 3902.5996 -4.6771277 - 7750 17751.083 615.46827 0 3902.7058 7.3637076 - 7800 20724.904 64.633157 0 3902.5784 5.2079592 - 7850 19966.924 204.60327 0 3902.1817 6.4943932 - 7900 19730.339 248.88701 0 3902.6536 8.4392109 - 7950 19907.748 216.06587 0 3902.6859 -5.1989259 - 8000 18217.971 528.46486 0 3902.1632 -15.394144 - 8050 17868.898 592.98294 0 3902.0381 9.1139508 - 8100 19370.601 315.22753 0 3902.3759 7.9651368 - 8150 18199.01 532.43818 0 3902.6252 10.07163 - 8200 20646.337 79.222148 0 3902.6179 0.17396159 - 8250 20811.938 48.374613 0 3902.4372 -14.594973 - 8300 20906.571 30.626024 0 3902.2132 -12.34909 - 8350 19873.431 221.86861 0 3902.1335 7.1435615 - 8400 20374.979 127.96219 0 3901.1064 10.527044 - 8450 20701.502 68.073078 0 3901.6846 2.5071154 - 8500 20452.423 113.98399 0 3901.4698 4.2164058 - 8550 19695.059 253.87834 0 3901.1115 8.0656507 - 8600 19447.531 299.45597 0 3900.8505 -0.71982287 - 8650 17202.668 714.55842 0 3900.2378 -16.743518 - 8700 18579.153 459.20676 0 3899.7906 3.4494692 - 8750 20247.204 150.39086 0 3899.8731 -0.1022032 - 8800 18520.797 469.57224 0 3899.3494 5.7412252 - 8850 16011.411 934.80107 0 3899.8772 34.500452 - 8900 19045.914 372.92529 0 3899.9464 10.001612 - 8950 19798.369 233.70991 0 3900.0746 9.3270865 - 9000 17141.02 725.70858 0 3899.9716 -6.7470927 - 9050 17722.847 617.81927 0 3899.828 -10.909071 - 9100 20811.604 45.701413 0 3899.7021 -12.300065 - 9150 18066.034 554.62654 0 3900.1884 -5.7606837 - 9200 19259.884 332.49612 0 3899.1412 -40.231609 - 9250 19116.782 359.42396 0 3899.5689 0.68271469 - 9300 18785.022 421.1178 0 3899.8256 -20.433345 - 9350 19018.32 377.90289 0 3899.814 3.2963902 - 9400 17321.798 691.93839 0 3899.6788 24.552549 - 9450 18318.437 507.12661 0 3899.4297 6.1367468 - 9500 16431.681 857.32722 0 3900.2311 25.431389 - 9550 17920.939 581.45381 0 3900.1462 9.1734747 - 9600 16603.394 825.79291 0 3900.4954 -5.9643183 - 9650 17753.931 607.15019 0 3894.9151 2.2302338 - 9700 17452.305 668.30613 0 3900.2145 2.4635322 - 9750 15955.164 945.80159 0 3900.4617 20.290857 - 9800 17958.495 574.7055 0 3900.3526 12.218625 - 9850 18759.766 423.66965 0 3897.7005 -4.8999337 - 9900 19798.529 232.2507 0 3898.6449 0.10312101 - 9950 18260.87 517.50071 0 3899.1432 5.7261992 - 10000 19116.279 359.58291 0 3899.6345 3.2110764 -Loop time of 3.40298 on 1 procs for 10000 steps with 81 atoms - -Performance: 25389.516 tau/day, 2938.601 timesteps/s, 238.027 katom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.068835 | 0.068835 | 0.068835 | 0.0 | 2.02 -Neigh | 0.078603 | 0.078603 | 0.078603 | 0.0 | 2.31 -Comm | 0.013957 | 0.013957 | 0.013957 | 0.0 | 0.41 -Output | 0.0034786 | 0.0034786 | 0.0034786 | 0.0 | 0.10 -Modify | 3.2212 | 3.2212 | 3.2212 | 0.0 | 94.66 -Other | | 0.01692 | | | 0.50 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 105 ave 105 max 105 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 498 ave 498 max 498 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 498 -Ave neighs/atom = 6.1481481 -Neighbor list builds = 1202 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.poems5.g++.4 b/examples/rigid/log.25Mar24.rigid.poems5.g++.4 deleted file mode 100644 index 78f4d4417b..0000000000 --- a/examples/rigid/log.25Mar24.rigid.poems5.g++.4 +++ /dev/null @@ -1,329 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems file connected-bodies2.dat -2 clusters, 9 bodies, 7 joints, 81 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- fix poems command: doi:10.1016/j.ijnonlinmec.2008.04.003 - -@Article{Mukherjee08, - author = {R. M. Mukherjee and P. S. Crozier and S. J. Plimpton and K. S. Anderson}, - title = {Substructured Molecular Dynamics Using Multibody Dynamics Algorithms}, - journal = {Intl.\ J.\ Non-Linear Mechanics}, - year = 2008, - volume = 43, - number = 10, - pages = {1040--1055} -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12774.759 1538.7378 0 3904.434 18.086356 - 100 19803.641 237.21132 0 3904.5523 -3.1528278 - 150 20259.6 152.62032 0 3904.3981 -4.6173548 - 200 20705.978 69.977442 0 3904.4178 9.0928146 - 250 19552.211 283.50525 0 3904.285 15.670465 - 300 19266.324 333.5792 0 3901.4169 7.2119197 - 350 20738.325 63.738945 0 3904.1694 -23.03999 - 400 20616.682 86.082444 0 3903.9864 -13.783584 - 450 19831.326 230.13858 0 3902.6063 0.42074361 - 500 20365.825 131.47271 0 3902.9217 0.69215592 - 550 20794.102 52.163238 0 3902.9229 4.5895354 - 600 20853.873 40.899172 0 3902.7275 2.3593042 - 650 19255.802 336.29509 0 3902.1844 10.341742 - 700 18526.969 471.02462 0 3901.9448 -0.61898691 - 750 18960.662 391.26068 0 3902.4944 12.04731 - 800 20142.432 172.05197 0 3902.1319 4.6838632 - 850 19932.48 210.71175 0 3901.9118 3.4716031 - 900 20243.528 153.13972 0 3901.9411 3.6490762 - 950 20388.132 126.88722 0 3902.4671 -4.4518463 - 1000 20076.333 184.61916 0 3902.4586 -2.272315 - 1050 20859.506 39.696992 0 3902.5684 6.45166 - 1100 15284.661 1072.1906 0 3902.6833 21.194041 - 1150 19658.317 261.99809 0 3902.4272 -2.8744196 - 1200 20767.681 56.717093 0 3902.5839 -34.817444 - 1250 20625.583 82.586396 0 3902.1388 11.697328 - 1300 20690.013 71.006479 0 3902.4903 -29.292783 - 1350 20936.019 26.022787 0 3903.0634 1.0316031 - 1400 19753.56 244.81777 0 3902.8844 6.713847 - 1450 15690.145 998.34279 0 3903.9252 48.124638 - 1500 20234.455 155.92476 0 3903.0461 13.17218 - 1550 20779.631 55.063072 0 3903.1428 -2.6390427 - 1600 20642.756 80.233303 0 3902.9659 -2.4688077 - 1650 18785.71 423.90132 0 3902.7365 -5.6468182 - 1700 20965.076 20.760481 0 3903.182 -0.45377448 - 1750 18935.45 396.95247 0 3903.5173 25.912353 - 1800 20581.523 91.763662 0 3903.1567 3.8225817 - 1850 20616.962 85.182351 0 3903.1382 4.1907744 - 1900 16601.061 828.59343 0 3902.8639 -0.49284971 - 1950 20175.618 166.51633 0 3902.7419 5.6031735 - 2000 20266.439 149.55931 0 3902.6036 -1.1956447 - 2050 20159.308 169.44017 0 3902.6453 -0.7983344 - 2100 19743.72 245.40822 0 3901.6527 3.5301052 - 2150 20674.556 74.284034 0 3902.9055 0.61532081 - 2200 19950.784 208.30189 0 3902.8915 7.6523945 - 2250 19817.161 232.7485 0 3902.5932 3.4492756 - 2300 20459.058 114.2307 0 3902.9451 -11.066393 - 2350 18359.21 503.25787 0 3903.1115 -9.0741539 - 2400 19952.914 207.84881 0 3902.8328 -0.53972874 - 2450 19661.352 259.78979 0 3900.781 7.8669927 - 2500 20917.293 29.699201 0 3903.2719 1.1433085 - 2550 20763.955 57.990256 0 3903.1671 -1.1088372 - 2600 20640.005 80.556339 0 3902.7795 9.6127007 - 2650 20823.227 47.292746 0 3903.446 2.2923503 - 2700 20401.43 125.53141 0 3903.5739 -8.0683618 - 2750 20689.918 72.242212 0 3903.7084 0.22078527 - 2800 20783.922 54.87309 0 3903.7476 2.0668249 - 2850 19258.563 336.84835 0 3903.2488 4.2704683 - 2900 20565.694 95.184831 0 3903.6468 -0.24799068 - 2950 20915.041 30.344751 0 3903.5004 -2.9900907 - 3000 19571.964 278.74004 0 3903.1778 12.195325 - 3050 20356.693 133.43974 0 3903.1976 0.11608195 - 3100 20047.888 190.69627 0 3903.268 -4.5895546 - 3150 19834.363 230.59072 0 3903.6209 -1.4352632 - 3200 20213.412 160.25129 0 3903.4757 3.7488266 - 3250 19286.774 332.04497 0 3903.6699 -5.0835358 - 3300 20952.226 23.774103 0 3903.816 0.10019546 - 3350 20407.952 124.62932 0 3903.8798 0.4403531 - 3400 19401.716 311.03567 0 3903.9461 1.8034568 - 3450 20880.78 37.20558 0 3904.0167 6.3948533 - 3500 19529.313 287.50301 0 3904.0425 12.311168 - 3550 20943.604 25.677677 0 3904.1228 5.1786098 - 3600 20272.725 149.91697 0 3904.1254 1.196909 - 3650 19781.047 240.95421 0 3904.1111 -8.5091671 - 3700 20613.433 86.53896 0 3903.8414 -9.1622102 - 3750 20567.605 95.294456 0 3904.1101 -0.11887825 - 3800 19891.98 220.32932 0 3904.0292 6.8801146 - 3850 20669.735 76.407858 0 3904.1365 -7.4310509 - 3900 20908.711 32.197181 0 3904.1807 -4.6573356 - 3950 20822.78 48.03134 0 3904.1018 0.086779759 - 4000 20199.055 163.66262 0 3904.2283 2.0027771 - 4050 20072.638 187.07041 0 3904.2256 4.4103784 - 4100 17724.651 619.7903 0 3902.1331 11.210006 - 4150 20760.201 60.001382 0 3904.4831 -3.8510009 - 4200 19159.102 356.30472 0 3904.2865 -2.3503308 - 4250 19403.974 311.3497 0 3904.6783 -1.2458384 - 4300 20858.687 42.000734 0 3904.7206 2.1750528 - 4350 20486.989 110.94383 0 3904.8306 5.017245 - 4400 20231.073 158.28825 0 3904.7832 7.4295979 - 4450 16369.689 873.39361 0 3904.8175 14.371454 - 4500 20745.196 63.11427 0 3904.8172 -7.855609 - 4550 18688.003 443.85636 0 3904.5977 9.8067426 - 4600 17755.672 616.68475 0 3904.7721 -3.9654703 - 4650 19843.131 230.34486 0 3904.9988 -0.13553926 - 4700 18873.202 409.99341 0 3905.0308 15.912724 - 4750 20605.355 89.223116 0 3905.0295 2.0847611 - 4800 20136.483 176.1278 0 3905.1062 -1.7091113 - 4850 19808.073 236.83278 0 3904.9945 5.0982271 - 4900 19142.083 359.55764 0 3904.3878 8.2072008 - 4950 20539.687 101.08198 0 3904.7277 8.0469319 - 5000 20840.809 45.759021 0 3905.168 4.771755 - 5050 20009.696 199.45528 0 3904.9546 6.1191423 - 5100 20882.034 38.247578 0 3905.2909 -6.3068822 - 5150 20329.869 140.47458 0 3905.2651 -21.720979 - 5200 17334.411 695.67098 0 3905.7471 -9.8243617 - 5250 19602.025 275.17282 0 3905.1775 -3.2371379 - 5300 20858.74 42.630642 0 3905.3603 0.38011789 - 5350 20828.619 48.188698 0 3905.3403 5.7187945 - 5400 20978.428 20.447148 0 3905.3413 6.1168011 - 5450 20115.374 179.9294 0 3904.9987 8.6440563 - 5500 20522.744 104.7733 0 3905.2815 -2.6561664 - 5550 20625.724 85.600795 0 3905.1792 -1.327206 - 5600 19559.638 282.68742 0 3904.8426 17.893028 - 5650 20552.224 98.978098 0 3904.9455 2.4489071 - 5700 19982.142 204.09989 0 3904.4966 9.9034011 - 5750 20408.825 125.30875 0 3904.7209 1.2515548 - 5800 19773.143 243.02134 0 3904.7144 -2.6729948 - 5850 20781.934 56.310486 0 3904.8168 -1.659054 - 5900 19807.668 236.54392 0 3904.6306 0.49776361 - 5950 20741.237 63.921667 0 3904.8916 4.2800039 - 6000 20322.7 140.98125 0 3904.4442 7.4978024 - 6050 20858.439 42.383629 0 3905.0575 -4.6872323 - 6100 20212.538 162.022 0 3905.0847 -7.0796165 - 6150 18513.957 476.7087 0 3905.2193 7.107138 - 6200 20802.734 52.621638 0 3904.9797 3.7242428 - 6250 20818.044 49.717458 0 3904.9109 -0.91041774 - 6300 19987.245 203.4635 0 3904.8052 -0.86714551 - 6350 20806.906 51.449749 0 3904.5806 -4.0699629 - 6400 20530.3 103.09809 0 3905.0055 1.660177 - 6450 20667.085 77.715553 0 3904.9535 0.99217521 - 6500 20515.816 105.81762 0 3905.0428 3.0994091 - 6550 20548.348 99.627131 0 3904.8769 -0.77417688 - 6600 19827.378 232.99889 0 3904.7355 3.295082 - 6650 19237.199 342.94808 0 3905.3923 -6.2226637 - 6700 19611.621 273.139 0 3904.9206 -3.5465535 - 6750 20874.805 39.1893 0 3904.8939 -0.051336814 - 6800 19433.717 305.99952 0 3904.8361 -19.858865 - 6850 20119.223 179.19987 0 3904.9818 4.6466283 - 6900 20467.389 114.77871 0 3905.0359 10.290214 - 6950 20334.202 139.43289 0 3905.0259 7.5448433 - 7000 20504.591 107.86929 0 3905.0158 -0.10092084 - 7050 17969.214 576.83722 0 3904.4694 10.852897 - 7100 19186.398 351.80467 0 3904.8414 0.24779979 - 7150 20261.23 152.54684 0 3904.6265 -7.0175844 - 7200 20696.821 71.985154 0 3904.7298 3.9649146 - 7250 18456.212 487.1819 0 3904.9989 5.8280225 - 7300 17705.1 625.95928 0 3904.6816 6.8298215 - 7350 17032.039 750.96958 0 3905.051 11.833303 - 7400 20557.431 97.599213 0 3904.5308 0.43747863 - 7450 20466.847 114.5693 0 3904.7261 1.9786538 - 7500 20416.862 123.31643 0 3904.2168 -2.9094738 - 7550 18433.95 487.50767 0 3901.2022 4.0921479 - 7600 19950.107 209.92208 0 3904.3863 3.9114888 - 7650 16037.844 934.94785 0 3904.9189 -1.2183461 - 7700 20145.239 173.99945 0 3904.5993 3.1185554 - 7750 18672.579 446.35236 0 3904.2373 4.1086445 - 7800 19740.616 249.10395 0 3904.7737 4.6048428 - 7850 20801.917 52.742096 0 3904.9489 1.5978265 - 7900 20305.348 144.57749 0 3904.8272 2.7348725 - 7950 20221.086 159.31958 0 3903.9652 7.1592496 - 8000 20826.907 47.953835 0 3904.7884 6.2728901 - 8050 18646.418 452.02126 0 3905.0617 5.9716218 - 8100 20653.653 80.183024 0 3904.9336 -1.8274783 - 8150 20843.275 45.172279 0 3905.0379 -6.9445524 - 8200 20364.78 133.45082 0 3904.7064 -12.094533 - 8250 18163.745 541.08818 0 3904.7447 -2.6103997 - 8300 20889.664 36.793018 0 3905.2494 -9.2650749 - 8350 20307.367 144.33088 0 3904.9543 -0.65999546 - 8400 20485.202 111.41317 0 3904.9691 -0.42802224 - 8450 20864.395 41.146879 0 3904.9238 7.7084978 - 8500 20901.899 34.291267 0 3905.0132 -5.2070823 - 8550 20211.78 162.02611 0 3904.9484 -5.8363409 - 8600 19639.538 268.05291 0 3905.0044 3.8180903 - 8650 19919.356 216.24885 0 3905.0185 0.17130921 - 8700 19499.449 293.97522 0 3904.9843 -4.897872 - 8750 20270.687 151.1571 0 3904.9879 0.28558082 - 8800 18804.137 422.61651 0 3904.864 15.351015 - 8850 20654.443 80.110976 0 3905.0078 4.1368065 - 8900 19953.725 209.81046 0 3904.9447 10.71743 - 8950 18195.013 536.67764 0 3906.1245 21.497802 - 9000 20478.531 112.78923 0 3905.1098 -13.053056 - 9050 20866.484 40.901611 0 3905.0653 -3.6134066 - 9100 20322.595 141.61419 0 3905.0577 15.459697 - 9150 20855.456 42.94311 0 3905.0646 4.9123213 - 9200 20208.201 162.79363 0 3905.0531 2.5454472 - 9250 18394.203 498.63686 0 3904.9707 0.041811692 - 9300 18776.997 427.7118 0 3904.9335 -7.652483 - 9350 18330.751 510.07857 0 3904.6621 8.3424059 - 9400 17538.366 657.08623 0 3904.9319 8.5478668 - 9450 20309.605 143.77142 0 3904.8093 6.6831447 - 9500 19982.331 203.81545 0 3904.2471 -7.6711411 - 9550 19410.612 310.1139 0 3904.6717 5.3983286 - 9600 19198.225 349.06634 0 3904.2932 -4.107658 - 9650 19388.043 314.31566 0 3904.6939 6.1198194 - 9700 18849.37 414.1045 0 3904.7286 5.4468861 - 9750 18263.312 523.38716 0 3905.4819 -0.56480349 - 9800 20421.858 122.53973 0 3904.3653 -15.641399 - 9850 17678.959 631.15683 0 3905.0381 -1.805446 - 9900 19421.046 306.67446 0 3903.1644 7.0287747 - 9950 18460.64 483.18902 0 3901.8261 3.658774 - 10000 19781.151 239.38136 0 3902.5575 6.3312911 -Loop time of 3.21586 on 4 procs for 10000 steps with 81 atoms - -Performance: 26866.868 tau/day, 3109.591 timesteps/s, 251.877 katom-step/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0068055 | 0.017185 | 0.043838 | 11.8 | 0.53 -Neigh | 0.010594 | 0.021601 | 0.042532 | 8.5 | 0.67 -Comm | 0.068664 | 0.091849 | 0.10748 | 4.8 | 2.86 -Output | 0.0038351 | 0.0044469 | 0.0057465 | 1.1 | 0.14 -Modify | 2.8494 | 2.9033 | 2.9663 | 2.5 | 90.28 -Other | | 0.1775 | | | 5.52 - -Nlocal: 20.25 ave 36 max 0 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Nghost: 38.25 ave 50 max 28 min -Histogram: 1 0 1 0 0 1 0 0 0 1 -Neighs: 126.5 ave 213 max 0 min -Histogram: 1 0 0 0 1 0 0 0 0 2 - -Total # of neighbors = 506 -Ave neighs/atom = 6.2469136 -Neighbor list builds = 1207 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/rigid/log.25Mar24.rigid.property.g++.1 b/examples/rigid/log.25Mar24.rigid.property.g++.1 deleted file mode 100644 index 0a3d0da63a..0000000000 --- a/examples/rigid/log.25Mar24.rigid.property.g++.1 +++ /dev/null @@ -1,343 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -fix 0 all property/atom i_bodies - -read_data data.rigid-property fix 0 NULL Clumps -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -# assemble bodies from per-atom custom integer property bodies -fix 1 all rigid custom i_bodies - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.42 | 4.42 | 4.42 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690665 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.0007653281 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652436 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589881 0 5269.4979 12.062708 - 9750 16738.013 0.13550093 0 5269.5101 11.407245 - 9800 16738.512 -0.01162033 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270581 0 5269.5237 11.395098 - 9900 16738.489 -0.0002498458 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.13897 on 1 procs for 10000 steps with 81 atoms - -Performance: 621716.264 tau/day, 71957.901 timesteps/s, 5.829 Matom-step/s -98.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0095014 | 0.0095014 | 0.0095014 | 0.0 | 6.84 -Neigh | 0.050174 | 0.050174 | 0.050174 | 0.0 | 36.10 -Comm | 0.0091698 | 0.0091698 | 0.0091698 | 0.0 | 6.60 -Output | 0.0016255 | 0.0016255 | 0.0016255 | 0.0 | 1.17 -Modify | 0.060968 | 0.060968 | 0.060968 | 0.0 | 43.87 -Other | | 0.007531 | | | 5.42 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.property.g++.4 b/examples/rigid/log.25Mar24.rigid.property.g++.4 deleted file mode 100644 index 5195cd4eb6..0000000000 --- a/examples/rigid/log.25Mar24.rigid.property.g++.4 +++ /dev/null @@ -1,343 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic -atom_modify map array - -pair_style lj/cut 2.5 - -fix 0 all property/atom i_bodies - -read_data data.rigid-property fix 0 NULL Clumps -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -# assemble bodies from per-atom custom integer property bodies -fix 1 all rigid custom i_bodies - 9 rigid bodies with 81 atoms - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.3 | 4.394 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722867e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706558 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156158 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 - 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589886 0 5269.4979 12.062708 - 9750 16738.013 0.13550089 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270567 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984578 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.145717 on 4 procs for 10000 steps with 81 atoms - -Performance: 592928.932 tau/day, 68626.034 timesteps/s, 5.559 Matom-step/s -98.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0017512 | 0.002579 | 0.0032423 | 1.1 | 1.77 -Neigh | 0.01337 | 0.01442 | 0.016488 | 1.0 | 9.90 -Comm | 0.066749 | 0.068666 | 0.070799 | 0.7 | 47.12 -Output | 0.0018563 | 0.0020346 | 0.0025278 | 0.6 | 1.40 -Modify | 0.040991 | 0.042542 | 0.044042 | 0.6 | 29.19 -Other | | 0.01548 | | | 10.62 - -Nlocal: 20.25 ave 37 max 3 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.small.g++.1 b/examples/rigid/log.25Mar24.rigid.small.g++.1 deleted file mode 100644 index 7c1c88364b..0000000000 --- a/examples/rigid/log.25Mar24.rigid.small.g++.1 +++ /dev/null @@ -1,321 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.002 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/small molecule - create bodies CPU = 0.000 seconds - 9 rigid bodies with 81 atoms - 1.2247449 = max distance from body owner to body atom - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722853e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.05932751 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934369 0 5269.4889 12.025288 - 3750 16737.731 0.20706559 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690669 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646805 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532808 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652431 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156156 0 5269.5203 12.011611 - 9600 16738.549 -0.026814366 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589875 0 5269.4979 12.062708 - 9750 16738.013 0.13550135 0 5269.5101 11.407245 - 9800 16738.512 -0.01162033 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270544 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984555 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.159025 on 1 procs for 10000 steps with 81 atoms - -Performance: 543312.198 tau/day, 62883.356 timesteps/s, 5.094 Matom-step/s -98.3% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0094515 | 0.0094515 | 0.0094515 | 0.0 | 5.94 -Bond | 0.00045015 | 0.00045015 | 0.00045015 | 0.0 | 0.28 -Neigh | 0.066186 | 0.066186 | 0.066186 | 0.0 | 41.62 -Comm | 0.0097819 | 0.0097819 | 0.0097819 | 0.0 | 6.15 -Output | 0.0021947 | 0.0021947 | 0.0021947 | 0.0 | 1.38 -Modify | 0.062923 | 0.062923 | 0.062923 | 0.0 | 39.57 -Other | | 0.008038 | | | 5.05 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.small.g++.4 b/examples/rigid/log.25Mar24.rigid.small.g++.4 deleted file mode 100644 index 1b0d54f7b3..0000000000 --- a/examples/rigid/log.25Mar24.rigid.small.g++.4 +++ /dev/null @@ -1,321 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/small molecule - create bodies CPU = 0.000 seconds - 9 rigid bodies with 81 atoms - 1.2247449 = max distance from body owner to body atom - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722842e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554428 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934367 0 5269.4889 12.025288 - 3750 16737.731 0.20706557 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690662 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532814 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.0003765244 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 - 9600 16738.549 -0.026814371 0 5269.5163 12.011415 - 9650 16738.765 -0.10191524 0 5269.5092 12.011013 - 9700 16735.041 1.0589896 0 5269.4979 12.062708 - 9750 16738.013 0.13550091 0 5269.5101 11.407245 - 9800 16738.512 -0.011620327 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984566 0 5269.5242 11.395085 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.200426 on 4 procs for 10000 steps with 81 atoms - -Performance: 431082.236 tau/day, 49893.777 timesteps/s, 4.041 Matom-step/s -97.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.001863 | 0.0024669 | 0.0029246 | 0.8 | 1.23 -Bond | 0.00033475 | 0.00034422 | 0.00035273 | 0.0 | 0.17 -Neigh | 0.016097 | 0.017035 | 0.018935 | 0.9 | 8.50 -Comm | 0.066051 | 0.06822 | 0.070253 | 0.7 | 34.04 -Output | 0.0020466 | 0.0021927 | 0.0026005 | 0.5 | 1.09 -Modify | 0.094972 | 0.096687 | 0.098173 | 0.4 | 48.24 -Other | | 0.01348 | | | 6.73 - -Nlocal: 20.25 ave 37 max 3 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.small.infile.g++.1 b/examples/rigid/log.25Mar24.rigid.small.infile.g++.1 deleted file mode 100644 index 8c441d5d00..0000000000 --- a/examples/rigid/log.25Mar24.rigid.small.infile.g++.1 +++ /dev/null @@ -1,322 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.003 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/small molecule infile bodyinfo.dat - create bodies CPU = 0.000 seconds - 9 rigid bodies with 81 atoms - 1.2247449 = max distance from body owner to body atom - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Reading rigid body data for 4 bodies from file bodyinfo.dat -Per MPI rank memory allocation (min/avg/max) = 9.034 | 9.034 | 9.034 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722875e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.059327511 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 - 3750 16737.731 0.20706559 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690667 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532809 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652433 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156155 0 5269.5203 12.011611 - 9600 16738.549 -0.026814367 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589876 0 5269.4979 12.062708 - 9750 16738.013 0.13550105 0 5269.5101 11.407245 - 9800 16738.512 -0.011620331 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270584 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984576 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395074 -Loop time of 0.154542 on 1 procs for 10000 steps with 81 atoms - -Performance: 559072.380 tau/day, 64707.451 timesteps/s, 5.241 Matom-step/s -98.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0094322 | 0.0094322 | 0.0094322 | 0.0 | 6.10 -Bond | 0.00037544 | 0.00037544 | 0.00037544 | 0.0 | 0.24 -Neigh | 0.062048 | 0.062048 | 0.062048 | 0.0 | 40.15 -Comm | 0.0095533 | 0.0095533 | 0.0095533 | 0.0 | 6.18 -Output | 0.0022247 | 0.0022247 | 0.0022247 | 0.0 | 1.44 -Modify | 0.06281 | 0.06281 | 0.06281 | 0.0 | 40.64 -Other | | 0.008098 | | | 5.24 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.small.infile.g++.4 b/examples/rigid/log.25Mar24.rigid.small.infile.g++.4 deleted file mode 100644 index e4c45a4523..0000000000 --- a/examples/rigid/log.25Mar24.rigid.small.infile.g++.4 +++ /dev/null @@ -1,322 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style bond - -pair_style lj/cut 2.5 - -read_data data.rigid.small -Reading data file ... - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.001 seconds - -velocity all create 100.0 4928459 - -# unconnected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 10 18 -9 atoms in group clump2 -group clump3 id <> 19 27 -9 atoms in group clump3 -group clump4 id <> 28 36 -9 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 46 54 -9 atoms in group clump6 -group clump7 id <> 55 63 -9 atoms in group clump7 -group clump8 id <> 64 72 -9 atoms in group clump8 -group clump9 id <> 73 81 -9 atoms in group clump9 - -fix 1 all rigid/small molecule infile bodyinfo.dat - create bodies CPU = 0.000 seconds - 9 rigid bodies with 81 atoms - 1.2247449 = max distance from body owner to body atom - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Reading rigid body data for 4 bodies from file bodyinfo.dat -Per MPI rank memory allocation (min/avg/max) = 8.892 | 8.94 | 9.049 Mbytes - Step Temp E_pair E_mol TotEng Press - 0 115.29439 5235.9179 0 5272.2142 -2.7403788 - 50 14910.685 571.71558 0 5265.82 32.006171 - 100 16298.442 136.66184 0 5267.653 16.444229 - 150 16682.606 17.490511 0 5269.4219 14.900344 - 200 16733.929 1.372872 0 5269.4617 14.569267 - 250 16738.853 -0.15252816 0 5269.4864 14.496404 - 300 16738.588 -0.055171335 0 5269.5002 14.496025 - 350 16738.492 -0.017444677 0 5269.5077 14.496446 - 400 16738.464 -0.0060102023 0 5269.5104 14.496618 - 450 16738.455 -0.0012713351 0 5269.5124 14.496701 - 500 16738.455 -0.00081068621 0 5269.5128 14.496709 - 550 16738.455 -0.00083203497 0 5269.5129 14.496707 - 600 16738.455 -0.00058355356 0 5269.5131 14.496709 - 650 16738.455 -0.00047226704 0 5269.5131 14.496708 - 700 16738.455 0 0 5269.5136 14.496713 - 750 16738.455 0 0 5269.5136 14.49671 - 800 16738.455 0 0 5269.5137 14.496709 - 850 16738.455 0 0 5269.5137 14.49671 - 900 16738.456 0 0 5269.5138 14.496713 - 950 16738.462 -0.0035323872 0 5269.5122 14.496671 - 1000 16738.586 -0.051135144 0 5269.5036 14.496229 - 1050 16737.358 0.32995057 0 5269.4981 14.525763 - 1100 16737.892 0.16210246 0 5269.4984 14.531983 - 1150 16738.703 -0.089235095 0 5269.5025 14.509899 - 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 - 1250 16738.456 0 0 5269.514 14.510704 - 1300 16738.457 0 0 5269.5141 14.510701 - 1350 16738.457 0 0 5269.5141 14.510699 - 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 - 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 - 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 - 1550 16738.457 0 0 5269.5143 14.51071 - 1600 16738.457 0 0 5269.5144 14.510712 - 1650 16738.457 0 0 5269.5144 14.510712 - 1700 16738.458 0 0 5269.5144 14.51071 - 1750 16738.458 0 0 5269.5145 14.510708 - 1800 16738.458 0 0 5269.5145 14.510706 - 1850 16738.458 0 0 5269.5146 14.510705 - 1900 16738.458 0 0 5269.5146 14.510706 - 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 - 2000 16738.491 -0.013255268 0 5269.5117 14.510532 - 2050 16738.556 -0.0365811 0 5269.5087 14.51029 - 2100 16738.633 -0.063209659 0 5269.5065 14.510219 - 2150 16738.607 -0.05601761 0 5269.5055 14.510231 - 2200 16738.557 -0.038423032 0 5269.5072 14.510404 - 2250 16738.515 -0.023709918 0 5269.5088 14.510539 - 2300 16738.489 -0.013249035 0 5269.5111 14.510621 - 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 - 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 - 2450 16738.464 -0.0023259756 0 5269.514 14.510746 - 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 - 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722864e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 - 2700 16738.761 -0.10614946 0 5269.5038 14.499584 - 2750 16733.973 1.4038179 0 5269.5064 14.598107 - 2800 16738.585 -0.046813448 0 5269.5076 14.511073 - 2850 16738.487 -0.012558719 0 5269.5111 14.510111 - 2900 16738.465 -0.0026252725 0 5269.514 14.510277 - 2950 16738.476 -0.0082220764 0 5269.512 14.510223 - 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 - 3100 16653.226 26.818761 0 5269.5009 14.496764 - 3150 16739.351 -0.30690375 0 5269.4886 13.643904 - 3200 16733.238 1.6025328 0 5269.4737 12.016934 - 3250 16734.374 1.2554429 0 5269.4841 11.963561 - 3300 16732.156 1.9585967 0 5269.4893 12.234024 - 3350 16738.655 -0.079693236 0 5269.497 12.092757 - 3400 16738.543 -0.042215005 0 5269.4991 12.092809 - 3450 16738.591 -0.05932751 0 5269.4972 12.092536 - 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 - 3600 16734.939 1.0821936 0 5269.4891 12.173591 - 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934369 0 5269.4889 12.025288 - 3750 16737.731 0.20706559 0 5269.4927 12.061948 - 3800 16738.578 -0.05582043 0 5269.4965 12.035665 - 3850 16738.471 -0.016307928 0 5269.5024 12.035302 - 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 - 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 - 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 - 4050 16738.437 0 0 5269.5078 12.035454 - 4100 16738.437 0 0 5269.508 12.035435 - 4150 16738.438 0 0 5269.5081 12.035426 - 4200 16738.438 0 0 5269.5083 12.035432 - 4250 16738.439 0 0 5269.5085 12.035447 - 4300 16738.439 0 0 5269.5086 12.035463 - 4350 16738.44 0 0 5269.5087 12.035474 - 4400 16738.44 0 0 5269.5088 12.035478 - 4450 16738.44 0 0 5269.5089 12.035474 - 4500 16738.44 0 0 5269.509 12.035462 - 4550 16738.441 0 0 5269.5092 12.035449 - 4600 16738.441 0 0 5269.5093 12.035445 - 4650 16738.442 0 0 5269.5095 12.035451 - 4700 16738.442 0 0 5269.5096 12.03546 - 4750 16738.443 0 0 5269.5097 12.035465 - 4800 16738.443 0 0 5269.5098 12.035466 - 4850 16738.443 0 0 5269.51 12.035463 - 4900 16738.444 0 0 5269.5101 12.035456 - 4950 16738.444 0 0 5269.5102 12.035447 - 5000 16738.445 0 0 5269.5104 12.03544 - 5050 16738.445 0 0 5269.5105 12.035442 - 5100 16738.446 0 0 5269.5107 12.035455 - 5150 16738.446 0 0 5269.5108 12.03547 - 5200 16738.446 0 0 5269.5109 12.035479 - 5250 16738.447 0 0 5269.511 12.035479 - 5300 16738.447 0 0 5269.5111 12.03547 - 5350 16738.447 0 0 5269.5112 12.035454 - 5400 16738.448 0 0 5269.5113 12.035434 - 5450 16738.448 0 0 5269.5115 12.03542 - 5500 16738.449 0 0 5269.5117 12.035422 - 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 - 5600 16738.51 -0.021618357 0 5269.5092 12.035106 - 5650 16738.622 -0.059214788 0 5269.507 12.035694 - 5700 16395.28 108.06942 0 5269.5463 24.369038 - 5750 16738.544 -0.033973429 0 5269.5077 12.011261 - 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 - 5850 16738.451 0 0 5269.5123 12.011709 - 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 - 5950 16738.452 -0.00024253348 0 5269.5124 12.011678 - 6000 16738.452 0 0 5269.5128 12.011688 - 6050 16738.453 0 0 5269.513 12.011702 - 6100 16738.453 0 0 5269.5131 12.011716 - 6150 16738.454 0 0 5269.5132 12.011725 - 6200 16738.454 0 0 5269.5133 12.011728 - 6250 16738.454 0 0 5269.5134 12.011723 - 6300 16738.455 0 0 5269.5135 12.011712 - 6350 16738.455 0 0 5269.5137 12.0117 - 6400 16738.456 0 0 5269.5138 12.011697 - 6450 16738.456 0 0 5269.514 12.011704 - 6500 16738.456 0 0 5269.5141 12.011714 - 6550 16738.457 0 0 5269.5142 12.011719 - 6600 16738.457 0 0 5269.5143 12.011718 - 6650 16738.458 0 0 5269.5144 12.011713 - 6700 16738.458 0 0 5269.5146 12.011705 - 6750 16738.459 0 0 5269.5147 12.011696 - 6800 16738.459 0 0 5269.5149 12.01169 - 6850 16738.46 0 0 5269.515 12.011695 - 6900 16738.46 0 0 5269.5152 12.01171 - 6950 16738.46 0 0 5269.5153 12.011726 - 7000 16738.461 0 0 5269.5154 12.011736 - 7050 16738.461 0 0 5269.5155 12.011737 - 7100 16738.461 0 0 5269.5155 12.011728 - 7150 16738.461 0 0 5269.5156 12.011712 - 7200 16738.462 0 0 5269.5158 12.011691 - 7250 16738.463 0 0 5269.516 12.011676 - 7300 16738.463 0 0 5269.5162 12.011677 - 7350 16738.464 0 0 5269.5164 12.011693 - 7400 16738.464 0 0 5269.5165 12.011713 - 7450 16738.465 0 0 5269.5166 12.011729 - 7500 16738.465 0 0 5269.5167 12.011736 - 7550 16738.465 0 0 5269.5168 12.011734 - 7600 16738.465 0 0 5269.5168 12.011722 - 7650 16738.466 0 0 5269.517 12.011704 - 7700 16738.466 0 0 5269.5171 12.011687 - 7750 16738.467 0 0 5269.5173 12.011681 - 7800 16738.467 0 0 5269.5175 12.011687 - 7850 16738.468 0 0 5269.5176 12.0117 - 7900 16738.468 0 0 5269.5178 12.011712 - 7950 16738.469 0 0 5269.5179 12.011721 - 8000 16738.469 0 0 5269.518 12.011724 - 8050 16738.469 0 0 5269.5181 12.01172 - 8100 16738.47 0 0 5269.5182 12.011709 - 8150 16738.47 0 0 5269.5183 12.0117 - 8200 16738.47 0 0 5269.5185 12.0117 - 8250 16738.471 0 0 5269.5186 12.011709 - 8300 16738.471 0 0 5269.5187 12.011719 - 8350 16738.472 0 0 5269.5189 12.011723 - 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690668 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646805 0 5269.5182 12.011643 - 8550 16738.483 -0.0045307408 0 5269.5178 12.011621 - 8600 16738.474 -0.00076532808 0 5269.5189 12.011681 - 8650 16738.474 0 0 5269.5197 12.011699 - 8700 16738.475 0 0 5269.5199 12.011715 - 8750 16738.475 0 0 5269.52 12.011732 - 8800 16738.475 0 0 5269.52 12.011743 - 8850 16738.476 0 0 5269.5201 12.011744 - 8900 16738.476 0 0 5269.5202 12.011735 - 8950 16738.476 0 0 5269.5203 12.011719 - 9000 16738.477 0 0 5269.5205 12.011698 - 9050 16738.477 0 0 5269.5206 12.011683 - 9100 16738.478 0 0 5269.5208 12.011684 - 9150 16738.479 0 0 5269.521 12.011701 - 9200 16738.479 0 0 5269.5212 12.011722 - 9250 16738.479 0 0 5269.5213 12.011738 - 9300 16738.48 0 0 5269.5214 12.011746 - 9350 16738.48 0 0 5269.5214 12.011744 - 9400 16738.48 0 0 5269.5215 12.011732 - 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652432 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156155 0 5269.5203 12.011611 - 9600 16738.549 -0.026814366 0 5269.5163 12.011415 - 9650 16738.765 -0.10191522 0 5269.5092 12.011013 - 9700 16735.041 1.0589874 0 5269.4979 12.062708 - 9750 16738.013 0.1355012 0 5269.5101 11.407245 - 9800 16738.512 -0.011620331 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270574 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984568 0 5269.5242 11.395084 - 9950 16738.49 0 0 5269.5245 11.395076 - 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.194899 on 4 procs for 10000 steps with 81 atoms - -Performance: 443306.036 tau/day, 51308.569 timesteps/s, 4.156 Matom-step/s -98.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0017487 | 0.0024215 | 0.0028965 | 0.9 | 1.24 -Bond | 0.00032501 | 0.00033082 | 0.0003413 | 0.0 | 0.17 -Neigh | 0.015692 | 0.016603 | 0.018578 | 0.9 | 8.52 -Comm | 0.063465 | 0.066081 | 0.068061 | 0.8 | 33.91 -Output | 0.0019654 | 0.0021191 | 0.0025315 | 0.5 | 1.09 -Modify | 0.092199 | 0.094298 | 0.096149 | 0.5 | 48.38 -Other | | 0.01305 | | | 6.69 - -Nlocal: 20.25 ave 37 max 3 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 0 -Neighbor list builds = 1552 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/rigid/log.25Mar24.rigid.tnr.g++.1 b/examples/rigid/log.25Mar24.rigid.tnr.g++.1 deleted file mode 100644 index be58bf94b9..0000000000 --- a/examples/rigid/log.25Mar24.rigid.tnr.g++.1 +++ /dev/null @@ -1,475 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Tethered nanorods - -atom_style molecular - -read_data data.rigid.tnr -Reading data file ... - orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 5600 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 1600 bonds -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.027 seconds - -# Specify bond parameters - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 - -special_bonds fene -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - -# Specify initial velocities - -velocity all create 1.4 109345 - -# Specify rigid components - -group rods type 2 -4000 atoms in group rods -group tethers subtract all rods -1600 atoms in group tethers - -neigh_modify exclude molecule/intra rods delay 0 every 1 - -# Specify the pair potentials - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff * * 1.0 1.0 1.122 -pair_coeff 2 2 1.0 1.0 2.5 - -# Specify output - -thermo 100 -thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz -thermo_modify flush yes lost warn - -timestep 0.005 - -fix 1 rods rigid molecule - 800 rigid bodies with 4000 atoms -fix 2 tethers nve -fix 3 all langevin 1.4 1.4 1.0 437624 - -run 5000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 45 45 45 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 8.017 | 8.017 | 8.017 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 - 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248 - 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036 - 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998 - 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801 - 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745 - 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581 - 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883 - 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271 - 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788 - 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119 - 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748 - 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115 - 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625 - 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021 - 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242 - 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334 - 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014 - 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797 - 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268 - 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673 - 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825 - 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911 - 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296 - 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402 - 2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677 - 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948 - 2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371 - 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106 - 2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713 - 3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611 - 3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039 - 3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251 - 3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362 - 3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524 - 3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699 - 3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752 - 3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797 - 3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772 - 3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034 - 4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065 - 4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387 - 4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557 - 4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574 - 4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421 - 4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711 - 4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462 - 4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986 - 4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278 - 4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891 - 5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248 -Loop time of 5.54157 on 1 procs for 5000 steps with 5600 atoms - -Performance: 389781.415 tau/day, 902.272 timesteps/s, 5.053 Matom-step/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.40156 | 0.40156 | 0.40156 | 0.0 | 7.25 -Bond | 0.172 | 0.172 | 0.172 | 0.0 | 3.10 -Neigh | 1.6573 | 1.6573 | 1.6573 | 0.0 | 29.91 -Comm | 0.10679 | 0.10679 | 0.10679 | 0.0 | 1.93 -Output | 0.0033706 | 0.0033706 | 0.0033706 | 0.0 | 0.06 -Modify | 3.0948 | 3.0948 | 3.0948 | 0.0 | 55.85 -Other | | 0.1058 | | | 1.91 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1351 ave 1351 max 1351 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5254 ave 5254 max 5254 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5254 -Ave neighs/atom = 0.93821429 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 766 -Dangerous builds = 0 - -# Replace fix rigid and fix langevin with new ones - -unfix 1 -unfix 3 - -fix 3 tethers langevin 1.4 1.4 1.0 198450 - -# Test different integrators for rods - -fix 1 rods rigid/nve molecule - 800 rigid bodies with 4000 atoms -print "rigid/nve" -rigid/nve -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 8.018 | 8.018 | 8.018 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575 - 5100 1.439608 5.9052128 7.0359478 0.0060989876 7.2985886 62.244 62.244 62.244 0.0087364154 0.0040228411 0.0055377063 - 5200 1.4120671 5.9102569 7.01936 0.0064301456 7.2962615 62.244 62.244 62.244 0.0082738088 0.0038925707 0.0071240574 - 5300 1.4452434 5.8842166 7.0193778 0.0081724166 7.3713067 62.244 62.244 62.244 0.0077715644 0.0068924374 0.0098532479 - 5400 1.4170243 5.887522 7.0005186 0.00086566653 7.0377968 62.244 62.244 62.244 -9.179779e-05 -0.0020237494 0.0047125468 - 5500 1.4209084 5.875892 6.9919394 0.009363414 7.3951563 62.244 62.244 62.244 0.0088769611 0.0087092372 0.010504044 - 5600 1.4132978 5.8798939 6.9899636 0.0014877902 7.0540323 62.244 62.244 62.244 -0.0023427699 0.0045593956 0.0022467449 - 5700 1.4065055 5.8875412 6.9922759 0.002808316 7.1132105 62.244 62.244 62.244 0.0025187553 0.00051088905 0.0053953037 - 5800 1.4079049 5.8940749 6.9999087 0.0015946903 7.0685809 62.244 62.244 62.244 0.0037830352 0.00021762631 0.00078340928 - 5900 1.4076048 5.8941588 6.9997569 0.0051902121 7.2232631 62.244 62.244 62.244 -0.00093181434 0.0096405899 0.0068618607 - 6000 1.4322812 5.8903503 7.0153305 0.00029722379 7.0281298 62.244 62.244 62.244 0.0019139164 -0.00073870179 -0.00028354325 -Loop time of 1.21399 on 1 procs for 1000 steps with 5600 atoms - -Performance: 355850.342 tau/day, 823.728 timesteps/s, 4.613 Matom-step/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.12141 | 0.12141 | 0.12141 | 0.0 | 10.00 -Bond | 0.038739 | 0.038739 | 0.038739 | 0.0 | 3.19 -Neigh | 0.39335 | 0.39335 | 0.39335 | 0.0 | 32.40 -Comm | 0.023806 | 0.023806 | 0.023806 | 0.0 | 1.96 -Output | 0.00074295 | 0.00074295 | 0.00074295 | 0.0 | 0.06 -Modify | 0.61212 | 0.61212 | 0.61212 | 0.0 | 50.42 -Other | | 0.02383 | | | 1.96 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1347 ave 1347 max 1347 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5399 ave 5399 max 5399 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5399 -Ave neighs/atom = 0.96410714 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 153 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 - 800 rigid bodies with 4000 atoms -print "rigid/nvt" -rigid/nvt -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 8.018 | 8.018 | 8.018 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 6000 1.4322812 5.8903503 7.0153305 0.012984296 7.5744734 62.244 62.244 62.244 0.058323772 0.007366828 -0.026737713 - 6100 1.4199781 5.8764024 6.9917192 0.0054080227 7.2246049 62.244 62.244 62.244 0.0092282159 0.0019631398 0.0050327123 - 6200 1.3976803 5.8924474 6.9902504 0.00044474719 7.0094026 62.244 62.244 62.244 -0.0022979183 -0.0004943354 0.0041264952 - 6300 1.4076912 5.8847607 6.9904268 0.0066261457 7.2757686 62.244 62.244 62.244 0.0057923777 0.0091772934 0.0049087658 - 6400 1.3749242 5.8816641 6.9615934 0.0075045379 7.2847615 62.244 62.244 62.244 0.012318395 0.003979389 0.0062158299 - 6500 1.3467602 5.888001 6.945809 -6.1011018e-05 6.9431817 62.244 62.244 62.244 0.0031945051 -0.0013048764 -0.0020726618 - 6600 1.3638321 5.8744775 6.9456945 0.005780579 7.1946237 62.244 62.244 62.244 0.0060765968 0.0058486743 0.0054164658 - 6700 1.3933343 5.8833797 6.9777691 0.0026007197 7.089764 62.244 62.244 62.244 0.0029828101 0.0019631585 0.0028561905 - 6800 1.4025439 5.901019 7.0026421 0.0033759718 7.1480216 62.244 62.244 62.244 0.0059683617 0.0016890885 0.002470465 - 6900 1.4165405 5.8901618 7.0027785 0.0048537306 7.2117948 62.244 62.244 62.244 0.0031937581 0.0089194691 0.0024479647 - 7000 1.4256345 5.8979889 7.0177485 0.0076603683 7.347627 62.244 62.244 62.244 0.0064499957 0.0096400261 0.0068910831 -Loop time of 1.16587 on 1 procs for 1000 steps with 5600 atoms - -Performance: 370540.281 tau/day, 857.732 timesteps/s, 4.803 Matom-step/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.11675 | 0.11675 | 0.11675 | 0.0 | 10.01 -Bond | 0.03628 | 0.03628 | 0.03628 | 0.0 | 3.11 -Neigh | 0.36879 | 0.36879 | 0.36879 | 0.0 | 31.63 -Comm | 0.022201 | 0.022201 | 0.022201 | 0.0 | 1.90 -Output | 0.00070791 | 0.00070791 | 0.00070791 | 0.0 | 0.06 -Modify | 0.59859 | 0.59859 | 0.59859 | 0.0 | 51.34 -Other | | 0.02255 | | | 1.93 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1284 ave 1284 max 1284 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5691 ave 5691 max 5691 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5691 -Ave neighs/atom = 1.01625 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 151 -Dangerous builds = 0 -unfix 1 - -compute myTemp all temp - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all - 800 rigid bodies with 4000 atoms -print "rigid/npt iso" -rigid/npt iso -fix_modify 1 temp myTemp - -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 8.018 | 8.018 | 8.018 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 7000 1.4256345 5.8979889 7.0177485 0.030670312 8.3385046 62.244 62.244 62.244 0.019152979 0.028037341 0.044820616 - 7100 1.4830481 5.8740667 7.0389215 0.021216954 7.7436467 57.083193 57.083193 57.083193 0.015785563 0.020078182 0.027787115 - 7200 1.5225973 5.8364439 7.0323626 0.015560962 7.3866118 50.329217 50.329217 50.329217 0.017379604 0.02205435 0.0072489313 - 7300 1.5589134 5.7874972 7.0119402 0.020613279 7.3515942 45.188285 45.188285 45.188285 0.019963793 0.02165546 0.020220585 - 7400 1.5629259 5.7523794 6.9799739 0.035363756 7.4299227 41.456971 41.456971 41.456971 0.030810521 0.041559103 0.033721646 - 7500 1.5735285 5.706087 6.9420093 0.033186427 7.2889675 38.830074 38.830074 38.830074 0.030605548 0.018770943 0.050182791 - 7600 1.5546074 5.6815832 6.902644 0.027297758 7.1446412 36.752801 36.752801 36.752801 0.027154479 0.030653039 0.024085757 - 7700 1.5396727 5.6293114 6.8386418 0.030528746 7.0744265 35.101973 35.101973 35.101973 0.022542269 0.025802901 0.043241069 - 7800 1.5249769 5.5826711 6.7804588 0.067321436 7.2458344 33.82824 33.82824 33.82824 0.063820368 0.072156874 0.065987065 - 7900 1.5017937 5.5660576 6.7456361 0.04770857 7.0497596 32.926623 32.926623 32.926623 0.035259576 0.06869573 0.039170404 - 8000 1.5105319 5.5459012 6.7323431 0.053301062 7.0487429 32.153588 32.153588 32.153588 0.076450314 0.07417732 0.0092755526 -Loop time of 2.49405 on 1 procs for 1000 steps with 5600 atoms - -Performance: 173212.568 tau/day, 400.955 timesteps/s, 2.245 Matom-step/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.29712 | 0.29712 | 0.29712 | 0.0 | 11.91 -Bond | 0.044611 | 0.044611 | 0.044611 | 0.0 | 1.79 -Neigh | 1.2735 | 1.2735 | 1.2735 | 0.0 | 51.06 -Comm | 0.048469 | 0.048469 | 0.048469 | 0.0 | 1.94 -Output | 0.0007418 | 0.0007418 | 0.0007418 | 0.0 | 0.03 -Modify | 0.7991 | 0.7991 | 0.7991 | 0.0 | 32.04 -Other | | 0.03048 | | | 1.22 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2993 ave 2993 max 2993 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 25312 ave 25312 max 25312 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 25312 -Ave neighs/atom = 4.52 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 335 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all - 800 rigid bodies with 4000 atoms -print "rigid/npt x" -rigid/npt x -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 8.033 | 8.033 | 8.033 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 8000 1.5105319 5.5459012 6.7323431 -0.15611622 5.8056235 32.153588 32.153588 32.153588 -0.25823552 0.036861264 -0.24697441 - 8100 1.4816536 5.5214096 6.6851691 0.051659716 6.9889314 31.85012 32.153588 32.153588 0.042525917 0.079045459 0.033407772 - 8200 1.4364335 5.5026881 6.6309297 0.030961663 6.8100555 31.337401 32.153588 32.153588 0.062969827 0.0077436471 0.022171514 - 8300 1.4159126 5.504273 6.6163965 0.050231597 6.9027629 30.879771 32.153588 32.153588 0.047512875 0.071477224 0.031704693 - 8400 1.4479331 5.4732237 6.6104975 0.037171033 6.8195306 30.460678 32.153588 32.153588 0.016306171 0.072770628 0.022436301 - 8500 1.4126922 5.4616331 6.5712271 0.069137703 6.9521816 29.846079 32.153588 32.153588 0.075972518 0.063305384 0.068135208 - 8600 1.4129562 5.4397649 6.5495663 0.068287674 6.9190398 29.306917 32.153588 32.153588 0.077820831 0.076960087 0.050082105 - 8700 1.4199417 5.408767 6.5240551 0.046952367 6.7741118 28.847632 32.153588 32.153588 0.078496327 0.013710756 0.048650018 - 8800 1.415092 5.4082456 6.5197246 0.017068201 6.6091852 28.39051 32.153588 32.153588 0.01803734 0.0086202553 0.024547008 - 8900 1.4080943 5.3806524 6.486635 0.006282149 6.5189723 27.882074 32.153588 32.153588 0.023331732 0.01130818 -0.015793465 - 9000 1.4188356 5.3687142 6.4831335 0.078333785 6.8770321 27.237322 32.153588 32.153588 0.092873218 0.033643462 0.10848468 -Loop time of 2.35076 on 1 procs for 1000 steps with 5600 atoms - -Performance: 183770.370 tau/day, 425.394 timesteps/s, 2.382 Matom-step/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.45082 | 0.45082 | 0.45082 | 0.0 | 19.18 -Bond | 0.045157 | 0.045157 | 0.045157 | 0.0 | 1.92 -Neigh | 0.98655 | 0.98655 | 0.98655 | 0.0 | 41.97 -Comm | 0.039968 | 0.039968 | 0.039968 | 0.0 | 1.70 -Output | 0.00072296 | 0.00072296 | 0.00072296 | 0.0 | 0.03 -Modify | 0.80394 | 0.80394 | 0.80394 | 0.0 | 34.20 -Other | | 0.0236 | | | 1.00 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3422 ave 3422 max 3422 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 31084 ave 31084 max 31084 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 31084 -Ave neighs/atom = 5.5507143 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 167 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all - 800 rigid bodies with 4000 atoms -print "rigid/nph iso" -rigid/nph iso -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 8.036 | 8.036 | 8.036 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 9000 1.4188356 5.3687142 6.4831335 0.066940268 6.8197402 27.237322 32.153588 32.153588 0.020750172 0.14461869 0.035451941 - 9100 1.418441 5.3523211 6.4664305 0.016522511 6.5489637 27.17712 32.08252 32.08252 0.01137531 0.0028933886 0.035298833 - 9200 1.4433401 5.3458252 6.4794915 0.038961106 6.6708176 27.023003 31.900585 31.900585 0.012667867 0.094480325 0.0097351253 - 9300 1.4806575 5.309105 6.4720822 0.11806636 7.0379478 26.804952 31.643176 31.643176 0.063001935 0.11667303 0.17452413 - 9400 1.4835179 5.3103383 6.4755622 0.098990545 6.9362503 26.543432 31.334452 31.334452 0.13023767 0.084360197 0.08237377 - 9500 1.4855723 5.2906327 6.4574702 -0.0012789282 6.4516456 26.352845 31.109465 31.109465 0.053813822 -0.016098782 -0.041551825 - 9600 1.4959395 5.2553176 6.4302979 0.036958035 6.5952607 26.176506 30.901298 30.901298 0.077457004 -0.035314705 0.068731807 - 9700 1.4470266 5.289874 6.4264359 0.065648447 6.7177609 26.125849 30.841497 30.841497 0.064764383 0.041383889 0.090797069 - 9800 1.4525327 5.2808561 6.4217428 0.0076421133 6.4554682 26.077575 30.78451 30.78451 -0.01978363 0.013568065 0.029141905 - 9900 1.4603761 5.269343 6.4163902 0.079488558 6.7651749 26.027767 30.725712 30.725712 0.06210239 0.062690336 0.11367295 - 10000 1.4437445 5.2626116 6.3965955 0.0024175103 6.4072252 26.045744 30.746933 30.746933 0.0020903338 0.023283622 -0.018121425 -Loop time of 2.42718 on 1 procs for 1000 steps with 5600 atoms - -Performance: 177984.690 tau/day, 412.002 timesteps/s, 2.307 Matom-step/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.52411 | 0.52411 | 0.52411 | 0.0 | 21.59 -Bond | 0.04594 | 0.04594 | 0.04594 | 0.0 | 1.89 -Neigh | 1.0079 | 1.0079 | 1.0079 | 0.0 | 41.53 -Comm | 0.040182 | 0.040182 | 0.040182 | 0.0 | 1.66 -Output | 0.00070663 | 0.00070663 | 0.00070663 | 0.0 | 0.03 -Modify | 0.78582 | 0.78582 | 0.78582 | 0.0 | 32.38 -Other | | 0.02253 | | | 0.93 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3638 ave 3638 max 3638 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 35778 ave 35778 max 35778 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 35778 -Ave neighs/atom = 6.3889286 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 161 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all - 800 rigid bodies with 4000 atoms -print "rigid/nph xy couple" -rigid/nph xy couple -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 8.041 | 8.041 | 8.041 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 10000 1.4437445 5.2626116 6.3965955 0.043852305 6.5894123 26.045744 30.746933 30.746933 -0.10594451 -0.016019605 0.25352103 - 10100 1.4544517 5.2536075 6.3960014 0.040252547 6.5723133 25.995896 30.688087 30.746933 0.036481947 0.058195014 0.026080679 - 10200 1.4465796 5.2533056 6.3895164 0.043103918 6.5797343 26.093233 30.802994 30.746933 0.047509548 0.023387048 0.058415158 - 10300 1.4703558 5.2311222 6.3860079 0.02952279 6.5179005 26.253791 30.992532 30.746933 0.067825843 -1.1742127e-05 0.020754268 - 10400 1.4264151 5.2426153 6.362988 0.043320767 6.5561801 26.230542 30.965087 30.746933 0.036437179 0.069318063 0.02420706 - 10500 1.4718495 5.213542 6.3696009 0.028876649 6.4965877 26.047535 30.749047 30.746933 0.044470994 0.03304953 0.0091094235 - 10600 1.4550996 5.2087392 6.3516419 0.049130073 6.5647387 25.868744 30.537985 30.746933 0.056613289 0.028555571 0.062221359 - 10700 1.4755834 5.1912236 6.3502153 0.0027128909 6.3617831 25.648895 30.278455 30.746933 0.035708882 0.02165412 -0.04922433 - 10800 1.4801906 5.1863989 6.3490092 0.030220134 6.4763468 25.497097 30.099256 30.746933 0.035963119 0.021549561 0.033147721 - 10900 1.4318851 5.1785312 6.3032002 0.095502071 6.7019424 25.380506 29.961622 30.746933 0.1040397 0.10708089 0.075385625 - 11000 1.4500789 5.1660716 6.3050309 0.072030914 6.6026703 25.249123 29.806525 30.746933 0.073199983 0.0091150749 0.13377768 -Loop time of 2.55647 on 1 procs for 1000 steps with 5600 atoms - -Performance: 168982.932 tau/day, 391.164 timesteps/s, 2.191 Matom-step/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.5683 | 0.5683 | 0.5683 | 0.0 | 22.23 -Bond | 0.044877 | 0.044877 | 0.044877 | 0.0 | 1.76 -Neigh | 1.0732 | 1.0732 | 1.0732 | 0.0 | 41.98 -Comm | 0.041328 | 0.041328 | 0.041328 | 0.0 | 1.62 -Output | 0.00078717 | 0.00078717 | 0.00078717 | 0.0 | 0.03 -Modify | 0.80433 | 0.80433 | 0.80433 | 0.0 | 31.46 -Other | | 0.02363 | | | 0.92 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3699 ave 3699 max 3699 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 39523 ave 39523 max 39523 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 39523 -Ave neighs/atom = 7.0576786 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 163 -Dangerous builds = 0 - -Total wall time: 0:00:17 diff --git a/examples/rigid/log.25Mar24.rigid.tnr.g++.4 b/examples/rigid/log.25Mar24.rigid.tnr.g++.4 deleted file mode 100644 index 6d98088472..0000000000 --- a/examples/rigid/log.25Mar24.rigid.tnr.g++.4 +++ /dev/null @@ -1,475 +0,0 @@ -LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-306-gf3391199e7-modified) - using 1 OpenMP thread(s) per MPI task -# Tethered nanorods - -atom_style molecular - -read_data data.rigid.tnr -Reading data file ... - orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 5600 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 1600 bonds -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.017 seconds - -# Specify bond parameters - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 - -special_bonds fene -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000 seconds - -# Specify initial velocities - -velocity all create 1.4 109345 - -# Specify rigid components - -group rods type 2 -4000 atoms in group rods -group tethers subtract all rods -1600 atoms in group tethers - -neigh_modify exclude molecule/intra rods delay 0 every 1 - -# Specify the pair potentials - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff * * 1.0 1.0 1.122 -pair_coeff 2 2 1.0 1.0 2.5 - -# Specify output - -thermo 100 -thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz -thermo_modify flush yes lost warn - -timestep 0.005 - -fix 1 rods rigid molecule - 800 rigid bodies with 4000 atoms -fix 2 tethers nve -fix 3 all langevin 1.4 1.4 1.0 437624 - -run 5000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 45 45 45 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.552 | 7.555 | 7.559 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 - 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624 - 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719 - 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786 - 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141 - 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529 - 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222 - 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907 - 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859 - 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971 - 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735 - 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195 - 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658 - 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474 - 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314 - 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432 - 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699 - 1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975 - 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981 - 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291 - 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901 - 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978 - 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521 - 2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595 - 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026 - 2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414204 0.0039571831 0.0048428538 - 2600 1.3876469 5.9249124 7.0148347 -0.0017777225 6.9382806 62.244 62.244 62.244 -0.00047616393 -0.0025484918 -0.0023085117 - 2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812866 0.0032048359 - 2800 1.4444643 5.9283432 7.0628925 0.0019400023 7.1464349 62.244 62.244 62.244 0.0014895078 0.0046367397 -0.00030624049 - 2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403268 -0.0046971891 - 3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147657 - 3100 1.3569137 5.9171753 6.9829583 -0.0028266769 6.8612331 62.244 62.244 62.244 -0.0069507251 0.0010084401 -0.0025377458 - 3200 1.4004275 5.905939 7.0058998 0.0054394667 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594139 0.00020680257 - 3300 1.3641217 5.9145275 6.985972 -0.0027212813 6.8687854 62.244 62.244 62.244 -0.00065933696 -0.005771301 -0.001733206 - 3400 1.3868722 5.9059546 6.9952684 0.0092591263 7.3939943 62.244 62.244 62.244 0.010690877 0.01075252 0.0063339817 - 3500 1.3939169 5.8992292 6.9940762 0.0074340014 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252538 0.0077394438 - 3600 1.3982507 5.9219461 7.0201971 0.0056794512 7.2647714 62.244 62.244 62.244 0.0023367131 0.0080592141 0.0066424266 - 3700 1.4019908 5.9059957 7.0071844 0.0065915518 7.2910365 62.244 62.244 62.244 0.0049554052 0.010827013 0.0039922376 - 3800 1.3960736 5.902079 6.9986201 0.0027763672 7.1181788 62.244 62.244 62.244 -0.0015907142 0.0025862031 0.0073336126 - 3900 1.4352825 5.8986216 7.0259591 0.003498295 7.1766062 62.244 62.244 62.244 0.0030417173 0.0027739456 0.0046792221 - 4000 1.4121845 5.9079028 7.0170981 0.0050462581 7.2344052 62.244 62.244 62.244 0.0045543085 0.0064113637 0.0041731022 - 4100 1.3989579 5.9082397 7.0070461 0.00042870391 7.0255074 62.244 62.244 62.244 0.0025733986 0.0025181076 -0.0038053944 - 4200 1.399883 5.8998147 6.9993477 0.0042777423 7.1835602 62.244 62.244 62.244 0.0013744675 0.0064699404 0.0049888191 - 4300 1.4076025 5.9044509 7.0100472 0.0066788698 7.2976595 62.244 62.244 62.244 0.007361029 0.0048139331 0.0078616474 - 4400 1.4161078 5.9064334 7.0187102 -0.0011844913 6.9677025 62.244 62.244 62.244 -0.001908963 -0.0037556847 0.0021111739 - 4500 1.429225 5.8980089 7.0205885 0.0018498822 7.10025 62.244 62.244 62.244 0.0041143046 0.0010156504 0.00041969169 - 4600 1.3958783 5.894313 6.9907006 0.0041483111 7.1693394 62.244 62.244 62.244 0.0033996217 0.0041616835 0.004883628 - 4700 1.3856609 5.8886843 6.9770467 0.0013148711 7.033669 62.244 62.244 62.244 -0.00051706505 0.0030872136 0.0013744648 - 4800 1.4016792 5.902351 7.0032949 0.0025050908 7.1111717 62.244 62.244 62.244 0.0016540384 -0.00018095286 0.0060421869 - 4900 1.4466248 5.9050606 7.0413069 -0.0026620212 6.9266722 62.244 62.244 62.244 -0.00069094879 -0.0073956145 0.00010049979 - 5000 1.4387209 5.9077482 7.0377864 0.0049404333 7.2505363 62.244 62.244 62.244 0.0042769255 0.0046681652 0.0058762093 -Loop time of 2.72962 on 4 procs for 5000 steps with 5600 atoms - -Performance: 791319.942 tau/day, 1831.759 timesteps/s, 10.258 Matom-step/s -99.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.06605 | 0.10369 | 0.14557 | 11.7 | 3.80 -Bond | 0.03005 | 0.045571 | 0.06035 | 6.5 | 1.67 -Neigh | 0.61326 | 0.61489 | 0.61678 | 0.2 | 22.53 -Comm | 0.14416 | 0.19908 | 0.25001 | 11.1 | 7.29 -Output | 0.0017405 | 0.0025188 | 0.0028143 | 0.9 | 0.09 -Modify | 1.522 | 1.6149 | 1.699 | 6.3 | 59.16 -Other | | 0.1489 | | | 5.46 - -Nlocal: 1400 ave 1868 max 905 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Nghost: 648.25 ave 688 max 598 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Neighs: 1202.5 ave 1821 max 698 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 4810 -Ave neighs/atom = 0.85892857 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 759 -Dangerous builds = 0 - -# Replace fix rigid and fix langevin with new ones - -unfix 1 -unfix 3 - -fix 3 tethers langevin 1.4 1.4 1.0 198450 - -# Test different integrators for rods - -fix 1 rods rigid/nve molecule - 800 rigid bodies with 4000 atoms -print "rigid/nve" -rigid/nve -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 7.557 | 7.566 | 7.574 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 5000 1.4387209 5.9077482 7.0377864 0.0036839327 7.1964276 62.244 62.244 62.244 0.025677952 -0.016670649 0.002044495 - 5100 1.4449629 5.8876265 7.0225675 0.0023125815 7.1221542 62.244 62.244 62.244 0.0045991271 0.0036872425 -0.0013486251 - 5200 1.4271279 5.9160281 7.0369606 0.0020315691 7.1244461 62.244 62.244 62.244 -0.0022476411 0.0039290288 0.0044133197 - 5300 1.4143266 5.9052803 7.0161581 0.0064093985 7.2921661 62.244 62.244 62.244 0.0090986577 0.0026397649 0.0074897729 - 5400 1.4426551 5.9087477 7.041876 0.0020419183 7.1298072 62.244 62.244 62.244 0.0043078454 1.5623413e-05 0.001802286 - 5500 1.4280605 5.9038941 7.0255591 0.00057730336 7.0504195 62.244 62.244 62.244 0.0058938228 0.00065558729 -0.0048175 - 5600 1.4315004 5.902394 7.0267609 0.0096531882 7.4424563 62.244 62.244 62.244 0.0054225258 0.011780272 0.011756766 - 5700 1.4074659 5.9076093 7.0130984 0.0052032455 7.2371658 62.244 62.244 62.244 0.0029612305 0.003678953 0.008969553 - 5800 1.4216898 5.9047983 7.0214595 0.0015109698 7.0865264 62.244 62.244 62.244 -6.4662019e-05 0.0023994389 0.0021981326 - 5900 1.4052133 5.8920187 6.9957385 0.0065755622 7.278902 62.244 62.244 62.244 0.0062703932 0.011367786 0.002088507 - 6000 1.3958734 5.9025061 6.9988899 0.0071783223 7.3080101 62.244 62.244 62.244 0.0088905564 0.0025533521 0.010091058 -Loop time of 0.646284 on 4 procs for 1000 steps with 5600 atoms - -Performance: 668436.315 tau/day, 1547.306 timesteps/s, 8.665 Matom-step/s -99.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.01802 | 0.028926 | 0.041262 | 6.4 | 4.48 -Bond | 0.0066363 | 0.0098826 | 0.012811 | 2.9 | 1.53 -Neigh | 0.14233 | 0.14273 | 0.14311 | 0.1 | 22.08 -Comm | 0.029365 | 0.044453 | 0.057955 | 6.3 | 6.88 -Output | 0.00034317 | 0.00049475 | 0.00055796 | 0.0 | 0.08 -Modify | 0.35817 | 0.37856 | 0.40064 | 2.8 | 58.57 -Other | | 0.04124 | | | 6.38 - -Nlocal: 1400 ave 1850 max 932 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 642.25 ave 730 max 550 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Neighs: 1267.25 ave 1805 max 729 min -Histogram: 1 1 0 0 0 0 0 0 1 1 - -Total # of neighbors = 5069 -Ave neighs/atom = 0.90517857 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 154 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 - 800 rigid bodies with 4000 atoms -print "rigid/nvt" -rigid/nvt -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 7.557 | 7.566 | 7.574 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 6000 1.3958734 5.9025061 6.9988899 0.0021028569 7.0894453 62.244 62.244 62.244 0.013626393 0.019990521 -0.027308344 - 6100 1.403297 5.9008111 7.0030257 0.0034667159 7.152313 62.244 62.244 62.244 0.00094173119 0.0074633638 0.0019950526 - 6200 1.4025256 5.8966477 6.9982564 -0.00020483779 6.9894355 62.244 62.244 62.244 -0.0064238043 0.0010245391 0.0047847518 - 6300 1.4394011 5.9052004 7.0357728 0.0054604133 7.2709147 62.244 62.244 62.244 0.0096132747 0.002164465 0.0046035003 - 6400 1.408769 5.8824709 6.9889834 0.005608612 7.2305072 62.244 62.244 62.244 0.0042736813 0.0053311794 0.0072209755 - 6500 1.3956548 5.8831208 6.9793329 0.0085962528 7.3495135 62.244 62.244 62.244 0.0082055979 0.011231962 0.0063511989 - 6600 1.3758562 5.8829365 6.9635978 0.0065047826 7.2437134 62.244 62.244 62.244 0.005468046 0.0069917695 0.0070545323 - 6700 1.3804704 5.8923062 6.9765917 0.0057976076 7.2262542 62.244 62.244 62.244 0.0052851407 0.011935403 0.00017227886 - 6800 1.396967 5.8774293 6.974672 0.0018361999 7.0537443 62.244 62.244 62.244 1.5181397e-05 0.0031700121 0.0023234062 - 6900 1.3966118 5.8872183 6.9841821 0.0029553371 7.1114478 62.244 62.244 62.244 -0.0022750426 0.0055197498 0.005621304 - 7000 1.3992657 5.8918087 6.990857 0.0033614376 7.1356106 62.244 62.244 62.244 0.0019626838 -0.0019054573 0.010027086 -Loop time of 0.627583 on 4 procs for 1000 steps with 5600 atoms - -Performance: 688355.013 tau/day, 1593.414 timesteps/s, 8.923 Matom-step/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.017522 | 0.028358 | 0.041297 | 6.2 | 4.52 -Bond | 0.0060681 | 0.0092563 | 0.012417 | 2.9 | 1.47 -Neigh | 0.13625 | 0.13667 | 0.13709 | 0.1 | 21.78 -Comm | 0.027966 | 0.043787 | 0.057522 | 6.2 | 6.98 -Output | 0.00035478 | 0.00049121 | 0.00055892 | 0.0 | 0.08 -Modify | 0.35811 | 0.37631 | 0.39333 | 2.6 | 59.96 -Other | | 0.03272 | | | 5.21 - -Nlocal: 1400 ave 1883 max 958 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 665 ave 803 max 565 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Neighs: 1272.25 ave 1895 max 762 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 5089 -Ave neighs/atom = 0.90875 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 150 -Dangerous builds = 0 -unfix 1 - -compute myTemp all temp - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all - 800 rigid bodies with 4000 atoms -print "rigid/npt iso" -rigid/npt iso -fix_modify 1 temp myTemp - -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 7.557 | 7.566 | 7.574 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 7000 1.3992657 5.8918087 6.990857 0.016459779 7.6996647 62.244 62.244 62.244 0.056781831 -0.019577361 0.012174866 - 7100 1.5086944 5.8706667 7.0556653 0.011656301 7.4412826 57.006966 57.006966 57.006966 0.015012728 0.015151838 0.0048043378 - 7200 1.5444857 5.8347072 7.047818 0.025893976 7.6357076 50.283831 50.283831 50.283831 0.021166084 0.027070838 0.029445006 - 7300 1.5460527 5.7950177 7.0093593 0.02162991 7.3688559 45.318555 45.318555 45.318555 0.014747735 0.037527921 0.012614075 - 7400 1.5613693 5.7516603 6.9780323 0.034798817 7.4279201 41.678228 41.678228 41.678228 0.041296806 0.025288632 0.037811012 - 7500 1.5582169 5.7359749 6.9598708 0.029878761 7.2757008 38.972622 38.972622 38.972622 0.031657651 0.020061922 0.037916711 - 7600 1.5578367 5.6988812 6.9224785 0.045695884 7.3351888 36.981577 36.981577 36.981577 0.040243029 0.039644927 0.057199697 - 7700 1.5148812 5.6528692 6.8427272 0.022439627 7.0209705 35.43196 35.43196 35.43196 0.010631952 0.017769669 0.03891726 - 7800 1.529109 5.6051059 6.8061392 0.054079172 7.1911354 34.161596 34.161596 34.161596 0.034939239 0.071325426 0.05597285 - 7900 1.5182819 5.5708546 6.7633838 0.066345571 7.1933547 33.108416 33.108416 33.108416 0.060359678 0.07068182 0.067995216 - 8000 1.4677372 5.5540248 6.7068537 0.033729921 6.90804 32.205032 32.205032 32.205032 0.049412183 0.016101823 0.035675755 -Loop time of 1.1282 on 4 procs for 1000 steps with 5600 atoms - -Performance: 382910.795 tau/day, 886.368 timesteps/s, 4.964 Matom-step/s -99.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.047245 | 0.075421 | 0.11065 | 10.1 | 6.69 -Bond | 0.0077964 | 0.011056 | 0.014794 | 2.9 | 0.98 -Neigh | 0.47306 | 0.4737 | 0.47434 | 0.1 | 41.99 -Comm | 0.047565 | 0.086613 | 0.11788 | 10.3 | 7.68 -Output | 0.00031206 | 0.00038703 | 0.00060877 | 0.0 | 0.03 -Modify | 0.43174 | 0.44726 | 0.46676 | 2.3 | 39.64 -Other | | 0.03376 | | | 2.99 - -Nlocal: 1400 ave 1845 max 1051 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 1558.25 ave 1732 max 1431 min -Histogram: 1 0 1 0 1 0 0 0 0 1 -Neighs: 6210.75 ave 9543 max 3698 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 24843 -Ave neighs/atom = 4.43625 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 335 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all - 800 rigid bodies with 4000 atoms -print "rigid/npt x" -rigid/npt x -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 7.567 | 7.579 | 7.596 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 8000 1.4677372 5.5540248 6.7068537 -0.017850632 6.6003814 32.205032 32.205032 32.205032 -0.10278017 -0.1824093 0.23163757 - 8100 1.4540331 5.5388671 6.6809322 0.022562574 6.8139144 31.823315 32.205032 32.205032 0.028408548 0.028883436 0.010395737 - 8200 1.4702497 5.4971666 6.6519689 0.031541665 6.8340274 31.164985 32.205032 32.205032 0.05198967 0.017790558 0.024844767 - 8300 1.4895576 5.4752966 6.6452643 0.049612462 6.9245663 30.396516 32.205032 32.205032 0.050583662 0.041684528 0.056569197 - 8400 1.4546023 5.4627064 6.6052185 0.014637455 6.6862795 29.901065 32.205032 32.205032 0.022874978 -0.0061332581 0.027170646 - 8500 1.4485789 5.4330137 6.5707949 0.06887386 6.9450276 29.337823 32.205032 32.205032 0.082103679 0.041682043 0.082835857 - 8600 1.4443937 5.4261726 6.5606664 0.02551672 6.6959898 28.63444 32.205032 32.205032 0.028149026 0.066325162 -0.017924027 - 8700 1.4329121 5.409813 6.5352887 0.028828984 6.6848753 28.015854 32.205032 32.205032 0.015384578 0.050827744 0.02027463 - 8800 1.4015747 5.4009279 6.5017898 0.046423411 6.7374794 27.41221 32.205032 32.205032 0.099149897 0.019633915 0.020486421 - 8900 1.411353 5.3728016 6.4813438 0.046095308 6.711069 26.908695 32.205032 32.205032 0.04716092 0.029778906 0.061346098 - 9000 1.3987178 5.3528351 6.451453 0.029891295 6.5977498 26.425959 32.205032 32.205032 0.033096258 0.039059663 0.017517965 -Loop time of 1.05732 on 4 procs for 1000 steps with 5600 atoms - -Performance: 408581.873 tau/day, 945.791 timesteps/s, 5.296 Matom-step/s -99.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.084017 | 0.12178 | 0.1674 | 10.7 | 11.52 -Bond | 0.0087866 | 0.011339 | 0.014172 | 2.1 | 1.07 -Neigh | 0.35177 | 0.35194 | 0.35221 | 0.0 | 33.29 -Comm | 0.046529 | 0.094466 | 0.13331 | 12.7 | 8.93 -Output | 0.00031081 | 0.00038714 | 0.00061511 | 0.0 | 0.04 -Modify | 0.43779 | 0.45007 | 0.46334 | 1.8 | 42.57 -Other | | 0.02734 | | | 2.59 - -Nlocal: 1400 ave 1718 max 1133 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 1700.75 ave 1793 max 1533 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Neighs: 7936.75 ave 10967 max 5250 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 31747 -Ave neighs/atom = 5.6691071 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 169 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all - 800 rigid bodies with 4000 atoms -print "rigid/nph iso" -rigid/nph iso -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.58 | 7.597 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 9000 1.3987178 5.3528351 6.451453 0.26585248 7.7526137 26.425959 32.205032 32.205032 0.02018168 0.47782722 0.29954855 - 9100 1.4351747 5.3304458 6.4576986 0.051746697 6.707501 26.305023 32.057649 32.057649 0.073064096 0.037508173 0.044667823 - 9200 1.442609 5.3185643 6.4516564 0.026933669 6.5768423 25.974904 31.655336 31.655336 0.0097800385 0.035425194 0.035595776 - 9300 1.4528107 5.2812305 6.4223354 0.074634951 6.7601945 25.747306 31.377965 31.377965 0.12937272 0.031196451 0.063335685 - 9400 1.4778194 5.2625966 6.4233445 0.0179548 6.5034822 25.626311 31.23051 31.23051 0.042627054 -0.047901197 0.059138542 - 9500 1.4406019 5.2661826 6.3976982 0.048963663 6.6143417 25.551982 31.139926 31.139926 0.097226703 -0.0051171725 0.054781458 - 9600 1.4463517 5.2420508 6.3780826 0.033338493 6.5253103 25.535743 31.120136 31.120136 0.013953126 0.066958907 0.019103444 - 9700 1.4040075 5.264089 6.3668617 0.075486855 6.6986983 25.496763 31.072631 31.072631 0.051974464 0.097239496 0.077246606 - 9800 1.4369291 5.25259 6.3812208 0.062882837 6.6532231 25.359898 30.905835 30.905835 0.088614069 0.087884794 0.012149647 - 9900 1.4426697 5.2270989 6.3602387 0.070910381 6.6603048 25.175015 30.68052 30.68052 0.081294501 0.056618911 0.07481773 - 10000 1.4714476 5.2051468 6.3608901 0.038441228 6.5234989 25.171919 30.676748 30.676748 0.021691591 0.0086967032 0.084935388 -Loop time of 1.07529 on 4 procs for 1000 steps with 5600 atoms - -Performance: 401751.573 tau/day, 929.980 timesteps/s, 5.208 Matom-step/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.10178 | 0.14349 | 0.18701 | 10.0 | 13.34 -Bond | 0.0094369 | 0.011359 | 0.01342 | 1.5 | 1.06 -Neigh | 0.35737 | 0.35764 | 0.35787 | 0.0 | 33.26 -Comm | 0.048562 | 0.093503 | 0.13651 | 12.7 | 8.70 -Output | 0.00029714 | 0.00035903 | 0.0005404 | 0.0 | 0.03 -Modify | 0.43477 | 0.44365 | 0.45263 | 1.3 | 41.26 -Other | | 0.0253 | | | 2.35 - -Nlocal: 1400 ave 1650 max 1148 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Nghost: 1770.5 ave 1864 max 1640 min -Histogram: 1 0 0 0 0 1 0 0 1 1 -Neighs: 9370.75 ave 12213 max 6410 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 37483 -Ave neighs/atom = 6.6933929 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 162 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all - 800 rigid bodies with 4000 atoms -print "rigid/nph xy couple" -rigid/nph xy couple -run 1000 -Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule -Per MPI rank memory allocation (min/avg/max) = 7.569 | 7.58 | 7.597 Mbytes - Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 10000 1.4714476 5.2051468 6.3608901 -0.096738415 5.9516804 25.171919 30.676748 30.676748 -0.07465944 0.069571401 -0.28512721 - 10100 1.4336012 5.2129069 6.3389239 0.069305782 6.6336186 25.237381 30.756525 30.676748 0.1042358 0.062982076 0.040699467 - 10200 1.3850266 5.2255115 6.3133757 -0.026502584 6.1990129 25.423835 30.983755 30.676748 -0.018638813 -0.01225392 -0.048615018 - 10300 1.4059572 5.2273228 6.3316268 0.026841528 6.4477936 25.461278 31.029386 30.676748 0.0032748153 0.054971756 0.022278013 - 10400 1.4085811 5.2218002 6.3281652 0.087028058 6.7005137 25.315588 30.851835 30.676748 0.095488962 0.059423478 0.10617173 - 10500 1.4323046 5.1961285 6.321127 0.011963636 6.3715428 25.124329 30.61875 30.676748 0.047765438 -0.013073535 0.0011990069 - 10600 1.4401614 5.1744178 6.3055874 0.065577091 6.5770196 24.899891 30.345229 30.676748 0.05130409 0.11923748 0.026189709 - 10700 1.45262 5.1656069 6.3065622 0.019979844 6.3873914 24.616776 30.0002 30.676748 0.062077837 0.01564587 -0.017784176 - 10800 1.436593 5.1491998 6.2775666 0.06467682 6.5343926 24.388662 29.722201 30.676748 0.055509186 0.081686998 0.056834275 - 10900 1.4221057 5.1580272 6.2750151 0.10779715 6.6964287 24.198783 29.490797 30.676748 0.11821126 0.13388181 0.071298392 - 11000 1.4318097 5.1652839 6.2898937 0.12207839 6.7635101 24.106649 29.378514 30.676748 0.13281999 0.095712525 0.13770264 -Loop time of 1.05977 on 4 procs for 1000 steps with 5600 atoms - -Performance: 407635.235 tau/day, 943.600 timesteps/s, 5.284 Matom-step/s -99.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.11531 | 0.15482 | 0.18642 | 8.0 | 14.61 -Bond | 0.0095915 | 0.011316 | 0.012716 | 1.2 | 1.07 -Neigh | 0.34708 | 0.34732 | 0.34748 | 0.0 | 32.77 -Comm | 0.050629 | 0.082561 | 0.12326 | 11.1 | 7.79 -Output | 0.00029841 | 0.00036751 | 0.00057311 | 0.0 | 0.03 -Modify | 0.43421 | 0.44242 | 0.45027 | 0.9 | 41.75 -Other | | 0.02097 | | | 1.98 - -Nlocal: 1400 ave 1551 max 1205 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Nghost: 1831.5 ave 1910 max 1688 min -Histogram: 1 0 0 0 0 1 0 0 0 2 -Neighs: 10203.8 ave 12647 max 7619 min -Histogram: 1 0 1 0 0 0 0 1 0 1 - -Total # of neighbors = 40815 -Ave neighs/atom = 7.2883929 -Ave special neighs/atom = 0.57142857 -Neighbor list builds = 161 -Dangerous builds = 0 - -Total wall time: 0:00:08 diff --git a/examples/rigid/log.27Nov18.rigid.atomfile.g++.1 b/examples/rigid/log.27Nov18.rigid.atomfile.g++.1 new file mode 100644 index 0000000000..e3e539eada --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.atomfile.g++.1 @@ -0,0 +1,338 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atomfile bodies.txt +fix 1 all rigid custom v_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.109 | 4.109 | 4.109 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.153749 on 1 procs for 10000 steps with 81 atoms + +Performance: 561955.786 tau/day, 65041.179 timesteps/s +98.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0098538 | 0.0098538 | 0.0098538 | 0.0 | 6.41 +Neigh | 0.040308 | 0.040308 | 0.040308 | 0.0 | 26.22 +Comm | 0.013034 | 0.013034 | 0.013034 | 0.0 | 8.48 +Output | 0.0017202 | 0.0017202 | 0.0017202 | 0.0 | 1.12 +Modify | 0.083709 | 0.083709 | 0.083709 | 0.0 | 54.45 +Other | | 0.005123 | | | 3.33 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.atomfile.g++.4 b/examples/rigid/log.27Nov18.rigid.atomfile.g++.4 new file mode 100644 index 0000000000..1e28766101 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.atomfile.g++.4 @@ -0,0 +1,338 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atomfile bodies.txt +fix 1 all rigid custom v_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.174 | 4.455 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 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5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.202963 on 4 procs for 10000 steps with 81 atoms + +Performance: 425693.239 tau/day, 49270.051 timesteps/s +89.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0025978 | 0.0033882 | 0.0042055 | 1.0 | 1.67 +Neigh | 0.012025 | 0.013416 | 0.01623 | 1.4 | 6.61 +Comm | 0.080375 | 0.087468 | 0.090782 | 1.4 | 43.10 +Output | 0.0031407 | 0.0039954 | 0.0065427 | 2.3 | 1.97 +Modify | 0.086613 | 0.087285 | 0.087619 | 0.1 | 43.01 +Other | | 0.00741 | | | 3.65 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.atomvar.g++.1 b/examples/rigid/log.27Nov18.rigid.atomvar.g++.1 new file mode 100644 index 0000000000..58834ebf3d --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.atomvar.g++.1 @@ -0,0 +1,338 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) +fix 1 all rigid custom v_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.984 | 3.984 | 3.984 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 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16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 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12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.15622 on 1 procs for 10000 steps with 81 atoms + +Performance: 553065.489 tau/day, 64012.209 timesteps/s +95.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0098181 | 0.0098181 | 0.0098181 | 0.0 | 6.28 +Neigh | 0.040912 | 0.040912 | 0.040912 | 0.0 | 26.19 +Comm | 0.013111 | 0.013111 | 0.013111 | 0.0 | 8.39 +Output | 0.0016305 | 0.0016305 | 0.0016305 | 0.0 | 1.04 +Modify | 0.085361 | 0.085361 | 0.085361 | 0.0 | 54.64 +Other | | 0.005387 | | | 3.45 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.atomvar.g++.4 b/examples/rigid/log.27Nov18.rigid.atomvar.g++.4 new file mode 100644 index 0000000000..42b8a52768 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.atomvar.g++.4 @@ -0,0 +1,338 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) +fix 1 all rigid custom v_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.955 | 4.049 | 4.33 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.199799 on 4 procs for 10000 steps with 81 atoms + +Performance: 432434.078 tau/day, 50050.241 timesteps/s +91.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.002665 | 0.0034567 | 0.0040557 | 0.9 | 1.73 +Neigh | 0.012185 | 0.013168 | 0.014083 | 0.8 | 6.59 +Comm | 0.079331 | 0.082804 | 0.084927 | 0.7 | 41.44 +Output | 0.0031595 | 0.0039212 | 0.0061827 | 2.1 | 1.96 +Modify | 0.088465 | 0.090202 | 0.091938 | 0.4 | 45.15 +Other | | 0.006247 | | | 3.13 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.early.g++.1 b/examples/rigid/log.27Nov18.rigid.early.g++.1 new file mode 100644 index 0000000000..3c8022423f --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.early.g++.1 @@ -0,0 +1,337 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.152593 on 1 procs for 10000 steps with 81 atoms + +Performance: 566210.692 tau/day, 65533.645 timesteps/s +96.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0098324 | 0.0098324 | 0.0098324 | 0.0 | 6.44 +Neigh | 0.040376 | 0.040376 | 0.040376 | 0.0 | 26.46 +Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 8.03 +Output | 0.0016036 | 0.0016036 | 0.0016036 | 0.0 | 1.05 +Modify | 0.083605 | 0.083605 | 0.083605 | 0.0 | 54.79 +Other | | 0.00493 | | | 3.23 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.early.g++.4 b/examples/rigid/log.27Nov18.rigid.early.g++.4 new file mode 100644 index 0000000000..91f091b799 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.early.g++.4 @@ -0,0 +1,337 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.198859 on 4 procs for 10000 steps with 81 atoms + +Performance: 434479.274 tau/day, 50286.953 timesteps/s +91.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.002526 | 0.0034331 | 0.0041001 | 1.0 | 1.73 +Neigh | 0.012097 | 0.013092 | 0.013992 | 0.8 | 6.58 +Comm | 0.075266 | 0.07972 | 0.084679 | 1.2 | 40.09 +Output | 0.0030892 | 0.0043746 | 0.0081537 | 3.3 | 2.20 +Modify | 0.088037 | 0.091924 | 0.095021 | 0.9 | 46.23 +Other | | 0.006316 | | | 3.18 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.g++.1 b/examples/rigid/log.27Nov18.rigid.g++.1 new file mode 100644 index 0000000000..9dff202069 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.g++.1 @@ -0,0 +1,335 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 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0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.152143 on 1 procs for 10000 steps with 81 atoms + +Performance: 567885.005 tau/day, 65727.431 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0097773 | 0.0097773 | 0.0097773 | 0.0 | 6.43 +Neigh | 0.040602 | 0.040602 | 0.040602 | 0.0 | 26.69 +Comm | 0.012049 | 0.012049 | 0.012049 | 0.0 | 7.92 +Output | 0.0016172 | 0.0016172 | 0.0016172 | 0.0 | 1.06 +Modify | 0.083104 | 0.083104 | 0.083104 | 0.0 | 54.62 +Other | | 0.004994 | | | 3.28 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.g++.4 b/examples/rigid/log.27Nov18.rigid.g++.4 new file mode 100644 index 0000000000..36e602f1f1 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.g++.4 @@ -0,0 +1,335 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 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14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 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0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.201762 on 4 procs for 10000 steps with 81 atoms + +Performance: 428226.262 tau/day, 49563.225 timesteps/s +89.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0025356 | 0.0033935 | 0.0042305 | 1.0 | 1.68 +Neigh | 0.012009 | 0.012959 | 0.015092 | 1.1 | 6.42 +Comm | 0.07666 | 0.086213 | 0.092506 | 2.0 | 42.73 +Output | 0.0032623 | 0.0052034 | 0.011 | 4.6 | 2.58 +Modify | 0.084815 | 0.087869 | 0.089999 | 0.6 | 43.55 +Other | | 0.006125 | | | 3.04 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.nve.early.g++.1 b/examples/rigid/log.27Nov18.rigid.nve.early.g++.1 new file mode 100644 index 0000000000..1e426d397e --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.nve.early.g++.1 @@ -0,0 +1,337 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.69 571.70921 0 5265.8153 32.005816 + 100 16298.128 136.75661 0 5267.6488 16.449029 + 150 16682.532 17.504156 0 5269.4124 14.901186 + 200 16733.906 1.3755079 0 5269.4571 14.571305 + 250 16738.861 -0.15272039 0 5269.4886 14.498342 + 300 16738.608 -0.055216883 0 5269.5066 14.498 + 350 16738.5 -0.017457072 0 5269.5104 14.498392 + 400 16738.451 -0.0060161309 0 5269.5063 14.49851 + 450 16738.435 -0.001271965 0 5269.5059 14.498571 + 500 16738.443 -0.00081074175 0 5269.509 14.498598 + 550 16738.452 -0.00083208965 0 5269.5118 14.498618 + 600 16738.45 -0.00058358431 0 5269.5116 14.498617 + 650 16738.443 -0.00047228525 0 5269.5093 14.4986 + 700 16738.444 0 0 5269.5102 14.498612 + 750 16738.461 0 0 5269.5157 14.498654 + 800 16738.479 0 0 5269.521 14.498697 + 850 16738.473 0 0 5269.5192 14.498683 + 900 16738.449 0 0 5269.5116 14.498624 + 950 16738.438 -0.0035324203 0 5269.5046 14.498537 + 1000 16738.562 -0.051134242 0 5269.4963 14.498093 + 1050 16737.343 0.32970192 0 5269.4934 14.527634 + 1100 16737.878 0.16213235 0 5269.4941 14.533864 + 1150 16738.682 -0.089236256 0 5269.4959 14.511765 + 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 + 1250 16738.45 0 0 5269.5119 14.512611 + 1300 16738.475 0 0 5269.5199 14.512673 + 1350 16738.484 0 0 5269.5228 14.512696 + 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 + 1450 16738.45 -0.0010933363 0 5269.511 14.512595 + 1500 16738.445 -0.00057484239 0 5269.51 14.512591 + 1550 16738.451 0 0 5269.5123 14.512615 + 1600 16738.452 0 0 5269.5127 14.512618 + 1650 16738.443 0 0 5269.5099 14.512596 + 1700 16738.433 0 0 5269.5068 14.512572 + 1750 16738.438 0 0 5269.5084 14.512584 + 1800 16738.459 0 0 5269.5149 14.512635 + 1850 16738.473 0 0 5269.5193 14.51267 + 1900 16738.462 0 0 5269.5159 14.512644 + 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 + 2000 16738.463 -0.013425408 0 5269.5027 14.512382 + 2050 16738.535 -0.036964311 0 5269.5017 14.512152 + 2100 16738.621 -0.063490509 0 5269.5023 14.512108 + 2150 16738.594 -0.056143934 0 5269.5012 14.512117 + 2200 16738.536 -0.038486645 0 5269.5007 14.512277 + 2250 16738.496 -0.023712406 0 5269.503 14.51242 + 2300 16738.488 -0.013209094 0 5269.5109 14.51255 + 2350 16738.486 -0.0045244524 0 5269.519 14.512693 + 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 + 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 + 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 + 2550 16738.552 -0.04420046 0 5269.4998 14.512177 + 2600 16738.42 -0.004347531 0 5269.4982 14.512783 + 2650 16734.241 1.3131302 0 5269.5 14.577195 + 2700 16738.737 -0.10612056 0 5269.4961 14.503874 + 2750 16732.705 1.7939719 0 5269.4974 14.629294 + 2800 16738.558 -0.042867033 0 5269.5032 14.519893 + 2850 16738.499 -0.01271227 0 5269.5146 14.518524 + 2900 16738.486 -0.0032778045 0 5269.52 14.518712 + 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 + 3000 16738.647 -0.070862542 0 5269.5031 14.51803 + 3050 16678.313 18.829038 0 5269.409 15.533426 + 3100 16632.312 33.399217 0 5269.4975 14.588597 + 3150 16739.318 -0.31388148 0 5269.4715 13.520782 + 3200 16727.951 3.26736 0 5269.4741 12.288358 + 3250 16686.364 16.353793 0 5269.4682 14.152517 + 3300 16738.532 -0.031574462 0 5269.5064 13.310615 + 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 + 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 + 3450 16738.489 -0.021623738 0 5269.5026 13.308001 + 3500 16737.78 0.19719043 0 5269.4983 13.325999 + 3550 16658.578 25.116206 0 5269.4834 13.778249 + 3600 16738.51 -0.032864725 0 5269.4981 12.392389 + 3650 16738.899 -0.15952703 0 5269.4938 12.383503 + 3700 16738.879 -0.16025994 0 5269.487 12.382575 + 3750 16738.878 -0.16608251 0 5269.4806 12.382765 + 3800 16738.591 -0.078679341 0 5269.4776 12.383227 + 3850 16738.429 -0.024729409 0 5269.4807 12.382942 + 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 + 3950 16738.428 -0.002521266 0 5269.5027 12.383324 + 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 + 4050 16738.488 0 0 5269.5241 12.383531 + 4100 16738.468 0 0 5269.5178 12.383482 + 4150 16738.422 0 0 5269.5033 12.383369 + 4200 16738.387 0 0 5269.4921 12.383281 + 4250 16738.383 0 0 5269.4908 12.38327 + 4300 16738.4 0 0 5269.4964 12.383314 + 4350 16738.423 0 0 5269.5036 12.38337 + 4400 16738.441 0 0 5269.5092 12.383414 + 4450 16738.45 0 0 5269.5121 12.383437 + 4500 16738.45 0 0 5269.5122 12.383438 + 4550 16738.442 0 0 5269.5095 12.383417 + 4600 16738.425 0 0 5269.5042 12.383376 + 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 + 4700 16738.444 -0.024020551 0 5269.4862 12.382975 + 4750 16738.49 -0.04852143 0 5269.4761 12.385777 + 4800 16735.057 1.0347216 0 5269.4786 12.43543 + 4850 16735.441 0.92650925 0 5269.4913 12.418653 + 4900 16723.839 4.5908974 0 5269.5033 13.410103 + 4950 16738.531 -0.02153767 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589697 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 + 5100 16738.404 0 0 5269.4976 13.090032 + 5150 16738.421 0 0 5269.5029 13.090073 + 5200 16738.44 0 0 5269.5087 13.090119 + 5250 16738.448 -0.001279392 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376391 0 5269.5075 13.090026 + 5350 16738.479 -0.020383841 0 5269.5007 13.089897 + 5400 16735.845 0.7988947 0 5269.4909 13.136244 + 5450 16735.558 0.87620022 0 5269.4778 12.324482 + 5500 16711.494 8.4724178 0 5269.4984 12.656579 + 5550 16454.525 89.074815 0 5269.2031 16.996503 + 5600 16713.084 7.9801418 0 5269.5065 13.774979 + 5650 16738.676 -0.079987748 0 5269.5033 13.168297 + 5700 16446.281 91.866085 0 5269.399 23.764663 + 5750 16738.549 -0.039869084 0 5269.5034 13.378122 + 5800 16738.487 -0.014994478 0 5269.5086 13.378399 + 5850 16738.466 -0.0051267616 0 5269.512 13.37856 + 5900 16738.462 -0.0043690142 0 5269.5113 13.378573 + 5950 16738.528 -0.032727415 0 5269.5039 13.378197 + 6000 16702.774 10.969438 0 5269.2502 13.788852 + 6050 16682.271 17.483137 0 5269.3092 13.353101 + 6100 16738.508 -0.028838222 0 5269.5016 12.521084 + 6150 16738.425 -0.0067595536 0 5269.4974 12.521223 + 6200 16738.401 -0.0011499893 0 5269.4955 12.521254 + 6250 16738.455 0 0 5269.5135 12.52141 + 6300 16738.523 0 0 5269.5352 12.52158 + 6350 16738.503 0 0 5269.5287 12.521531 + 6400 16738.427 0 0 5269.5047 12.521344 + 6450 16738.399 0 0 5269.496 12.521274 + 6500 16738.425 0 0 5269.5042 12.521337 + 6550 16738.441 0 0 5269.5093 12.521378 + 6600 16738.42 0 0 5269.5025 12.521326 + 6650 16738.398 0 0 5269.4957 12.521272 + 6700 16738.435 0 0 5269.5074 12.521362 + 6750 16738.505 0 0 5269.5293 12.521534 + 6800 16738.508 0 0 5269.5303 12.521543 + 6850 16738.446 0 0 5269.5108 12.521391 + 6900 16738.414 0 0 5269.5009 12.521312 + 6950 16738.432 0 0 5269.5063 12.521354 + 7000 16738.444 0 0 5269.5102 12.521385 + 7050 16738.421 0 0 5269.5029 12.521329 + 7100 16738.393 0 0 5269.4941 12.521259 + 7150 16738.419 0 0 5269.5022 12.521322 + 7200 16738.489 0 0 5269.5244 12.521495 + 7250 16738.505 0 0 5269.5293 12.521535 + 7300 16738.443 0 0 5269.5098 12.521383 + 7350 16738.404 0 0 5269.4976 12.521287 + 7400 16738.43 0 0 5269.5058 12.52135 + 7450 16738.461 0 0 5269.5156 12.521427 + 7500 16738.447 0 0 5269.5109 12.521392 + 7550 16738.407 0 0 5269.4986 12.521295 + 7600 16738.412 0 0 5269.5002 12.521306 + 7650 16738.478 0 0 5269.5208 12.521467 + 7700 16738.51 0 0 5269.5309 12.521547 + 7750 16738.454 0 0 5269.5135 12.521412 + 7800 16738.398 0 0 5269.4958 12.521273 + 7850 16738.407 -0.0002118108 0 5269.4982 12.521289 + 7900 16738.441 -0.00021679711 0 5269.509 12.521373 + 7950 16738.446 -0.00023848139 0 5269.5107 12.521386 + 8000 16738.423 0 0 5269.5035 12.521333 + 8050 16738.423 0 0 5269.5034 12.521332 + 8100 16738.478 -0.00069622994 0 5269.52 12.521454 + 8150 16738.523 -0.0040058408 0 5269.531 12.521501 + 8200 16738.486 -0.0092298229 0 5269.5142 12.521334 + 8250 16738.458 -0.023189671 0 5269.4914 12.521014 + 8300 16738.513 -0.045845677 0 5269.4861 12.520779 + 8350 16723.745 4.5690412 0 5269.4516 12.849325 + 8400 16738.466 -0.020158442 0 5269.497 12.835773 + 8450 16738.437 -0.012822892 0 5269.4952 12.829936 + 8500 16738.408 -0.0016837088 0 5269.4972 12.830061 + 8550 16738.464 -0.00097379467 0 5269.5155 12.830216 + 8600 16738.669 -0.050578079 0 5269.5304 12.829934 + 8650 15917.563 250.28318 0 5261.3678 24.54572 + 8700 16738.445 0.0012168759 0 5269.5117 10.589499 + 8750 16738.473 -0.010164589 0 5269.509 10.588414 + 8800 16738.468 0 0 5269.5177 10.588633 + 8850 16738.508 0 0 5269.5304 10.588733 + 8900 16738.509 0 0 5269.5307 10.588736 + 8950 16738.496 0 0 5269.5266 10.588705 + 9000 16738.477 0 0 5269.5204 10.588656 + 9050 16738.455 0 0 5269.5135 10.588602 + 9100 16738.477 0 0 5269.5206 10.588656 + 9150 16738.512 0 0 5269.5316 10.588743 + 9200 16738.502 0 0 5269.5285 10.58872 + 9250 16738.493 0 0 5269.5255 10.588696 + 9300 16738.482 0 0 5269.522 10.588669 + 9350 16738.46 0 0 5269.5151 10.588615 + 9400 16738.481 0 0 5269.5217 10.588665 + 9450 16738.509 0 0 5269.5307 10.588736 + 9500 16738.491 0 0 5269.5248 10.58869 + 9550 16738.484 0 0 5269.5227 10.588674 + 9600 16738.483 0 0 5269.5223 10.588671 + 9650 16738.464 0 0 5269.5166 10.588626 + 9700 16738.484 0 0 5269.5229 10.588674 + 9750 16738.507 0 0 5269.5301 10.588731 + 9800 16738.482 0 0 5269.5221 10.588669 + 9850 16738.478 0 0 5269.5208 10.588659 + 9900 16738.487 -0.00030979474 0 5269.5233 10.588675 + 9950 16738.476 -0.00095968581 0 5269.5193 10.588632 + 10000 16738.494 -0.00062717822 0 5269.5253 10.588684 +Loop time of 0.168577 on 1 procs for 10000 steps with 81 atoms + +Performance: 512524.843 tau/day, 59320.005 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.010812 | 0.010812 | 0.010812 | 0.0 | 6.41 +Neigh | 0.04144 | 0.04144 | 0.04144 | 0.0 | 24.58 +Comm | 0.012082 | 0.012082 | 0.012082 | 0.0 | 7.17 +Output | 0.0016394 | 0.0016394 | 0.0016394 | 0.0 | 0.97 +Modify | 0.097466 | 0.097466 | 0.097466 | 0.0 | 57.82 +Other | | 0.005139 | | | 3.05 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 49 ave 49 max 49 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3 +Ave neighs/atom = 0.037037 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.nve.early.g++.4 b/examples/rigid/log.27Nov18.rigid.nve.early.g++.4 new file mode 100644 index 0000000000..5b775d969a --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.nve.early.g++.4 @@ -0,0 +1,337 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.69 571.70921 0 5265.8153 32.005816 + 100 16298.128 136.75661 0 5267.6488 16.449029 + 150 16682.532 17.504156 0 5269.4124 14.901186 + 200 16733.906 1.3755079 0 5269.4571 14.571305 + 250 16738.861 -0.15272039 0 5269.4886 14.498342 + 300 16738.608 -0.055216883 0 5269.5066 14.498 + 350 16738.5 -0.017457072 0 5269.5104 14.498392 + 400 16738.451 -0.0060161309 0 5269.5063 14.49851 + 450 16738.435 -0.001271965 0 5269.5059 14.498571 + 500 16738.443 -0.00081074175 0 5269.509 14.498598 + 550 16738.452 -0.00083208965 0 5269.5118 14.498618 + 600 16738.45 -0.00058358431 0 5269.5116 14.498617 + 650 16738.443 -0.00047228525 0 5269.5093 14.4986 + 700 16738.444 0 0 5269.5102 14.498612 + 750 16738.461 0 0 5269.5157 14.498654 + 800 16738.479 0 0 5269.521 14.498697 + 850 16738.473 0 0 5269.5192 14.498683 + 900 16738.449 0 0 5269.5116 14.498624 + 950 16738.438 -0.0035324203 0 5269.5046 14.498537 + 1000 16738.562 -0.051134242 0 5269.4963 14.498093 + 1050 16737.343 0.32970192 0 5269.4934 14.527634 + 1100 16737.878 0.16213235 0 5269.4941 14.533864 + 1150 16738.682 -0.089236256 0 5269.4959 14.511765 + 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 + 1250 16738.45 0 0 5269.5119 14.512611 + 1300 16738.475 0 0 5269.5199 14.512673 + 1350 16738.484 0 0 5269.5228 14.512696 + 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 + 1450 16738.45 -0.0010933363 0 5269.511 14.512595 + 1500 16738.445 -0.00057484239 0 5269.51 14.512591 + 1550 16738.451 0 0 5269.5123 14.512615 + 1600 16738.452 0 0 5269.5127 14.512618 + 1650 16738.443 0 0 5269.5099 14.512596 + 1700 16738.433 0 0 5269.5068 14.512572 + 1750 16738.438 0 0 5269.5084 14.512584 + 1800 16738.459 0 0 5269.5149 14.512635 + 1850 16738.473 0 0 5269.5193 14.51267 + 1900 16738.462 0 0 5269.5159 14.512644 + 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 + 2000 16738.463 -0.013425408 0 5269.5027 14.512382 + 2050 16738.535 -0.036964311 0 5269.5017 14.512152 + 2100 16738.621 -0.063490509 0 5269.5023 14.512108 + 2150 16738.594 -0.056143934 0 5269.5012 14.512117 + 2200 16738.536 -0.038486645 0 5269.5007 14.512277 + 2250 16738.496 -0.023712406 0 5269.503 14.51242 + 2300 16738.488 -0.013209094 0 5269.5109 14.51255 + 2350 16738.486 -0.0045244524 0 5269.519 14.512693 + 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 + 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 + 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 + 2550 16738.552 -0.04420046 0 5269.4998 14.512177 + 2600 16738.42 -0.004347531 0 5269.4982 14.512783 + 2650 16734.241 1.3131302 0 5269.5 14.577195 + 2700 16738.737 -0.10612056 0 5269.4961 14.503874 + 2750 16732.705 1.7939719 0 5269.4974 14.629294 + 2800 16738.558 -0.042867033 0 5269.5032 14.519893 + 2850 16738.499 -0.01271227 0 5269.5146 14.518524 + 2900 16738.486 -0.0032778045 0 5269.52 14.518712 + 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 + 3000 16738.647 -0.070862542 0 5269.5031 14.51803 + 3050 16678.313 18.829038 0 5269.409 15.533426 + 3100 16632.312 33.399217 0 5269.4975 14.588597 + 3150 16739.318 -0.31388148 0 5269.4715 13.520782 + 3200 16727.951 3.26736 0 5269.4741 12.288358 + 3250 16686.364 16.353793 0 5269.4682 14.152517 + 3300 16738.532 -0.031574462 0 5269.5064 13.310615 + 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 + 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 + 3450 16738.489 -0.021623738 0 5269.5026 13.308001 + 3500 16737.78 0.19719043 0 5269.4983 13.325999 + 3550 16658.578 25.116206 0 5269.4834 13.778249 + 3600 16738.51 -0.032864725 0 5269.4981 12.392389 + 3650 16738.899 -0.15952703 0 5269.4938 12.383503 + 3700 16738.879 -0.16025994 0 5269.487 12.382575 + 3750 16738.878 -0.16608251 0 5269.4806 12.382765 + 3800 16738.591 -0.078679341 0 5269.4776 12.383227 + 3850 16738.429 -0.024729409 0 5269.4807 12.382942 + 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 + 3950 16738.428 -0.002521266 0 5269.5027 12.383324 + 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 + 4050 16738.488 0 0 5269.5241 12.383531 + 4100 16738.468 0 0 5269.5178 12.383482 + 4150 16738.422 0 0 5269.5033 12.383369 + 4200 16738.387 0 0 5269.4921 12.383281 + 4250 16738.383 0 0 5269.4908 12.38327 + 4300 16738.4 0 0 5269.4964 12.383314 + 4350 16738.423 0 0 5269.5036 12.38337 + 4400 16738.441 0 0 5269.5092 12.383414 + 4450 16738.45 0 0 5269.5121 12.383437 + 4500 16738.45 0 0 5269.5122 12.383438 + 4550 16738.442 0 0 5269.5095 12.383417 + 4600 16738.425 0 0 5269.5042 12.383376 + 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 + 4700 16738.444 -0.024020551 0 5269.4862 12.382975 + 4750 16738.49 -0.048521428 0 5269.4761 12.385777 + 4800 16735.057 1.0347217 0 5269.4786 12.43543 + 4850 16735.441 0.92650925 0 5269.4913 12.418653 + 4900 16723.839 4.5908973 0 5269.5033 13.410103 + 4950 16738.531 -0.02153767 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589696 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 + 5100 16738.404 0 0 5269.4976 13.090032 + 5150 16738.421 0 0 5269.5029 13.090073 + 5200 16738.44 0 0 5269.5087 13.090119 + 5250 16738.448 -0.001279392 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376392 0 5269.5075 13.090026 + 5350 16738.479 -0.020383842 0 5269.5007 13.089897 + 5400 16735.845 0.79889474 0 5269.4909 13.136244 + 5450 16735.558 0.87619992 0 5269.4778 12.324482 + 5500 16711.494 8.4724208 0 5269.4984 12.656579 + 5550 16454.525 89.074816 0 5269.2031 16.996503 + 5600 16713.084 7.9801334 0 5269.5065 13.774977 + 5650 16738.676 -0.079987764 0 5269.5033 13.168295 + 5700 16446.281 91.866085 0 5269.399 23.764662 + 5750 16738.549 -0.039869084 0 5269.5034 13.378121 + 5800 16738.487 -0.014994475 0 5269.5086 13.378397 + 5850 16738.466 -0.0051267556 0 5269.512 13.378559 + 5900 16738.462 -0.0043690097 0 5269.5113 13.378572 + 5950 16738.528 -0.03272741 0 5269.5039 13.378195 + 6000 16702.774 10.969434 0 5269.2502 13.788851 + 6050 16682.271 17.483158 0 5269.3092 13.3531 + 6100 16738.508 -0.028838239 0 5269.5016 12.521082 + 6150 16738.425 -0.0067595542 0 5269.4974 12.521221 + 6200 16738.401 -0.0011499896 0 5269.4955 12.521252 + 6250 16738.455 0 0 5269.5135 12.521408 + 6300 16738.523 0 0 5269.5352 12.521578 + 6350 16738.503 0 0 5269.5287 12.52153 + 6400 16738.427 0 0 5269.5047 12.521342 + 6450 16738.399 0 0 5269.496 12.521273 + 6500 16738.425 0 0 5269.5042 12.521336 + 6550 16738.441 0 0 5269.5093 12.521377 + 6600 16738.42 0 0 5269.5025 12.521324 + 6650 16738.398 0 0 5269.4957 12.52127 + 6700 16738.435 0 0 5269.5074 12.52136 + 6750 16738.505 0 0 5269.5293 12.521532 + 6800 16738.508 0 0 5269.5303 12.521541 + 6850 16738.446 0 0 5269.5108 12.521389 + 6900 16738.414 0 0 5269.5009 12.521311 + 6950 16738.432 0 0 5269.5063 12.521353 + 7000 16738.444 0 0 5269.5102 12.521383 + 7050 16738.421 0 0 5269.5029 12.521327 + 7100 16738.393 0 0 5269.4941 12.521258 + 7150 16738.419 0 0 5269.5022 12.52132 + 7200 16738.489 0 0 5269.5244 12.521494 + 7250 16738.505 0 0 5269.5293 12.521533 + 7300 16738.443 0 0 5269.5098 12.521381 + 7350 16738.404 0 0 5269.4976 12.521285 + 7400 16738.43 0 0 5269.5058 12.521348 + 7450 16738.461 0 0 5269.5156 12.521425 + 7500 16738.447 0 0 5269.5109 12.52139 + 7550 16738.407 0 0 5269.4986 12.521293 + 7600 16738.412 0 0 5269.5002 12.521305 + 7650 16738.478 0 0 5269.5208 12.521465 + 7700 16738.51 0 0 5269.5309 12.521546 + 7750 16738.454 0 0 5269.5135 12.52141 + 7800 16738.398 0 0 5269.4958 12.521272 + 7850 16738.407 -0.00021180981 0 5269.4982 12.521288 + 7900 16738.441 -0.0002167964 0 5269.509 12.521371 + 7950 16738.446 -0.00023848065 0 5269.5107 12.521385 + 8000 16738.423 0 0 5269.5035 12.521331 + 8050 16738.423 0 0 5269.5034 12.52133 + 8100 16738.478 -0.00069623408 0 5269.52 12.521452 + 8150 16738.523 -0.0040058355 0 5269.531 12.521499 + 8200 16738.486 -0.0092298325 0 5269.5142 12.521332 + 8250 16738.458 -0.023189665 0 5269.4914 12.521012 + 8300 16738.513 -0.045846242 0 5269.4861 12.520778 + 8350 16723.742 4.5698786 0 5269.4516 12.849386 + 8400 16738.466 -0.02016972 0 5269.497 12.835784 + 8450 16738.437 -0.012822703 0 5269.4952 12.829948 + 8500 16738.408 -0.0016836132 0 5269.4972 12.830073 + 8550 16738.464 -0.00097380297 0 5269.5155 12.830227 + 8600 16738.669 -0.050578946 0 5269.5304 12.829946 + 8650 15917.707 250.24016 0 5261.3702 24.544744 + 8700 16738.445 0.0010615265 0 5269.5117 10.589987 + 8750 16738.473 -0.010158834 0 5269.509 10.588904 + 8800 16738.468 0 0 5269.5176 10.589124 + 8850 16738.508 0 0 5269.5304 10.589223 + 8900 16738.509 0 0 5269.5306 10.589226 + 8950 16738.496 0 0 5269.5266 10.589195 + 9000 16738.477 0 0 5269.5204 10.589147 + 9050 16738.455 0 0 5269.5135 10.589092 + 9100 16738.477 0 0 5269.5206 10.589146 + 9150 16738.512 0 0 5269.5316 10.589233 + 9200 16738.502 0 0 5269.5285 10.58921 + 9250 16738.493 0 0 5269.5255 10.589186 + 9300 16738.482 0 0 5269.522 10.589159 + 9350 16738.46 0 0 5269.5151 10.589105 + 9400 16738.481 0 0 5269.5217 10.589155 + 9450 16738.509 0 0 5269.5307 10.589226 + 9500 16738.491 0 0 5269.5248 10.589181 + 9550 16738.484 0 0 5269.5227 10.589164 + 9600 16738.483 0 0 5269.5223 10.589161 + 9650 16738.464 0 0 5269.5166 10.589116 + 9700 16738.484 0 0 5269.5228 10.589164 + 9750 16738.507 0 0 5269.5301 10.589221 + 9800 16738.482 0 0 5269.5221 10.589159 + 9850 16738.478 0 0 5269.5208 10.589149 + 9900 16738.487 -0.00030979591 0 5269.5233 10.589165 + 9950 16738.476 -0.0009596827 0 5269.5193 10.589123 + 10000 16738.494 -0.0006271698 0 5269.5253 10.589175 +Loop time of 0.213152 on 4 procs for 10000 steps with 81 atoms + +Performance: 405345.239 tau/day, 46914.958 timesteps/s +91.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0029514 | 0.0038354 | 0.005348 | 1.5 | 1.80 +Neigh | 0.01178 | 0.013139 | 0.0167 | 1.8 | 6.16 +Comm | 0.073879 | 0.078553 | 0.081131 | 1.0 | 36.85 +Output | 0.0031943 | 0.0037987 | 0.0055451 | 1.6 | 1.78 +Modify | 0.10553 | 0.10763 | 0.1096 | 0.4 | 50.49 +Other | | 0.0062 | | | 2.91 + +Nlocal: 20.25 ave 34 max 9 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 38.5 ave 43 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 0.75 ave 2 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 3 +Ave neighs/atom = 0.037037 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.nve.g++.1 b/examples/rigid/log.27Nov18.rigid.nve.g++.1 new file mode 100644 index 0000000000..c3805dc42e --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.nve.g++.1 @@ -0,0 +1,335 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.69 571.70921 0 5265.8153 32.005816 + 100 16298.128 136.75661 0 5267.6488 16.449029 + 150 16682.532 17.504156 0 5269.4124 14.901186 + 200 16733.906 1.3755079 0 5269.4571 14.571305 + 250 16738.861 -0.15272039 0 5269.4886 14.498342 + 300 16738.608 -0.055216883 0 5269.5066 14.498 + 350 16738.5 -0.017457072 0 5269.5104 14.498392 + 400 16738.451 -0.0060161309 0 5269.5063 14.49851 + 450 16738.435 -0.001271965 0 5269.5059 14.498571 + 500 16738.443 -0.00081074175 0 5269.509 14.498598 + 550 16738.452 -0.00083208965 0 5269.5118 14.498618 + 600 16738.45 -0.00058358431 0 5269.5116 14.498617 + 650 16738.443 -0.00047228525 0 5269.5093 14.4986 + 700 16738.444 0 0 5269.5102 14.498612 + 750 16738.461 0 0 5269.5157 14.498654 + 800 16738.479 0 0 5269.521 14.498697 + 850 16738.473 0 0 5269.5192 14.498683 + 900 16738.449 0 0 5269.5116 14.498624 + 950 16738.438 -0.0035324203 0 5269.5046 14.498537 + 1000 16738.562 -0.051134242 0 5269.4963 14.498093 + 1050 16737.343 0.32970192 0 5269.4934 14.527634 + 1100 16737.878 0.16213235 0 5269.4941 14.533864 + 1150 16738.682 -0.089236256 0 5269.4959 14.511765 + 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 + 1250 16738.45 0 0 5269.5119 14.512611 + 1300 16738.475 0 0 5269.5199 14.512673 + 1350 16738.484 0 0 5269.5228 14.512696 + 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 + 1450 16738.45 -0.0010933363 0 5269.511 14.512595 + 1500 16738.445 -0.00057484239 0 5269.51 14.512591 + 1550 16738.451 0 0 5269.5123 14.512615 + 1600 16738.452 0 0 5269.5127 14.512618 + 1650 16738.443 0 0 5269.5099 14.512596 + 1700 16738.433 0 0 5269.5068 14.512572 + 1750 16738.438 0 0 5269.5084 14.512584 + 1800 16738.459 0 0 5269.5149 14.512635 + 1850 16738.473 0 0 5269.5193 14.51267 + 1900 16738.462 0 0 5269.5159 14.512644 + 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 + 2000 16738.463 -0.013425408 0 5269.5027 14.512382 + 2050 16738.535 -0.036964311 0 5269.5017 14.512152 + 2100 16738.621 -0.063490509 0 5269.5023 14.512108 + 2150 16738.594 -0.056143934 0 5269.5012 14.512117 + 2200 16738.536 -0.038486645 0 5269.5007 14.512277 + 2250 16738.496 -0.023712406 0 5269.503 14.51242 + 2300 16738.488 -0.013209094 0 5269.5109 14.51255 + 2350 16738.486 -0.0045244524 0 5269.519 14.512693 + 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 + 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 + 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 + 2550 16738.552 -0.04420046 0 5269.4998 14.512177 + 2600 16738.42 -0.004347531 0 5269.4982 14.512783 + 2650 16734.241 1.3131302 0 5269.5 14.577195 + 2700 16738.737 -0.10612056 0 5269.4961 14.503874 + 2750 16732.705 1.7939719 0 5269.4974 14.629294 + 2800 16738.558 -0.042867033 0 5269.5032 14.519893 + 2850 16738.499 -0.01271227 0 5269.5146 14.518524 + 2900 16738.486 -0.0032778045 0 5269.52 14.518712 + 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 + 3000 16738.647 -0.070862542 0 5269.5031 14.51803 + 3050 16678.313 18.829038 0 5269.409 15.533426 + 3100 16632.312 33.399217 0 5269.4975 14.588597 + 3150 16739.318 -0.31388148 0 5269.4715 13.520782 + 3200 16727.951 3.26736 0 5269.4741 12.288358 + 3250 16686.364 16.353793 0 5269.4682 14.152517 + 3300 16738.532 -0.031574462 0 5269.5064 13.310615 + 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 + 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 + 3450 16738.489 -0.021623738 0 5269.5026 13.308001 + 3500 16737.78 0.19719043 0 5269.4983 13.325999 + 3550 16658.578 25.116206 0 5269.4834 13.778249 + 3600 16738.51 -0.032864725 0 5269.4981 12.392389 + 3650 16738.899 -0.15952703 0 5269.4938 12.383503 + 3700 16738.879 -0.16025994 0 5269.487 12.382575 + 3750 16738.878 -0.16608251 0 5269.4806 12.382765 + 3800 16738.591 -0.078679341 0 5269.4776 12.383227 + 3850 16738.429 -0.024729409 0 5269.4807 12.382942 + 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 + 3950 16738.428 -0.002521266 0 5269.5027 12.383324 + 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 + 4050 16738.488 0 0 5269.5241 12.383531 + 4100 16738.468 0 0 5269.5178 12.383482 + 4150 16738.422 0 0 5269.5033 12.383369 + 4200 16738.387 0 0 5269.4921 12.383281 + 4250 16738.383 0 0 5269.4908 12.38327 + 4300 16738.4 0 0 5269.4964 12.383314 + 4350 16738.423 0 0 5269.5036 12.38337 + 4400 16738.441 0 0 5269.5092 12.383414 + 4450 16738.45 0 0 5269.5121 12.383437 + 4500 16738.45 0 0 5269.5122 12.383438 + 4550 16738.442 0 0 5269.5095 12.383417 + 4600 16738.425 0 0 5269.5042 12.383376 + 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 + 4700 16738.444 -0.024020551 0 5269.4862 12.382975 + 4750 16738.49 -0.04852143 0 5269.4761 12.385777 + 4800 16735.057 1.0347216 0 5269.4786 12.43543 + 4850 16735.441 0.92650925 0 5269.4913 12.418653 + 4900 16723.839 4.5908974 0 5269.5033 13.410103 + 4950 16738.531 -0.02153767 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589697 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 + 5100 16738.404 0 0 5269.4976 13.090032 + 5150 16738.421 0 0 5269.5029 13.090073 + 5200 16738.44 0 0 5269.5087 13.090119 + 5250 16738.448 -0.001279392 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376391 0 5269.5075 13.090026 + 5350 16738.479 -0.020383841 0 5269.5007 13.089897 + 5400 16735.845 0.7988947 0 5269.4909 13.136244 + 5450 16735.558 0.87620022 0 5269.4778 12.324482 + 5500 16711.494 8.4724178 0 5269.4984 12.656579 + 5550 16454.525 89.074815 0 5269.2031 16.996503 + 5600 16713.084 7.9801418 0 5269.5065 13.774979 + 5650 16738.676 -0.079987748 0 5269.5033 13.168297 + 5700 16446.281 91.866085 0 5269.399 23.764663 + 5750 16738.549 -0.039869084 0 5269.5034 13.378122 + 5800 16738.487 -0.014994478 0 5269.5086 13.378399 + 5850 16738.466 -0.0051267616 0 5269.512 13.37856 + 5900 16738.462 -0.0043690142 0 5269.5113 13.378573 + 5950 16738.528 -0.032727415 0 5269.5039 13.378197 + 6000 16702.774 10.969438 0 5269.2502 13.788852 + 6050 16682.271 17.483137 0 5269.3092 13.353101 + 6100 16738.508 -0.028838222 0 5269.5016 12.521084 + 6150 16738.425 -0.0067595536 0 5269.4974 12.521223 + 6200 16738.401 -0.0011499893 0 5269.4955 12.521254 + 6250 16738.455 0 0 5269.5135 12.52141 + 6300 16738.523 0 0 5269.5352 12.52158 + 6350 16738.503 0 0 5269.5287 12.521531 + 6400 16738.427 0 0 5269.5047 12.521344 + 6450 16738.399 0 0 5269.496 12.521274 + 6500 16738.425 0 0 5269.5042 12.521337 + 6550 16738.441 0 0 5269.5093 12.521378 + 6600 16738.42 0 0 5269.5025 12.521326 + 6650 16738.398 0 0 5269.4957 12.521272 + 6700 16738.435 0 0 5269.5074 12.521362 + 6750 16738.505 0 0 5269.5293 12.521534 + 6800 16738.508 0 0 5269.5303 12.521543 + 6850 16738.446 0 0 5269.5108 12.521391 + 6900 16738.414 0 0 5269.5009 12.521312 + 6950 16738.432 0 0 5269.5063 12.521354 + 7000 16738.444 0 0 5269.5102 12.521385 + 7050 16738.421 0 0 5269.5029 12.521329 + 7100 16738.393 0 0 5269.4941 12.521259 + 7150 16738.419 0 0 5269.5022 12.521322 + 7200 16738.489 0 0 5269.5244 12.521495 + 7250 16738.505 0 0 5269.5293 12.521535 + 7300 16738.443 0 0 5269.5098 12.521383 + 7350 16738.404 0 0 5269.4976 12.521287 + 7400 16738.43 0 0 5269.5058 12.52135 + 7450 16738.461 0 0 5269.5156 12.521427 + 7500 16738.447 0 0 5269.5109 12.521392 + 7550 16738.407 0 0 5269.4986 12.521295 + 7600 16738.412 0 0 5269.5002 12.521306 + 7650 16738.478 0 0 5269.5208 12.521467 + 7700 16738.51 0 0 5269.5309 12.521547 + 7750 16738.454 0 0 5269.5135 12.521412 + 7800 16738.398 0 0 5269.4958 12.521273 + 7850 16738.407 -0.0002118108 0 5269.4982 12.521289 + 7900 16738.441 -0.00021679711 0 5269.509 12.521373 + 7950 16738.446 -0.00023848139 0 5269.5107 12.521386 + 8000 16738.423 0 0 5269.5035 12.521333 + 8050 16738.423 0 0 5269.5034 12.521332 + 8100 16738.478 -0.00069622994 0 5269.52 12.521454 + 8150 16738.523 -0.0040058408 0 5269.531 12.521501 + 8200 16738.486 -0.0092298229 0 5269.5142 12.521334 + 8250 16738.458 -0.023189671 0 5269.4914 12.521014 + 8300 16738.513 -0.045845677 0 5269.4861 12.520779 + 8350 16723.745 4.5690412 0 5269.4516 12.849325 + 8400 16738.466 -0.020158442 0 5269.497 12.835773 + 8450 16738.437 -0.012822892 0 5269.4952 12.829936 + 8500 16738.408 -0.0016837088 0 5269.4972 12.830061 + 8550 16738.464 -0.00097379467 0 5269.5155 12.830216 + 8600 16738.669 -0.050578079 0 5269.5304 12.829934 + 8650 15917.563 250.28318 0 5261.3678 24.54572 + 8700 16738.445 0.0012168759 0 5269.5117 10.589499 + 8750 16738.473 -0.010164589 0 5269.509 10.588414 + 8800 16738.468 0 0 5269.5177 10.588633 + 8850 16738.508 0 0 5269.5304 10.588733 + 8900 16738.509 0 0 5269.5307 10.588736 + 8950 16738.496 0 0 5269.5266 10.588705 + 9000 16738.477 0 0 5269.5204 10.588656 + 9050 16738.455 0 0 5269.5135 10.588602 + 9100 16738.477 0 0 5269.5206 10.588656 + 9150 16738.512 0 0 5269.5316 10.588743 + 9200 16738.502 0 0 5269.5285 10.58872 + 9250 16738.493 0 0 5269.5255 10.588696 + 9300 16738.482 0 0 5269.522 10.588669 + 9350 16738.46 0 0 5269.5151 10.588615 + 9400 16738.481 0 0 5269.5217 10.588665 + 9450 16738.509 0 0 5269.5307 10.588736 + 9500 16738.491 0 0 5269.5248 10.58869 + 9550 16738.484 0 0 5269.5227 10.588674 + 9600 16738.483 0 0 5269.5223 10.588671 + 9650 16738.464 0 0 5269.5166 10.588626 + 9700 16738.484 0 0 5269.5229 10.588674 + 9750 16738.507 0 0 5269.5301 10.588731 + 9800 16738.482 0 0 5269.5221 10.588669 + 9850 16738.478 0 0 5269.5208 10.588659 + 9900 16738.487 -0.00030979474 0 5269.5233 10.588675 + 9950 16738.476 -0.00095968581 0 5269.5193 10.588632 + 10000 16738.494 -0.00062717822 0 5269.5253 10.588684 +Loop time of 0.171181 on 1 procs for 10000 steps with 81 atoms + +Performance: 504728.317 tau/day, 58417.629 timesteps/s +97.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.011004 | 0.011004 | 0.011004 | 0.0 | 6.43 +Neigh | 0.041984 | 0.041984 | 0.041984 | 0.0 | 24.53 +Comm | 0.012262 | 0.012262 | 0.012262 | 0.0 | 7.16 +Output | 0.0017002 | 0.0017002 | 0.0017002 | 0.0 | 0.99 +Modify | 0.098894 | 0.098894 | 0.098894 | 0.0 | 57.77 +Other | | 0.005337 | | | 3.12 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 49 ave 49 max 49 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3 +Ave neighs/atom = 0.037037 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.nve.g++.4 b/examples/rigid/log.27Nov18.rigid.nve.g++.4 new file mode 100644 index 0000000000..bc79d9730f --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.nve.g++.4 @@ -0,0 +1,335 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.69 571.70921 0 5265.8153 32.005816 + 100 16298.128 136.75661 0 5267.6488 16.449029 + 150 16682.532 17.504156 0 5269.4124 14.901186 + 200 16733.906 1.3755079 0 5269.4571 14.571305 + 250 16738.861 -0.15272039 0 5269.4886 14.498342 + 300 16738.608 -0.055216883 0 5269.5066 14.498 + 350 16738.5 -0.017457072 0 5269.5104 14.498392 + 400 16738.451 -0.0060161309 0 5269.5063 14.49851 + 450 16738.435 -0.001271965 0 5269.5059 14.498571 + 500 16738.443 -0.00081074175 0 5269.509 14.498598 + 550 16738.452 -0.00083208965 0 5269.5118 14.498618 + 600 16738.45 -0.00058358431 0 5269.5116 14.498617 + 650 16738.443 -0.00047228525 0 5269.5093 14.4986 + 700 16738.444 0 0 5269.5102 14.498612 + 750 16738.461 0 0 5269.5157 14.498654 + 800 16738.479 0 0 5269.521 14.498697 + 850 16738.473 0 0 5269.5192 14.498683 + 900 16738.449 0 0 5269.5116 14.498624 + 950 16738.438 -0.0035324203 0 5269.5046 14.498537 + 1000 16738.562 -0.051134242 0 5269.4963 14.498093 + 1050 16737.343 0.32970192 0 5269.4934 14.527634 + 1100 16737.878 0.16213235 0 5269.4941 14.533864 + 1150 16738.682 -0.089236256 0 5269.4959 14.511765 + 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 + 1250 16738.45 0 0 5269.5119 14.512611 + 1300 16738.475 0 0 5269.5199 14.512673 + 1350 16738.484 0 0 5269.5228 14.512696 + 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 + 1450 16738.45 -0.0010933363 0 5269.511 14.512595 + 1500 16738.445 -0.00057484239 0 5269.51 14.512591 + 1550 16738.451 0 0 5269.5123 14.512615 + 1600 16738.452 0 0 5269.5127 14.512618 + 1650 16738.443 0 0 5269.5099 14.512596 + 1700 16738.433 0 0 5269.5068 14.512572 + 1750 16738.438 0 0 5269.5084 14.512584 + 1800 16738.459 0 0 5269.5149 14.512635 + 1850 16738.473 0 0 5269.5193 14.51267 + 1900 16738.462 0 0 5269.5159 14.512644 + 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 + 2000 16738.463 -0.013425408 0 5269.5027 14.512382 + 2050 16738.535 -0.036964311 0 5269.5017 14.512152 + 2100 16738.621 -0.063490509 0 5269.5023 14.512108 + 2150 16738.594 -0.056143934 0 5269.5012 14.512117 + 2200 16738.536 -0.038486645 0 5269.5007 14.512277 + 2250 16738.496 -0.023712406 0 5269.503 14.51242 + 2300 16738.488 -0.013209094 0 5269.5109 14.51255 + 2350 16738.486 -0.0045244524 0 5269.519 14.512693 + 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 + 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 + 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 + 2550 16738.552 -0.04420046 0 5269.4998 14.512177 + 2600 16738.42 -0.004347531 0 5269.4982 14.512783 + 2650 16734.241 1.3131302 0 5269.5 14.577195 + 2700 16738.737 -0.10612056 0 5269.4961 14.503874 + 2750 16732.705 1.7939719 0 5269.4974 14.629294 + 2800 16738.558 -0.042867033 0 5269.5032 14.519893 + 2850 16738.499 -0.01271227 0 5269.5146 14.518524 + 2900 16738.486 -0.0032778045 0 5269.52 14.518712 + 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 + 3000 16738.647 -0.070862542 0 5269.5031 14.51803 + 3050 16678.313 18.829038 0 5269.409 15.533426 + 3100 16632.312 33.399217 0 5269.4975 14.588597 + 3150 16739.318 -0.31388148 0 5269.4715 13.520782 + 3200 16727.951 3.26736 0 5269.4741 12.288358 + 3250 16686.364 16.353793 0 5269.4682 14.152517 + 3300 16738.532 -0.031574462 0 5269.5064 13.310615 + 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 + 3400 16738.445 -0.0049349125 0 5269.5055 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16738.45 0 0 5269.5122 12.383438 + 4550 16738.442 0 0 5269.5095 12.383417 + 4600 16738.425 0 0 5269.5042 12.383376 + 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 + 4700 16738.444 -0.024020551 0 5269.4862 12.382975 + 4750 16738.49 -0.048521428 0 5269.4761 12.385777 + 4800 16735.057 1.0347217 0 5269.4786 12.43543 + 4850 16735.441 0.92650925 0 5269.4913 12.418653 + 4900 16723.839 4.5908973 0 5269.5033 13.410103 + 4950 16738.531 -0.02153767 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589696 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 + 5100 16738.404 0 0 5269.4976 13.090032 + 5150 16738.421 0 0 5269.5029 13.090073 + 5200 16738.44 0 0 5269.5087 13.090119 + 5250 16738.448 -0.001279392 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376392 0 5269.5075 13.090026 + 5350 16738.479 -0.020383842 0 5269.5007 13.089897 + 5400 16735.845 0.79889474 0 5269.4909 13.136244 + 5450 16735.558 0.87619992 0 5269.4778 12.324482 + 5500 16711.494 8.4724208 0 5269.4984 12.656579 + 5550 16454.525 89.074816 0 5269.2031 16.996503 + 5600 16713.084 7.9801334 0 5269.5065 13.774977 + 5650 16738.676 -0.079987764 0 5269.5033 13.168295 + 5700 16446.281 91.866085 0 5269.399 23.764662 + 5750 16738.549 -0.039869084 0 5269.5034 13.378121 + 5800 16738.487 -0.014994475 0 5269.5086 13.378397 + 5850 16738.466 -0.0051267556 0 5269.512 13.378559 + 5900 16738.462 -0.0043690097 0 5269.5113 13.378572 + 5950 16738.528 -0.03272741 0 5269.5039 13.378195 + 6000 16702.774 10.969434 0 5269.2502 13.788851 + 6050 16682.271 17.483158 0 5269.3092 13.3531 + 6100 16738.508 -0.028838239 0 5269.5016 12.521082 + 6150 16738.425 -0.0067595542 0 5269.4974 12.521221 + 6200 16738.401 -0.0011499896 0 5269.4955 12.521252 + 6250 16738.455 0 0 5269.5135 12.521408 + 6300 16738.523 0 0 5269.5352 12.521578 + 6350 16738.503 0 0 5269.5287 12.52153 + 6400 16738.427 0 0 5269.5047 12.521342 + 6450 16738.399 0 0 5269.496 12.521273 + 6500 16738.425 0 0 5269.5042 12.521336 + 6550 16738.441 0 0 5269.5093 12.521377 + 6600 16738.42 0 0 5269.5025 12.521324 + 6650 16738.398 0 0 5269.4957 12.52127 + 6700 16738.435 0 0 5269.5074 12.52136 + 6750 16738.505 0 0 5269.5293 12.521532 + 6800 16738.508 0 0 5269.5303 12.521541 + 6850 16738.446 0 0 5269.5108 12.521389 + 6900 16738.414 0 0 5269.5009 12.521311 + 6950 16738.432 0 0 5269.5063 12.521353 + 7000 16738.444 0 0 5269.5102 12.521383 + 7050 16738.421 0 0 5269.5029 12.521327 + 7100 16738.393 0 0 5269.4941 12.521258 + 7150 16738.419 0 0 5269.5022 12.52132 + 7200 16738.489 0 0 5269.5244 12.521494 + 7250 16738.505 0 0 5269.5293 12.521533 + 7300 16738.443 0 0 5269.5098 12.521381 + 7350 16738.404 0 0 5269.4976 12.521285 + 7400 16738.43 0 0 5269.5058 12.521348 + 7450 16738.461 0 0 5269.5156 12.521425 + 7500 16738.447 0 0 5269.5109 12.52139 + 7550 16738.407 0 0 5269.4986 12.521293 + 7600 16738.412 0 0 5269.5002 12.521305 + 7650 16738.478 0 0 5269.5208 12.521465 + 7700 16738.51 0 0 5269.5309 12.521546 + 7750 16738.454 0 0 5269.5135 12.52141 + 7800 16738.398 0 0 5269.4958 12.521272 + 7850 16738.407 -0.00021180981 0 5269.4982 12.521288 + 7900 16738.441 -0.0002167964 0 5269.509 12.521371 + 7950 16738.446 -0.00023848065 0 5269.5107 12.521385 + 8000 16738.423 0 0 5269.5035 12.521331 + 8050 16738.423 0 0 5269.5034 12.52133 + 8100 16738.478 -0.00069623408 0 5269.52 12.521452 + 8150 16738.523 -0.0040058355 0 5269.531 12.521499 + 8200 16738.486 -0.0092298325 0 5269.5142 12.521332 + 8250 16738.458 -0.023189665 0 5269.4914 12.521012 + 8300 16738.513 -0.045846242 0 5269.4861 12.520778 + 8350 16723.742 4.5698786 0 5269.4516 12.849386 + 8400 16738.466 -0.02016972 0 5269.497 12.835784 + 8450 16738.437 -0.012822703 0 5269.4952 12.829948 + 8500 16738.408 -0.0016836132 0 5269.4972 12.830073 + 8550 16738.464 -0.00097380297 0 5269.5155 12.830227 + 8600 16738.669 -0.050578946 0 5269.5304 12.829946 + 8650 15917.707 250.24016 0 5261.3702 24.544744 + 8700 16738.445 0.0010615265 0 5269.5117 10.589987 + 8750 16738.473 -0.010158834 0 5269.509 10.588904 + 8800 16738.468 0 0 5269.5176 10.589124 + 8850 16738.508 0 0 5269.5304 10.589223 + 8900 16738.509 0 0 5269.5306 10.589226 + 8950 16738.496 0 0 5269.5266 10.589195 + 9000 16738.477 0 0 5269.5204 10.589147 + 9050 16738.455 0 0 5269.5135 10.589092 + 9100 16738.477 0 0 5269.5206 10.589146 + 9150 16738.512 0 0 5269.5316 10.589233 + 9200 16738.502 0 0 5269.5285 10.58921 + 9250 16738.493 0 0 5269.5255 10.589186 + 9300 16738.482 0 0 5269.522 10.589159 + 9350 16738.46 0 0 5269.5151 10.589105 + 9400 16738.481 0 0 5269.5217 10.589155 + 9450 16738.509 0 0 5269.5307 10.589226 + 9500 16738.491 0 0 5269.5248 10.589181 + 9550 16738.484 0 0 5269.5227 10.589164 + 9600 16738.483 0 0 5269.5223 10.589161 + 9650 16738.464 0 0 5269.5166 10.589116 + 9700 16738.484 0 0 5269.5228 10.589164 + 9750 16738.507 0 0 5269.5301 10.589221 + 9800 16738.482 0 0 5269.5221 10.589159 + 9850 16738.478 0 0 5269.5208 10.589149 + 9900 16738.487 -0.00030979591 0 5269.5233 10.589165 + 9950 16738.476 -0.0009596827 0 5269.5193 10.589123 + 10000 16738.494 -0.0006271698 0 5269.5253 10.589175 +Loop time of 0.212511 on 4 procs for 10000 steps with 81 atoms + +Performance: 406566.385 tau/day, 47056.295 timesteps/s +91.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0032909 | 0.0039915 | 0.0048544 | 0.9 | 1.88 +Neigh | 0.011434 | 0.01325 | 0.016991 | 1.9 | 6.24 +Comm | 0.076038 | 0.082493 | 0.088069 | 1.5 | 38.82 +Output | 0.0031183 | 0.0045295 | 0.0086036 | 3.5 | 2.13 +Modify | 0.099662 | 0.10206 | 0.10679 | 0.9 | 48.02 +Other | | 0.00619 | | | 2.91 + +Nlocal: 20.25 ave 34 max 9 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 38.5 ave 43 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 0.75 ave 2 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 3 +Ave neighs/atom = 0.037037 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.property.g++.1 b/examples/rigid/log.27Nov18.rigid.property.g++.1 new file mode 100644 index 0000000000..e6ab4ed102 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.property.g++.1 @@ -0,0 +1,340 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +fix 0 all property/atom i_bodies + +read_data data.rigid-property fix 0 NULL Bodies + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +# assemble bodies from per-atom custom integer property bodies +fix 1 all rigid custom i_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.046 | 4.046 | 4.046 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.156049 on 1 procs for 10000 steps with 81 atoms + +Performance: 553673.043 tau/day, 64082.528 timesteps/s +97.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.010187 | 0.010187 | 0.010187 | 0.0 | 6.53 +Neigh | 0.040601 | 0.040601 | 0.040601 | 0.0 | 26.02 +Comm | 0.013221 | 0.013221 | 0.013221 | 0.0 | 8.47 +Output | 0.0016611 | 0.0016611 | 0.0016611 | 0.0 | 1.06 +Modify | 0.085107 | 0.085107 | 0.085107 | 0.0 | 54.54 +Other | | 0.005271 | | | 3.38 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.property.g++.4 b/examples/rigid/log.27Nov18.rigid.property.g++.4 new file mode 100644 index 0000000000..f63e34bc4b --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.property.g++.4 @@ -0,0 +1,340 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +fix 0 all property/atom i_bodies + +read_data data.rigid-property fix 0 NULL Bodies + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +# assemble bodies from per-atom custom integer property bodies +fix 1 all rigid custom i_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.017 | 4.111 | 4.392 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.198069 on 4 procs for 10000 steps with 81 atoms + +Performance: 436211.675 tau/day, 50487.462 timesteps/s +91.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0026007 | 0.0034987 | 0.0043218 | 1.0 | 1.77 +Neigh | 0.012213 | 0.013261 | 0.014237 | 0.8 | 6.70 +Comm | 0.073581 | 0.082048 | 0.087982 | 2.1 | 41.42 +Output | 0.0047908 | 0.0058783 | 0.009093 | 2.4 | 2.97 +Modify | 0.081998 | 0.086993 | 0.09176 | 1.4 | 43.92 +Other | | 0.00639 | | | 3.23 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.27Nov18.rigid.tnr.g++.1 b/examples/rigid/log.27Nov18.rigid.tnr.g++.1 new file mode 100644 index 0000000000..bf29e0b94b --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.tnr.g++.1 @@ -0,0 +1,458 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Tethered nanorods + +atom_style molecular + +read_data data.rigid.tnr + orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5600 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 1600 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +# Specify bond parameters + +bond_style fene +bond_coeff 1 30.0 1.5 1.0 1.0 + +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + +# Specify initial velocities + +velocity all create 1.4 109345 + +# Specify rigid components + +group rods type 2 +4000 atoms in group rods +group tethers subtract all rods +1600 atoms in group tethers + +neigh_modify exclude molecule/intra rods delay 0 every 1 + +# Specify the pair potentials + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff * * 1.0 1.0 1.122 +pair_coeff 2 2 1.0 1.0 2.5 + +# Specify output + +thermo 100 +thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz +thermo_modify flush yes lost warn + +timestep 0.005 + +fix 1 rods rigid molecule +800 rigid bodies with 4000 atoms +fix 2 tethers nve +fix 3 all langevin 1.4 1.4 1.0 437624 + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 45 45 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 + 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248 + 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036 + 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998 + 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801 + 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745 + 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581 + 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883 + 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271 + 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788 + 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119 + 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748 + 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115 + 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625 + 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021 + 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242 + 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334 + 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014 + 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797 + 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268 + 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673 + 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825 + 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911 + 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296 + 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402 + 2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677 + 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948 + 2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371 + 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106 + 2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713 + 3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611 + 3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039 + 3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251 + 3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362 + 3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524 + 3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699 + 3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752 + 3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797 + 3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772 + 3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034 + 4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065 + 4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387 + 4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557 + 4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574 + 4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421 + 4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711 + 4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462 + 4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986 + 4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278 + 4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891 + 5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248 +Loop time of 6.84203 on 1 procs for 5000 steps with 5600 atoms + +Performance: 315695.745 tau/day, 730.777 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.53182 | 0.53182 | 0.53182 | 0.0 | 7.77 +Bond | 0.18231 | 0.18231 | 0.18231 | 0.0 | 2.66 +Neigh | 1.8709 | 1.8709 | 1.8709 | 0.0 | 27.34 +Comm | 0.18452 | 0.18452 | 0.18452 | 0.0 | 2.70 +Output | 0.0043087 | 0.0043087 | 0.0043087 | 0.0 | 0.06 +Modify | 3.8809 | 3.8809 | 3.8809 | 0.0 | 56.72 +Other | | 0.1873 | | | 2.74 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1351 ave 1351 max 1351 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5254 ave 5254 max 5254 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5254 +Ave neighs/atom = 0.938214 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 766 +Dangerous builds = 0 + +# Replace fix rigid and fix langevin with new ones + +unfix 1 +unfix 3 + +fix 3 tethers langevin 1.4 1.4 1.0 198450 + +# Test different integrators for rods + +fix 1 rods rigid/nve molecule +800 rigid bodies with 4000 atoms +print "rigid/nve" +rigid/nve +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575 + 5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041 + 5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551 + 5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518 + 5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493 + 5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038 + 5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751 + 5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035 + 5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927 + 5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509 + 6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075 +Loop time of 1.40593 on 1 procs for 1000 steps with 5600 atoms + +Performance: 307270.224 tau/day, 711.274 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14844 | 0.14844 | 0.14844 | 0.0 | 10.56 +Bond | 0.036852 | 0.036852 | 0.036852 | 0.0 | 2.62 +Neigh | 0.40537 | 0.40537 | 0.40537 | 0.0 | 28.83 +Comm | 0.036592 | 0.036592 | 0.036592 | 0.0 | 2.60 +Output | 0.00085831 | 0.00085831 | 0.00085831 | 0.0 | 0.06 +Modify | 0.74053 | 0.74053 | 0.74053 | 0.0 | 52.67 +Other | | 0.03729 | | | 2.65 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1347 ave 1347 max 1347 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5399 ave 5399 max 5399 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5399 +Ave neighs/atom = 0.964107 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 153 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 +800 rigid bodies with 4000 atoms +print "rigid/nvt" +rigid/nvt +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547 + 6100 1.4199699 5.8764035 6.9917138 0.0054065561 7.2245364 62.244 62.244 62.244 0.009227645 0.0019623802 0.0050296432 + 6200 1.3976825 5.8924426 6.9902474 0.00043900876 7.0091524 62.244 62.244 62.244 -0.0023073124 -0.00049925318 0.0041235918 + 6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018934 0.0091933877 0.0049242093 + 6400 1.3749203 5.8817073 6.9616336 0.0074967162 7.2844648 62.244 62.244 62.244 0.012281887 0.0039781589 0.0062301027 + 6500 1.3467096 5.8881264 6.9458946 -0.00011926349 6.9407588 62.244 62.244 62.244 0.0030721967 -0.0013265863 -0.0021034009 + 6600 1.3646558 5.8739857 6.9458497 0.0056064043 7.1872784 62.244 62.244 62.244 0.0059660337 0.0057680048 0.0050851745 + 6700 1.3927251 5.883612 6.9775229 0.0025583824 7.0876946 62.244 62.244 62.244 0.0030974706 0.0018499606 0.002727716 + 6800 1.4016999 5.9015886 7.0025488 0.0039070678 7.1707989 62.244 62.244 62.244 0.0068320586 0.0020056859 0.002883459 + 6900 1.4136745 5.8914714 7.001837 0.0051755091 7.22471 62.244 62.244 62.244 0.0028467792 0.0094052519 0.0032744962 + 7000 1.4286639 5.893567 7.0157059 0.0062957476 7.2868198 62.244 62.244 62.244 0.0047242086 0.0093408867 0.0048221474 +Loop time of 1.41045 on 1 procs for 1000 steps with 5600 atoms + +Performance: 306284.404 tau/day, 708.992 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.1497 | 0.1497 | 0.1497 | 0.0 | 10.61 +Bond | 0.036719 | 0.036719 | 0.036719 | 0.0 | 2.60 +Neigh | 0.40272 | 0.40272 | 0.40272 | 0.0 | 28.55 +Comm | 0.036315 | 0.036315 | 0.036315 | 0.0 | 2.57 +Output | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 0.06 +Modify | 0.747 | 0.747 | 0.747 | 0.0 | 52.96 +Other | | 0.03715 | | | 2.63 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1284 ave 1284 max 1284 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5677 ave 5677 max 5677 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5677 +Ave neighs/atom = 1.01375 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 151 +Dangerous builds = 0 +unfix 1 + +compute myTemp all temp + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt iso" +rigid/npt iso +fix_modify 1 temp myTemp + +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 7000 1.4286639 5.893567 7.0157059 0.032101512 8.3980939 62.244 62.244 62.244 0.0040045405 0.040447803 0.051852194 + 7100 1.4709161 5.8870949 7.0424207 0.019697134 7.6953761 57.045689 57.045689 57.045689 0.012929484 0.020492532 0.025669387 + 7200 1.5163078 5.8421187 7.0330973 0.018916867 7.46241 50.277171 50.277171 50.277171 0.017823354 0.026688031 0.012239218 + 7300 1.5675309 5.7752739 7.0064855 0.022899743 7.3829781 45.154874 45.154874 45.154874 0.019324617 0.024318577 0.025056034 + 7400 1.5432228 5.7513096 6.9634284 0.024381819 7.272744 41.416613 41.416613 41.416613 0.032026791 0.022254425 0.018864241 + 7500 1.5511419 5.7072564 6.9255953 0.030632381 7.2405167 38.613262 38.613262 38.613262 0.041572196 0.012539031 0.037785916 + 7600 1.5437461 5.6656571 6.8781869 0.031293788 7.1486082 36.440994 36.440994 36.440994 0.036220762 0.02125772 0.036402883 + 7700 1.5873874 5.6134986 6.8603063 0.04807003 7.221002 34.765744 34.765744 34.765744 0.031608235 0.053442472 0.059159381 + 7800 1.5079648 5.601961 6.7863866 0.031128515 6.9971673 33.59594 33.59594 33.59594 0.032932226 0.015950578 0.044502741 + 7900 1.4737447 5.5644198 6.7219673 0.099246661 7.3415696 32.698542 32.698542 32.698542 0.071386679 0.10758014 0.11877317 + 8000 1.4727947 5.5161158 6.6729171 0.072190554 7.0973199 32.050043 32.050043 32.050043 0.072806068 0.06277287 0.080992723 +Loop time of 3.15299 on 1 procs for 1000 steps with 5600 atoms + +Performance: 137012.841 tau/day, 317.159 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.37069 | 0.37069 | 0.37069 | 0.0 | 11.76 +Bond | 0.05046 | 0.05046 | 0.05046 | 0.0 | 1.60 +Neigh | 1.4844 | 1.4844 | 1.4844 | 0.0 | 47.08 +Comm | 0.081178 | 0.081178 | 0.081178 | 0.0 | 2.57 +Output | 0.00083494 | 0.00083494 | 0.00083494 | 0.0 | 0.03 +Modify | 1.1163 | 1.1163 | 1.1163 | 0.0 | 35.41 +Other | | 0.0491 | | | 1.56 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2954 ave 2954 max 2954 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25585 ave 25585 max 25585 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25585 +Ave neighs/atom = 4.56875 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 334 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt x" +rigid/npt x +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.785 | 7.785 | 7.785 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 8000 1.4727947 5.5161158 6.6729171 0.13628586 7.4741313 32.050043 32.050043 32.050043 -0.030897367 0.27196335 0.1677916 + 8100 1.4522497 5.5136331 6.6542974 0.057107124 6.9895036 32.000184 32.050043 32.050043 0.049932793 0.056130194 0.065258384 + 8200 1.4407937 5.5014539 6.6331202 0.024119241 6.7733276 31.691157 32.050043 32.050043 0.041526366 0.022503949 0.0083274089 + 8300 1.4542258 5.496977 6.6391934 0.043395674 6.887667 31.215092 32.050043 32.050043 0.025407647 0.075227689 0.029551686 + 8400 1.4375595 5.4901345 6.6192605 0.013578023 6.6952098 30.494249 32.050043 32.050043 -0.0045150608 0.033500673 0.011748456 + 8500 1.4410736 5.4540565 6.5859426 0.017121222 6.679397 29.757445 32.050043 32.050043 0.035675932 -0.032105 0.047792733 + 8600 1.4372413 5.4150437 6.5439197 0.084045699 6.9949237 29.254706 32.050043 32.050043 0.10347392 0.073148157 0.075515024 + 8700 1.4299119 5.3982284 6.5213476 0.00045273296 6.5237411 28.822481 32.050043 32.050043 0.0093093459 0.0081538479 -0.016104995 + 8800 1.4677947 5.3637715 6.5166456 0.028621833 6.6651924 28.294159 32.050043 32.050043 0.033527613 0.036046563 0.016291323 + 8900 1.4625499 5.3483914 6.4971459 0.032843022 6.6649394 27.852402 32.050043 32.050043 0.040751528 0.055865445 0.0019120942 + 9000 1.4488382 5.3486741 6.4866589 0.087522574 6.9279711 27.488856 32.050043 32.050043 0.059432129 0.10936517 0.093770421 +Loop time of 3.09429 on 1 procs for 1000 steps with 5600 atoms + +Performance: 139611.779 tau/day, 323.175 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.57714 | 0.57714 | 0.57714 | 0.0 | 18.65 +Bond | 0.051715 | 0.051715 | 0.051715 | 0.0 | 1.67 +Neigh | 1.223 | 1.223 | 1.223 | 0.0 | 39.52 +Comm | 0.066183 | 0.066183 | 0.066183 | 0.0 | 2.14 +Output | 0.00086594 | 0.00086594 | 0.00086594 | 0.0 | 0.03 +Modify | 1.1355 | 1.1355 | 1.1355 | 0.0 | 36.70 +Other | | 0.03994 | | | 1.29 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3381 ave 3381 max 3381 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 31737 ave 31737 max 31737 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 31737 +Ave neighs/atom = 5.66732 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 169 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph iso" +rigid/nph iso +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.788 | 7.788 | 7.788 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 9000 1.4488382 5.3486741 6.4866589 0.20124138 7.5013717 27.488856 32.050043 32.050043 0.22160189 0.42145658 -0.039334342 + 9100 1.4408457 5.3612674 6.4929746 0.076331412 6.8758499 27.440968 31.994208 31.994208 0.083838068 0.041724506 0.10343166 + 9200 1.4870445 5.3340546 6.5020483 0.01010773 6.5521592 27.334266 31.869802 31.869802 0.024563803 -0.0068003493 0.012559737 + 9300 1.4376808 5.3295183 6.4587396 0.10720051 6.9752889 27.076116 31.568817 31.568817 0.11844426 0.10444301 0.09871425 + 9400 1.4621325 5.3011274 6.4495541 0.071127232 6.7846388 26.873295 31.332342 31.332342 0.091608834 0.02680694 0.094965923 + 9500 1.4463444 5.3005044 6.4365304 0.0011545049 6.4418432 26.664 31.088319 31.088319 -0.030551889 0.036011952 -0.0019965484 + 9600 1.4473406 5.2912939 6.4281024 0.066132857 6.7281169 26.537276 30.940568 30.940568 0.12276096 0.013455525 0.06218208 + 9700 1.4520445 5.2707214 6.4112246 0.077219765 6.757956 26.446587 30.834832 30.834832 0.073829267 0.11047347 0.047356559 + 9800 1.4825713 5.246644 6.4111243 0.061402527 6.6831281 26.327581 30.696078 30.696078 0.091860222 0.022619578 0.06972778 + 9900 1.4795219 5.2344495 6.3965347 0.086345107 6.7729623 26.187615 30.532888 30.532888 0.077396265 0.11142542 0.07021363 + 10000 1.4527053 5.2126819 6.3537041 0.045117764 6.5474705 26.057038 30.380645 30.380645 0.011087188 0.058029185 0.066236921 +Loop time of 3.25046 on 1 procs for 1000 steps with 5600 atoms + +Performance: 132904.162 tau/day, 307.649 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.68223 | 0.68223 | 0.68223 | 0.0 | 20.99 +Bond | 0.05211 | 0.05211 | 0.05211 | 0.0 | 1.60 +Neigh | 1.2617 | 1.2617 | 1.2617 | 0.0 | 38.82 +Comm | 0.069407 | 0.069407 | 0.069407 | 0.0 | 2.14 +Output | 0.00085688 | 0.00085688 | 0.00085688 | 0.0 | 0.03 +Modify | 1.1438 | 1.1438 | 1.1438 | 0.0 | 35.19 +Other | | 0.04037 | | | 1.24 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3756 ave 3756 max 3756 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37360 ave 37360 max 37360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37360 +Ave neighs/atom = 6.67143 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 158 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph xy couple" +rigid/nph xy couple +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.795 | 7.795 | 7.795 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 10000 1.4527053 5.2126819 6.3537041 0.056937886 6.5982342 26.057038 30.380645 30.380645 -0.37001102 0.18554825 0.35527643 + 10100 1.4606958 5.2220088 6.3693071 0.10308269 6.8132489 26.093341 30.422971 30.380645 0.12567436 0.057087258 0.12648646 + 10200 1.4429187 5.2134399 6.3467753 0.022637194 6.4450326 26.195743 30.542365 30.380645 0.010739012 0.071921542 -0.014748971 + 10300 1.4559104 5.2293511 6.3728908 0.0079467818 6.4073504 26.182966 30.527467 30.380645 -0.014274944 0.032205181 0.0059101087 + 10400 1.4741126 5.2072221 6.3650586 0.095611559 6.7814715 26.240156 30.594148 30.380645 0.073579289 0.092441893 0.12081349 + 10500 1.4411698 5.2173262 6.3492878 0.010458046 6.3947259 26.208633 30.557393 30.380645 0.036794882 -0.0051462954 -0.00027444949 + 10600 1.4492728 5.1940541 6.3323802 0.042602534 6.5163992 26.132032 30.468083 30.380645 0.090116773 0.0022769844 0.035413845 + 10700 1.4599974 5.1895935 6.3363432 0.05533717 6.573197 26.013045 30.329352 30.380645 0.070180878 0.08084881 0.014981824 + 10800 1.4781084 5.1724704 6.3334454 0.031843587 6.4690539 25.947295 30.252692 30.380645 0.0041524129 0.077618702 0.013759645 + 10900 1.4410507 5.1708846 6.3027527 0.020221033 6.3881531 25.839719 30.127267 30.380645 -0.0014092876 0.014833141 0.047239245 + 11000 1.4150286 5.1756927 6.2871219 0.039768792 6.45242 25.63435 29.887821 30.380645 0.034930907 0.032278926 0.052096542 +Loop time of 3.43774 on 1 procs for 1000 steps with 5600 atoms + +Performance: 125663.855 tau/day, 290.889 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.75066 | 0.75066 | 0.75066 | 0.0 | 21.84 +Bond | 0.053177 | 0.053177 | 0.053177 | 0.0 | 1.55 +Neigh | 1.3577 | 1.3577 | 1.3577 | 0.0 | 39.49 +Comm | 0.07294 | 0.07294 | 0.07294 | 0.0 | 2.12 +Output | 0.00086403 | 0.00086403 | 0.00086403 | 0.0 | 0.03 +Modify | 1.1612 | 1.1612 | 1.1612 | 0.0 | 33.78 +Other | | 0.0412 | | | 1.20 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3904 ave 3904 max 3904 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 39666 ave 39666 max 39666 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 39666 +Ave neighs/atom = 7.08321 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 159 +Dangerous builds = 0 + +Total wall time: 0:00:22 diff --git a/examples/rigid/log.27Nov18.rigid.tnr.g++.4 b/examples/rigid/log.27Nov18.rigid.tnr.g++.4 new file mode 100644 index 0000000000..1fa53eb8d3 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.tnr.g++.4 @@ -0,0 +1,458 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Tethered nanorods + +atom_style molecular + +read_data data.rigid.tnr + orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 5600 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 1600 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +# Specify bond parameters + +bond_style fene +bond_coeff 1 30.0 1.5 1.0 1.0 + +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + +# Specify initial velocities + +velocity all create 1.4 109345 + +# Specify rigid components + +group rods type 2 +4000 atoms in group rods +group tethers subtract all rods +1600 atoms in group tethers + +neigh_modify exclude molecule/intra rods delay 0 every 1 + +# Specify the pair potentials + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff * * 1.0 1.0 1.122 +pair_coeff 2 2 1.0 1.0 2.5 + +# Specify output + +thermo 100 +thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz +thermo_modify flush yes lost warn + +timestep 0.005 + +fix 1 rods rigid molecule +800 rigid bodies with 4000 atoms +fix 2 tethers nve +fix 3 all langevin 1.4 1.4 1.0 437624 + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 45 45 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 + 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624 + 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719 + 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786 + 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141 + 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529 + 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222 + 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907 + 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859 + 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971 + 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735 + 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195 + 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658 + 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474 + 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314 + 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432 + 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699 + 1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975 + 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981 + 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291 + 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901 + 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978 + 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521 + 2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595 + 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026 + 2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538 + 2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116 + 2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359 + 2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055 + 2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189 + 3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657 + 3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458 + 3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265 + 3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057 + 3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981 + 3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447 + 3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317 + 3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268 + 3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977 + 3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851 + 4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779 + 4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267 + 4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436 + 4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353 + 4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015 + 4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655 + 4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475 + 4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828 + 4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007 + 4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05 + 5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114 +Loop time of 3.70354 on 4 procs for 5000 steps with 5600 atoms + +Performance: 583225.455 tau/day, 1350.059 timesteps/s +92.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.081073 | 0.13498 | 0.20108 | 14.4 | 3.64 +Bond | 0.032352 | 0.048566 | 0.066671 | 7.0 | 1.31 +Neigh | 0.71345 | 0.72477 | 0.73658 | 1.3 | 19.57 +Comm | 0.29998 | 0.37027 | 0.42722 | 8.9 | 10.00 +Output | 0.0026417 | 0.0048325 | 0.0085185 | 3.2 | 0.13 +Modify | 1.9807 | 2.1035 | 2.263 | 8.1 | 56.80 +Other | | 0.3166 | | | 8.55 + +Nlocal: 1400 ave 1868 max 905 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 648.25 ave 688 max 598 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 1202.5 ave 1821 max 698 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 4810 +Ave neighs/atom = 0.858929 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 759 +Dangerous builds = 0 + +# Replace fix rigid and fix langevin with new ones + +unfix 1 +unfix 3 + +fix 3 tethers langevin 1.4 1.4 1.0 198450 + +# Test different integrators for rods + +fix 1 rods rigid/nve molecule +800 rigid bodies with 4000 atoms +print "rigid/nve" +rigid/nve +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407 + 5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113 + 5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599 + 5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984 + 5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427 + 5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784 + 5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228 + 5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215 + 5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708 + 5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003 + 6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208 +Loop time of 0.84847 on 4 procs for 1000 steps with 5600 atoms + +Performance: 509151.820 tau/day, 1178.592 timesteps/s +94.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.020741 | 0.03547 | 0.053064 | 7.5 | 4.18 +Bond | 0.0064373 | 0.0096895 | 0.013065 | 3.0 | 1.14 +Neigh | 0.14992 | 0.15174 | 0.15392 | 0.4 | 17.88 +Comm | 0.068751 | 0.081259 | 0.10084 | 4.2 | 9.58 +Output | 0.00054288 | 0.00096381 | 0.0017593 | 0.0 | 0.11 +Modify | 0.45914 | 0.48587 | 0.51316 | 2.8 | 57.26 +Other | | 0.08348 | | | 9.84 + +Nlocal: 1400 ave 1868 max 935 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 633.75 ave 695 max 541 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 1263 ave 1799 max 710 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 5052 +Ave neighs/atom = 0.902143 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 153 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 +800 rigid bodies with 4000 atoms +print "rigid/nvt" +rigid/nvt +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535 + 6100 1.3829575 5.9055308 6.9917699 0.0022904842 7.090405 62.244 62.244 62.244 -0.00045870123 0.0040556461 0.0032745076 + 6200 1.3942692 5.90506 7.0001838 0.0046406766 7.2000253 62.244 62.244 62.244 0.0042263485 0.0051632793 0.0045324021 + 6300 1.4009885 5.902399 7.0028005 0.0077682466 7.3373246 62.244 62.244 62.244 0.0071636876 0.0098268446 0.0063142075 + 6400 1.3627532 5.9075588 6.9779284 0.0093180831 7.3791932 62.244 62.244 62.244 0.0062401458 0.01302262 0.0086914833 + 6500 1.3341203 5.9012967 6.9491767 0.01010805 7.3844599 62.244 62.244 62.244 0.0031876185 0.011099561 0.01603697 + 6600 1.3572847 5.8915298 6.9576042 -0.00034416901 6.9427833 62.244 62.244 62.244 0.0025579012 -0.0011308802 -0.0024595281 + 6700 1.366374 5.8985277 6.9717413 0.0029472772 7.0986599 62.244 62.244 62.244 0.0022469424 -0.00042869772 0.0070235868 + 6800 1.381673 5.8909304 6.9761606 -9.1063397e-05 6.9722391 62.244 62.244 62.244 -0.0048194377 -0.00080972169 0.0053559692 + 6900 1.4011472 5.8881927 6.9887188 0.0010086058 7.0321524 62.244 62.244 62.244 0.0012132619 -0.0025916747 0.0044042301 + 7000 1.3973658 5.8867938 6.9843498 0.0070015187 7.2858563 62.244 62.244 62.244 0.0058913402 0.0076802028 0.0074330131 +Loop time of 0.902266 on 4 procs for 1000 steps with 5600 atoms + +Performance: 478794.425 tau/day, 1108.320 timesteps/s +92.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022644 | 0.037091 | 0.054025 | 7.4 | 4.11 +Bond | 0.0066526 | 0.0098482 | 0.012934 | 2.8 | 1.09 +Neigh | 0.15815 | 0.16028 | 0.16242 | 0.5 | 17.76 +Comm | 0.086046 | 0.10069 | 0.11568 | 3.7 | 11.16 +Output | 0.00047731 | 0.00090772 | 0.0016732 | 0.0 | 0.10 +Modify | 0.46692 | 0.49338 | 0.52973 | 3.5 | 54.68 +Other | | 0.1001 | | | 11.09 + +Nlocal: 1400 ave 1832 max 970 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 652.5 ave 749 max 561 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 1407.5 ave 2071 max 748 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +Total # of neighbors = 5630 +Ave neighs/atom = 1.00536 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 149 +Dangerous builds = 0 +unfix 1 + +compute myTemp all temp + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt iso" +rigid/npt iso +fix_modify 1 temp myTemp + +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 7000 1.3973658 5.8867938 6.9843498 0.0026564535 7.0987447 62.244 62.244 62.244 0.033711862 -0.0068580786 -0.018884423 + 7100 1.463906 5.861189 7.0110088 0.011521299 7.3924648 57.022165 57.022165 57.022165 0.010788399 0.0093706759 0.014404821 + 7200 1.4950346 5.817724 6.9919936 0.023104537 7.516484 50.28164 50.28164 50.28164 0.023252537 0.018108267 0.027952807 + 7300 1.5103539 5.7757334 6.9620355 0.02265972 7.3367664 45.242961 45.242961 45.242961 0.023588139 0.022279352 0.022111669 + 7400 1.5583184 5.7576833 6.9816589 0.028383162 7.3460731 41.582206 41.582206 41.582206 0.027312172 0.029876235 0.027961079 + 7500 1.5988886 5.6930714 6.9489127 0.046500933 7.4415595 39.00204 39.00204 39.00204 0.057497139 0.031007247 0.050998413 + 7600 1.5458926 5.6844397 6.8986555 0.034168406 7.2068206 36.96428 36.96428 36.96428 0.037874991 0.027247969 0.037382258 + 7700 1.5179913 5.6416448 6.8339457 0.070322183 7.3856048 35.284894 35.284894 35.284894 0.054248771 0.10402305 0.052694729 + 7800 1.4797888 5.6045532 6.7668481 0.07801402 7.3126319 33.963465 33.963465 33.963465 0.096058241 0.061172194 0.076811627 + 7900 1.4846305 5.54982 6.7159177 0.065303374 7.1325712 32.936376 32.936376 32.936376 0.089117046 0.06069295 0.046100127 + 8000 1.4352665 5.5157472 6.6430722 0.065962965 7.0326574 32.099391 32.099391 32.099391 0.032126133 0.070109418 0.095653344 +Loop time of 1.72334 on 4 procs for 1000 steps with 5600 atoms + +Performance: 250675.661 tau/day, 580.268 timesteps/s +92.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.060282 | 0.099801 | 0.13824 | 10.8 | 5.79 +Bond | 0.0095227 | 0.013491 | 0.017217 | 3.2 | 0.78 +Neigh | 0.58793 | 0.59546 | 0.60654 | 1.0 | 34.55 +Comm | 0.17903 | 0.21403 | 0.24615 | 6.5 | 12.42 +Output | 0.00045562 | 0.00076783 | 0.0017018 | 0.0 | 0.04 +Modify | 0.64959 | 0.68513 | 0.70671 | 2.8 | 39.76 +Other | | 0.1147 | | | 6.65 + +Nlocal: 1400 ave 1768 max 981 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 1574 ave 1663 max 1447 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 6338 ave 9521 max 3068 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 25352 +Ave neighs/atom = 4.52714 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 337 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt x" +rigid/npt x +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.226 | 7.412 | 7.597 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 8000 1.4352665 5.5157472 6.6430722 0.073641793 7.0780095 32.099391 32.099391 32.099391 0.13359913 0.13991003 -0.052583787 + 8100 1.4385682 5.5149882 6.6449064 0.092621097 7.1894426 31.952972 32.099391 32.099391 0.10729401 0.11619987 0.054369411 + 8200 1.42735 5.5149024 6.6360094 0.023903894 6.7756304 31.745099 32.099391 32.099391 0.051524189 0.013370811 0.006816681 + 8300 1.4335369 5.5031396 6.629106 0.024536474 6.7705237 31.324638 32.099391 32.099391 0.042356568 -0.0039258365 0.035178692 + 8400 1.4502714 5.4659017 6.6050122 0.06575457 6.9774701 30.785462 32.099391 32.099391 0.056998298 0.084852971 0.055412441 + 8500 1.4432366 5.4541505 6.5877355 0.03322226 6.7725932 30.241461 32.099391 32.099391 0.045871758 0.024443739 0.029351281 + 8600 1.436491 5.4272043 6.5554911 0.039811655 6.7732608 29.729098 32.099391 32.099391 0.037709456 0.060942551 0.020782958 + 8700 1.4099251 5.4106713 6.5180919 0.013490442 6.590596 29.209958 32.099391 32.099391 0.025833003 -0.0021161354 0.016754458 + 8800 1.3801478 5.3926425 6.4766747 0.028808964 6.6280205 28.552039 32.099391 32.099391 0.012603549 0.018713073 0.055110271 + 8900 1.4411695 5.3583474 6.4903088 0.053464468 6.7655624 27.980937 32.099391 32.099391 0.055084927 0.073292013 0.032016464 + 9000 1.4264395 5.3680298 6.4884216 0.066557314 6.8276318 27.69922 32.099391 32.099391 0.05380086 0.069450871 0.076420212 +Loop time of 1.45936 on 4 procs for 1000 steps with 5600 atoms + +Performance: 296020.704 tau/day, 685.233 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.097855 | 0.1563 | 0.20542 | 12.5 | 10.71 +Bond | 0.010222 | 0.01371 | 0.016844 | 2.6 | 0.94 +Neigh | 0.43646 | 0.44419 | 0.4668 | 2.0 | 30.44 +Comm | 0.10136 | 0.14589 | 0.19563 | 11.6 | 10.00 +Output | 0.00046229 | 0.00076181 | 0.0016556 | 0.0 | 0.05 +Modify | 0.59971 | 0.62524 | 0.65776 | 2.9 | 42.84 +Other | | 0.07327 | | | 5.02 + +Nlocal: 1400 ave 1680 max 1049 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 1627.25 ave 1775 max 1488 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 7842 ave 10600 max 4326 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 31368 +Ave neighs/atom = 5.60143 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 166 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph iso" +rigid/nph iso +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.412 | 7.597 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 9000 1.4264395 5.3680298 6.4884216 0.0098629166 6.5386881 27.69922 32.099391 32.099391 -0.32352455 -0.020288613 0.37340191 + 9100 1.4501008 5.3468478 6.4858243 0.059250929 6.7846766 27.60347 31.988431 31.988431 0.076039445 0.051409059 0.050304282 + 9200 1.4635102 5.3406895 6.4901983 0.035210102 6.6656151 27.490192 31.857158 31.857158 0.0079484246 0.066653954 0.031027926 + 9300 1.4503713 5.3595734 6.4987624 0.020794 6.6013231 27.398334 31.750708 31.750708 0.053098983 0.0019379163 0.0073450997 + 9400 1.4701421 5.3186993 6.4734172 0.039118143 6.6618027 27.181055 31.498913 31.498913 0.076457868 -0.0028405762 0.043737137 + 9500 1.4495442 5.323167 6.4617063 0.073591495 6.8091096 27.000921 31.290164 31.290164 0.037777789 0.097624306 0.085372389 + 9600 1.4668438 5.3002222 6.4523494 0.06758294 6.7648428 26.814997 31.074705 31.074705 0.057941415 0.09775976 0.047047645 + 9700 1.4926839 5.2883964 6.4608196 0.059125916 6.7288224 26.637713 30.869258 30.869258 0.049817515 0.032285203 0.095275031 + 9800 1.4644558 5.2702597 6.4205112 0.0076221617 6.4543756 26.460515 30.663911 30.663911 -0.0060723629 0.010616271 0.018322577 + 9900 1.4669549 5.2511861 6.4034006 0.044167302 6.5961243 26.30195 30.480157 30.480157 0.026274163 0.013826125 0.092401618 + 10000 1.460983 5.2470476 6.3945715 0.10536479 6.8483021 26.186495 30.346361 30.346361 0.088951294 0.11273872 0.11440435 +Loop time of 1.61361 on 4 procs for 1000 steps with 5600 atoms + +Performance: 267722.758 tau/day, 619.729 timesteps/s +93.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.13322 | 0.18643 | 0.259 | 12.5 | 11.55 +Bond | 0.012367 | 0.014462 | 0.016771 | 1.6 | 0.90 +Neigh | 0.46284 | 0.46471 | 0.46675 | 0.3 | 28.80 +Comm | 0.10183 | 0.17241 | 0.22246 | 12.4 | 10.68 +Output | 0.00044584 | 0.00074542 | 0.0016396 | 0.0 | 0.05 +Modify | 0.691 | 0.7057 | 0.72761 | 1.8 | 43.73 +Other | | 0.06915 | | | 4.29 + +Nlocal: 1400 ave 1633 max 1183 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1747.75 ave 1847 max 1624 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 9290.75 ave 12454 max 6621 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 37163 +Ave neighs/atom = 6.63625 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 162 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph xy couple" +rigid/nph xy couple +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 10000 1.460983 5.2470476 6.3945715 0.18376191 7.1859023 26.186495 30.346361 30.346361 0.015959435 0.68341409 -0.14808778 + 10100 1.4487259 5.2485513 6.3864479 0.060157728 6.6465409 26.238844 30.407026 30.346361 0.10289596 0.022823411 0.05475381 + 10200 1.4335646 5.2420513 6.3680395 0.013676852 6.4271554 26.235255 30.402867 30.346361 -0.017328522 0.040786509 0.017572569 + 10300 1.4334952 5.2377534 6.3636871 0.030978458 6.4967192 26.150168 30.304264 30.346361 0.044154015 0.036133394 0.012647966 + 10400 1.4209473 5.2242736 6.3403516 -0.00094467594 6.3363148 26.085773 30.22964 30.346361 0.030664991 0.018005544 -0.051504563 + 10500 1.4262805 5.2044624 6.3247294 0.045042501 6.5149748 25.934148 30.053928 30.346361 0.031103656 0.045410964 0.058612885 + 10600 1.4516048 5.2017459 6.3419036 0.069565209 6.6313867 25.741959 29.831208 30.346361 0.021768778 0.11302833 0.073898515 + 10700 1.4841074 5.1911212 6.356808 0.046866825 6.5493087 25.574636 29.637306 30.346361 0.073969059 0.064901506 0.0017299084 + 10800 1.4646257 5.1958815 6.3462665 0.050747116 6.5534926 25.500146 29.550982 30.346361 0.076646556 0.070734108 0.004860682 + 10900 1.461356 5.1821605 6.3299773 0.069060447 6.610166 25.417723 29.455466 30.346361 0.051399011 0.065631311 0.090151019 + 11000 1.4395386 5.1786243 6.3093047 -0.0087983274 6.2737059 25.383039 29.415273 30.346361 -0.060891892 0.037235898 -0.0027389884 +Loop time of 1.56065 on 4 procs for 1000 steps with 5600 atoms + +Performance: 276807.605 tau/day, 640.758 timesteps/s +94.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.15892 | 0.20364 | 0.2564 | 9.2 | 13.05 +Bond | 0.011486 | 0.014652 | 0.01918 | 2.6 | 0.94 +Neigh | 0.43915 | 0.43981 | 0.44125 | 0.1 | 28.18 +Comm | 0.093711 | 0.14431 | 0.18183 | 9.9 | 9.25 +Output | 0.00044441 | 0.00073904 | 0.0016198 | 0.0 | 0.05 +Modify | 0.66889 | 0.68497 | 0.70418 | 1.5 | 43.89 +Other | | 0.07254 | | | 4.65 + +Nlocal: 1400 ave 1610 max 1237 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1832 ave 1919 max 1765 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 10008.2 ave 12428 max 7982 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 40033 +Ave neighs/atom = 7.14875 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 157 +Dangerous builds = 0 + +Total wall time: 0:00:11 diff --git a/src/math_eigen.cpp b/src/math_eigen.cpp index 99c8d38290..65c3fa806a 100644 --- a/src/math_eigen.cpp +++ b/src/math_eigen.cpp @@ -44,7 +44,7 @@ int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v1 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_INCREASING_EVALS); + int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_DECREASING_EVALS); // transpose the evec matrix @@ -67,7 +67,7 @@ int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v2 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_INCREASING_EVALS); + int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_DECREASING_EVALS); // transpose the evec matrix diff --git a/unittest/force-styles/tests/fix-timestep-rigid_group.yaml b/unittest/force-styles/tests/fix-timestep-rigid_group.yaml index b5c77af975..e28e0abb08 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_group.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_group.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:00:59 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -15,65 +14,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4245356937318909e+03 -1.4496493315649632e+03 -3.6144360984225123e+03 8.4840626828644361e+02 2.0318336761612773e+02 -6.0622397707969583e+02 -global_scalar: 15.711521423178084 + -1.4245356937318884e+03 -1.4496493315649691e+03 -3.6144360984224995e+03 8.4840626828644076e+02 2.0318336761611761e+02 -6.0622397707970140e+02 +global_scalar: 15.711521423178082 run_pos: ! |2 - 1 -2.7899546863891755e-01 2.4731857340328198e+00 -1.7290667740241461e-01 - 2 3.0296221610263996e-01 2.9517129916957550e+00 -8.5798904387772190e-01 - 3 -6.9368802364134963e-01 1.2445115421754176e+00 -6.2281111198650141e-01 - 4 -1.5764879647103172e+00 1.4919714415841279e+00 -1.2492069414674598e+00 - 5 -8.9434512967430235e-01 9.3651699743510453e-01 4.0191726558261442e-01 - 6 2.9454439634451712e-01 2.2724545792544146e-01 -1.2845195053960266e+00 - 7 3.4049112903270240e-01 -9.4655678322404235e-03 -2.4634480020857055e+00 - 8 1.1644354555804877e+00 -4.8367776650961403e-01 -6.7663643940735962e-01 - 9 1.3781717822696455e+00 -2.5332509530011083e-01 2.6864954436590072e-01 - 10 2.0186368606041905e+00 -1.4285861423625785e+00 -9.6712491252780486e-01 - 11 1.7929137227577487e+00 -1.9875455388407386e+00 -1.8836565352266592e+00 - 12 3.0032775230399622e+00 -4.8983022415173583e-01 -1.6190248017343625e+00 - 13 4.0448964162125964e+00 -9.0213155122390454e-01 -1.6385398399479547e+00 - 14 2.6035151245015857e+00 -4.0874995493218413e-01 -2.6555999074786598e+00 - 15 2.9761196776172323e+00 5.6287237454109007e-01 -1.2442626196083335e+00 - 16 2.6517373021566182e+00 -2.3957035508393734e+00 3.3389262100686046e-02 - 17 2.2311114924744961e+00 -2.1018393228798584e+00 1.1496088522377494e+00 - 18 2.1390642573201792e+00 3.0164773560693803e+00 -3.5143984803853883e+00 - 19 1.5353246655146293e+00 2.6305911186316160e+00 -4.2455871034737100e+00 - 20 2.7649421538938399e+00 3.6818603528430875e+00 -3.9364115785985545e+00 - 21 4.9043112657298966e+00 -4.0774268210397882e+00 -3.6200836396129850e+00 - 22 4.3665322424283417e+00 -4.2075138112953612e+00 -4.4636587264885925e+00 - 23 5.7355405581985277e+00 -3.5789558641908901e+00 -3.8805763324089995e+00 - 24 2.0692780332810012e+00 3.1504920436415969e+00 3.1571131300668829e+00 - 25 1.3007297593168976e+00 3.2745259354179459e+00 2.5110163874103693e+00 - 26 2.5819416446099637e+00 4.0104903120756576e+00 3.2150249624526102e+00 + 1 -2.7899546863891400e-01 2.4731857340328229e+00 -1.7290667740242271e-01 + 2 3.0296221610264262e-01 2.9517129916957545e+00 -8.5798904387773245e-01 + 3 -6.9368802364134741e-01 1.2445115421754194e+00 -6.2281111198650418e-01 + 4 -1.5764879647103154e+00 1.4919714415841279e+00 -1.2492069414674623e+00 + 5 -8.9434512967429969e-01 9.3651699743511030e-01 4.0191726558261276e-01 + 6 2.9454439634451712e-01 2.2724545792544038e-01 -1.2845195053960268e+00 + 7 3.4049112903270051e-01 -9.4655678322458359e-03 -2.4634480020857055e+00 + 8 1.1644354555804874e+00 -4.8367776650961336e-01 -6.7663643940735863e-01 + 9 1.3781717822696469e+00 -2.5332509530010694e-01 2.6864954436590061e-01 + 10 2.0186368606041896e+00 -1.4285861423625796e+00 -9.6712491252780131e-01 + 11 1.7929137227577452e+00 -1.9875455388407426e+00 -1.8836565352266534e+00 + 12 3.0032775230399604e+00 -4.8983022415174027e-01 -1.6190248017343642e+00 + 13 4.0448964162125947e+00 -9.0213155122391020e-01 -1.6385398399479558e+00 + 14 2.6035151245015822e+00 -4.0874995493219213e-01 -2.6555999074786607e+00 + 15 2.9761196776172318e+00 5.6287237454108674e-01 -1.2442626196083388e+00 + 16 2.6517373021566168e+00 -2.3957035508393707e+00 3.3389262100692263e-02 + 17 2.2311114924744970e+00 -2.1018393228798513e+00 1.1496088522377543e+00 + 18 2.1390642573201784e+00 3.0164773560693781e+00 -3.5143984803853878e+00 + 19 1.5353246655146278e+00 2.6305911186316133e+00 -4.2455871034737074e+00 + 20 2.7649421538938390e+00 3.6818603528430849e+00 -3.9364115785985550e+00 + 21 4.9043112657298877e+00 -4.0774268210397882e+00 -3.6200836396129836e+00 + 22 4.3665322424283310e+00 -4.2075138112953594e+00 -4.4636587264885881e+00 + 23 5.7355405581985188e+00 -3.5789558641908918e+00 -3.8805763324089981e+00 + 24 2.0692780332810115e+00 3.1504920436416004e+00 3.1571131300668789e+00 + 25 1.3007297593169076e+00 3.2745259354179481e+00 2.5110163874103675e+00 + 26 2.5819416446099739e+00 4.0104903120756576e+00 3.2150249624526035e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093289825842437e-04 2.6351122778447999e-04 -4.4905093064114823e-04 - 2 4.9594625316470473e-04 9.4561370489632928e-05 -5.4581359894047732e-04 - 3 3.3306085115756054e-04 2.3224943880673362e-04 -2.3659455671746045e-04 - 4 3.3692327392261130e-04 2.1926810694051292e-04 -2.4716631558862576e-04 - 5 3.3642542694185899e-04 4.1797578013265770e-04 -1.8011341766657654e-04 - 6 2.0926869754934769e-04 2.6449308951579106e-05 -1.0508938983871929e-04 - 7 1.4629043007908003e-04 -1.6873376665349995e-04 -6.8354048774352968e-05 - 8 1.5844101624224859e-04 3.7728761274000288e-05 -1.9162715667092141e-05 - 9 2.1299362072601887e-04 1.6917140529157517e-04 -6.3528165037845917e-05 - 10 5.4261629412254576e-05 -9.4655528376811157e-05 1.0511362869146505e-04 - 11 -3.2194160796502236e-05 -2.2025095264758700e-04 2.0300202946212152e-04 - 12 1.2640586304750429e-04 -2.9851080445664956e-04 -7.9476371818247574e-05 - 13 8.4523575162143312e-05 -4.0583135407330399e-04 -4.7551111331702557e-05 - 14 9.9954050381271961e-05 -4.2610816481298121e-04 -7.9255633594381943e-05 - 15 2.4417481119789894e-04 -2.3521002264677784e-04 -2.4875318161049020e-04 - 16 -9.0958138549668516e-06 3.7774817121217089e-06 2.4035199548834928e-04 - 17 5.7507224523611227e-05 2.2629217444843685e-04 2.0686920072684740e-04 - 18 2.9220264989359860e-04 -6.2478376436796244e-04 8.4222594596602409e-04 - 19 2.0572616567799204e-04 -5.0334424271726607e-04 8.4953929443210702e-04 - 20 4.1224811789513060e-04 -7.4115205416011543e-04 8.3678612337507964e-04 - 21 -1.0671858777656406e-03 -1.1531171045499533e-03 7.3720674900162007e-04 - 22 -1.1066511338291734e-03 -1.0433933757600477e-03 7.4544544325708432e-04 - 23 -9.7629260480941644e-04 -1.3100872491594124e-03 7.2687284219704641e-04 - 24 4.3308126651259382e-04 -6.6527658087322671e-04 8.4451298670663671e-04 - 25 4.4565811905442982e-04 -5.1298436273584133e-04 8.5878867884521635e-04 - 26 5.9865972692022961e-04 -7.6385263287080262e-04 8.4259943226842242e-04 + 1 4.7093289825842508e-04 2.6351122778447809e-04 -4.4905093064114883e-04 + 2 4.9594625316470506e-04 9.4561370489630299e-05 -5.4581359894047775e-04 + 3 3.3306085115756103e-04 2.3224943880673259e-04 -2.3659455671746018e-04 + 4 3.3692327392261152e-04 2.1926810694051179e-04 -2.4716631558862516e-04 + 5 3.3642542694186002e-04 4.1797578013265738e-04 -1.8011341766657675e-04 + 6 2.0926869754934769e-04 2.6449308951578185e-05 -1.0508938983871811e-04 + 7 1.4629043007907940e-04 -1.6873376665350122e-04 -6.8354048774350921e-05 + 8 1.5844101624224881e-04 3.7728761273999780e-05 -1.9162715667090996e-05 + 9 2.1299362072601952e-04 1.6917140529157474e-04 -6.3528165037845483e-05 + 10 5.4261629412254495e-05 -9.4655528376811482e-05 1.0511362869146690e-04 + 11 -3.2194160796502724e-05 -2.2025095264758716e-04 2.0300202946212429e-04 + 12 1.2640586304750378e-04 -2.9851080445665107e-04 -7.9476371818245798e-05 + 13 8.4523575162142608e-05 -4.0583135407330561e-04 -4.7551111331700511e-05 + 14 9.9954050381270972e-05 -4.2610816481298294e-04 -7.9255633594379530e-05 + 15 2.4417481119789862e-04 -2.3521002264677992e-04 -2.4875318161048917e-04 + 16 -9.0958138549664992e-06 3.7774817121222391e-06 2.4035199548835096e-04 + 17 5.7507224523612230e-05 2.2629217444843764e-04 2.0686920072684822e-04 + 18 2.9220264989359833e-04 -6.2478376436796265e-04 8.4222594596602366e-04 + 19 2.0572616567799188e-04 -5.0334424271726639e-04 8.4953929443210648e-04 + 20 4.1224811789513022e-04 -7.4115205416011554e-04 8.3678612337507920e-04 + 21 -1.0671858777656393e-03 -1.1531171045499515e-03 7.3720674900162159e-04 + 22 -1.1066511338291710e-03 -1.0433933757600460e-03 7.4544544325708573e-04 + 23 -9.7629260480941525e-04 -1.3100872491594103e-03 7.2687284219704804e-04 + 24 4.3308126651259312e-04 -6.6527658087322801e-04 8.4451298670663606e-04 + 25 4.4565811905442889e-04 -5.1298436273584285e-04 8.5878867884521559e-04 + 26 5.9865972692022765e-04 -7.6385263287080381e-04 8.4259943226842166e-04 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml b/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml index a73c8cd112..d667942e49 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:00:59 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -15,8 +14,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00 -global_scalar: 18.340560167414402 + -4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00 +global_scalar: 18.3405601674144 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -35,15 +34,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588271301e+00 3.0171068018412783e+00 -3.5144628518856353e+00 - 19 1.5366124997074575e+00 2.6286809834111740e+00 -4.2452547844370221e+00 - 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 - 21 4.9036621347791236e+00 -4.0757648442838548e+00 -3.6192617654515908e+00 - 22 4.3655322291888474e+00 -4.2084949965552561e+00 -4.4622011117402343e+00 - 23 5.7380414793463110e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 + 18 2.1392027588271301e+00 3.0171068018412779e+00 -3.5144628518856349e+00 + 19 1.5366124997074571e+00 2.6286809834111748e+00 -4.2452547844370221e+00 + 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352554e+00 + 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515904e+00 + 22 4.3655322291888483e+00 -4.2084949965552561e+00 -4.4622011117402334e+00 + 23 5.7380414793463101e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 24 2.0701314765323930e+00 3.1499370533342330e+00 3.1565324852522938e+00 - 25 1.3030170721374787e+00 3.2711173927682244e+00 2.5081940917429759e+00 - 26 2.5776230782480041e+00 4.0127347068243884e+00 3.2182355138709284e+00 + 25 1.3030170721374779e+00 3.2711173927682249e+00 2.5081940917429768e+00 + 26 2.5776230782480045e+00 4.0127347068243875e+00 3.2182355138709275e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -65,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704849e-04 -3.1032459262908286e-04 8.1043030117346052e-04 - 19 8.5103884665345473e-04 -1.4572280596788095e-03 1.0163621287634121e-03 - 20 -6.5204659278590661e-04 4.3989037444289755e-04 4.9909839028507901e-04 - 21 -1.3888125881903906e-03 -3.1978049143082342e-04 1.1455681499836646e-03 - 22 -1.6084223477729526e-03 -1.5355394240821163e-03 1.4772010826232394e-03 - 23 2.6392672378804821e-04 -3.9375414431174795e-03 -3.6991583139728377e-04 - 24 8.6062827067890269e-04 -9.4179873474469291e-04 5.5396395550012388e-04 - 25 1.5933645477487551e-03 -2.2139156625681673e-03 -5.5078029695647250e-04 - 26 -1.5679561743998888e-03 3.5146224354726068e-04 2.4446924193334487e-03 + 18 3.6149625095704914e-04 -3.1032459262908286e-04 8.1043030117346052e-04 + 19 8.5103884665345452e-04 -1.4572280596788108e-03 1.0163621287634116e-03 + 20 -6.5204659278590683e-04 4.3989037444289853e-04 4.9909839028507901e-04 + 21 -1.3888125881903923e-03 -3.1978049143082385e-04 1.1455681499836646e-03 + 22 -1.6084223477729510e-03 -1.5355394240821117e-03 1.4772010826232375e-03 + 23 2.6392672378805124e-04 -3.9375414431174821e-03 -3.6991583139728095e-04 + 24 8.6062827067890247e-04 -9.4179873474469237e-04 5.5396395550012453e-04 + 25 1.5933645477487538e-03 -2.2139156625681695e-03 -5.5078029695647401e-04 + 26 -1.5679561743998840e-03 3.5146224354726100e-04 2.4446924193334478e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml index 9e362dd3ac..304db9fd60 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:00 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-12 skip_tests: prerequisites: ! | @@ -16,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134789653e+01 -2.6907707565986087e+01 -6.0080860422267843e+00 -2.5620423972100063e+01 -1.3450224059983270e+01 -1.4947288486998982e+00 -global_scalar: 18.340560167414335 + -4.9200116134788658e+01 -2.6907707565985344e+01 -6.0080860422268874e+00 -2.5620423972099733e+01 -1.3450224059983656e+01 -1.4947288487000705e+00 +global_scalar: 18.340560167414306 run_pos: ! |2 1 -2.7993683669226854e-01 2.4726588069312836e+00 -1.7200860244148508e-01 2 3.0197083955402171e-01 2.9515239068888608e+00 -8.5689735572907555e-01 @@ -37,14 +36,14 @@ run_pos: ! |2 16 2.6517554244980301e+00 -2.3957110424978438e+00 3.2908335999177751e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 18 2.1392027588271310e+00 3.0171068018412779e+00 -3.5144628518856349e+00 - 19 1.5366124997074584e+00 2.6286809834111722e+00 -4.2452547844370230e+00 + 19 1.5366124997074566e+00 2.6286809834111740e+00 -4.2452547844370239e+00 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 - 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515900e+00 - 22 4.3655322291888465e+00 -4.2084949965552578e+00 -4.4622011117402343e+00 + 21 4.9036621347791245e+00 -4.0757648442838557e+00 -3.6192617654515900e+00 + 22 4.3655322291888465e+00 -4.2084949965552569e+00 -4.4622011117402334e+00 23 5.7380414793463101e+00 -3.5841969195032686e+00 -3.8827839830470232e+00 24 2.0701314765323913e+00 3.1499370533342308e+00 3.1565324852522920e+00 - 25 1.3030170721374779e+00 3.2711173927682236e+00 2.5081940917429755e+00 - 26 2.5776230782480036e+00 4.0127347068243875e+00 3.2182355138709280e+00 + 25 1.3030170721374770e+00 3.2711173927682236e+00 2.5081940917429755e+00 + 26 2.5776230782480054e+00 4.0127347068243875e+00 3.2182355138709262e+00 27 -1.9613581876744357e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678509e+00 29 -1.3108232656499084e+00 -3.5992986322410765e+00 2.2680459788743512e+00 @@ -66,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704659e-04 -3.1032459262907825e-04 8.1043030117346085e-04 - 19 8.5103884665346059e-04 -1.4572280596788099e-03 1.0163621287634082e-03 - 20 -6.5204659278590227e-04 4.3989037444289446e-04 4.9909839028508150e-04 - 21 -1.3888125881903869e-03 -3.1978049143081757e-04 1.1455681499836596e-03 - 22 -1.6084223477729556e-03 -1.5355394240821013e-03 1.4772010826232407e-03 - 23 2.6392672378803953e-04 -3.9375414431174656e-03 -3.6991583139727423e-04 - 24 8.6062827067889998e-04 -9.4179873474469411e-04 5.5396395550012377e-04 - 25 1.5933645477487516e-03 -2.2139156625681634e-03 -5.5078029695647109e-04 - 26 -1.5679561743998922e-03 3.5146224354726068e-04 2.4446924193334543e-03 + 18 3.6149625095704681e-04 -3.1032459262907857e-04 8.1043030117346074e-04 + 19 8.5103884665345820e-04 -1.4572280596788108e-03 1.0163621287634073e-03 + 20 -6.5204659278590271e-04 4.3989037444289630e-04 4.9909839028508215e-04 + 21 -1.3888125881903852e-03 -3.1978049143082049e-04 1.1455681499836594e-03 + 22 -1.6084223477729513e-03 -1.5355394240820970e-03 1.4772010826232351e-03 + 23 2.6392672378803975e-04 -3.9375414431174569e-03 -3.6991583139727910e-04 + 24 8.6062827067889835e-04 -9.4179873474469346e-04 5.5396395550012518e-04 + 25 1.5933645477487516e-03 -2.2139156625681669e-03 -5.5078029695647542e-04 + 26 -1.5679561743998831e-03 3.5146224354726187e-04 2.4446924193334495e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml index 420e54be25..c80a70b428 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:00 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -15,38 +14,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |2- - 4.3578059175768836e+01 1.7275105168781163e+01 6.7372361277896715e+01 5.1985075050485008e+01 -2.0990677388216337e+01 -7.5321398110797180e+00 -global_scalar: 29.023636439584656 + 4.3578059172167876e+01 1.7275105166465000e+01 6.7372361276631054e+01 5.1985075049901745e+01 -2.0990677389800993e+01 -7.5321398101844359e+00 +global_scalar: 29.023636440847998 run_pos: ! |2 - 1 -6.3472039825540794e-01 3.0113983126285611e+00 -8.8148450172186088e-02 - 2 6.4798884173342230e-02 3.5870486860061987e+00 -9.1146271255438371e-01 - 3 -1.1328967478843275e+00 1.5344674077764573e+00 -6.2949567786978555e-01 - 4 -2.1941320441845233e+00 1.8319737599532644e+00 -1.3824693495475202e+00 - 5 -1.3741175247363868e+00 1.1637763350571468e+00 6.0220861483099597e-01 - 6 5.5368589242003274e-02 3.1209253712249918e-01 -1.4252606627468261e+00 - 7 1.1075313780254881e-01 2.8008314824818470e-02 -2.8425552056440617e+00 - 8 1.1011987966103707e+00 -5.4254536577072621e-01 -6.9472264392662098e-01 - 9 1.3580030945400878e+00 -2.6595138115347083e-01 4.4172536708308918e-01 - 10 2.1282964643832170e+00 -1.6781145595678604e+00 -1.0442216631471855e+00 - 11 1.8571593172392049e+00 -2.3497452731073896e+00 -2.1462323657667168e+00 - 12 3.3117732698472082e+00 -5.4913311816195076e-01 -1.8274356036323969e+00 - 13 4.5640183918456607e+00 -1.0445083545908531e+00 -1.8509716390299671e+00 - 14 2.8312769330519618e+00 -4.5135848464346928e-01 -3.0735173792334827e+00 - 15 3.2788434490966321e+00 7.1618295543705379e-01 -1.3765217601453177e+00 - 16 2.8895075000233756e+00 -2.8409365554013446e+00 1.5818504152563229e-01 - 17 2.3837073405560343e+00 -2.4882133308171808e+00 1.5000885103551624e+00 - 18 2.2738793194332434e+00 3.6743407122541889e+00 -4.1408965121171795e+00 - 19 1.6572750518219337e+00 3.2770314238270633e+00 -4.8886441786700008e+00 - 20 2.9120476452894675e+00 4.3568412674987194e+00 -4.5732834167653644e+00 - 21 5.6058485051319096e+00 -4.8495065176594299e+00 -4.2655497599906971e+00 - 22 5.0552709232924169e+00 -4.9851876754509741e+00 -5.1280564952785888e+00 - 23 6.4593933583860359e+00 -4.3461765101804879e+00 -4.5350231457223327e+00 - 24 2.1823354618683570e+00 3.8552931130563355e+00 3.8953804330779889e+00 - 25 1.3973696115700545e+00 3.9794119229082359e+00 3.2321313265764022e+00 - 26 2.7018361229436465e+00 4.7379517630364116e+00 3.9583193477161114e+00 - 27 -2.6559803075362858e+00 -5.1969823689084436e+00 2.6552621488559236e+00 - 28 -3.5927802460212725e+00 -4.7943885088607452e+00 2.0214142204098309e+00 - 29 -1.8739632618342856e+00 -4.2877858778718556e+00 2.8450749793922920e+00 + 1 -6.3472039825517168e-01 3.0113983126282058e+00 -8.8148450172235826e-02 + 2 6.4798884173500326e-02 3.5870486860057795e+00 -9.1146271255434463e-01 + 3 -1.1328967478840362e+00 1.5344674077762583e+00 -6.2949567786977667e-01 + 4 -2.1941320441841130e+00 1.8319737599530370e+00 -1.3824693495474225e+00 + 5 -1.3741175247360697e+00 1.1637763350569887e+00 6.0220861483086097e-01 + 6 5.5368589242158706e-02 3.1209253712244411e-01 -1.4252606627467266e+00 + 7 1.1075313780270069e-01 2.8008314824797154e-02 -2.8425552056438050e+00 + 8 1.1011987966104080e+00 -5.4254536577068713e-01 -6.9472264392660854e-01 + 9 1.3580030945401020e+00 -2.6595138115345840e-01 4.4172536708297194e-01 + 10 2.1282964643831388e+00 -1.6781145595676907e+00 -1.0442216631471304e+00 + 11 1.8571593172391605e+00 -2.3497452731071471e+00 -2.1462323657665392e+00 + 12 3.3117732698469986e+00 -5.4913311816190635e-01 -1.8274356036322548e+00 + 13 4.5640183918453143e+00 -1.0445083545907554e+00 -1.8509716390298214e+00 + 14 2.8312769330518019e+00 -4.5135848464344086e-01 -3.0735173792331993e+00 + 15 3.2788434490964296e+00 7.1618295543695254e-01 -1.3765217601452289e+00 + 16 2.8895075000232158e+00 -2.8409365554010479e+00 1.5818504152554702e-01 + 17 2.3837073405559277e+00 -2.4882133308169232e+00 1.5000885103549333e+00 + 18 2.2738793194357232e+00 3.6743407122553755e+00 -4.1408965121163197e+00 + 19 1.6572750518209336e+00 3.2770314238152451e+00 -4.8886441786593569e+00 + 20 2.9120476452800226e+00 4.3568412675031851e+00 -4.5732834167769187e+00 + 21 5.6058485050774536e+00 -4.8495065176300871e+00 -4.2655497599953458e+00 + 22 5.0552709232982114e+00 -4.9851876752032496e+00 -5.1280564953560424e+00 + 23 6.4593933585948218e+00 -4.3461765105422652e+00 -4.5350231456236889e+00 + 24 2.1823354619125279e+00 3.8552931130470363e+00 3.8953804330431208e+00 + 25 1.3973696115403698e+00 3.9794119228484153e+00 3.2321313266194949e+00 + 26 2.7018361227965517e+00 4.7379517631305443e+00 3.9583193478092706e+00 + 27 -2.6559803075358257e+00 -5.1969823689078796e+00 2.6552621488555683e+00 + 28 -3.5927802460207046e+00 -4.7943885088602283e+00 2.0214142204095413e+00 + 29 -1.8739632618339108e+00 -4.2877858778713946e+00 2.8450749793919066e+00 run_vel: ! |2 1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04 2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03 @@ -65,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.0094600492089644e-04 -2.4312792028464785e-04 6.5542049134054972e-04 - 19 7.4731683460624917e-04 -1.2894119671240515e-03 8.4327024053305281e-04 - 20 -6.2333686369944134e-04 4.4115361644063580e-04 3.7135656432041769e-04 - 21 -1.1457423794330429e-03 -1.7337748206069275e-04 9.4510018428907005e-04 - 22 -1.3457150585185161e-03 -1.2816797348700177e-03 1.2470992253076274e-03 - 23 3.6277645495226573e-04 -3.4719859038751704e-03 -4.3796817878355291e-04 - 24 7.2410992459670032e-04 -7.6012809759399148e-04 4.3327155120505761e-04 - 25 1.3921349891892136e-03 -1.9207002802470530e-03 -5.7453335098663809e-04 - 26 -1.4901465945625111e-03 4.2012923513626559e-04 2.1578545406129137e-03 + 18 3.0094600491564739e-04 -2.4312792027781263e-04 6.5542049134062323e-04 + 19 7.4731683462770076e-04 -1.2894119671278408e-03 8.4327024053533397e-04 + 20 -6.2333686369976551e-04 4.4115361641690044e-04 3.7135656431834220e-04 + 21 -1.1457423793218525e-03 -1.7337748161437940e-04 9.4510018429417686e-04 + 22 -1.3457150581639313e-03 -1.2816797357047471e-03 1.2470992250388096e-03 + 23 3.6277645415306518e-04 -3.4719859048227848e-03 -4.3796817853449118e-04 + 24 7.2410992462873655e-04 -7.6012809744767037e-04 4.3327155128124943e-04 + 25 1.3921349892629666e-03 -1.9207002802664867e-03 -5.7453335109528090e-04 + 26 -1.4901465947638008e-03 4.2012923457099966e-04 2.1578545404178418e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml index 4d16fc12a0..3894815950 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:00 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 6.5e-13 skip_tests: prerequisites: ! | @@ -15,38 +14,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |2- - 2.7340318979717416e+01 4.7963870104375275e+00 6.8884396847589585e+01 2.9853310005453281e+01 -1.0857139898599751e+01 -5.1889756547311965e+00 -global_scalar: 9.776787862991728 + 2.7340318973870396e+01 4.7963870091858283e+00 6.8884396847592512e+01 2.9853310007358935e+01 -1.0857139901347722e+01 -5.1889756561454785e+00 +global_scalar: 9.77678786310451 run_pos: ! |2 - 1 -5.1121862036689958e-01 2.8134872171089729e+00 -4.8993015395755179e-02 - 2 1.4735952487989756e-01 3.3535825972289093e+00 -9.3694001270719340e-01 - 3 -9.8023793775484513e-01 1.4277788160415970e+00 -6.3283768722997102e-01 - 4 -1.9793617512989155e+00 1.7069097152786199e+00 -1.4449221382951762e+00 - 5 -1.2073406578723613e+00 1.0799834439085494e+00 6.9555923026634758e-01 - 6 1.3848116183685821e-01 2.8090381873868608e-01 -1.4910727029123834e+00 - 7 1.9062418945961834e-01 1.4366032742524126e-02 -3.0196292835188681e+00 - 8 1.1231015082843996e+00 -5.2094745136412257e-01 -7.0318517336038155e-01 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-5.1868156516245785e+00 + 20 2.8608613711028656e+00 4.1100452338287408e+00 -4.8694049549907970e+00 + 21 5.3613621396958795e+00 -4.5653056926475841e+00 -4.5681019697305372e+00 + 22 4.8144754754921184e+00 -4.6999404674483083e+00 -5.4362066556130868e+00 + 23 6.2091840278795729e+00 -4.0659479262420684e+00 -4.8393130641864568e+00 + 24 2.1433208912603074e+00 3.5960988832146015e+00 4.2399236066404100e+00 + 25 1.3636453973491918e+00 3.7192408266342980e+00 3.5723762826473990e+00 + 26 2.6593036729945752e+00 4.4718649490241678e+00 4.3032623333405660e+00 + 27 -2.4141791756398536e+00 -4.8879035738852403e+00 2.9097838637418292e+00 + 28 -3.2961505257539048e+00 -4.5101758871984199e+00 2.2261768979308005e+00 + 29 -1.6779316575994301e+00 -4.0348635219024889e+00 3.1144975929056571e+00 run_vel: ! |2 1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04 2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03 @@ -65,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.1638284997600319e-04 -2.6313163919763335e-04 6.1054395248685519e-04 - 19 7.6494647250110288e-04 -1.3190724749175438e-03 7.9947132612783736e-04 - 20 -6.1620104632483571e-04 4.2577138776739548e-04 3.2526261653790590e-04 - 21 -1.2063428872614197e-03 -2.2879409923923591e-04 8.9132836537741717e-04 - 22 -1.4151473875545966e-03 -1.3502255384792933e-03 1.1972773112250280e-03 - 23 3.1280366189902534e-04 -3.5563936883846667e-03 -4.9548546556753227e-04 - 24 7.5594375538112746e-04 -8.1321044009394260e-04 3.9340911288157350e-04 - 25 1.4373446730968913e-03 -1.9778020567293151e-03 -6.1842201907436371e-04 - 26 -1.4806168648243687e-03 3.7766934332225264e-04 2.1280924227258073e-03 + 18 3.1638284997073272e-04 -2.6313163919070405e-04 6.1054395248656961e-04 + 19 7.6494647252307673e-04 -1.3190724749214326e-03 7.9947132612985723e-04 + 20 -6.1620104632513929e-04 4.2577138774295274e-04 3.2526261653548693e-04 + 21 -1.2063428871524097e-03 -2.2879409878999576e-04 8.9132836538734445e-04 + 22 -1.4151473871894464e-03 -1.3502255393198256e-03 1.1972773109437849e-03 + 23 3.1280366109607172e-04 -3.5563936893394407e-03 -4.9548546532774958e-04 + 24 7.5594375541558026e-04 -8.1321043994394464e-04 3.9340911295780739e-04 + 25 1.4373446731689036e-03 -1.9778020567486213e-03 -6.1842201918304478e-04 + 26 -1.4806168650325999e-03 3.7766934274110835e-04 2.1280924225288342e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml index 5504ed4686..f5965e53ff 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:01 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,65 +13,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.6326314448662429e+03 -1.4727331978532245e+03 -3.8557370515929042e+03 5.5052891601619581e+02 4.7346742977256520e+02 -6.2035591882208064e+02 -global_scalar: 106.86683072474244 + -1.6326314448663306e+03 -1.4727331978532295e+03 -3.8557370515932275e+03 5.5052891601644615e+02 4.7346742977310657e+02 -6.2035591882122355e+02 +global_scalar: 106.86683072474125 run_pos: ! |2 - 1 -2.6314711410917102e-01 2.4664715027243860e+00 -1.7093568570953632e-01 - 2 3.1632911015962950e-01 2.9434731493852171e+00 -8.5432214735883338e-01 - 3 -6.7623447816593352e-01 1.2410822625695497e+00 -6.1935152269929450e-01 - 4 -1.5552134736907304e+00 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-2.0274707260294341e-04 + 13 2.0597404142686670e-04 -1.0865778699535151e-03 -1.1731137935658918e-04 + 14 2.4719215573349161e-04 -1.1410575874168858e-03 -2.0209037936298231e-04 + 15 6.3286464043726845e-04 -6.3068988069288313e-04 -6.5527927471360488e-04 + 16 -4.4100406048953834e-05 8.6869240444187047e-06 6.5198761255923199e-04 + 17 1.3407421346950653e-04 6.0357565278263911e-04 5.6233596575975121e-04 + 18 7.9277804690569076e-04 -1.5618239874425175e-03 2.1367192719678593e-03 + 19 5.6167660797942776e-04 -1.2371794194922848e-03 2.1562222137424714e-03 + 20 1.1137406410123489e-03 -1.8729421751430327e-03 2.1222207985340819e-03 + 21 -2.8426953558137740e-03 -2.9730185469781381e-03 1.8564402246257748e-03 + 22 -2.9480844379790165e-03 -2.6797216173769360e-03 1.8784164631754769e-03 + 23 -2.5997293519674958e-03 -3.3926375081633348e-03 1.8288830284141459e-03 + 24 1.1689404599043950e-03 -1.6701257754515662e-03 2.1428138286394673e-03 + 25 1.2027302640333160e-03 -1.2630861421196525e-03 2.1808987508670514e-03 + 26 1.6116362268906780e-03 -1.9337182438138849e-03 2.1377249582867843e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml index d04c58e083..3b13658e19 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:01 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,38 +13,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -8.7531774640811420e+01 5.5811525750281774e+00 -5.5468297761715007e+01 -1.5316306336726905e+02 1.4641268095299071e+02 1.7263710083146290e+01 -global_scalar: 77.78983430422252 + -8.7531774769722489e+01 5.5811525017966304e+00 -5.5468297744356747e+01 -1.5316306343483370e+02 1.4641268097314367e+02 1.7263710089631324e+01 +global_scalar: 77.78983430293286 run_pos: ! |2 - 1 -4.6333219629057343e-01 2.7511450055078264e+00 -1.2865946102794723e-01 - 2 1.7937148390171043e-01 3.2800405238548382e+00 -8.8510337855745913e-01 - 3 -9.2104620265733672e-01 1.3941717929290096e+00 -6.2603796687147195e-01 - 4 -1.8960869879720148e+00 1.6675144043874610e+00 -1.3178544214442827e+00 - 5 -1.1426748052076219e+00 1.0535885915282748e+00 5.0562616550083384e-01 - 6 1.7070712623507234e-01 2.7107933832768616e-01 -1.3571701846609390e+00 - 7 2.2159329060507194e-01 1.0068698962099276e-02 -2.6593507556865532e+00 - 8 1.1315940381700180e+00 -5.1414408469817374e-01 -6.8596713849766644e-01 - 9 1.3675404538221745e+00 -2.6001531899018637e-01 3.5817751536688647e-01 - 10 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1.0068698962042433e-02 -2.6593507556860114e+00 + 8 1.1315940381701060e+00 -5.1414408469809381e-01 -6.8596713849763802e-01 + 9 1.3675404538221994e+00 -2.6001531899016506e-01 3.5817751536664133e-01 + 10 2.0752698846777218e+00 -1.5574812996955254e+00 -1.0070795245589492e+00 + 11 1.8261547470632067e+00 -2.1745615463231482e+00 -2.0195839000288469e+00 + 12 3.1626236108721066e+00 -5.2019677375525752e-01 -1.7266801053747978e+00 + 13 4.3131602274134853e+00 -9.7533717592326674e-01 -1.7483045222380902e+00 + 14 2.7211536303664605e+00 -4.3036348628163701e-01 -2.8715539682060491e+00 + 15 3.1323683805788374e+00 6.4234915962457073e-01 -1.3123899007466848e+00 + 16 2.7746546569032322e+00 -2.6258578189755974e+00 9.7666596945726880e-02 + 17 2.3099360535750506e+00 -2.3017831004883886e+00 1.3305794265747686e+00 + 18 2.2091748314094701e+00 3.3564440703097080e+00 -3.8370878208998480e+00 + 19 1.5986312961639815e+00 2.9614993054417287e+00 -4.5778944294436021e+00 + 20 2.8405364052167421e+00 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-9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 7.2384391137821785e-04 -6.0015829219183913e-04 1.5957533239005792e-03 - 19 1.7583138220942001e-03 -3.0158245949231362e-03 2.0310435058145879e-03 - 20 -1.4153552733289841e-03 9.7835305963750062e-04 9.3881222515317965e-04 - 21 -2.7591188784018856e-03 -5.1180651254767841e-04 2.2758295071625967e-03 - 22 -3.2319732438308327e-03 -3.0809796341686479e-03 2.9861065796802132e-03 - 23 6.9767443960831559e-04 -8.1543313047864312e-03 -8.9929523012053270e-04 - 24 1.7345816996818938e-03 -1.8508160077951139e-03 1.0723416139084840e-03 - 25 3.2855417748809557e-03 -4.5284294761711655e-03 -1.2529298997977286e-03 - 26 -3.4004728777299181e-03 8.5952141335802687e-04 5.0505027869618231e-03 + 18 7.2384391131466940e-04 -6.0015829212802722e-04 1.5957533238990559e-03 + 19 1.7583138222551384e-03 -3.0158245948490804e-03 2.0310435058142470e-03 + 20 -1.4153552732353322e-03 9.7835305930749246e-04 9.3881222516217474e-04 + 21 -2.7591188772323472e-03 -5.1180650802276303e-04 2.2758295071994400e-03 + 22 -3.2319732401280494e-03 -3.0809796427949646e-03 2.9861065768383484e-03 + 23 6.9767443123301817e-04 -8.1543313142268207e-03 -8.9929522742256325e-04 + 24 1.7345816999787505e-03 -1.8508160062822962e-03 1.0723416147087287e-03 + 25 3.2855417755407162e-03 -4.5284294762327620e-03 -1.2529299007822618e-03 + 26 -3.4004728795728936e-03 8.5952140737749613e-04 5.0505027847540665e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml index fc5948cb52..b20d639fd4 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:02 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -15,65 +14,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4245356938011316e+03 -1.4496493316650758e+03 -3.6144360982530934e+03 8.4840626794790273e+02 2.0318336802433893e+02 -6.0622397695991208e+02 -global_scalar: 15.711521423178162 + -1.4245356938011610e+03 -1.4496493316650424e+03 -3.6144360982532016e+03 8.4840626794792252e+02 2.0318336802442886e+02 -6.0622397695978805e+02 +global_scalar: 15.711521423178128 run_pos: ! |2 - 1 -2.7899546863904412e-01 2.4731857340327541e+00 -1.7290667740243348e-01 - 2 3.0296221610251317e-01 2.9517129916957181e+00 -8.5798904387771990e-01 - 3 -6.9368802364141358e-01 1.2445115421753392e+00 -6.2281111198654315e-01 - 4 -1.5764879647103740e+00 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2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml index 0f36c31a95..839ac060a5 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:02 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -15,8 +14,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200114760030708e+01 -2.6907707699312748e+01 -6.0080872440179061e+00 -2.5620425767600064e+01 -1.3450222535184853e+01 -1.4947348700253382e+00 -global_scalar: 18.340560165889197 + -4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00 +global_scalar: 18.340560167364448 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -35,15 +34,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588241729e+00 3.0171068018404634e+00 -3.5144628518858858e+00 - 19 1.5366124996944652e+00 2.6286809834366300e+00 -4.2452547844429631e+00 - 20 2.7628161763703827e+00 3.6842251687412753e+00 -3.9370881219283147e+00 - 21 4.9036621349084646e+00 -4.0757648444931904e+00 -3.6192617654848509e+00 - 22 4.3655322292057255e+00 -4.2084949967079632e+00 -4.4622011117106153e+00 - 23 5.7380414788131207e+00 -3.5841969185149058e+00 -3.8827839829438688e+00 - 24 2.0701314764430685e+00 3.1499370533656190e+00 3.1565324853444698e+00 - 25 1.3030170721374645e+00 3.2711173928413317e+00 2.5081940917372791e+00 - 26 2.5776230786045939e+00 4.0127347066259897e+00 3.2182355135086644e+00 + 18 2.1392027588270928e+00 3.0171068018423082e+00 -3.5144628518853867e+00 + 19 1.5366124996934336e+00 2.6286809834236959e+00 -4.2452547844313493e+00 + 20 2.7628161763597592e+00 3.6842251687468450e+00 -3.9370881219419189e+00 + 21 4.9036621348471368e+00 -4.0757648444604762e+00 -3.6192617654906609e+00 + 22 4.3655322292129357e+00 -4.2084949964269480e+00 -4.4622011117992786e+00 + 23 5.7380414790507261e+00 -3.5841969189265162e+00 -3.8827839828320116e+00 + 24 2.0701314764933532e+00 3.1499370533556008e+00 3.1565324853054118e+00 + 25 1.3030170721038390e+00 3.2711173927738786e+00 2.5081940917867680e+00 + 26 2.5776230784374867e+00 4.0127347067334345e+00 3.2182355136150917e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -65,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095571725e-04 -3.1032459263052550e-04 8.1043030117473349e-04 - 19 8.5103884662188244e-04 -1.4572280597071525e-03 1.0163621287543638e-03 - 20 -6.5204659274901945e-04 4.3989037447700791e-04 4.9909839028904252e-04 - 21 -1.3888125889514069e-03 -3.1978049248194420e-04 1.1455681505565557e-03 - 22 -1.6084223477996385e-03 -1.5355394224557757e-03 1.4772010822781041e-03 - 23 2.6392672685288674e-04 -3.9375414405480738e-03 -3.6991583333937880e-04 - 24 8.6062827042478370e-04 -9.4179873506334828e-04 5.5396395546095014e-04 - 25 1.5933645477524167e-03 -2.2139156628045932e-03 -5.5078029709943691e-04 - 26 -1.5679561733890424e-03 3.5146224505578228e-04 2.4446924196328459e-03 + 18 3.6149625094898067e-04 -3.1032459262177040e-04 8.1043030117471950e-04 + 19 8.5103884664914254e-04 -1.4572280597118469e-03 1.0163621287571445e-03 + 20 -6.5204659274939057e-04 4.3989037444674739e-04 4.9909839028631532e-04 + 21 -1.3888125888095134e-03 -3.1978049191290817e-04 1.1455681505629727e-03 + 22 -1.6084223473476296e-03 -1.5355394235202363e-03 1.4772010819351844e-03 + 23 2.6392672583440717e-04 -3.9375414417551127e-03 -3.6991583302200246e-04 + 24 8.6062827046548790e-04 -9.4179873487668705e-04 5.5396395555797203e-04 + 25 1.5933645478462865e-03 -2.2139156628290975e-03 -5.5078029723780941e-04 + 26 -1.5679561736454237e-03 3.5146224433513641e-04 2.4446924193838983e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml index 6a8c54f4a9..854e8b4d45 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:03 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -15,26 +14,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3754817467882813e+03 -1.4228425246442055e+03 -3.6087196200592184e+03 8.7407043142559792e+02 2.1665316510417179e+02 -6.0480791467761571e+02 -global_scalar: 4.531423038570381 + -1.3754817467882767e+03 -1.4228425246441275e+03 -3.6087196200592489e+03 8.7407043142559303e+02 2.1665316510426268e+02 -6.0480791467747542e+02 +global_scalar: 4.531423038570333 run_pos: ! |2 - 1 -2.7899546859705771e-01 2.4731857340428069e+00 -1.7290667720877784e-01 - 2 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-1.8836565351901273e+00 + 12 3.0032775230343667e+00 -4.8983022415922672e-01 -1.6190248016125368e+00 + 13 4.0448964161972993e+00 -9.0213155125590028e-01 -1.6385398398261621e+00 + 14 2.6035151245156412e+00 -4.0874995488520105e-01 -2.6555999073601511e+00 + 15 2.9761196776308623e+00 5.6287237451808192e-01 -1.2442626194415292e+00 + 16 2.6517373020764632e+00 -2.3957035509096389e+00 3.3389262134244646e-02 + 17 2.2311114923824555e+00 -2.1018393229880719e+00 1.1496088522768189e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -48,23 +47,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093296226165618e-04 2.6351124312058857e-04 -4.4905063547614403e-04 - 2 4.9594635271877252e-04 9.4561409237151983e-05 -5.4581325723054321e-04 - 3 3.3306088119082413e-04 2.3224949911015692e-04 -2.3659435306899455e-04 - 4 3.3692332940285378e-04 2.1926824120529077e-04 -2.4716611858554389e-04 - 5 3.3642541894623611e-04 4.1797578053944765e-04 -1.8011323945926958e-04 - 6 2.0926870695907706e-04 2.6449376032434591e-05 -1.0508922741400673e-04 - 7 1.4629046128361865e-04 -1.6873362379725188e-04 -6.8353900724066446e-05 - 8 1.5844098346817927e-04 3.7728756087617390e-05 -1.9162577392845779e-05 - 9 2.1299357198253474e-04 1.6917133003967807e-04 -6.3528006071197993e-05 - 10 5.4261569071247645e-05 -9.4655546204705848e-05 1.0511372702289633e-04 - 11 -3.2194218121526927e-05 -2.2025090185604412e-04 2.0300208519293052e-04 - 12 1.2640585449264128e-04 -2.9851081600947238e-04 -7.9476186245595616e-05 - 13 8.4523551795112752e-05 -4.0583140303608579e-04 -4.7550925831960783e-05 - 14 9.9954071734163598e-05 -4.2610809338915548e-04 -7.9255453072680826e-05 - 15 2.4417483202630842e-04 -2.3521005781668527e-04 -2.4875292755154548e-04 - 16 -9.0959360838764895e-06 3.7773746063197473e-06 2.4035204669042547e-04 - 17 5.7507084250817169e-05 2.2629200960630572e-04 2.0686926033795233e-04 + 1 4.7093296226164550e-04 2.6351124312060223e-04 -4.4905063547613568e-04 + 2 4.9594635271876775e-04 9.4561409237174846e-05 -5.4581325723053790e-04 + 3 3.3306088119081919e-04 2.3224949911015709e-04 -2.3659435306899653e-04 + 4 3.3692332940285361e-04 2.1926824120528752e-04 -2.4716611858555457e-04 + 5 3.3642541894622217e-04 4.1797578053944250e-04 -1.8011323945926332e-04 + 6 2.0926870695908031e-04 2.6449376032433555e-05 -1.0508922741401509e-04 + 7 1.4629046128363305e-04 -1.6873362379725323e-04 -6.8353900724087087e-05 + 8 1.5844098346817862e-04 3.7728756087615553e-05 -1.9162577392847385e-05 + 9 2.1299357198252531e-04 1.6917133003967874e-04 -6.3528006071188683e-05 + 10 5.4261569071251603e-05 -9.4655546204709643e-05 1.0511372702289179e-04 + 11 -3.2194218121513917e-05 -2.2025090185605342e-04 2.0300208519291412e-04 + 12 1.2640585449265036e-04 -2.9851081600945991e-04 -7.9476186245599681e-05 + 13 8.4523551795123310e-05 -4.0583140303606936e-04 -4.7550925831962545e-05 + 14 9.9954071734181717e-05 -4.2610809338914382e-04 -7.9255453072696249e-05 + 15 2.4417483202631243e-04 -2.3521005781666407e-04 -2.4875292755154228e-04 + 16 -9.0959360838797421e-06 3.7773746063106756e-06 2.4035204669042973e-04 + 17 5.7507084250803101e-05 2.2629200960629499e-04 2.0686926033796699e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml index 7b702a4f2a..664921b147 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:03 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -15,8 +14,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200114760030708e+01 -2.6907707699312748e+01 -6.0080872440179061e+00 -2.5620425767600064e+01 -1.3450222535184853e+01 -1.4947348700253382e+00 -global_scalar: 0.5007318719399354 + -4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00 +global_scalar: 0.5007318719663203 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -35,15 +34,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588241729e+00 3.0171068018404634e+00 -3.5144628518858858e+00 - 19 1.5366124996944652e+00 2.6286809834366300e+00 -4.2452547844429631e+00 - 20 2.7628161763703827e+00 3.6842251687412753e+00 -3.9370881219283147e+00 - 21 4.9036621349084646e+00 -4.0757648444931904e+00 -3.6192617654848509e+00 - 22 4.3655322292057255e+00 -4.2084949967079632e+00 -4.4622011117106153e+00 - 23 5.7380414788131207e+00 -3.5841969185149058e+00 -3.8827839829438688e+00 - 24 2.0701314764430685e+00 3.1499370533656190e+00 3.1565324853444698e+00 - 25 1.3030170721374645e+00 3.2711173928413317e+00 2.5081940917372791e+00 - 26 2.5776230786045939e+00 4.0127347066259897e+00 3.2182355135086644e+00 + 18 2.1392027588270928e+00 3.0171068018423082e+00 -3.5144628518853867e+00 + 19 1.5366124996934336e+00 2.6286809834236959e+00 -4.2452547844313493e+00 + 20 2.7628161763597592e+00 3.6842251687468450e+00 -3.9370881219419189e+00 + 21 4.9036621348471368e+00 -4.0757648444604762e+00 -3.6192617654906609e+00 + 22 4.3655322292129357e+00 -4.2084949964269480e+00 -4.4622011117992786e+00 + 23 5.7380414790507261e+00 -3.5841969189265162e+00 -3.8827839828320116e+00 + 24 2.0701314764933532e+00 3.1499370533556008e+00 3.1565324853054118e+00 + 25 1.3030170721038390e+00 3.2711173927738786e+00 2.5081940917867680e+00 + 26 2.5776230784374867e+00 4.0127347067334345e+00 3.2182355136150917e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -65,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095571725e-04 -3.1032459263052550e-04 8.1043030117473349e-04 - 19 8.5103884662188244e-04 -1.4572280597071525e-03 1.0163621287543638e-03 - 20 -6.5204659274901945e-04 4.3989037447700791e-04 4.9909839028904252e-04 - 21 -1.3888125889514069e-03 -3.1978049248194420e-04 1.1455681505565557e-03 - 22 -1.6084223477996385e-03 -1.5355394224557757e-03 1.4772010822781041e-03 - 23 2.6392672685288674e-04 -3.9375414405480738e-03 -3.6991583333937880e-04 - 24 8.6062827042478370e-04 -9.4179873506334828e-04 5.5396395546095014e-04 - 25 1.5933645477524167e-03 -2.2139156628045932e-03 -5.5078029709943691e-04 - 26 -1.5679561733890424e-03 3.5146224505578228e-04 2.4446924196328459e-03 + 18 3.6149625094898067e-04 -3.1032459262177040e-04 8.1043030117471950e-04 + 19 8.5103884664914254e-04 -1.4572280597118469e-03 1.0163621287571445e-03 + 20 -6.5204659274939057e-04 4.3989037444674739e-04 4.9909839028631532e-04 + 21 -1.3888125888095134e-03 -3.1978049191290817e-04 1.1455681505629727e-03 + 22 -1.6084223473476296e-03 -1.5355394235202363e-03 1.4772010819351844e-03 + 23 2.6392672583440717e-04 -3.9375414417551127e-03 -3.6991583302200246e-04 + 24 8.6062827046548790e-04 -9.4179873487668705e-04 5.5396395555797203e-04 + 25 1.5933645478462865e-03 -2.2139156628290975e-03 -5.5078029723780941e-04 + 26 -1.5679561736454237e-03 3.5146224433513641e-04 2.4446924193838983e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml index b8ec6036a3..a49508ca15 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml @@ -1,8 +1,7 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:03 2024 -epsilon: 1e-12 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 +epsilon: 5e-13 skip_tests: prerequisites: ! | atom full @@ -14,26 +13,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3123962047758187e+03 -1.3675423591720764e+03 -3.5468492999580299e+03 7.8271738572394452e+02 2.6480486115379637e+02 -7.6950536863892899e+02 -global_scalar: 68.08659647424867 + -1.3123962047757550e+03 -1.3675423591710460e+03 -3.5468492999583855e+03 7.8271738572396373e+02 2.6480486115495069e+02 -7.6950536863736306e+02 +global_scalar: 68.08659647423171 run_pos: ! |2 - 1 -2.7802951913978302e-01 2.4737132264315886e+00 -1.7381271738770820e-01 - 2 3.0397800832462774e-01 2.9519031941430738e+00 -8.5908822750493219e-01 - 3 -6.9299720296403144e-01 1.2449766685867643e+00 -6.2329294828390935e-01 - 4 -1.5757894675977402e+00 1.4924105480969891e+00 -1.2497098747245081e+00 - 5 -8.9364750934382919e-01 9.3735293261092456e-01 4.0154813851965188e-01 - 6 2.9498813449158368e-01 2.2729986882934847e-01 -1.2847387164261186e+00 - 7 3.4080910884973536e-01 -9.8008218373410172e-03 -2.4635938021178290e+00 - 8 1.1647778042705941e+00 -4.8360070140696521e-01 -6.7668409924193851e-01 - 9 1.3786230528162504e+00 -2.5298559880063631e-01 2.6851325883859889e-01 - 10 2.0187712935465760e+00 -1.4287732348423197e+00 -9.6692440387075651e-01 - 11 1.7928755785828601e+00 -1.9879833661321924e+00 -1.8832605388677695e+00 - 12 3.0035558347417104e+00 -4.9042429038332558e-01 -1.6191927838349707e+00 - 13 4.0450911337528455e+00 -9.0293975523220671e-01 -1.6386440514139291e+00 - 14 2.6037405819188639e+00 -4.0959881564248080e-01 -2.6557674031623937e+00 - 15 2.9766330093333795e+00 5.6240461100740513e-01 -1.2447686007445669e+00 - 16 2.6517453810150675e+00 -2.3956939898019254e+00 3.3859750044092363e-02 - 17 2.2312525656155877e+00 -2.1013855689248668e+00 1.1500124166847305e+00 + 1 -2.7802951913990959e-01 2.4737132264311215e+00 -1.7381271738602289e-01 + 2 3.0397800832473609e-01 2.9519031941431444e+00 -8.5908822750267100e-01 + 3 -6.9299720296404743e-01 1.2449766685866726e+00 -6.2329294828335358e-01 + 4 -1.5757894675975461e+00 1.4924105480974301e+00 -1.2497098747240374e+00 + 5 -8.9364750934418624e-01 9.3735293261000852e-01 4.0154813851989335e-01 + 6 2.9498813449175199e-01 2.2729986882976547e-01 -1.2847387164260673e+00 + 7 3.4080910885027837e-01 -9.8008218359699473e-03 -2.4635938021179546e+00 + 8 1.1647778042705452e+00 -4.8360070140706557e-01 -6.7668409924218165e-01 + 9 1.3786230528159027e+00 -2.5298559880150862e-01 2.6851325883861188e-01 + 10 2.0187712935465942e+00 -1.4287732348422091e+00 -9.6692440387148870e-01 + 11 1.7928755785831587e+00 -1.9879833661313322e+00 -1.8832605388690278e+00 + 12 3.0035558347419657e+00 -4.9042429038271507e-01 -1.6191927838346238e+00 + 13 4.0450911337530959e+00 -9.0293975523160919e-01 -1.6386440514135796e+00 + 14 2.6037405819194577e+00 -4.0959881564101863e-01 -2.6557674031621108e+00 + 15 2.9766330093335447e+00 5.6240461100771322e-01 -1.2447686007433758e+00 + 16 2.6517453810147344e+00 -2.3956939898026426e+00 3.3859750042781744e-02 + 17 2.2312525656149020e+00 -2.1013855689264771e+00 1.1500124166835219e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -47,23 +46,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 1.8443993556507550e-03 1.0121779580008364e-03 -1.7361326034906117e-03 - 2 1.9401022924561704e-03 3.6428754787474148e-04 -2.1069540627809144e-03 - 3 1.3158623602986111e-03 8.9265747656469769e-04 -9.2144725682167822e-04 - 4 1.3306255280096579e-03 8.4281508656016844e-04 -9.6194026572521364e-04 - 5 1.3289682243418409e-03 1.6048237018838117e-03 -7.0511232123120064e-04 - 6 8.4113718611817723e-04 1.0389683283156166e-04 -4.1697370456838980e-04 - 7 5.9950574545550414e-04 -6.4437674895204296e-04 -2.7586696717479603e-04 - 8 6.4634547270655271e-04 1.4734228826538870e-04 -8.7540766366732192e-05 - 9 8.5561404484556399e-04 6.5123532540342654e-04 -2.5782947158584915e-04 - 10 2.4688038968457540e-04 -3.5995975344040265e-04 3.8912416843293944e-04 - 11 -8.4672359473939376e-05 -8.4134349031586390e-04 7.6463157764299549e-04 - 12 5.2321633256271539e-04 -1.1418047427487572e-03 -3.1842516233546950e-04 - 13 3.6258187754852045e-04 -1.5531581259503574e-03 -1.9590476904008422e-04 - 14 4.2166181631227780e-04 -1.6310415916636891e-03 -3.1740232809282303e-04 - 15 9.7471807923364706e-04 -8.9939841791107037e-04 -9.6757308853435780e-04 - 16 4.1534888650543531e-06 1.7705740203412426e-05 9.0753010117785768e-04 - 17 2.5969943716097897e-04 8.7075266710338634e-04 7.7887058799558893e-04 + 1 1.8443993556501188e-03 1.0121779580014884e-03 -1.7361326034900006e-03 + 2 1.9401022924558343e-03 3.6428754787592733e-04 -2.1069540627804634e-03 + 3 1.3158623602983108e-03 8.9265747656461540e-04 -9.2144725682164657e-04 + 4 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8.7075266710270492e-04 7.7887058799645239e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml index deeee40b52..6068993094 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:04 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +13,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4827261099624999e+02 -1.8411194282828326e+01 -1.0752762861573947e+02 -2.1814511471949461e+02 1.7027764305079162e+02 2.1058942246396320e+01 -global_scalar: 0.9532609552151339 + -1.4827261116680472e+02 -1.8411194349753309e+01 -1.0752762859308649e+02 -2.1814511477016276e+02 1.7027764307147623e+02 2.1058942244057214e+01 +global_scalar: 0.9532609554739606 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +33,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1395635672857165e+00 3.0168023048413781e+00 -3.5136606977888540e+00 - 19 1.5374727853296883e+00 2.6272080573369379e+00 -4.2442423140961818e+00 - 20 2.7621434608442974e+00 3.6846842324506923e+00 -3.9366036440451500e+00 - 21 4.9022821627727593e+00 -4.0760572705753884e+00 -3.6181235130648650e+00 - 22 4.3639257458473608e+00 -4.2100277337137149e+00 -4.4607219426242057e+00 - 23 5.7383384123314833e+00 -3.5881799299869201e+00 -3.8831848693467652e+00 - 24 2.0709922900187268e+00 3.1490053461587983e+00 3.1570777021928031e+00 - 25 1.3046262535950772e+00 3.2688902578410239e+00 2.5076144139609013e+00 - 26 2.5760050692220648e+00 4.0131166908053464e+00 3.2207051908683750e+00 + 18 2.1395635672981443e+00 3.0168023048492310e+00 -3.5136606977867388e+00 + 19 1.5374727853253387e+00 2.6272080572819609e+00 -4.2442423140467360e+00 + 20 2.7621434607990372e+00 3.6846842324743214e+00 -3.9366036441030396e+00 + 21 4.9022821625125470e+00 -4.0760572704380627e+00 -3.6181235130909242e+00 + 22 4.3639257458824501e+00 -4.2100277325126187e+00 -4.4607219430080747e+00 + 23 5.7383384133351401e+00 -3.5881799317362106e+00 -3.8831848688588710e+00 + 24 2.0709922902331592e+00 3.1490053461169678e+00 3.1570777020268803e+00 + 25 1.3046262534530633e+00 3.2688902575528282e+00 2.5076144141701078e+00 + 26 2.5760050685080813e+00 4.0131166912605272e+00 3.2207051913215210e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +63,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 7.8522439447394326e-04 -6.6826115070004464e-04 1.7528441282176825e-03 - 19 1.8628941717384645e-03 -3.1840047052822556e-03 2.2062694140226819e-03 - 20 -1.4430972532419690e-03 9.7564145880034414e-04 1.0686492192457362e-03 - 21 -3.0047717260078453e-03 -6.6139344410253201e-04 2.4784169376928207e-03 - 22 -3.4980341614361554e-03 -3.3380963226435131e-03 3.2191614012082861e-03 - 23 5.9333931535562748e-04 -8.6231086111150188e-03 -8.2692040667271425e-04 - 24 1.8727912307694413e-03 -2.0349136837727452e-03 1.1951471743788897e-03 - 25 3.4887365951187166e-03 -4.8232966888750181e-03 -1.2263764478999317e-03 - 26 -3.4770257989604671e-03 7.8662050913487318e-04 5.3381090686904524e-03 + 18 7.8522439440007537e-04 -6.6826115062653757e-04 1.7528441282153480e-03 + 19 1.8628941719211862e-03 -3.1840047051916367e-03 2.2062694140207390e-03 + 20 -1.4430972531298200e-03 9.7564145841628493e-04 1.0686492192569898e-03 + 21 -3.0047717246574385e-03 -6.6139343888744974e-04 2.4784169377340712e-03 + 22 -3.4980341571643784e-03 -3.3380963325931002e-03 3.2191613979274040e-03 + 23 5.9333930569297746e-04 -8.6231086219834968e-03 -8.2692040355627789e-04 + 24 1.8727912311097641e-03 -2.0349136820274911e-03 1.1951471753018509e-03 + 25 3.4887365958745920e-03 -4.8232966889391266e-03 -1.2263764490291313e-03 + 26 -3.4770258010749858e-03 7.8662050223200905e-04 5.3381090661352298e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml index a8087adef5..02acb437d9 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:04 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 7.5e-13 skip_tests: prerequisites: ! | @@ -15,26 +14,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3754817466835991e+03 -1.4228425246166084e+03 -3.6087196201914162e+03 8.7407043149699155e+02 2.1665316519769920e+02 -6.0480791462032153e+02 -global_scalar: 4.531423038570312 + -1.3754817466835989e+03 -1.4228425246166137e+03 -3.6087196201914348e+03 8.7407043149698916e+02 2.1665316519769885e+02 -6.0480791462033073e+02 +global_scalar: 4.531423038570297 run_pos: ! |2 - 1 -2.7899546859693225e-01 2.4731857340428771e+00 -1.7290667720876018e-01 - 2 3.0296221616793617e-01 2.9517129917211538e+00 -8.5798904365354822e-01 - 3 -6.9368802362166271e-01 1.2445115422149740e+00 -6.2281111185285387e-01 - 4 -1.5764879646739496e+00 1.4919714416722003e+00 -1.2492069413381550e+00 - 5 -8.9434512967954460e-01 9.3651699743538508e-01 4.0191726569957453e-01 - 6 2.9454439635065910e-01 2.2724545796943096e-01 -1.2845195052894227e+00 - 7 3.4049112905311785e-01 -9.4655677385578896e-03 -2.4634480019885232e+00 - 8 1.1644354555589664e+00 -4.8367776651302741e-01 -6.7663643931660822e-01 - 9 1.3781717822376678e+00 -2.5332509534947639e-01 2.6864954447021405e-01 - 10 2.0186368605645768e+00 -1.4285861423742912e+00 -9.6712491246325705e-01 - 11 1.7929137227200933e+00 -1.9875455388074468e+00 -1.8836565351900401e+00 - 12 3.0032775230343129e+00 -4.8983022415935129e-01 -1.6190248016126136e+00 - 13 4.0448964161972292e+00 -9.0213155125606781e-01 -1.6385398398262672e+00 - 14 2.6035151245155359e+00 -4.0874995488537874e-01 -2.6555999073602123e+00 - 15 2.9761196776308694e+00 5.6287237451798344e-01 -1.2442626194416739e+00 - 16 2.6517373020764223e+00 -2.3957035509096416e+00 3.3389262134313369e-02 - 17 2.2311114923824853e+00 -2.1018393229879830e+00 1.1496088522768906e+00 + 1 -2.7899546859693136e-01 2.4731857340428784e+00 -1.7290667720876285e-01 + 2 3.0296221616793728e-01 2.9517129917211546e+00 -8.5798904365355155e-01 + 3 -6.9368802362166204e-01 1.2445115422149751e+00 -6.2281111185285498e-01 + 4 -1.5764879646739487e+00 1.4919714416722010e+00 -1.2492069413381564e+00 + 5 -8.9434512967954416e-01 9.3651699743538730e-01 4.0191726569957442e-01 + 6 2.9454439635065910e-01 2.2724545796943096e-01 -1.2845195052894232e+00 + 7 3.4049112905311751e-01 -9.4655677385591108e-03 -2.4634480019885228e+00 + 8 1.1644354555589662e+00 -4.8367776651302724e-01 -6.7663643931660777e-01 + 9 1.3781717822376680e+00 -2.5332509534947545e-01 2.6864954447021416e-01 + 10 2.0186368605645764e+00 -1.4285861423742918e+00 -9.6712491246325605e-01 + 11 1.7929137227200918e+00 -1.9875455388074483e+00 -1.8836565351900385e+00 + 12 3.0032775230343125e+00 -4.8983022415935312e-01 -1.6190248016126132e+00 + 13 4.0448964161972283e+00 -9.0213155125606947e-01 -1.6385398398262669e+00 + 14 2.6035151245155355e+00 -4.0874995488538129e-01 -2.6555999073602123e+00 + 15 2.9761196776308694e+00 5.6287237451798222e-01 -1.2442626194416753e+00 + 16 2.6517373020764219e+00 -2.3957035509096407e+00 3.3389262134315700e-02 + 17 2.2311114923824857e+00 -2.1018393229879817e+00 1.1496088522768926e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -48,23 +47,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093296226165726e-04 2.6351124312057366e-04 -4.4905063547614750e-04 - 2 4.9594635271877263e-04 9.4561409237139244e-05 -5.4581325723053519e-04 - 3 3.3306088119083079e-04 2.3224949911015511e-04 -2.3659435306900900e-04 - 4 3.3692332940286722e-04 2.1926824120529738e-04 -2.4716611858556574e-04 - 5 3.3642541894624012e-04 4.1797578053943767e-04 -1.8011323945929113e-04 - 6 2.0926870695908297e-04 2.6449376032441903e-05 -1.0508922741401427e-04 - 7 1.4629046128362941e-04 -1.6873362379723111e-04 -6.8353900724071745e-05 - 8 1.5844098346817935e-04 3.7728756087619165e-05 -1.9162577392849147e-05 - 9 2.1299357198252962e-04 1.6917133003966793e-04 -6.3528006071199972e-05 - 10 5.4261569071245965e-05 -9.4655546204698774e-05 1.0511372702289789e-04 - 11 -3.2194218121522970e-05 -2.2025090185602350e-04 2.0300208519292848e-04 - 12 1.2640585449263589e-04 -2.9851081600946756e-04 -7.9476186245575178e-05 - 13 8.4523551795102697e-05 -4.0583140303608210e-04 -4.7550925831930561e-05 - 14 9.9954071734164248e-05 -4.2610809338913878e-04 -7.9255453072661758e-05 - 15 2.4417483202630007e-04 -2.3521005781669015e-04 -2.4875292755151984e-04 - 16 -9.0959360838839976e-06 3.7773746063194848e-06 2.4035204669042588e-04 - 17 5.7507084250806896e-05 2.2629200960629374e-04 2.0686926033794661e-04 + 1 4.7093296226165759e-04 2.6351124312057290e-04 -4.4905063547614669e-04 + 2 4.9594635271877263e-04 9.4561409237138512e-05 -5.4581325723053421e-04 + 3 3.3306088119083101e-04 2.3224949911015481e-04 -2.3659435306900835e-04 + 4 3.3692332940286717e-04 2.1926824120529722e-04 -2.4716611858556465e-04 + 5 3.3642541894624077e-04 4.1797578053943724e-04 -1.8011323945929064e-04 + 6 2.0926870695908283e-04 2.6449376032441855e-05 -1.0508922741401397e-04 + 7 1.4629046128362884e-04 -1.6873362379723068e-04 -6.8353900724071325e-05 + 8 1.5844098346817943e-04 3.7728756087619084e-05 -1.9162577392849316e-05 + 9 2.1299357198253002e-04 1.6917133003966749e-04 -6.3528006071200284e-05 + 10 5.4261569071245856e-05 -9.4655546204698666e-05 1.0511372702289738e-04 + 11 -3.2194218121523431e-05 -2.2025090185602293e-04 2.0300208519292805e-04 + 12 1.2640585449263546e-04 -2.9851081600946745e-04 -7.9476186245575585e-05 + 13 8.4523551795102263e-05 -4.0583140303608199e-04 -4.7550925831931374e-05 + 14 9.9954071734163435e-05 -4.2610809338913835e-04 -7.9255453072661880e-05 + 15 2.4417483202629980e-04 -2.3521005781669047e-04 -2.4875292755152005e-04 + 16 -9.0959360838836724e-06 3.7773746063194780e-06 2.4035204669042463e-04 + 17 5.7507084250807628e-05 2.2629200960629336e-04 2.0686926033794547e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml index 0eae9f7559..92754f85f5 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml @@ -1,7 +1,6 @@ --- -lammps_version: 7 Feb 2024 -tags: -date_generated: Mon Mar 25 20:01:05 2024 +lammps_version: 17 Feb 2022 +date_generated: Fri Mar 18 22:18:00 2022 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -15,8 +14,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00 -global_scalar: 18.340560167414402 + -4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00 +global_scalar: 18.3405601674144 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -35,15 +34,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588271301e+00 3.0171068018412783e+00 -3.5144628518856353e+00 - 19 1.5366124997074575e+00 2.6286809834111740e+00 -4.2452547844370221e+00 - 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 - 21 4.9036621347791236e+00 -4.0757648442838548e+00 -3.6192617654515908e+00 - 22 4.3655322291888474e+00 -4.2084949965552561e+00 -4.4622011117402343e+00 - 23 5.7380414793463110e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 + 18 2.1392027588271301e+00 3.0171068018412779e+00 -3.5144628518856349e+00 + 19 1.5366124997074571e+00 2.6286809834111748e+00 -4.2452547844370221e+00 + 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352554e+00 + 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515904e+00 + 22 4.3655322291888483e+00 -4.2084949965552561e+00 -4.4622011117402334e+00 + 23 5.7380414793463101e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 24 2.0701314765323930e+00 3.1499370533342330e+00 3.1565324852522938e+00 - 25 1.3030170721374787e+00 3.2711173927682244e+00 2.5081940917429759e+00 - 26 2.5776230782480041e+00 4.0127347068243884e+00 3.2182355138709284e+00 + 25 1.3030170721374779e+00 3.2711173927682249e+00 2.5081940917429768e+00 + 26 2.5776230782480045e+00 4.0127347068243875e+00 3.2182355138709275e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -65,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704849e-04 -3.1032459262908286e-04 8.1043030117346052e-04 - 19 8.5103884665345473e-04 -1.4572280596788095e-03 1.0163621287634121e-03 - 20 -6.5204659278590661e-04 4.3989037444289755e-04 4.9909839028507901e-04 - 21 -1.3888125881903906e-03 -3.1978049143082342e-04 1.1455681499836646e-03 - 22 -1.6084223477729526e-03 -1.5355394240821163e-03 1.4772010826232394e-03 - 23 2.6392672378804821e-04 -3.9375414431174795e-03 -3.6991583139728377e-04 - 24 8.6062827067890269e-04 -9.4179873474469291e-04 5.5396395550012388e-04 - 25 1.5933645477487551e-03 -2.2139156625681673e-03 -5.5078029695647250e-04 - 26 -1.5679561743998888e-03 3.5146224354726068e-04 2.4446924193334487e-03 + 18 3.6149625095704914e-04 -3.1032459262908286e-04 8.1043030117346052e-04 + 19 8.5103884665345452e-04 -1.4572280596788108e-03 1.0163621287634116e-03 + 20 -6.5204659278590683e-04 4.3989037444289853e-04 4.9909839028507901e-04 + 21 -1.3888125881903923e-03 -3.1978049143082385e-04 1.1455681499836646e-03 + 22 -1.6084223477729510e-03 -1.5355394240821117e-03 1.4772010826232375e-03 + 23 2.6392672378805124e-04 -3.9375414431174821e-03 -3.6991583139728095e-04 + 24 8.6062827067890247e-04 -9.4179873474469237e-04 5.5396395550012453e-04 + 25 1.5933645477487538e-03 -2.2139156625681695e-03 -5.5078029695647401e-04 + 26 -1.5679561743998840e-03 3.5146224354726100e-04 2.4446924193334478e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index 15ce3ae605..1da2dfa33c 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -1922,58 +1922,70 @@ TEST_F(AtomStyleTest, tri) EXPECT_NEAR(radius[GETIDX(5)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(6)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 13.982119044342252, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 13.982119044342252, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 13.945895752275419, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 0.10811427523057447, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 0.10811427523057447, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 0.23541253382609079, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 19.018309360029388, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 19.018309360029388, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 18.948744087979012, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 0.36886008861549813, EPSILON); - EXPECT_NEAR(bonus[0].quat[0], 0.92373678792937974, EPSILON); - EXPECT_NEAR(bonus[0].quat[1], 0.0067268233964605136, EPSILON); - EXPECT_NEAR(bonus[0].quat[2], 0.016239988275423622, EPSILON); - EXPECT_NEAR(bonus[0].quat[3], -0.38262430562330857, EPSILON); - EXPECT_NEAR(bonus[1].quat[0], 0.63633478678991862, EPSILON); - EXPECT_NEAR(bonus[1].quat[1], 0.66894644809679971, EPSILON); - EXPECT_NEAR(bonus[1].quat[2], 0.26478147716387457, EPSILON); - EXPECT_NEAR(bonus[1].quat[3], 0.27835132126616718, EPSILON); - EXPECT_NEAR(bonus[2].quat[0], 0.90191325590647375, EPSILON); - EXPECT_NEAR(bonus[2].quat[1], 0.2009681312851252, EPSILON); - EXPECT_NEAR(bonus[2].quat[2], 0.1002758475123109, EPSILON); - EXPECT_NEAR(bonus[2].quat[3], 0.36892959143125958, EPSILON); - EXPECT_NEAR(bonus[3].quat[0], 0.34503278332913523, EPSILON); - EXPECT_NEAR(bonus[3].quat[1], 0.17090845404750615, EPSILON); - EXPECT_NEAR(bonus[3].quat[2], 0.44689296000042461, EPSILON); - EXPECT_NEAR(bonus[3].quat[3], 0.80748335033318219, EPSILON); - EXPECT_NEAR(bonus[0].c1[0], -0.14933690186163626, EPSILON); - EXPECT_NEAR(bonus[0].c1[2], -0.0052525338293288879, EPSILON); - EXPECT_NEAR(bonus[1].c1[0], -0.18681344121910512, EPSILON); - EXPECT_NEAR(bonus[1].c1[2], 0.18561232929671317, EPSILON); - EXPECT_NEAR(bonus[2].c1[0], -0.78775285695558628, EPSILON); - EXPECT_NEAR(bonus[2].c1[2], -0.22123552085772158, EPSILON); - EXPECT_NEAR(bonus[3].c1[0], -0.47901475403318072, EPSILON); - EXPECT_NEAR(bonus[3].c1[2], -0.69845793336676587, EPSILON); - EXPECT_NEAR(bonus[0].c2[0], 0.55733290519255363, EPSILON); - EXPECT_NEAR(bonus[0].c2[2], 0.019602723119529656, EPSILON); - EXPECT_NEAR(bonus[1].c2[0], -0.22223836695322477, EPSILON); - EXPECT_NEAR(bonus[1].c2[2], 0.22080949143752887, EPSILON); - EXPECT_NEAR(bonus[2].c2[0], 0.63043795621810073, EPSILON); - EXPECT_NEAR(bonus[2].c2[2], 0.17705460333259254, EPSILON); - EXPECT_NEAR(bonus[3].c2[0], 0.15093208974463557, EPSILON); - EXPECT_NEAR(bonus[3].c2[2], 0.22007613459534847, EPSILON); - EXPECT_NEAR(bonus[0].c3[0], -0.4079960033309174, EPSILON); - EXPECT_NEAR(bonus[0].c3[2], -0.014350189290200809, EPSILON); - EXPECT_NEAR(bonus[1].c3[0], 0.40905180817232961, EPSILON); - EXPECT_NEAR(bonus[1].c3[2], -0.40642182073424171, EPSILON); - EXPECT_NEAR(bonus[2].c3[0], 0.15731490073748589, EPSILON); - EXPECT_NEAR(bonus[2].c3[2], 0.044180917525128927, EPSILON); - EXPECT_NEAR(bonus[3].c3[0], 0.32808266428854477, EPSILON); - EXPECT_NEAR(bonus[3].c3[2], 0.4783817987714174, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 0.36886008861549813, EPSILON); + EXPECT_NEAR(bonus[0].quat[0], 0.66466395261228639, EPSILON); + EXPECT_NEAR(bonus[0].quat[1], -0.26579965871355399, EPSILON); + EXPECT_NEAR(bonus[0].quat[2], -0.64169714094040209, EPSILON); + EXPECT_NEAR(bonus[0].quat[3], -0.27531282359251713, EPSILON); + EXPECT_NEAR(bonus[1].quat[0], 0.63718542087921404, EPSILON); + EXPECT_NEAR(bonus[1].quat[1], 0.66984067651944412, EPSILON); + EXPECT_NEAR(bonus[1].quat[2], -0.26272786480888066, EPSILON); + EXPECT_NEAR(bonus[1].quat[3], -0.27619246288035992, EPSILON); + EXPECT_NEAR(bonus[2].quat[0], 0.70865471105868871, EPSILON); + EXPECT_NEAR(bonus[2].quat[1], 0.40297854431552654, EPSILON); + EXPECT_NEAR(bonus[2].quat[2], -0.56684324752832238, EPSILON); + EXPECT_NEAR(bonus[2].quat[3], 0.11876668744732566, EPSILON); + EXPECT_NEAR(bonus[3].quat[0], 0.55997606330452898, EPSILON); + EXPECT_NEAR(bonus[3].quat[1], 0.69182747953492685, EPSILON); + EXPECT_NEAR(bonus[3].quat[2], 0.072026021657128514, EPSILON); + EXPECT_NEAR(bonus[3].quat[3], 0.45012642589672475, EPSILON); + EXPECT_NEAR(bonus[0].c1[0], -0.0052525338293288905, EPSILON); + EXPECT_NEAR(bonus[0].c1[1], -0.55767753582520529, EPSILON); + EXPECT_NEAR(bonus[0].c1[2], 0.14933690186163631, EPSILON); + EXPECT_NEAR(bonus[1].c1[0], 0.18561232929671426, EPSILON); + EXPECT_NEAR(bonus[1].c1[1], 0.51379191773154387, EPSILON); + EXPECT_NEAR(bonus[1].c1[2], 0.18681344121910506, EPSILON); + EXPECT_NEAR(bonus[2].c1[0], -0.22123552085772166, EPSILON); + EXPECT_NEAR(bonus[2].c1[1], -0.28372571379613187, EPSILON); + EXPECT_NEAR(bonus[2].c1[2], 0.78775285695558617, EPSILON); + EXPECT_NEAR(bonus[3].c1[0], -0.69845793336676587, EPSILON); + EXPECT_NEAR(bonus[3].c1[1], 0.18083523090249506, EPSILON); + EXPECT_NEAR(bonus[3].c1[2], 0.47901475403318056, EPSILON); + EXPECT_NEAR(bonus[0].c2[0], 0.019602723119529659, EPSILON); + EXPECT_NEAR(bonus[0].c2[1], 0.14942924536134222, EPSILON); + EXPECT_NEAR(bonus[0].c2[2], -0.55733290519255385, EPSILON); + EXPECT_NEAR(bonus[1].c2[0], 0.2208094914375279, EPSILON); + EXPECT_NEAR(bonus[1].c2[1], -0.4849604211463005, EPSILON); + EXPECT_NEAR(bonus[1].c2[2], 0.22223836695322477, EPSILON); + EXPECT_NEAR(bonus[2].c2[0], 0.17705460333259249, EPSILON); + EXPECT_NEAR(bonus[2].c2[1], -0.56674478453558153, EPSILON); + EXPECT_NEAR(bonus[2].c2[2], -0.6304379562181005, EPSILON); + EXPECT_NEAR(bonus[3].c2[0], 0.22007613459534958, EPSILON); + EXPECT_NEAR(bonus[3].c2[1], -0.82388470022624394, EPSILON); + EXPECT_NEAR(bonus[3].c2[2], -0.15093208974463557, EPSILON); + EXPECT_NEAR(bonus[0].c3[0], -0.014350189290200811, EPSILON); + EXPECT_NEAR(bonus[0].c3[1], 0.40824829046386302, EPSILON); + EXPECT_NEAR(bonus[0].c3[2], 0.40799600333091751, EPSILON); + EXPECT_NEAR(bonus[1].c3[0], -0.40642182073424188, EPSILON); + EXPECT_NEAR(bonus[1].c3[1], -0.028831496585242929, EPSILON); + EXPECT_NEAR(bonus[1].c3[2], -0.40905180817232945, EPSILON); + EXPECT_NEAR(bonus[2].c3[0], 0.044180917525129149, EPSILON); + EXPECT_NEAR(bonus[2].c3[1], 0.85047049833171351, EPSILON); + EXPECT_NEAR(bonus[2].c3[2], -0.15731490073748589, EPSILON); + EXPECT_NEAR(bonus[3].c3[0], 0.47838179877141634, EPSILON); + EXPECT_NEAR(bonus[3].c3[1], 0.64304946932374796, EPSILON); + EXPECT_NEAR(bonus[3].c3[2], -0.32808266428854477, EPSILON); BEGIN_HIDE_OUTPUT(); command("group two id 2:4:2"); @@ -2036,58 +2048,70 @@ TEST_F(AtomStyleTest, tri) EXPECT_NEAR(radius[GETIDX(11)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(12)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 0.23541253382609079, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 0.23541253382609079, EPSILON); - EXPECT_NEAR(bonus[0].quat[0], 0.92373678792937974, EPSILON); - EXPECT_NEAR(bonus[0].quat[1], 0.0067268233964605136, EPSILON); - EXPECT_NEAR(bonus[0].quat[2], 0.016239988275423622, EPSILON); - EXPECT_NEAR(bonus[0].quat[3], -0.38262430562330857, EPSILON); - EXPECT_NEAR(bonus[1].quat[0], 0.90191325590647375, EPSILON); - EXPECT_NEAR(bonus[1].quat[1], 0.2009681312851252, EPSILON); - EXPECT_NEAR(bonus[1].quat[2], 0.1002758475123109, EPSILON); - EXPECT_NEAR(bonus[1].quat[3], 0.36892959143125958, EPSILON); - EXPECT_NEAR(bonus[2].quat[0], 0.92373678792937974, EPSILON); - EXPECT_NEAR(bonus[2].quat[1], 0.0067268233964605136, EPSILON); - EXPECT_NEAR(bonus[2].quat[2], 0.016239988275423622, EPSILON); - EXPECT_NEAR(bonus[2].quat[3], -0.38262430562330857, EPSILON); - EXPECT_NEAR(bonus[3].quat[0], 0.90191325590647375, EPSILON); - EXPECT_NEAR(bonus[3].quat[1], 0.2009681312851252, EPSILON); - EXPECT_NEAR(bonus[3].quat[2], 0.1002758475123109, EPSILON); - EXPECT_NEAR(bonus[3].quat[3], 0.36892959143125958, EPSILON); - EXPECT_NEAR(bonus[0].c1[0], -0.14933690186163626, EPSILON); - EXPECT_NEAR(bonus[0].c1[2], -0.0052525338293288879, EPSILON); - EXPECT_NEAR(bonus[1].c1[0], -0.78775285695558628, EPSILON); - EXPECT_NEAR(bonus[1].c1[2], -0.22123552085772158, EPSILON); - EXPECT_NEAR(bonus[2].c1[0], -0.14933690186163626, EPSILON); - EXPECT_NEAR(bonus[2].c1[2], -0.0052525338293288879, EPSILON); - EXPECT_NEAR(bonus[3].c1[0], -0.78775285695558628, EPSILON); - EXPECT_NEAR(bonus[3].c1[2], -0.22123552085772158, EPSILON); - EXPECT_NEAR(bonus[0].c2[0], 0.55733290519255363, EPSILON); - EXPECT_NEAR(bonus[0].c2[2], 0.019602723119529656, EPSILON); - EXPECT_NEAR(bonus[1].c2[0], 0.63043795621810073, EPSILON); - EXPECT_NEAR(bonus[1].c2[2], 0.17705460333259254, EPSILON); - EXPECT_NEAR(bonus[2].c2[0], 0.55733290519255363, EPSILON); - EXPECT_NEAR(bonus[2].c2[2], 0.019602723119529656, EPSILON); - EXPECT_NEAR(bonus[3].c2[0], 0.63043795621810073, EPSILON); - EXPECT_NEAR(bonus[3].c2[2], 0.17705460333259254, EPSILON); - EXPECT_NEAR(bonus[0].c3[0], -0.4079960033309174, EPSILON); - EXPECT_NEAR(bonus[0].c3[2], -0.014350189290200809, EPSILON); - EXPECT_NEAR(bonus[1].c3[0], 0.15731490073748589, EPSILON); - EXPECT_NEAR(bonus[1].c3[2], 0.044180917525128927, EPSILON); - EXPECT_NEAR(bonus[2].c3[0], -0.4079960033309174, EPSILON); - EXPECT_NEAR(bonus[2].c3[2], -0.014350189290200809, EPSILON); - EXPECT_NEAR(bonus[3].c3[0], 0.15731490073748589, EPSILON); - EXPECT_NEAR(bonus[3].c3[2], 0.044180917525128927, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[0].quat[0], 0.66466395261228639, EPSILON); + EXPECT_NEAR(bonus[0].quat[1], -0.26579965871355399, EPSILON); + EXPECT_NEAR(bonus[0].quat[2], -0.64169714094040209, EPSILON); + EXPECT_NEAR(bonus[0].quat[3], -0.27531282359251713, EPSILON); + EXPECT_NEAR(bonus[1].quat[0], 0.70865471105868871, EPSILON); + EXPECT_NEAR(bonus[1].quat[1], 0.40297854431552654, EPSILON); + EXPECT_NEAR(bonus[1].quat[2], -0.56684324752832238, EPSILON); + EXPECT_NEAR(bonus[1].quat[3], 0.11876668744732566, EPSILON); + EXPECT_NEAR(bonus[2].quat[0], 0.66466395261228639, EPSILON); + EXPECT_NEAR(bonus[2].quat[1], -0.26579965871355399, EPSILON); + EXPECT_NEAR(bonus[2].quat[2], -0.64169714094040209, EPSILON); + EXPECT_NEAR(bonus[2].quat[3], -0.27531282359251713, EPSILON); + EXPECT_NEAR(bonus[3].quat[0], 0.70865471105868871, EPSILON); + EXPECT_NEAR(bonus[3].quat[1], 0.40297854431552654, EPSILON); + EXPECT_NEAR(bonus[3].quat[2], -0.56684324752832238, EPSILON); + EXPECT_NEAR(bonus[3].quat[3], 0.11876668744732566, EPSILON); + EXPECT_NEAR(bonus[0].c1[0], -0.0052525338293288879, EPSILON); + EXPECT_NEAR(bonus[0].c1[1], -0.55767753582520529, EPSILON); + EXPECT_NEAR(bonus[0].c1[2], 0.14933690186163626, EPSILON); + EXPECT_NEAR(bonus[1].c1[0], -0.22123552085772158, EPSILON); + EXPECT_NEAR(bonus[1].c1[1], -0.28372571379613187, EPSILON); + EXPECT_NEAR(bonus[1].c1[2], 0.78775285695558628, EPSILON); + EXPECT_NEAR(bonus[2].c1[0], -0.0052525338293288905, EPSILON); + EXPECT_NEAR(bonus[2].c1[1], -0.55767753582520529, EPSILON); + EXPECT_NEAR(bonus[2].c1[2], 0.14933690186163631, EPSILON); + EXPECT_NEAR(bonus[3].c1[0], -0.22123552085772166, EPSILON); + EXPECT_NEAR(bonus[3].c1[1], -0.28372571379613187, EPSILON); + EXPECT_NEAR(bonus[3].c1[2], 0.78775285695558617, EPSILON); + EXPECT_NEAR(bonus[0].c2[0], 0.019602723119529659, EPSILON); + EXPECT_NEAR(bonus[0].c2[1], 0.14942924536134222, EPSILON); + EXPECT_NEAR(bonus[0].c2[2], -0.55733290519255385, EPSILON); + EXPECT_NEAR(bonus[1].c2[0], 0.17705460333259249, EPSILON); + EXPECT_NEAR(bonus[1].c2[1], -0.56674478453558153, EPSILON); + EXPECT_NEAR(bonus[1].c2[2], -0.6304379562181005, EPSILON); + EXPECT_NEAR(bonus[2].c2[0], 0.019602723119529659, EPSILON); + EXPECT_NEAR(bonus[2].c2[1], 0.14942924536134222, EPSILON); + EXPECT_NEAR(bonus[2].c2[2], -0.55733290519255385, EPSILON); + EXPECT_NEAR(bonus[3].c2[0], 0.17705460333259249, EPSILON); + EXPECT_NEAR(bonus[3].c2[1], -0.56674478453558153, EPSILON); + EXPECT_NEAR(bonus[3].c2[2], -0.6304379562181005, EPSILON); + EXPECT_NEAR(bonus[0].c3[0], -0.014350189290200811, EPSILON); + EXPECT_NEAR(bonus[0].c3[1], 0.40824829046386302, EPSILON); + EXPECT_NEAR(bonus[0].c3[2], 0.40799600333091751, EPSILON); + EXPECT_NEAR(bonus[1].c3[0], 0.044180917525129149, EPSILON); + EXPECT_NEAR(bonus[1].c3[1], 0.85047049833171351, EPSILON); + EXPECT_NEAR(bonus[1].c3[2], -0.15731490073748589, EPSILON); + EXPECT_NEAR(bonus[2].c3[0], -0.014350189290200811, EPSILON); + EXPECT_NEAR(bonus[2].c3[1], 0.40824829046386302, EPSILON); + EXPECT_NEAR(bonus[2].c3[2], 0.40799600333091751, EPSILON); + EXPECT_NEAR(bonus[3].c3[0], 0.044180917525129149, EPSILON); + EXPECT_NEAR(bonus[3].c3[1], 0.85047049833171351, EPSILON); + EXPECT_NEAR(bonus[3].c3[2], -0.15731490073748589, EPSILON); BEGIN_HIDE_OUTPUT(); command("reset_atoms id"); @@ -2116,18 +2140,18 @@ TEST_F(AtomStyleTest, tri) ASSERT_EQ(tri[GETIDX(6)], -1); ASSERT_EQ(tri[GETIDX(7)], 3); ASSERT_EQ(tri[GETIDX(8)], -1); - EXPECT_NEAR(bonus[0].inertia[2], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 0.23541253382609079, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 14.017974903242481, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 14.017974903242481, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 13.94589575227541, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 0.072258416330334363, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 19.15175691481879, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 0.072258416330334363, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 19.15175691481879, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 18.948744087979005, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 0.23541253382609079, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 0.23541253382609079, EPSILON); } TEST_F(AtomStyleTest, body_nparticle) @@ -2323,18 +2347,18 @@ TEST_F(AtomStyleTest, body_nparticle) EXPECT_NEAR(radius[GETIDX(5)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(6)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 2.0, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 2.0, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 2.0, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 0.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 4.5, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 0.0, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 4.5, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 4.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 0.5, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 1.7746273249544022, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 0.5, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 1.7746273249544022, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 1.67188, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 0.49099767504559777, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 12.0, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 0.49099767504559777, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 12.0, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 12.0, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 0.0, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[0], 1.0, EPSILON); EXPECT_NEAR(bonus[0].quat[1], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[2], 0.0, EPSILON); @@ -2495,18 +2519,18 @@ TEST_F(AtomStyleTest, body_nparticle) EXPECT_NEAR(radius[GETIDX(5)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(6)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 2.0, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 2.0, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 2.0, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 0.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 4.5, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 0.0, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 4.5, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 4.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 0.5, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 1.7746273249544022, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 0.5, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 1.7746273249544022, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 1.67188, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 0.49099767504559777, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 12.0, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 0.49099767504559777, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 12.0, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 12.0, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 0.0, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[0], 1.0, EPSILON); EXPECT_NEAR(bonus[0].quat[1], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[2], 0.0, EPSILON); @@ -2519,10 +2543,10 @@ TEST_F(AtomStyleTest, body_nparticle) EXPECT_NEAR(bonus[2].quat[1], 0.25056280708573159, EPSILON); EXPECT_NEAR(bonus[2].quat[2], 0.0, EPSILON); EXPECT_NEAR(bonus[2].quat[3], 0.25056280708573148, EPSILON); - EXPECT_NEAR(bonus[3].quat[0], 0.070424771223903379, EPSILON); - EXPECT_NEAR(bonus[3].quat[1], 0.81345375914352225, EPSILON); - EXPECT_NEAR(bonus[3].quat[2], 0.56848787755882768, EPSILON); - EXPECT_NEAR(bonus[3].quat[3], -0.10077135705145905, EPSILON); + EXPECT_NEAR(bonus[3].quat[0], 0.62499650256800654, EPSILON); + EXPECT_NEAR(bonus[3].quat[1], 0.47323774316465234, EPSILON); + EXPECT_NEAR(bonus[3].quat[2], 0.33072552332373728, EPSILON); + EXPECT_NEAR(bonus[3].quat[3], 0.52540083597613996, EPSILON); ASSERT_EQ(bonus[0].ilocal, 0); ASSERT_EQ(bonus[1].ilocal, 1); ASSERT_EQ(bonus[2].ilocal, 2); @@ -2610,18 +2634,18 @@ TEST_F(AtomStyleTest, body_nparticle) EXPECT_NEAR(radius[GETIDX(9)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(11)], 0.5, EPSILON); EXPECT_NEAR(radius[GETIDX(12)], 0.5, EPSILON); - EXPECT_NEAR(bonus[0].inertia[2], 2.0, EPSILON); + EXPECT_NEAR(bonus[0].inertia[0], 2.0, EPSILON); EXPECT_NEAR(bonus[0].inertia[1], 2.0, EPSILON); - EXPECT_NEAR(bonus[0].inertia[0], 0.0, EPSILON); - EXPECT_NEAR(bonus[1].inertia[2], 1.7746273249544022, EPSILON); + EXPECT_NEAR(bonus[0].inertia[2], 0.0, EPSILON); + EXPECT_NEAR(bonus[1].inertia[0], 1.7746273249544022, EPSILON); EXPECT_NEAR(bonus[1].inertia[1], 1.67188, EPSILON); - EXPECT_NEAR(bonus[1].inertia[0], 0.49099767504559777, EPSILON); - EXPECT_NEAR(bonus[2].inertia[2], 2.0, EPSILON); + EXPECT_NEAR(bonus[1].inertia[2], 0.49099767504559777, EPSILON); + EXPECT_NEAR(bonus[2].inertia[0], 2.0, EPSILON); EXPECT_NEAR(bonus[2].inertia[1], 2.0, EPSILON); - EXPECT_NEAR(bonus[2].inertia[0], 0.0, EPSILON); - EXPECT_NEAR(bonus[3].inertia[2], 1.7746273249544022, EPSILON); + EXPECT_NEAR(bonus[2].inertia[2], 0.0, EPSILON); + EXPECT_NEAR(bonus[3].inertia[0], 1.7746273249544022, EPSILON); EXPECT_NEAR(bonus[3].inertia[1], 1.67188, EPSILON); - EXPECT_NEAR(bonus[3].inertia[0], 0.49099767504559777, EPSILON); + EXPECT_NEAR(bonus[3].inertia[2], 0.49099767504559777, EPSILON); EXPECT_NEAR(bonus[0].quat[0], 1.0, EPSILON); EXPECT_NEAR(bonus[0].quat[1], 0.0, EPSILON); EXPECT_NEAR(bonus[0].quat[2], 0.0, EPSILON); From 78a3a7b9c24ef099297fc038b7acff281aef7ff8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Apr 2024 23:28:14 -0400 Subject: [PATCH 26/40] add optional argument to enable overriding sort order or eigenvalues/vectors --- src/math_eigen.cpp | 24 ++++++++++++++++++++---- src/math_eigen.h | 5 +++-- 2 files changed, 23 insertions(+), 6 deletions(-) diff --git a/src/math_eigen.cpp b/src/math_eigen.cpp index 65c3fa806a..c79a61f84a 100644 --- a/src/math_eigen.cpp +++ b/src/math_eigen.cpp @@ -31,7 +31,7 @@ using namespace MathEigen; typedef Jacobi Jacobi_v1; typedef Jacobi Jacobi_v2; -int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) +int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort) { // make copy of const matrix @@ -44,7 +44,15 @@ int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v1 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_DECREASING_EVALS); + int ierror = 1; + if (sort == -1) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_DECREASING_EVALS); + else if (sort == 0) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::DO_NOT_SORT); + else if (sort == 1) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_INCREASING_EVALS); + + if (ierror) return ierror; // transpose the evec matrix @@ -54,7 +62,7 @@ int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) return ierror; } -int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec) +int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort) { // make copy of const matrix @@ -67,7 +75,15 @@ int MathEigen::jacobi3(double const *const *mat, double *eval, double **evec) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v2 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_DECREASING_EVALS); + int ierror = 1; + if (sort == -1) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_DECREASING_EVALS); + else if (sort == 0) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::DO_NOT_SORT); + else if (sort == 1) + ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_INCREASING_EVALS); + + if (ierror) return ierror; // transpose the evec matrix diff --git a/src/math_eigen.h b/src/math_eigen.h index 9f2431e14a..c7a3853767 100644 --- a/src/math_eigen.h +++ b/src/math_eigen.h @@ -22,13 +22,14 @@ namespace MathEigen { * \param mat the 3x3 matrix you wish to diagonalize * \param eval store the eigenvalues here * \param evec store the eigenvectors here... + * \param sort order eigenvalues and -vectors (-1 decreasing (default), 1 increasing, 0 unsorted) * \return 0 if eigenvalue calculation converged, 1 if it failed */ -int jacobi3(double const *const *mat, double *eval, double **evec); +int jacobi3(double const *const *mat, double *eval, double **evec, int sort = -1); /** \overload */ -int jacobi3(double const mat[3][3], double *eval, double evec[3][3]); +int jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort = -1); } // namespace MathEigen From c0abefeacbe931f5b2b359d80833369fbe85fdf4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Apr 2024 23:53:25 -0400 Subject: [PATCH 27/40] update links in manual to jacobi3() docs --- doc/src/Developer_utils.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst index 625ce15202..76e90e17ba 100644 --- a/doc/src/Developer_utils.rst +++ b/doc/src/Developer_utils.rst @@ -635,10 +635,10 @@ Tohoku University (under MIT license) ---------- -.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec) +.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort) :project: progguide -.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) +.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort) :project: progguide --------------------------- From d06b86916ac342ef6b1bd88adb1fd4bdddd7e844 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 3 Apr 2024 11:11:16 -0600 Subject: [PATCH 28/40] more debugging --- src/math_eigen.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/math_eigen.cpp b/src/math_eigen.cpp index 42d95a1288..99c8d38290 100644 --- a/src/math_eigen.cpp +++ b/src/math_eigen.cpp @@ -44,7 +44,7 @@ int MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3]) // create instance of generic Jacobi class and get eigenvalues and -vectors Jacobi_v1 ecalc3(3, M, midx); - int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_INCREASING_EVAL); + int ierror = ecalc3.Diagonalize(mat, eval, evec, Jacobi_v1::SORT_INCREASING_EVALS); // transpose the evec matrix From 4329c4c37f6a12cabaa7d2237242fd3949d4963f Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 3 Apr 2024 11:11:52 -0600 Subject: [PATCH 29/40] changes to rigid and rigid/small --- src/RIGID/fix_rigid.cpp | 57 ++++++++++++++++++++++++++++------- src/RIGID/fix_rigid_small.cpp | 46 +++++++++++++++++++++++++--- 2 files changed, 87 insertions(+), 16 deletions(-) diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 9553d0b9fc..c728c66c4f 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -39,7 +39,7 @@ #include // DEBUG -#define IBODY 42 +#define IBODY 10 using namespace LAMMPS_NS; using namespace FixConst; @@ -901,6 +901,14 @@ void FixRigid::setup(int vflag) ez_space[ibody],inertia[ibody],omega[ibody]); if (ibody == IBODY) printf("SETUP omega: %g %g %g\n", omega[ibody][0],omega[ibody][1],omega[ibody][2]); + printf("IBODY %d quat %g %g %g %g omega %g %g %g idiag %g %g %g ex %g %g %g ey %g %g %g ez %g %g %g\n", + ibody, + quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3], + omega[ibody][0],omega[ibody][1],omega[ibody][2], + inertia[ibody][0],inertia[ibody][1],inertia[ibody][2], + ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2], + ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2], + ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); } set_v(); @@ -951,7 +959,7 @@ void FixRigid::initial_integrate(int vflag) MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody], ez_space[ibody],inertia[ibody],omega[ibody]); - if (update->ntimestep % 1 == 0 && ibody == IBODY) { + if (update->ntimestep % 100 == 0 && ibody == IBODY) { printf("BODY %d: start of step %ld\n",ibody,update->ntimestep); printf(" interia %g %g %g\n", inertia[ibody][0],inertia[ibody][1],inertia[ibody][2]); @@ -972,7 +980,7 @@ void FixRigid::initial_integrate(int vflag) MathExtra::richardson(quat[ibody],angmom[ibody],omega[ibody], inertia[ibody],dtq); - if (update->ntimestep % 1 == 0 && ibody == IBODY) { + if (update->ntimestep % 100 == 0 && ibody == IBODY) { printf(" richardson omega %g %g %g\n", omega[ibody][0],omega[ibody][1],omega[ibody][2]); printf(" richardson quat %15.12g %15.12g %15.12g %15.12g\n", @@ -982,7 +990,7 @@ void FixRigid::initial_integrate(int vflag) MathExtra::q_to_exyz(quat[ibody], ex_space[ibody],ey_space[ibody],ez_space[ibody]); - if (update->ntimestep % 1 == 0 && ibody == IBODY) { + if (update->ntimestep % 100 == 0 && ibody == IBODY) { printf(" exnew %g %g %g\n", ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2]); printf(" eynew %g %g %g\n", @@ -1002,7 +1010,7 @@ void FixRigid::initial_integrate(int vflag) } */ - if (update->ntimestep % 1 == 0 && ibody == IBODY) { + if (update->ntimestep % 100 == 0 && ibody == IBODY) { printf(" quatnew2 %15.12g %15.12g %15.12g %15.12g\n", quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3]); printf(" exnew2 %g %g %g\n", @@ -1090,7 +1098,7 @@ void FixRigid::final_integrate() MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody], ez_space[ibody],inertia[ibody],omega[ibody]); - if (update->ntimestep % 1 == 0 && ibody == IBODY) { + if (update->ntimestep % 100 == 0 && ibody == IBODY) { printf("BODY %d: end of step %ld\n",ibody,update->ntimestep); printf(" interia %g %g %g\n", inertia[ibody][0],inertia[ibody][1],inertia[ibody][2]); @@ -1111,6 +1119,20 @@ void FixRigid::final_integrate() // virial is already setup from initial_integrate set_v(); + + if (update->ntimestep == 500) { + for (ibody = 0; ibody < nbody; ibody++) { + printf("IBODY %d quat %g %g %g %g omega %g %g %g idiag %g %g %g ex %g %g %g ey %g %g %g ez %g %g %g\n", + ibody, + quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3], + omega[ibody][0],omega[ibody][1],omega[ibody][2], + inertia[ibody][0],inertia[ibody][1],inertia[ibody][2], + ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2], + ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2], + ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); + } + } + } /* ---------------------------------------------------------------------- */ @@ -1314,11 +1336,6 @@ void FixRigid::enforce2d() angmom[ibody][1] = 0.0; omega[ibody][0] = 0.0; omega[ibody][1] = 0.0; - if (langflag && langextra) { - langextra[ibody][2] = 0.0; - langextra[ibody][3] = 0.0; - langextra[ibody][4] = 0.0; - } } } @@ -2038,6 +2055,7 @@ void FixRigid::setup_bodies_static() // diagonalize inertia tensor for each body via Jacobi rotations // inertia = 3 eigenvalues = principal moments of inertia + // jacobi3() returns them in ascending order, so that in 2d last evector is z-axis // evectors and exzy_space = 3 evectors = principal axes of rigid body int ierror; @@ -2066,6 +2084,23 @@ void FixRigid::setup_bodies_static() ez_space[ibody][1] = evectors[1][2]; ez_space[ibody][2] = evectors[2][2]; + // for 2d, ensure that evector along z axis is last + // necessary so that quaternion is a simple rotation around +z axis + // or a 180 degree rotation for a -z axis + // otherwise richardson() method for a body with a tiny evalue (near-linear) + // may not preserve the correct z-aligned quat and assocated evectors + // over time due to round-off accumulation + + if (domain->dimension == 2) { + if (fabs(ez_space[ibody][0]) > EPSILON || fabs(ez_space[ibody][1]) > EPSILON) { + printf("AAA EVEC SWAP %d\n",ibody); + std::swap(inertia[ibody][1],inertia[ibody][2]); + std::swap(ey_space[ibody][0],ez_space[ibody][0]); + std::swap(ey_space[ibody][1],ez_space[ibody][1]); + std::swap(ey_space[ibody][2],ez_space[ibody][2]); + } + } + // if any principal moment < scaled EPSILON, set to 0.0 double max; diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 9e185a4de2..b61d264d0a 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -704,6 +704,14 @@ void FixRigidSmall::setup(int vflag) Body *b = &body[ibody]; MathExtra::angmom_to_omega(b->angmom,b->ex_space,b->ey_space, b->ez_space,b->inertia,b->omega); + printf("IBODY %d quat %g %g %g %g omega %g %g %g idiag %g %g %g ex %g %g %g ey %g %g %g ez %g %g %g\n", + ibody, + b->quat[0],b->quat[1],b->quat[2],b->quat[3], + b->omega[0],b->omega[1],b->omega[2], + b->inertia[0],b->inertia[1],b->inertia[2], + b->ex_space[0],b->ex_space[1],b->ex_space[2], + b->ey_space[0],b->ey_space[1],b->ey_space[2], + b->ez_space[0],b->ez_space[1],b->ez_space[2]); } commflag = FINAL; @@ -871,6 +879,21 @@ void FixRigidSmall::final_integrate() // virial is already setup from initial_integrate set_v(); + + if (update->ntimestep == 1000) { + for (int ibody = 0; ibody < nlocal_body; ibody++) { + Body *b = &body[ibody]; + printf("IBODY %d quat %g %g %g %g omega %g %g %g idiag %g %g %g ex %g %g %g ey %g %g %g ez %g %g %g\n", + ibody, + b->quat[0],b->quat[1],b->quat[2],b->quat[3], + b->omega[0],b->omega[1],b->omega[2], + b->inertia[0],b->inertia[1],b->inertia[2], + b->ex_space[0],b->ex_space[1],b->ex_space[2], + b->ey_space[0],b->ey_space[1],b->ey_space[2], + b->ez_space[0],b->ez_space[1],b->ez_space[2]); + } + } + } /* ---------------------------------------------------------------------- */ @@ -1110,11 +1133,6 @@ void FixRigidSmall::enforce2d() b->angmom[1] = 0.0; b->omega[0] = 0.0; b->omega[1] = 0.0; - if (langflag && langextra) { - langextra[ibody][2] = 0.0; - langextra[ibody][3] = 0.0; - langextra[ibody][4] = 0.0; - } } } @@ -2102,6 +2120,7 @@ void FixRigidSmall::setup_bodies_static() // diagonalize inertia tensor for each body via Jacobi rotations // inertia = 3 eigenvalues = principal moments of inertia + // jacobi3() returns them in ascending order, so that in 2d last evector is z-axis // evectors and exzy_space = 3 evectors = principal axes of rigid body int ierror; @@ -2134,6 +2153,22 @@ void FixRigidSmall::setup_bodies_static() ez[1] = evectors[1][2]; ez[2] = evectors[2][2]; + // for 2d, ensure that evector along z axis is last + // necessary so that quaternion is a simple rotation around +z axis + // or a 180 degree rotation for a -z axis + // otherwise richardson() method for a body with a tiny evalue (near-linear) + // may not preserve the correct z-aligned quat and assocated evectors + // over time due to round-off accumulation + + if (domain->dimension == 2) { + if (fabs(ez[0]) > EPSILON || fabs(ez[1]) > EPSILON) { + std::swap(inertia[1],inertia[2]); + std::swap(ey[0],ez[0]); + std::swap(ey[1],ez[1]); + std::swap(ey[2],ez[2]); + } + } + // if any principal moment < scaled EPSILON, set to 0.0 double max; @@ -2156,6 +2191,7 @@ void FixRigidSmall::setup_bodies_static() // convert geometric center position to principal axis coordinates // xcm is wrapped, but xgc is not initially + xcm = body[ibody].xcm; xgc = body[ibody].xgc; double delta[3]; From 39d12e48d6c81fb84500ac99f40fcd0dd7b85063 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 3 Apr 2024 15:04:39 -0400 Subject: [PATCH 30/40] must always return nfaces=0 for less than 3 vertices --- src/BODY/body_rounded_polyhedron.cpp | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 991f52cac5..6aa15b740b 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -99,10 +99,9 @@ int BodyRoundedPolyhedron::nedges(AtomVecBody::Bonus *bonus) { int nvertices = bonus->ivalue[0]; int nedges = bonus->ivalue[1]; - //int nfaces = bonus->ivalue[2]; if (nvertices == 1) return 0; else if (nvertices == 2) return 1; - return nedges; //(nvertices+nfaces-2); // Euler formula: V-E+F=2 + return nedges; } /* ---------------------------------------------------------------------- */ @@ -116,6 +115,9 @@ double *BodyRoundedPolyhedron::edges(AtomVecBody::Bonus *bonus) int BodyRoundedPolyhedron::nfaces(AtomVecBody::Bonus *bonus) { + int nvertices = bonus->ivalue[0]; + if (nvertices < 3) return 0; + return bonus->ivalue[2]; } From ecd8fe71a1890aa4fac05f3cdcefa5a190cc046e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 3 Apr 2024 15:05:09 -0400 Subject: [PATCH 31/40] cosmetic --- src/BODY/pair_body_rounded_polygon.cpp | 12 ++++-------- src/BODY/pair_body_rounded_polyhedron.cpp | 21 +++++++-------------- 2 files changed, 11 insertions(+), 22 deletions(-) diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 432f1d5c9c..14f4f27582 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -415,17 +415,14 @@ void PairBodyRoundedPolygon::init_style() if (!avec) error->all(FLERR,"Pair body/rounded/polygon requires atom style body"); if (strcmp(avec->bptr->style,"rounded/polygon") != 0) - error->all(FLERR,"Pair body/rounded/polygon requires " - "body style rounded/polygon"); + error->all(FLERR,"Pair body/rounded/polygon requires body style rounded/polygon"); bptr = dynamic_cast(avec->bptr); if (force->newton_pair == 0) - error->all(FLERR,"Pair style body/rounded/polygon requires " - "newton pair on"); + error->all(FLERR,"Pair style body/rounded/polygon requires newton pair on"); if (comm->ghost_velocity == 0) - error->all(FLERR,"Pair body/rounded/polygon requires " - "ghost atoms store velocity"); + error->all(FLERR,"Pair body/rounded/polygon requires ghost atoms store velocity"); neighbor->add_request(this); @@ -570,8 +567,7 @@ void PairBodyRoundedPolygon::body2space(int i) } if ((body_num_edges > 0) && (edge_ends == nullptr)) - error->one(FLERR,"Inconsistent edge data for body of atom {}", - atom->tag[i]); + error->one(FLERR,"Inconsistent edge data for body of atom {}", atom->tag[i]); for (int m = 0; m < body_num_edges; m++) { edge[nedge][0] = static_cast(edge_ends[2*m+0]); diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 82660df1e0..e82b1bcaef 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -222,8 +222,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag) // sphere-sphere interaction if (npi == 1 && npj == 1) { - sphere_against_sphere(i, j, itype, jtype, delx, dely, delz, - rsq, v, f, evflag); + sphere_against_sphere(i, j, itype, jtype, delx, dely, delz, rsq, v, f, evflag); continue; } @@ -391,20 +390,16 @@ void PairBodyRoundedPolyhedron::coeff(int narg, char **arg) void PairBodyRoundedPolyhedron::init_style() { avec = dynamic_cast(atom->style_match("body")); - if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires " - "atom style body"); + if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires atom style body"); if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0) - error->all(FLERR,"Pair body/rounded/polyhedron requires " - "body style rounded/polyhedron"); + error->all(FLERR,"Pair body/rounded/polyhedron requires body style rounded/polyhedron"); bptr = dynamic_cast(avec->bptr); if (force->newton_pair == 0) - error->all(FLERR,"Pair style body/rounded/polyhedron requires " - "newton pair on"); + error->all(FLERR,"Pair style body/rounded/polyhedron requires newton pair on"); if (comm->ghost_velocity == 0) - error->all(FLERR,"Pair body/rounded/polyhedron requires " - "ghost atoms store velocity"); + error->all(FLERR,"Pair body/rounded/polyhedron requires ghost atoms store velocity"); neighbor->add_request(this); @@ -558,8 +553,7 @@ void PairBodyRoundedPolyhedron::body2space(int i) } if ((body_num_edges > 0) && (edge_ends == nullptr)) - error->one(FLERR,"Inconsistent edge data for body of atom {}", - atom->tag[i]); + error->one(FLERR,"Inconsistent edge data for body of atom {}", atom->tag[i]); for (int m = 0; m < body_num_edges; m++) { edge[nedge][0] = static_cast(edge_ends[2*m+0]); @@ -585,8 +579,7 @@ void PairBodyRoundedPolyhedron::body2space(int i) } if ((body_num_faces > 0) && (face_pts == nullptr)) - error->one(FLERR,"Inconsistent face data for body of atom {}", - atom->tag[i]); + error->one(FLERR,"Inconsistent face data for body of atom {}", atom->tag[i]); for (int m = 0; m < body_num_faces; m++) { for (int k = 0; k < MAX_FACE_SIZE; k++) From 4c9924984db90d47adb49fa76a64eb79d2e8efea Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 3 Apr 2024 15:58:24 -0400 Subject: [PATCH 32/40] modify access to fixes --- src/BODY/pair_body_rounded_polygon.cpp | 25 ++++++++++------------- src/BODY/pair_body_rounded_polyhedron.cpp | 24 +++++++++------------- 2 files changed, 21 insertions(+), 28 deletions(-) diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 14f4f27582..2293f56a98 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -460,27 +460,24 @@ void PairBodyRoundedPolygon::init_style() for (i = 1; i <= ntypes; i++) maxerad[i] = merad[i] = 0; - int ipour; - for (ipour = 0; ipour < modify->nfix; ipour++) - if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; - if (ipour == modify->nfix) ipour = -1; + Fix *fixpour = nullptr; + auto pours = modify->get_fix_by_style("^pour"); + if (pours.size() > 0) fixpour = pours[0]; + + Fix *fixdep = nullptr; + auto deps = modify->get_fix_by_style("^deposit"); + if (deps.size() > 0) fixdep = deps[0]; - int idep; - for (idep = 0; idep < modify->nfix; idep++) - if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; - if (idep == modify->nfix) idep = -1; for (i = 1; i <= ntypes; i++) { merad[i] = 0.0; - if (ipour >= 0) { + if (fixpour) { itype = i; - merad[i] = - *((double *) modify->fix[ipour]->extract("radius",itype)); + merad[i] = *((double *) fixpour->extract("radius",itype)); } - if (idep >= 0) { + if (fixdep) { itype = i; - merad[i] = - *((double *) modify->fix[idep]->extract("radius",itype)); + merad[i] = *((double *) fixdep->extract("radius",itype)); } } diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index e82b1bcaef..ed83dc49e2 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -441,27 +441,23 @@ void PairBodyRoundedPolyhedron::init_style() for (i = 1; i <= ntypes; i++) maxerad[i] = merad[i] = 0; - int ipour; - for (ipour = 0; ipour < modify->nfix; ipour++) - if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; - if (ipour == modify->nfix) ipour = -1; + Fix *fixpour = nullptr; + auto pours = modify->get_fix_by_style("^pour"); + if (pours.size() > 0) fixpour = pours[0]; - int idep; - for (idep = 0; idep < modify->nfix; idep++) - if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; - if (idep == modify->nfix) idep = -1; + Fix *fixdep = nullptr; + auto deps = modify->get_fix_by_style("^deposit"); + if (deps.size() > 0) fixdep = deps[0]; for (i = 1; i <= ntypes; i++) { merad[i] = 0.0; - if (ipour >= 0) { + if (fixpour) { itype = i; - merad[i] = - *((double *) modify->fix[ipour]->extract("radius",itype)); + merad[i] = *((double *) fixpour->extract("radius",itype)); } - if (idep >= 0) { + if (fixdep) { itype = i; - merad[i] = - *((double *) modify->fix[idep]->extract("radius",itype)); + merad[i] = *((double *) fixdep->extract("radius",itype)); } } From f637299ac5153033e3bdc320ab05e22d08823bb6 Mon Sep 17 00:00:00 2001 From: maitanemuba Date: Thu, 4 Apr 2024 18:18:10 +0200 Subject: [PATCH 33/40] Added symmetrization of cutoff in init_one() and fixed a print --- src/ASPHERE/pair_ylz.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ASPHERE/pair_ylz.cpp b/src/ASPHERE/pair_ylz.cpp index a678712619..833dc8e3e4 100644 --- a/src/ASPHERE/pair_ylz.cpp +++ b/src/ASPHERE/pair_ylz.cpp @@ -300,6 +300,7 @@ double PairYLZ::init_one(int i, int j) zeta[j][i] = zeta[i][j]; mu[j][i] = mu[i][j]; beta[j][i] = beta[i][j]; + cut[j][i] = cut[i][j]; return cut[i][j]; } @@ -409,7 +410,7 @@ void PairYLZ::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) - fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][i], sigma[i][i], cut[i][j], + fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][j], sigma[i][j], cut[i][j], zeta[i][j], mu[i][j], beta[i][j]); } From 65cdc76c992887c72115c558d155de986d48c897 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 4 Apr 2024 13:07:35 -0600 Subject: [PATCH 34/40] final changes for 2d rigid bodies with jacobi --- .../micelle/log.29Mar2019.micelle-rigid.g++.1 | 260 ----------------- .../micelle/log.29Mar2019.micelle-rigid.g++.4 | 260 ----------------- .../micelle/log.4Apr2024.micelle-rigid.g++.1 | 271 +++++++++++++++++ .../micelle/log.4Apr2024.micelle-rigid.g++.4 | 272 ++++++++++++++++++ src/RIGID/fix_rigid.cpp | 107 +------ src/RIGID/fix_rigid_small.cpp | 30 +- 6 files changed, 551 insertions(+), 649 deletions(-) delete mode 100644 examples/micelle/log.29Mar2019.micelle-rigid.g++.1 delete mode 100644 examples/micelle/log.29Mar2019.micelle-rigid.g++.4 create mode 100644 examples/micelle/log.4Apr2024.micelle-rigid.g++.1 create mode 100644 examples/micelle/log.4Apr2024.micelle-rigid.g++.4 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 deleted file mode 100644 index f1001e6cea..0000000000 --- a/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 +++ /dev/null @@ -1,260 +0,0 @@ -LAMMPS (29 Mar 2019) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000473022 secs - read_data CPU = 0.0024147 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.00022316 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 - 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 - 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 - 200 0.45 1.01454 0.10663502 1.5708 4.7598476 - 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 - 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 - 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 - 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 - 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 - 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 -Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms - -Performance: 2093802.885 tau/day, 4846.766 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21 -Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11 -Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64 -Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86 -Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17 -Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37 -Other | | 0.002726 | | | 2.64 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 197 ave 197 max 197 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3094 ave 3094 max 3094 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3094 -Ave neighs/atom = 2.57833 -Ave special neighs/atom = 0.5 -Neighbor list builds = 52 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 - 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 - 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 - 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 - 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 - 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 - 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 - 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 - 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 - 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 -Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms - -Performance: 1208012.705 tau/day, 2796.326 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17 -Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38 -Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92 -Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45 -Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10 -Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34 -Other | | 0.00293 | | | 1.64 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 416 ave 416 max 416 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8769 ave 8769 max 8769 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8769 -Ave neighs/atom = 7.3075 -Ave special neighs/atom = 0.5 -Neighbor list builds = 47 -Dangerous builds = 2 -unfix 2 -unfix 4 -unfix 5 -fix 5 solute rigid/small molecule - create bodies CPU = 0.00015378 secs -150 rigid bodies with 450 atoms - 1.30435 = max distance from body owner to body atom -fix 4 all enforce2d -run 500 -Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes -Step Temp E_pair E_mol TotEng Press - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 - 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 - 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 - 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 - 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 - 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 - 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 - 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 - 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 - 950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332 - 1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141 -Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms - -Performance: 1297278.008 tau/day, 3002.958 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51 -Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56 -Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83 -Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44 -Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11 -Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66 -Other | | 0.003141 | | | 1.89 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 415 ave 415 max 415 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8743 ave 8743 max 8743 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8743 -Ave neighs/atom = 7.28583 -Ave special neighs/atom = 0.5 -Neighbor list builds = 40 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 deleted file mode 100644 index e65f67a527..0000000000 --- a/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 +++ /dev/null @@ -1,260 +0,0 @@ -LAMMPS (29 Mar 2019) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000422001 secs - read_data CPU = 0.00473404 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000183344 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 - 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 - 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 - 200 0.45 1.01454 0.10663502 1.5708 4.7598476 - 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 - 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 - 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 - 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 - 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 - 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 -Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms - -Performance: 5066547.720 tau/day, 11728.120 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16 -Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95 -Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95 -Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78 -Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62 -Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28 -Other | | 0.002669 | | | 6.26 - -Nlocal: 300 ave 304 max 292 min -Histogram: 1 0 0 0 0 0 0 0 2 1 -Nghost: 103.5 ave 108 max 98 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Neighs: 773.5 ave 792 max 735 min -Histogram: 1 0 0 0 0 0 0 0 2 1 - -Total # of neighbors = 3094 -Ave neighs/atom = 2.57833 -Ave special neighs/atom = 0.5 -Neighbor list builds = 52 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 50 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 500 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 - 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 - 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 - 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 - 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 - 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 - 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 - 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 - 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 - 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 -Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms - -Performance: 2434100.210 tau/day, 5634.491 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74 -Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30 -Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32 -Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30 -Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29 -Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73 -Other | | 0.002938 | | | 3.31 - -Nlocal: 300 ave 309 max 291 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 218.75 ave 223 max 216 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Neighs: 2192.25 ave 2251 max 2113 min -Histogram: 1 0 0 1 0 0 0 0 0 2 - -Total # of neighbors = 8769 -Ave neighs/atom = 7.3075 -Ave special neighs/atom = 0.5 -Neighbor list builds = 47 -Dangerous builds = 2 -unfix 2 -unfix 4 -unfix 5 -fix 5 solute rigid/small molecule - create bodies CPU = 7.70092e-05 secs -150 rigid bodies with 450 atoms - 1.30435 = max distance from body owner to body atom -fix 4 all enforce2d -run 500 -Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes -Step Temp E_pair E_mol TotEng Press - 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 - 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 - 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 - 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 - 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 - 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 - 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 - 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 - 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 - 950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332 - 1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141 -Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms - -Performance: 3671840.233 tau/day, 8499.630 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47 -Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93 -Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98 -Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29 -Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42 -Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11 -Other | | 0.00224 | | | 3.81 - -Nlocal: 300 ave 303 max 295 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 219 ave 224 max 215 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -Neighs: 2185.75 ave 2244 max 2143 min -Histogram: 1 1 0 0 0 1 0 0 0 1 - -Total # of neighbors = 8743 -Ave neighs/atom = 7.28583 -Ave special neighs/atom = 0.5 -Neighbor list builds = 40 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/micelle/log.4Apr2024.micelle-rigid.g++.1 b/examples/micelle/log.4Apr2024.micelle-rigid.g++.1 new file mode 100644 index 0000000000..d3cb98940d --- /dev/null +++ b/examples/micelle/log.4Apr2024.micelle-rigid.g++.1 @@ -0,0 +1,271 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified) +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +Reading data file ... + orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.005 seconds +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) +Per MPI rank memory allocation (min/avg/max) = 4.148 | 4.148 | 4.148 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.0365221 on 1 procs for 500 steps with 1200 atoms + +Performance: 5914221.123 tau/day, 13690.327 timesteps/s, 16.428 Matom-step/s +89.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022939 | 0.022939 | 0.022939 | 0.0 | 62.81 +Bond | 0.00073851 | 0.00073851 | 0.00073851 | 0.0 | 2.02 +Neigh | 0.0078339 | 0.0078339 | 0.0078339 | 0.0 | 21.45 +Comm | 0.00072134 | 0.00072134 | 0.00072134 | 0.0 | 1.98 +Output | 7.1419e-05 | 7.1419e-05 | 7.1419e-05 | 0.0 | 0.20 +Modify | 0.0034868 | 0.0034868 | 0.0034868 | 0.0 | 9.55 +Other | | 0.0007314 | | | 2.00 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 197 ave 197 max 197 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3094 ave 3094 max 3094 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.5783333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 + 150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109 + 100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772 + 150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796 + 200 0.49410558 -1.7945459 0.13695201 -1.2565449 4.0469262 + 250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445 + 300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851 + 350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818 + 400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566 + 450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611 + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738 +Loop time of 0.0650638 on 1 procs for 500 steps with 1200 atoms + +Performance: 3319817.322 tau/day, 7684.762 timesteps/s, 9.222 Matom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.027565 | 0.027565 | 0.027565 | 0.0 | 42.37 +Bond | 0.0007043 | 0.0007043 | 0.0007043 | 0.0 | 1.08 +Neigh | 0.012724 | 0.012724 | 0.012724 | 0.0 | 19.56 +Comm | 0.00091442 | 0.00091442 | 0.00091442 | 0.0 | 1.41 +Output | 6.004e-05 | 6.004e-05 | 6.004e-05 | 0.0 | 0.09 +Modify | 0.022329 | 0.022329 | 0.022329 | 0.0 | 34.32 +Other | | 0.0007666 | | | 1.18 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 411 ave 411 max 411 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8759 ave 8759 max 8759 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8759 +Ave neighs/atom = 7.2991667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 46 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 0.000 seconds + 150 rigid bodies with 450 atoms + 1.3043524 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 9.306 | 9.306 | 9.306 Mbytes + Step Temp E_pair E_mol TotEng Press + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752 + 550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662 + 600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379 + 650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789 + 700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082 + 750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147 + 800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481 + 850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703 + 900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388 + 950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786 + 1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630988 +Loop time of 0.0592806 on 1 procs for 500 steps with 1200 atoms + +Performance: 3643690.276 tau/day, 8434.468 timesteps/s, 10.121 Matom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.026866 | 0.026866 | 0.026866 | 0.0 | 45.32 +Bond | 0.00071863 | 0.00071863 | 0.00071863 | 0.0 | 1.21 +Neigh | 0.010927 | 0.010927 | 0.010927 | 0.0 | 18.43 +Comm | 0.00084187 | 0.00084187 | 0.00084187 | 0.0 | 1.42 +Output | 6.8106e-05 | 6.8106e-05 | 6.8106e-05 | 0.0 | 0.11 +Modify | 0.019075 | 0.019075 | 0.019075 | 0.0 | 32.18 +Other | | 0.000783 | | | 1.32 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 417 ave 417 max 417 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8654 ave 8654 max 8654 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8654 +Ave neighs/atom = 7.2116667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 39 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.4Apr2024.micelle-rigid.g++.4 b/examples/micelle/log.4Apr2024.micelle-rigid.g++.4 new file mode 100644 index 0000000000..ce15cfec21 --- /dev/null +++ b/examples/micelle/log.4Apr2024.micelle-rigid.g++.4 @@ -0,0 +1,272 @@ +LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +Reading data file ... + orthogonal box = (0 0 -0.1) to (35.85686 35.85686 0.1) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730) +Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.0138659 on 4 procs for 500 steps with 1200 atoms + +Performance: 15577811.312 tau/day, 36059.748 timesteps/s, 43.272 Matom-step/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0053896 | 0.0057144 | 0.0060899 | 0.4 | 41.21 +Bond | 0.00020074 | 0.00021422 | 0.00022291 | 0.0 | 1.54 +Neigh | 0.0025301 | 0.0025401 | 0.0025501 | 0.0 | 18.32 +Comm | 0.0031194 | 0.0035074 | 0.0038196 | 0.4 | 25.30 +Output | 6.4137e-05 | 6.7743e-05 | 7.7909e-05 | 0.0 | 0.49 +Modify | 0.0013391 | 0.0013582 | 0.0013972 | 0.1 | 9.80 +Other | | 0.0004638 | | | 3.34 + +Nlocal: 300 ave 304 max 292 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Nghost: 103.5 ave 108 max 98 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 773.5 ave 792 max 735 min +Histogram: 1 0 0 0 0 0 0 0 2 1 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.5783333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 + 150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 5 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.375 | 5.375 | 5.375 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109 + 100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772 + 150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796 + 200 0.49410558 -1.7945459 0.13695201 -1.2565449 4.0469262 + 250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445 + 300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851 + 350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818 + 400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566 + 450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611 + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738 +Loop time of 0.0381773 on 4 procs for 500 steps with 1200 atoms + +Performance: 5657810.772 tau/day, 13096.784 timesteps/s, 15.716 Matom-step/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0059651 | 0.0062314 | 0.0066404 | 0.3 | 16.32 +Bond | 0.00021057 | 0.00022477 | 0.0002333 | 0.0 | 0.59 +Neigh | 0.0041424 | 0.0041487 | 0.0041512 | 0.0 | 10.87 +Comm | 0.004264 | 0.0047244 | 0.0050297 | 0.4 | 12.37 +Output | 8.2396e-05 | 8.6559e-05 | 9.6749e-05 | 0.0 | 0.23 +Modify | 0.021833 | 0.021946 | 0.022094 | 0.1 | 57.48 +Other | | 0.0008157 | | | 2.14 + +Nlocal: 300 ave 303 max 296 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 216.25 ave 219 max 214 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 2189.75 ave 2205 max 2173 min +Histogram: 1 0 0 0 1 0 1 0 0 1 + +Total # of neighbors = 8759 +Ave neighs/atom = 7.2991667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 46 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 0.000 seconds + 150 rigid bodies with 450 atoms + 1.3043524 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 9.233 | 9.233 | 9.234 Mbytes + Step Temp E_pair E_mol TotEng Press + 500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752 + 550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662 + 600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379 + 650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789 + 700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082 + 750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147 + 800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481 + 850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703 + 900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388 + 950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786 + 1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987 +Loop time of 0.0236819 on 4 procs for 500 steps with 1200 atoms + +Performance: 9120883.727 tau/day, 21113.157 timesteps/s, 25.336 Matom-step/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0058656 | 0.0059718 | 0.0061355 | 0.1 | 25.22 +Bond | 0.0002083 | 0.00022447 | 0.00023485 | 0.0 | 0.95 +Neigh | 0.0035477 | 0.0035644 | 0.0035824 | 0.0 | 15.05 +Comm | 0.0041037 | 0.0042227 | 0.0043024 | 0.1 | 17.83 +Output | 7.4355e-05 | 7.8273e-05 | 8.7777e-05 | 0.0 | 0.33 +Modify | 0.008976 | 0.0090549 | 0.0091663 | 0.1 | 38.24 +Other | | 0.0005654 | | | 2.39 + +Nlocal: 300 ave 306 max 295 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Nghost: 221 ave 226 max 217 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 2163.5 ave 2271 max 2100 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 8654 +Ave neighs/atom = 7.2116667 +Ave special neighs/atom = 0.5 +Neighbor list builds = 39 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index c728c66c4f..6f8a9a2b7d 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -896,20 +896,9 @@ void FixRigid::setup(int vflag) // set velocities from angmom & omega - for (ibody = 0; ibody < nbody; ibody++) { + for (ibody = 0; ibody < nbody; ibody++) MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody], ez_space[ibody],inertia[ibody],omega[ibody]); - if (ibody == IBODY) printf("SETUP omega: %g %g %g\n", - omega[ibody][0],omega[ibody][1],omega[ibody][2]); - printf("IBODY %d quat %g %g %g %g omega %g %g %g idiag %g %g %g ex %g %g %g ey %g %g %g ez %g %g %g\n", - ibody, - quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3], - omega[ibody][0],omega[ibody][1],omega[ibody][2], - inertia[ibody][0],inertia[ibody][1],inertia[ibody][2], - ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2], - ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2], - ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); - } set_v(); @@ -958,68 +947,10 @@ void FixRigid::initial_integrate(int vflag) MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody], ez_space[ibody],inertia[ibody],omega[ibody]); - - if (update->ntimestep % 100 == 0 && ibody == IBODY) { - printf("BODY %d: start of step %ld\n",ibody,update->ntimestep); - printf(" interia %g %g %g\n", - inertia[ibody][0],inertia[ibody][1],inertia[ibody][2]); - printf(" angmom %g %g %g\n", - angmom[ibody][0],angmom[ibody][1],angmom[ibody][2]); - printf(" omega %g %g %g\n", - omega[ibody][0],omega[ibody][1],omega[ibody][2]); - printf(" ex %g %g %g\n", - ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2]); - printf(" ey %g %g %g\n", - ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2]); - printf(" ez %g %g %g\n", - ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); - printf(" quat %15.12g %15.12g %15.12g %15.12g\n", - quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3]); - } - MathExtra::richardson(quat[ibody],angmom[ibody],omega[ibody], inertia[ibody],dtq); - - if (update->ntimestep % 100 == 0 && ibody == IBODY) { - printf(" richardson omega %g %g %g\n", - omega[ibody][0],omega[ibody][1],omega[ibody][2]); - printf(" richardson quat %15.12g %15.12g %15.12g %15.12g\n", - quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3]); - } - MathExtra::q_to_exyz(quat[ibody], ex_space[ibody],ey_space[ibody],ez_space[ibody]); - - if (update->ntimestep % 100 == 0 && ibody == IBODY) { - printf(" exnew %g %g %g\n", - ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2]); - printf(" eynew %g %g %g\n", - ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2]); - printf(" eznew %g %g %g\n", - ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); - } - - /* - if (ibody == 42) { - ex_space[ibody][0] = ex_space[ibody][1] = 0.0; - ex_space[ibody][2] = 1.0; - ey_space[ibody][2] = ez_space[ibody][2] = 0.0; - MathExtra::norm3(ey_space[ibody]); - MathExtra::norm3(ez_space[ibody]); - MathExtra::exyz_to_q(ex_space[ibody],ey_space[ibody],ez_space[ibody],quat[ibody]); - } - */ - - if (update->ntimestep % 100 == 0 && ibody == IBODY) { - printf(" quatnew2 %15.12g %15.12g %15.12g %15.12g\n", - quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3]); - printf(" exnew2 %g %g %g\n", - ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2]); - printf(" eynew2 %g %g %g\n", - ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2]); - printf(" eznew2 %g %g %g\n", - ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); - } } // virial setup before call to set_xv @@ -1097,42 +1028,12 @@ void FixRigid::final_integrate() MathExtra::angmom_to_omega(angmom[ibody],ex_space[ibody],ey_space[ibody], ez_space[ibody],inertia[ibody],omega[ibody]); - - if (update->ntimestep % 100 == 0 && ibody == IBODY) { - printf("BODY %d: end of step %ld\n",ibody,update->ntimestep); - printf(" interia %g %g %g\n", - inertia[ibody][0],inertia[ibody][1],inertia[ibody][2]); - printf(" angmom %g %g %g\n", - angmom[ibody][0],angmom[ibody][1],angmom[ibody][2]); - printf(" omega %g %g %g\n", - omega[ibody][0],omega[ibody][1],omega[ibody][2]); - printf(" ex %g %g %g\n", - ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2]); - printf(" ey %g %g %g\n", - ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2]); - printf(" ez %g %g %g\n", - ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); - } } // set velocity/rotation of atoms in rigid bodies // virial is already setup from initial_integrate set_v(); - - if (update->ntimestep == 500) { - for (ibody = 0; ibody < nbody; ibody++) { - printf("IBODY %d quat %g %g %g %g omega %g %g %g idiag %g %g %g ex %g %g %g ey %g %g %g ez %g %g %g\n", - ibody, - quat[ibody][0],quat[ibody][1],quat[ibody][2],quat[ibody][3], - omega[ibody][0],omega[ibody][1],omega[ibody][2], - inertia[ibody][0],inertia[ibody][1],inertia[ibody][2], - ex_space[ibody][0],ex_space[ibody][1],ex_space[ibody][2], - ey_space[ibody][0],ey_space[ibody][1],ey_space[ibody][2], - ez_space[ibody][0],ez_space[ibody][1],ez_space[ibody][2]); - } - } - } /* ---------------------------------------------------------------------- */ @@ -2055,7 +1956,8 @@ void FixRigid::setup_bodies_static() // diagonalize inertia tensor for each body via Jacobi rotations // inertia = 3 eigenvalues = principal moments of inertia - // jacobi3() returns them in ascending order, so that in 2d last evector is z-axis + // request that jacobi3() return them in ascending order, + /// so that in 2d last evector is z-axis // evectors and exzy_space = 3 evectors = principal axes of rigid body int ierror; @@ -2070,7 +1972,7 @@ void FixRigid::setup_bodies_static() tensor[0][2] = tensor[2][0] = all[ibody][4]; tensor[0][1] = tensor[1][0] = all[ibody][5]; - ierror = MathEigen::jacobi3(tensor,inertia[ibody],evectors); + ierror = MathEigen::jacobi3(tensor,inertia[ibody],evectors,1); if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for rigid body"); @@ -2093,7 +1995,6 @@ void FixRigid::setup_bodies_static() if (domain->dimension == 2) { if (fabs(ez_space[ibody][0]) > EPSILON || fabs(ez_space[ibody][1]) > EPSILON) { - printf("AAA EVEC SWAP %d\n",ibody); std::swap(inertia[ibody][1],inertia[ibody][2]); std::swap(ey_space[ibody][0],ez_space[ibody][0]); std::swap(ey_space[ibody][1],ez_space[ibody][1]); diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index b61d264d0a..4be8ce5571 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -704,16 +704,8 @@ void FixRigidSmall::setup(int vflag) Body *b = &body[ibody]; MathExtra::angmom_to_omega(b->angmom,b->ex_space,b->ey_space, b->ez_space,b->inertia,b->omega); - printf("IBODY %d quat %g %g %g %g omega %g %g %g idiag %g %g %g ex %g %g %g ey %g %g %g ez %g %g %g\n", - ibody, - b->quat[0],b->quat[1],b->quat[2],b->quat[3], - b->omega[0],b->omega[1],b->omega[2], - b->inertia[0],b->inertia[1],b->inertia[2], - b->ex_space[0],b->ex_space[1],b->ex_space[2], - b->ey_space[0],b->ey_space[1],b->ey_space[2], - b->ez_space[0],b->ez_space[1],b->ez_space[2]); } - + commflag = FINAL; comm->forward_comm(this,10); @@ -879,21 +871,6 @@ void FixRigidSmall::final_integrate() // virial is already setup from initial_integrate set_v(); - - if (update->ntimestep == 1000) { - for (int ibody = 0; ibody < nlocal_body; ibody++) { - Body *b = &body[ibody]; - printf("IBODY %d quat %g %g %g %g omega %g %g %g idiag %g %g %g ex %g %g %g ey %g %g %g ez %g %g %g\n", - ibody, - b->quat[0],b->quat[1],b->quat[2],b->quat[3], - b->omega[0],b->omega[1],b->omega[2], - b->inertia[0],b->inertia[1],b->inertia[2], - b->ex_space[0],b->ex_space[1],b->ex_space[2], - b->ey_space[0],b->ey_space[1],b->ey_space[2], - b->ez_space[0],b->ez_space[1],b->ez_space[2]); - } - } - } /* ---------------------------------------------------------------------- */ @@ -2120,7 +2097,8 @@ void FixRigidSmall::setup_bodies_static() // diagonalize inertia tensor for each body via Jacobi rotations // inertia = 3 eigenvalues = principal moments of inertia - // jacobi3() returns them in ascending order, so that in 2d last evector is z-axis + // request that jacobi3() returns them in ascending order, + // so that in 2d last evector is z-axis // evectors and exzy_space = 3 evectors = principal axes of rigid body int ierror; @@ -2137,7 +2115,7 @@ void FixRigidSmall::setup_bodies_static() tensor[0][1] = tensor[1][0] = itensor[ibody][5]; inertia = body[ibody].inertia; - ierror = MathEigen::jacobi3(tensor,inertia,evectors); + ierror = MathEigen::jacobi3(tensor,inertia,evectors,1); if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for rigid body"); ex = body[ibody].ex_space; From 03711c13da83ca847001f1b84335d332bd948071 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 4 Apr 2024 13:11:59 -0600 Subject: [PATCH 35/40] clean up --- src/RIGID/fix_rigid.cpp | 5 +---- src/RIGID/fix_rigid_small.cpp | 4 ++-- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 6f8a9a2b7d..8703fb4d37 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -38,9 +38,6 @@ #include #include -// DEBUG -#define IBODY 10 - using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; @@ -2001,7 +1998,7 @@ void FixRigid::setup_bodies_static() std::swap(ey_space[ibody][2],ez_space[ibody][2]); } } - + // if any principal moment < scaled EPSILON, set to 0.0 double max; diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 4be8ce5571..2fc1553bf1 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -705,7 +705,7 @@ void FixRigidSmall::setup(int vflag) MathExtra::angmom_to_omega(b->angmom,b->ex_space,b->ey_space, b->ez_space,b->inertia,b->omega); } - + commflag = FINAL; comm->forward_comm(this,10); @@ -2169,7 +2169,7 @@ void FixRigidSmall::setup_bodies_static() // convert geometric center position to principal axis coordinates // xcm is wrapped, but xgc is not initially - + xcm = body[ibody].xcm; xgc = body[ibody].xgc; double delta[3]; From 2c26586b1af88adee7030768a705d5bfd55a0638 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 4 Apr 2024 13:50:43 -0600 Subject: [PATCH 36/40] clean up --- src/variable.cpp | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/src/variable.cpp b/src/variable.cpp index 8e35bd8e18..c99e4a4761 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -1544,7 +1544,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) // wait to check index1 until after compute invocation // to allow for computes with size_vector_variable == 1 - + if (index1 > compute->size_vector) print_var_error(FLERR,"Variable formula compute vector is accessed out-of-range",ivar,0); @@ -1572,7 +1572,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (index1 > compute->size_array_rows) print_var_error(FLERR,"Variable formula compute array is accessed out-of-range",ivar,0); - + value1 = compute->array[index1-1][index2-1]; argstack[nargstack++] = value1; @@ -1645,7 +1645,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) // wait to check vector size until after compute invocation // to allow for computes with size_vector_variable == 1 - + if (compute->size_vector == 0) print_var_error(FLERR,"Variable formula compute vector is zero length",ivar); @@ -1671,14 +1671,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) compute->compute_array(); compute->invoked_flag |= Compute::INVOKED_ARRAY; } - // wait until after compute invocation to check size_array_rows - // b/c may be zero until after initial invocation - if (compute->size_array_rows == 0) - print_var_error(FLERR,"Variable formula compute array is zero length",ivar); // wait to check row count until after compute invocation // to allow for computes with size_array_rows_variable == 1 - + if (compute->size_array_rows == 0) print_var_error(FLERR,"Variable formula compute array has zero rows",ivar); From 66d042a0ee3e78b43d933a616ccd020d42a14701 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 4 Apr 2024 14:11:13 -0600 Subject: [PATCH 37/40] make checks for exceeding length of variable-length vectors more consistent --- src/EXTRA-FIX/fix_ave_correlate_long.cpp | 4 +++- src/fix_ave_correlate.cpp | 6 ++++-- src/fix_ave_histo.cpp | 6 ++++-- src/fix_ave_time.cpp | 5 +++-- src/thermo.cpp | 10 ++++++++-- 5 files changed, 22 insertions(+), 9 deletions(-) diff --git a/src/EXTRA-FIX/fix_ave_correlate_long.cpp b/src/EXTRA-FIX/fix_ave_correlate_long.cpp index fc1760b353..7c80365c57 100644 --- a/src/EXTRA-FIX/fix_ave_correlate_long.cpp +++ b/src/EXTRA-FIX/fix_ave_correlate_long.cpp @@ -454,6 +454,8 @@ void FixAveCorrelateLong::end_of_step() scalar = val.val.f->compute_vector(val.argindex-1); // evaluate equal-style or vector-style variable + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori } else if (val.which == ArgInfo::VARIABLE) { if (val.argindex == 0) @@ -462,7 +464,7 @@ void FixAveCorrelateLong::end_of_step() double *varvec; int nvec = input->variable->compute_vector(val.val.v,&varvec); int index = val.argindex; - if (nvec < index) scalar = 0.0; + if (index > nvec) scalar = 0.0; else scalar = varvec[index-1]; } } diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 4b9e316b9d..576ddb3c94 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -414,7 +414,9 @@ void FixAveCorrelate::end_of_step() scalar = val.val.f->compute_vector(val.argindex-1); // evaluate equal-style or vector-style variable - + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori + } else if (val.which == ArgInfo::VARIABLE) { if (val.argindex == 0) scalar = input->variable->compute_equal(val.val.v); @@ -422,7 +424,7 @@ void FixAveCorrelate::end_of_step() double *varvec; int nvec = input->variable->compute_vector(val.val.v,&varvec); int index = val.argindex; - if (nvec < index) scalar = 0.0; + if (index > nvec) scalar = 0.0; else scalar = varvec[index-1]; } } diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index b3ca9e1106..44e64c4d5a 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -600,6 +600,8 @@ void FixAveHisto::end_of_step() } // evaluate equal-style or vector-style or atom-style variable + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori } else if (val.which == ArgInfo::VARIABLE) { if (kind == GLOBAL && mode == SCALAR) { @@ -607,7 +609,7 @@ void FixAveHisto::end_of_step() else { double *varvec; int nvec = input->variable->compute_vector(val.val.v,&varvec); - if (nvec < j) bin_one(0.0); + if (j > nvec) bin_one(0.0); else bin_one(varvec[j-1]); } @@ -637,7 +639,7 @@ void FixAveHisto::end_of_step() modify->addstep_compute(nvalid); return; } - + irepeat = 0; nvalid = ntimestep + nfreq - static_cast(nrepeat-1)*nevery; modify->addstep_compute(nvalid); diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index c88d8e1659..417e0fd97a 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -562,7 +562,8 @@ void FixAveTime::invoke_scalar(bigint ntimestep) scalar = val.val.f->compute_vector(val.argindex-1); // evaluate equal-style or vector-style variable - // ensure no out-of-range access to vector-style variable + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori } else if (val.which == ArgInfo::VARIABLE) { if (val.argindex == 0) @@ -570,7 +571,7 @@ void FixAveTime::invoke_scalar(bigint ntimestep) else { double *varvec; int nvec = input->variable->compute_vector(val.val.v,&varvec); - if (nvec < val.argindex) scalar = 0.0; + if (val.argindex > nvec) scalar = 0.0; else scalar = varvec[val.argindex-1]; } } diff --git a/src/thermo.cpp b/src/thermo.cpp index dbb8b2530e..5ef5eb59b8 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -1515,6 +1515,8 @@ void Thermo::compute_fix() int m = field2index[ifield]; Fix *fix = fixes[m]; + // check for out-of-range access if vector/array is variable length + if (argindex1[ifield] == 0) { dvalue = fix->compute_scalar(); if (normflag && fix->extscalar) dvalue /= natoms; @@ -1544,13 +1546,17 @@ void Thermo::compute_variable() { int iarg = argindex1[ifield]; + // evaluate equal-style or vector-style variable + // if index exceeds vector length, use a zero value + // this can be useful if vector length is not known a priori + if (iarg == 0) dvalue = input->variable->compute_equal(variables[field2index[ifield]]); else { double *varvec; int nvec = input->variable->compute_vector(variables[field2index[ifield]], &varvec); - if (iarg > nvec) error->all(FLERR, "Thermo vector-style variable is accessed out-of-range"); - dvalue = varvec[iarg - 1]; + if (iarg > nvec) dvalue = 0.0; + else dvalue = varvec[iarg - 1]; } } From c45f2666ad0c0bc0a3f6ac44c7bc6010648e9e36 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 4 Apr 2024 14:21:55 -0600 Subject: [PATCH 38/40] clean-up whitespace --- src/fix_ave_correlate.cpp | 2 +- src/fix_ave_histo.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 576ddb3c94..08cd673122 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -416,7 +416,7 @@ void FixAveCorrelate::end_of_step() // evaluate equal-style or vector-style variable // if index exceeds vector length, use a zero value // this can be useful if vector length is not known a priori - + } else if (val.which == ArgInfo::VARIABLE) { if (val.argindex == 0) scalar = input->variable->compute_equal(val.val.v); diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 44e64c4d5a..d676bca0b7 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -639,7 +639,7 @@ void FixAveHisto::end_of_step() modify->addstep_compute(nvalid); return; } - + irepeat = 0; nvalid = ntimestep + nfreq - static_cast(nrepeat-1)*nevery; modify->addstep_compute(nvalid); From ec7b76454a22454cad10a9af065a261ddd944460 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 4 Apr 2024 14:37:03 -0600 Subject: [PATCH 39/40] fix spelling error --- src/RIGID/fix_rigid.cpp | 2 +- src/RIGID/fix_rigid_small.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 8703fb4d37..f4b82e1fd2 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -1987,7 +1987,7 @@ void FixRigid::setup_bodies_static() // necessary so that quaternion is a simple rotation around +z axis // or a 180 degree rotation for a -z axis // otherwise richardson() method for a body with a tiny evalue (near-linear) - // may not preserve the correct z-aligned quat and assocated evectors + // may not preserve the correct z-aligned quat and associated evectors // over time due to round-off accumulation if (domain->dimension == 2) { diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 2fc1553bf1..cb12bd96f7 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -2135,7 +2135,7 @@ void FixRigidSmall::setup_bodies_static() // necessary so that quaternion is a simple rotation around +z axis // or a 180 degree rotation for a -z axis // otherwise richardson() method for a body with a tiny evalue (near-linear) - // may not preserve the correct z-aligned quat and assocated evectors + // may not preserve the correct z-aligned quat and associated evectors // over time due to round-off accumulation if (domain->dimension == 2) { From a51174f6c3dd422fe9daa91677cc6e0ddf99ba41 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 4 Apr 2024 21:30:42 -0400 Subject: [PATCH 40/40] update unit test reference data for rigid fixes --- .../tests/fix-timestep-rigid_group.yaml | 113 ++++++++--------- .../tests/fix-timestep-rigid_molecule.yaml | 43 +++---- .../fix-timestep-rigid_molecule_tri.yaml | 37 +++--- .../tests/fix-timestep-rigid_nph.yaml | 85 ++++++------- .../tests/fix-timestep-rigid_nph_small.yaml | 85 ++++++------- .../tests/fix-timestep-rigid_npt.yaml | 119 +++++++++--------- .../tests/fix-timestep-rigid_npt_small.yaml | 85 ++++++------- .../tests/fix-timestep-rigid_nve_group.yaml | 113 ++++++++--------- .../fix-timestep-rigid_nve_molecule.yaml | 45 +++---- .../tests/fix-timestep-rigid_nve_single.yaml | 77 ++++++------ .../tests/fix-timestep-rigid_nve_small.yaml | 45 +++---- .../tests/fix-timestep-rigid_nvt.yaml | 79 ++++++------ .../tests/fix-timestep-rigid_nvt_small.yaml | 45 +++---- .../tests/fix-timestep-rigid_single.yaml | 77 ++++++------ .../tests/fix-timestep-rigid_small.yaml | 43 +++---- 15 files changed, 553 insertions(+), 538 deletions(-) diff --git a/unittest/force-styles/tests/fix-timestep-rigid_group.yaml b/unittest/force-styles/tests/fix-timestep-rigid_group.yaml index e28e0abb08..e434ace375 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_group.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_group.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:10 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,65 +15,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4245356937318884e+03 -1.4496493315649691e+03 -3.6144360984224995e+03 8.4840626828644076e+02 2.0318336761611761e+02 -6.0622397707970140e+02 -global_scalar: 15.711521423178082 + -1.4245356937318909e+03 -1.4496493315649632e+03 -3.6144360984225123e+03 8.4840626828644361e+02 2.0318336761612773e+02 -6.0622397707969583e+02 +global_scalar: 15.711521423178084 run_pos: ! |2 - 1 -2.7899546863891400e-01 2.4731857340328229e+00 -1.7290667740242271e-01 - 2 3.0296221610264262e-01 2.9517129916957545e+00 -8.5798904387773245e-01 - 3 -6.9368802364134741e-01 1.2445115421754194e+00 -6.2281111198650418e-01 - 4 -1.5764879647103154e+00 1.4919714415841279e+00 -1.2492069414674623e+00 - 5 -8.9434512967429969e-01 9.3651699743511030e-01 4.0191726558261276e-01 - 6 2.9454439634451712e-01 2.2724545792544038e-01 -1.2845195053960268e+00 - 7 3.4049112903270051e-01 -9.4655678322458359e-03 -2.4634480020857055e+00 - 8 1.1644354555804874e+00 -4.8367776650961336e-01 -6.7663643940735863e-01 - 9 1.3781717822696469e+00 -2.5332509530010694e-01 2.6864954436590061e-01 - 10 2.0186368606041896e+00 -1.4285861423625796e+00 -9.6712491252780131e-01 - 11 1.7929137227577452e+00 -1.9875455388407426e+00 -1.8836565352266534e+00 - 12 3.0032775230399604e+00 -4.8983022415174027e-01 -1.6190248017343642e+00 - 13 4.0448964162125947e+00 -9.0213155122391020e-01 -1.6385398399479558e+00 - 14 2.6035151245015822e+00 -4.0874995493219213e-01 -2.6555999074786607e+00 - 15 2.9761196776172318e+00 5.6287237454108674e-01 -1.2442626196083388e+00 - 16 2.6517373021566168e+00 -2.3957035508393707e+00 3.3389262100692263e-02 - 17 2.2311114924744970e+00 -2.1018393228798513e+00 1.1496088522377543e+00 - 18 2.1390642573201784e+00 3.0164773560693781e+00 -3.5143984803853878e+00 - 19 1.5353246655146278e+00 2.6305911186316133e+00 -4.2455871034737074e+00 - 20 2.7649421538938390e+00 3.6818603528430849e+00 -3.9364115785985550e+00 - 21 4.9043112657298877e+00 -4.0774268210397882e+00 -3.6200836396129836e+00 - 22 4.3665322424283310e+00 -4.2075138112953594e+00 -4.4636587264885881e+00 - 23 5.7355405581985188e+00 -3.5789558641908918e+00 -3.8805763324089981e+00 - 24 2.0692780332810115e+00 3.1504920436416004e+00 3.1571131300668789e+00 - 25 1.3007297593169076e+00 3.2745259354179481e+00 2.5110163874103675e+00 - 26 2.5819416446099739e+00 4.0104903120756576e+00 3.2150249624526035e+00 + 1 -2.7899546863891755e-01 2.4731857340328198e+00 -1.7290667740241461e-01 + 2 3.0296221610263996e-01 2.9517129916957550e+00 -8.5798904387772190e-01 + 3 -6.9368802364134963e-01 1.2445115421754176e+00 -6.2281111198650141e-01 + 4 -1.5764879647103172e+00 1.4919714415841279e+00 -1.2492069414674598e+00 + 5 -8.9434512967430235e-01 9.3651699743510453e-01 4.0191726558261442e-01 + 6 2.9454439634451712e-01 2.2724545792544146e-01 -1.2845195053960266e+00 + 7 3.4049112903270240e-01 -9.4655678322404235e-03 -2.4634480020857055e+00 + 8 1.1644354555804877e+00 -4.8367776650961403e-01 -6.7663643940735962e-01 + 9 1.3781717822696455e+00 -2.5332509530011083e-01 2.6864954436590072e-01 + 10 2.0186368606041905e+00 -1.4285861423625785e+00 -9.6712491252780486e-01 + 11 1.7929137227577487e+00 -1.9875455388407386e+00 -1.8836565352266592e+00 + 12 3.0032775230399622e+00 -4.8983022415173583e-01 -1.6190248017343625e+00 + 13 4.0448964162125964e+00 -9.0213155122390454e-01 -1.6385398399479547e+00 + 14 2.6035151245015857e+00 -4.0874995493218413e-01 -2.6555999074786598e+00 + 15 2.9761196776172323e+00 5.6287237454109007e-01 -1.2442626196083335e+00 + 16 2.6517373021566182e+00 -2.3957035508393734e+00 3.3389262100686046e-02 + 17 2.2311114924744961e+00 -2.1018393228798584e+00 1.1496088522377494e+00 + 18 2.1390642573201792e+00 3.0164773560693803e+00 -3.5143984803853883e+00 + 19 1.5353246655146293e+00 2.6305911186316160e+00 -4.2455871034737100e+00 + 20 2.7649421538938399e+00 3.6818603528430875e+00 -3.9364115785985545e+00 + 21 4.9043112657298966e+00 -4.0774268210397882e+00 -3.6200836396129850e+00 + 22 4.3665322424283417e+00 -4.2075138112953612e+00 -4.4636587264885925e+00 + 23 5.7355405581985277e+00 -3.5789558641908901e+00 -3.8805763324089995e+00 + 24 2.0692780332810012e+00 3.1504920436415969e+00 3.1571131300668829e+00 + 25 1.3007297593168976e+00 3.2745259354179459e+00 2.5110163874103693e+00 + 26 2.5819416446099637e+00 4.0104903120756576e+00 3.2150249624526102e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093289825842508e-04 2.6351122778447809e-04 -4.4905093064114883e-04 - 2 4.9594625316470506e-04 9.4561370489630299e-05 -5.4581359894047775e-04 - 3 3.3306085115756103e-04 2.3224943880673259e-04 -2.3659455671746018e-04 - 4 3.3692327392261152e-04 2.1926810694051179e-04 -2.4716631558862516e-04 - 5 3.3642542694186002e-04 4.1797578013265738e-04 -1.8011341766657675e-04 - 6 2.0926869754934769e-04 2.6449308951578185e-05 -1.0508938983871811e-04 - 7 1.4629043007907940e-04 -1.6873376665350122e-04 -6.8354048774350921e-05 - 8 1.5844101624224881e-04 3.7728761273999780e-05 -1.9162715667090996e-05 - 9 2.1299362072601952e-04 1.6917140529157474e-04 -6.3528165037845483e-05 - 10 5.4261629412254495e-05 -9.4655528376811482e-05 1.0511362869146690e-04 - 11 -3.2194160796502724e-05 -2.2025095264758716e-04 2.0300202946212429e-04 - 12 1.2640586304750378e-04 -2.9851080445665107e-04 -7.9476371818245798e-05 - 13 8.4523575162142608e-05 -4.0583135407330561e-04 -4.7551111331700511e-05 - 14 9.9954050381270972e-05 -4.2610816481298294e-04 -7.9255633594379530e-05 - 15 2.4417481119789862e-04 -2.3521002264677992e-04 -2.4875318161048917e-04 - 16 -9.0958138549664992e-06 3.7774817121222391e-06 2.4035199548835096e-04 - 17 5.7507224523612230e-05 2.2629217444843764e-04 2.0686920072684822e-04 - 18 2.9220264989359833e-04 -6.2478376436796265e-04 8.4222594596602366e-04 - 19 2.0572616567799188e-04 -5.0334424271726639e-04 8.4953929443210648e-04 - 20 4.1224811789513022e-04 -7.4115205416011554e-04 8.3678612337507920e-04 - 21 -1.0671858777656393e-03 -1.1531171045499515e-03 7.3720674900162159e-04 - 22 -1.1066511338291710e-03 -1.0433933757600460e-03 7.4544544325708573e-04 - 23 -9.7629260480941525e-04 -1.3100872491594103e-03 7.2687284219704804e-04 - 24 4.3308126651259312e-04 -6.6527658087322801e-04 8.4451298670663606e-04 - 25 4.4565811905442889e-04 -5.1298436273584285e-04 8.5878867884521559e-04 - 26 5.9865972692022765e-04 -7.6385263287080381e-04 8.4259943226842166e-04 + 1 4.7093289825842437e-04 2.6351122778447999e-04 -4.4905093064114823e-04 + 2 4.9594625316470473e-04 9.4561370489632928e-05 -5.4581359894047732e-04 + 3 3.3306085115756054e-04 2.3224943880673362e-04 -2.3659455671746045e-04 + 4 3.3692327392261130e-04 2.1926810694051292e-04 -2.4716631558862576e-04 + 5 3.3642542694185899e-04 4.1797578013265770e-04 -1.8011341766657654e-04 + 6 2.0926869754934769e-04 2.6449308951579106e-05 -1.0508938983871929e-04 + 7 1.4629043007908003e-04 -1.6873376665349995e-04 -6.8354048774352968e-05 + 8 1.5844101624224859e-04 3.7728761274000288e-05 -1.9162715667092141e-05 + 9 2.1299362072601887e-04 1.6917140529157517e-04 -6.3528165037845917e-05 + 10 5.4261629412254576e-05 -9.4655528376811157e-05 1.0511362869146505e-04 + 11 -3.2194160796502236e-05 -2.2025095264758700e-04 2.0300202946212152e-04 + 12 1.2640586304750429e-04 -2.9851080445664956e-04 -7.9476371818247574e-05 + 13 8.4523575162143312e-05 -4.0583135407330399e-04 -4.7551111331702557e-05 + 14 9.9954050381271961e-05 -4.2610816481298121e-04 -7.9255633594381943e-05 + 15 2.4417481119789894e-04 -2.3521002264677784e-04 -2.4875318161049020e-04 + 16 -9.0958138549668516e-06 3.7774817121217089e-06 2.4035199548834928e-04 + 17 5.7507224523611227e-05 2.2629217444843685e-04 2.0686920072684740e-04 + 18 2.9220264989359860e-04 -6.2478376436796244e-04 8.4222594596602409e-04 + 19 2.0572616567799204e-04 -5.0334424271726607e-04 8.4953929443210702e-04 + 20 4.1224811789513060e-04 -7.4115205416011543e-04 8.3678612337507964e-04 + 21 -1.0671858777656406e-03 -1.1531171045499533e-03 7.3720674900162007e-04 + 22 -1.1066511338291734e-03 -1.0433933757600477e-03 7.4544544325708432e-04 + 23 -9.7629260480941644e-04 -1.3100872491594124e-03 7.2687284219704641e-04 + 24 4.3308126651259382e-04 -6.6527658087322671e-04 8.4451298670663671e-04 + 25 4.4565811905442982e-04 -5.1298436273584133e-04 8.5878867884521635e-04 + 26 5.9865972692022961e-04 -7.6385263287080262e-04 8.4259943226842242e-04 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml b/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml index d667942e49..e871a351f6 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_molecule.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:10 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00 -global_scalar: 18.3405601674144 + -4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00 +global_scalar: 18.340560167414402 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588271301e+00 3.0171068018412779e+00 -3.5144628518856349e+00 - 19 1.5366124997074571e+00 2.6286809834111748e+00 -4.2452547844370221e+00 - 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352554e+00 - 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515904e+00 - 22 4.3655322291888483e+00 -4.2084949965552561e+00 -4.4622011117402334e+00 - 23 5.7380414793463101e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 + 18 2.1392027588271301e+00 3.0171068018412783e+00 -3.5144628518856353e+00 + 19 1.5366124997074575e+00 2.6286809834111740e+00 -4.2452547844370221e+00 + 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 + 21 4.9036621347791236e+00 -4.0757648442838548e+00 -3.6192617654515908e+00 + 22 4.3655322291888474e+00 -4.2084949965552561e+00 -4.4622011117402343e+00 + 23 5.7380414793463110e+00 -3.5841969195032672e+00 -3.8827839830470219e+00 24 2.0701314765323930e+00 3.1499370533342330e+00 3.1565324852522938e+00 - 25 1.3030170721374779e+00 3.2711173927682249e+00 2.5081940917429768e+00 - 26 2.5776230782480045e+00 4.0127347068243875e+00 3.2182355138709275e+00 + 25 1.3030170721374787e+00 3.2711173927682244e+00 2.5081940917429759e+00 + 26 2.5776230782480041e+00 4.0127347068243884e+00 3.2182355138709284e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704914e-04 -3.1032459262908286e-04 8.1043030117346052e-04 - 19 8.5103884665345452e-04 -1.4572280596788108e-03 1.0163621287634116e-03 - 20 -6.5204659278590683e-04 4.3989037444289853e-04 4.9909839028507901e-04 - 21 -1.3888125881903923e-03 -3.1978049143082385e-04 1.1455681499836646e-03 - 22 -1.6084223477729510e-03 -1.5355394240821117e-03 1.4772010826232375e-03 - 23 2.6392672378805124e-04 -3.9375414431174821e-03 -3.6991583139728095e-04 - 24 8.6062827067890247e-04 -9.4179873474469237e-04 5.5396395550012453e-04 - 25 1.5933645477487538e-03 -2.2139156625681695e-03 -5.5078029695647401e-04 - 26 -1.5679561743998840e-03 3.5146224354726100e-04 2.4446924193334478e-03 + 18 3.6149625095704849e-04 -3.1032459262908286e-04 8.1043030117346052e-04 + 19 8.5103884665345473e-04 -1.4572280596788095e-03 1.0163621287634121e-03 + 20 -6.5204659278590661e-04 4.3989037444289755e-04 4.9909839028507901e-04 + 21 -1.3888125881903906e-03 -3.1978049143082342e-04 1.1455681499836646e-03 + 22 -1.6084223477729526e-03 -1.5355394240821163e-03 1.4772010826232394e-03 + 23 2.6392672378804821e-04 -3.9375414431174795e-03 -3.6991583139728377e-04 + 24 8.6062827067890269e-04 -9.4179873474469291e-04 5.5396395550012388e-04 + 25 1.5933645477487551e-03 -2.2139156625681673e-03 -5.5078029695647250e-04 + 26 -1.5679561743998888e-03 3.5146224354726068e-04 2.4446924193334487e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml index 304db9fd60..672bf8946c 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_molecule_tri.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:11 2024 epsilon: 5e-12 skip_tests: prerequisites: ! | @@ -15,8 +16,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134788658e+01 -2.6907707565985344e+01 -6.0080860422268874e+00 -2.5620423972099733e+01 -1.3450224059983656e+01 -1.4947288487000705e+00 -global_scalar: 18.340560167414306 + -4.9200116134789653e+01 -2.6907707565986087e+01 -6.0080860422267843e+00 -2.5620423972100063e+01 -1.3450224059983270e+01 -1.4947288486998982e+00 +global_scalar: 18.340560167414335 run_pos: ! |2 1 -2.7993683669226854e-01 2.4726588069312836e+00 -1.7200860244148508e-01 2 3.0197083955402171e-01 2.9515239068888608e+00 -8.5689735572907555e-01 @@ -36,14 +37,14 @@ run_pos: ! |2 16 2.6517554244980301e+00 -2.3957110424978438e+00 3.2908335999177751e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 18 2.1392027588271310e+00 3.0171068018412779e+00 -3.5144628518856349e+00 - 19 1.5366124997074566e+00 2.6286809834111740e+00 -4.2452547844370239e+00 + 19 1.5366124997074584e+00 2.6286809834111722e+00 -4.2452547844370230e+00 20 2.7628161763455852e+00 3.6842251687634775e+00 -3.9370881219352558e+00 - 21 4.9036621347791245e+00 -4.0757648442838557e+00 -3.6192617654515900e+00 - 22 4.3655322291888465e+00 -4.2084949965552569e+00 -4.4622011117402334e+00 + 21 4.9036621347791245e+00 -4.0757648442838548e+00 -3.6192617654515900e+00 + 22 4.3655322291888465e+00 -4.2084949965552578e+00 -4.4622011117402343e+00 23 5.7380414793463101e+00 -3.5841969195032686e+00 -3.8827839830470232e+00 24 2.0701314765323913e+00 3.1499370533342308e+00 3.1565324852522920e+00 - 25 1.3030170721374770e+00 3.2711173927682236e+00 2.5081940917429755e+00 - 26 2.5776230782480054e+00 4.0127347068243875e+00 3.2182355138709262e+00 + 25 1.3030170721374779e+00 3.2711173927682236e+00 2.5081940917429755e+00 + 26 2.5776230782480036e+00 4.0127347068243875e+00 3.2182355138709280e+00 27 -1.9613581876744357e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678509e+00 29 -1.3108232656499084e+00 -3.5992986322410765e+00 2.2680459788743512e+00 @@ -65,15 +66,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625095704681e-04 -3.1032459262907857e-04 8.1043030117346074e-04 - 19 8.5103884665345820e-04 -1.4572280596788108e-03 1.0163621287634073e-03 - 20 -6.5204659278590271e-04 4.3989037444289630e-04 4.9909839028508215e-04 - 21 -1.3888125881903852e-03 -3.1978049143082049e-04 1.1455681499836594e-03 - 22 -1.6084223477729513e-03 -1.5355394240820970e-03 1.4772010826232351e-03 - 23 2.6392672378803975e-04 -3.9375414431174569e-03 -3.6991583139727910e-04 - 24 8.6062827067889835e-04 -9.4179873474469346e-04 5.5396395550012518e-04 - 25 1.5933645477487516e-03 -2.2139156625681669e-03 -5.5078029695647542e-04 - 26 -1.5679561743998831e-03 3.5146224354726187e-04 2.4446924193334495e-03 + 18 3.6149625095704659e-04 -3.1032459262907825e-04 8.1043030117346085e-04 + 19 8.5103884665346059e-04 -1.4572280596788099e-03 1.0163621287634082e-03 + 20 -6.5204659278590227e-04 4.3989037444289446e-04 4.9909839028508150e-04 + 21 -1.3888125881903869e-03 -3.1978049143081757e-04 1.1455681499836596e-03 + 22 -1.6084223477729556e-03 -1.5355394240821013e-03 1.4772010826232407e-03 + 23 2.6392672378803953e-04 -3.9375414431174656e-03 -3.6991583139727423e-04 + 24 8.6062827067889998e-04 -9.4179873474469411e-04 5.5396395550012377e-04 + 25 1.5933645477487516e-03 -2.2139156625681634e-03 -5.5078029695647109e-04 + 26 -1.5679561743998922e-03 3.5146224354726068e-04 2.4446924193334543e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml index c80a70b428..16ba7c079d 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:11 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,38 +15,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |2- - 4.3578059172167876e+01 1.7275105166465000e+01 6.7372361276631054e+01 5.1985075049901745e+01 -2.0990677389800993e+01 -7.5321398101844359e+00 -global_scalar: 29.023636440847998 + 4.3578059175768836e+01 1.7275105168781163e+01 6.7372361277896715e+01 5.1985075050485008e+01 -2.0990677388216337e+01 -7.5321398110797180e+00 +global_scalar: 29.023636439584656 run_pos: ! |2 - 1 -6.3472039825517168e-01 3.0113983126282058e+00 -8.8148450172235826e-02 - 2 6.4798884173500326e-02 3.5870486860057795e+00 -9.1146271255434463e-01 - 3 -1.1328967478840362e+00 1.5344674077762583e+00 -6.2949567786977667e-01 - 4 -2.1941320441841130e+00 1.8319737599530370e+00 -1.3824693495474225e+00 - 5 -1.3741175247360697e+00 1.1637763350569887e+00 6.0220861483086097e-01 - 6 5.5368589242158706e-02 3.1209253712244411e-01 -1.4252606627467266e+00 - 7 1.1075313780270069e-01 2.8008314824797154e-02 -2.8425552056438050e+00 - 8 1.1011987966104080e+00 -5.4254536577068713e-01 -6.9472264392660854e-01 - 9 1.3580030945401020e+00 -2.6595138115345840e-01 4.4172536708297194e-01 - 10 2.1282964643831388e+00 -1.6781145595676907e+00 -1.0442216631471304e+00 - 11 1.8571593172391605e+00 -2.3497452731071471e+00 -2.1462323657665392e+00 - 12 3.3117732698469986e+00 -5.4913311816190635e-01 -1.8274356036322548e+00 - 13 4.5640183918453143e+00 -1.0445083545907554e+00 -1.8509716390298214e+00 - 14 2.8312769330518019e+00 -4.5135848464344086e-01 -3.0735173792331993e+00 - 15 3.2788434490964296e+00 7.1618295543695254e-01 -1.3765217601452289e+00 - 16 2.8895075000232158e+00 -2.8409365554010479e+00 1.5818504152554702e-01 - 17 2.3837073405559277e+00 -2.4882133308169232e+00 1.5000885103549333e+00 - 18 2.2738793194357232e+00 3.6743407122553755e+00 -4.1408965121163197e+00 - 19 1.6572750518209336e+00 3.2770314238152451e+00 -4.8886441786593569e+00 - 20 2.9120476452800226e+00 4.3568412675031851e+00 -4.5732834167769187e+00 - 21 5.6058485050774536e+00 -4.8495065176300871e+00 -4.2655497599953458e+00 - 22 5.0552709232982114e+00 -4.9851876752032496e+00 -5.1280564953560424e+00 - 23 6.4593933585948218e+00 -4.3461765105422652e+00 -4.5350231456236889e+00 - 24 2.1823354619125279e+00 3.8552931130470363e+00 3.8953804330431208e+00 - 25 1.3973696115403698e+00 3.9794119228484153e+00 3.2321313266194949e+00 - 26 2.7018361227965517e+00 4.7379517631305443e+00 3.9583193478092706e+00 - 27 -2.6559803075358257e+00 -5.1969823689078796e+00 2.6552621488555683e+00 - 28 -3.5927802460207046e+00 -4.7943885088602283e+00 2.0214142204095413e+00 - 29 -1.8739632618339108e+00 -4.2877858778713946e+00 2.8450749793919066e+00 + 1 -6.3472039825540794e-01 3.0113983126285611e+00 -8.8148450172186088e-02 + 2 6.4798884173342230e-02 3.5870486860061987e+00 -9.1146271255438371e-01 + 3 -1.1328967478843275e+00 1.5344674077764573e+00 -6.2949567786978555e-01 + 4 -2.1941320441845233e+00 1.8319737599532644e+00 -1.3824693495475202e+00 + 5 -1.3741175247363868e+00 1.1637763350571468e+00 6.0220861483099597e-01 + 6 5.5368589242003274e-02 3.1209253712249918e-01 -1.4252606627468261e+00 + 7 1.1075313780254881e-01 2.8008314824818470e-02 -2.8425552056440617e+00 + 8 1.1011987966103707e+00 -5.4254536577072621e-01 -6.9472264392662098e-01 + 9 1.3580030945400878e+00 -2.6595138115347083e-01 4.4172536708308918e-01 + 10 2.1282964643832170e+00 -1.6781145595678604e+00 -1.0442216631471855e+00 + 11 1.8571593172392049e+00 -2.3497452731073896e+00 -2.1462323657667168e+00 + 12 3.3117732698472082e+00 -5.4913311816195076e-01 -1.8274356036323969e+00 + 13 4.5640183918456607e+00 -1.0445083545908531e+00 -1.8509716390299671e+00 + 14 2.8312769330519618e+00 -4.5135848464346928e-01 -3.0735173792334827e+00 + 15 3.2788434490966321e+00 7.1618295543705379e-01 -1.3765217601453177e+00 + 16 2.8895075000233756e+00 -2.8409365554013446e+00 1.5818504152563229e-01 + 17 2.3837073405560343e+00 -2.4882133308171808e+00 1.5000885103551624e+00 + 18 2.2738793194332434e+00 3.6743407122541889e+00 -4.1408965121171795e+00 + 19 1.6572750518219337e+00 3.2770314238270633e+00 -4.8886441786700008e+00 + 20 2.9120476452894675e+00 4.3568412674987194e+00 -4.5732834167653644e+00 + 21 5.6058485051319096e+00 -4.8495065176594299e+00 -4.2655497599906971e+00 + 22 5.0552709232924169e+00 -4.9851876754509741e+00 -5.1280564952785888e+00 + 23 6.4593933583860359e+00 -4.3461765101804879e+00 -4.5350231457223327e+00 + 24 2.1823354618683570e+00 3.8552931130563355e+00 3.8953804330779889e+00 + 25 1.3973696115700545e+00 3.9794119229082359e+00 3.2321313265764022e+00 + 26 2.7018361229436465e+00 4.7379517630364116e+00 3.9583193477161114e+00 + 27 -2.6559803075362858e+00 -5.1969823689084436e+00 2.6552621488559236e+00 + 28 -3.5927802460212725e+00 -4.7943885088607452e+00 2.0214142204098309e+00 + 29 -1.8739632618342856e+00 -4.2877858778718556e+00 2.8450749793922920e+00 run_vel: ! |2 1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04 2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.0094600491564739e-04 -2.4312792027781263e-04 6.5542049134062323e-04 - 19 7.4731683462770076e-04 -1.2894119671278408e-03 8.4327024053533397e-04 - 20 -6.2333686369976551e-04 4.4115361641690044e-04 3.7135656431834220e-04 - 21 -1.1457423793218525e-03 -1.7337748161437940e-04 9.4510018429417686e-04 - 22 -1.3457150581639313e-03 -1.2816797357047471e-03 1.2470992250388096e-03 - 23 3.6277645415306518e-04 -3.4719859048227848e-03 -4.3796817853449118e-04 - 24 7.2410992462873655e-04 -7.6012809744767037e-04 4.3327155128124943e-04 - 25 1.3921349892629666e-03 -1.9207002802664867e-03 -5.7453335109528090e-04 - 26 -1.4901465947638008e-03 4.2012923457099966e-04 2.1578545404178418e-03 + 18 3.0094600492089644e-04 -2.4312792028464785e-04 6.5542049134054972e-04 + 19 7.4731683460624917e-04 -1.2894119671240515e-03 8.4327024053305281e-04 + 20 -6.2333686369944134e-04 4.4115361644063580e-04 3.7135656432041769e-04 + 21 -1.1457423794330429e-03 -1.7337748206069275e-04 9.4510018428907005e-04 + 22 -1.3457150585185161e-03 -1.2816797348700177e-03 1.2470992253076274e-03 + 23 3.6277645495226573e-04 -3.4719859038751704e-03 -4.3796817878355291e-04 + 24 7.2410992459670032e-04 -7.6012809759399148e-04 4.3327155120505761e-04 + 25 1.3921349891892136e-03 -1.9207002802470530e-03 -5.7453335098663809e-04 + 26 -1.4901465945625111e-03 4.2012923513626559e-04 2.1578545406129137e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml index 3894815950..80cc4865c0 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nph_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:11 2024 epsilon: 6.5e-13 skip_tests: prerequisites: ! | @@ -14,38 +15,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |2- - 2.7340318973870396e+01 4.7963870091858283e+00 6.8884396847592512e+01 2.9853310007358935e+01 -1.0857139901347722e+01 -5.1889756561454785e+00 -global_scalar: 9.77678786310451 + 2.7340318979717416e+01 4.7963870104375275e+00 6.8884396847589585e+01 2.9853310005453281e+01 -1.0857139898599751e+01 -5.1889756547311965e+00 +global_scalar: 9.776787862991728 run_pos: ! |2 - 1 -5.1121862036604515e-01 2.8134872171079977e+00 -4.8993015395518924e-02 - 2 1.4735952488047133e-01 3.3535825972277546e+00 -9.3694001270735150e-01 - 3 -9.8023793775378820e-01 1.4277788160410712e+00 -6.3283768722999234e-01 - 4 -1.9793617512974304e+00 1.7069097152779946e+00 -1.4449221382955635e+00 - 5 -1.2073406578712120e+00 1.0799834439081337e+00 6.9555923026692668e-01 - 6 1.3848116183742931e-01 2.8090381873852976e-01 -1.4910727029127884e+00 - 7 1.9062418946016990e-01 1.4366032742456625e-02 -3.0196292835199614e+00 - 8 1.1231015082845541e+00 -5.2094745136401599e-01 -7.0318517336042774e-01 - 9 1.3648756844511976e+00 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-3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.1638284997073272e-04 -2.6313163919070405e-04 6.1054395248656961e-04 - 19 7.6494647252307673e-04 -1.3190724749214326e-03 7.9947132612985723e-04 - 20 -6.1620104632513929e-04 4.2577138774295274e-04 3.2526261653548693e-04 - 21 -1.2063428871524097e-03 -2.2879409878999576e-04 8.9132836538734445e-04 - 22 -1.4151473871894464e-03 -1.3502255393198256e-03 1.1972773109437849e-03 - 23 3.1280366109607172e-04 -3.5563936893394407e-03 -4.9548546532774958e-04 - 24 7.5594375541558026e-04 -8.1321043994394464e-04 3.9340911295780739e-04 - 25 1.4373446731689036e-03 -1.9778020567486213e-03 -6.1842201918304478e-04 - 26 -1.4806168650325999e-03 3.7766934274110835e-04 2.1280924225288342e-03 + 18 3.1638284997600319e-04 -2.6313163919763335e-04 6.1054395248685519e-04 + 19 7.6494647250110288e-04 -1.3190724749175438e-03 7.9947132612783736e-04 + 20 -6.1620104632483571e-04 4.2577138776739548e-04 3.2526261653790590e-04 + 21 -1.2063428872614197e-03 -2.2879409923923591e-04 8.9132836537741717e-04 + 22 -1.4151473875545966e-03 -1.3502255384792933e-03 1.1972773112250280e-03 + 23 3.1280366189902534e-04 -3.5563936883846667e-03 -4.9548546556753227e-04 + 24 7.5594375538112746e-04 -8.1321044009394260e-04 3.9340911288157350e-04 + 25 1.4373446730968913e-03 -1.9778020567293151e-03 -6.1842201907436371e-04 + 26 -1.4806168648243687e-03 3.7766934332225264e-04 2.1280924227258073e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml index f5965e53ff..6757db5703 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_npt.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:12 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -13,65 +14,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.6326314448663306e+03 -1.4727331978532295e+03 -3.8557370515932275e+03 5.5052891601644615e+02 4.7346742977310657e+02 -6.2035591882122355e+02 -global_scalar: 106.86683072474125 + -1.6326314448662429e+03 -1.4727331978532245e+03 -3.8557370515929042e+03 5.5052891601619581e+02 4.7346742977256520e+02 -6.2035591882208064e+02 +global_scalar: 106.86683072474244 run_pos: ! |2 - 1 -2.6314711410922875e-01 2.4664715027241684e+00 -1.7093568570875561e-01 - 2 3.1632911015968190e-01 2.9434731493852482e+00 -8.5432214735778889e-01 - 3 -6.7623447816593885e-01 1.2410822625695044e+00 -6.1935152269903870e-01 - 4 -1.5552134736906362e+00 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-2.0274707260289267e-04 + 13 2.0597404142668038e-04 -1.0865778699538143e-03 -1.1731137935657286e-04 + 14 2.4719215573317579e-04 -1.1410575874171004e-03 -2.0209037936272953e-04 + 15 6.3286464043720871e-04 -6.3068988069325653e-04 -6.5527927471369335e-04 + 16 -4.4100406048914694e-05 8.6869240445997393e-06 6.5198761255915100e-04 + 17 1.3407421346973834e-04 6.0357565278286712e-04 5.6233596575947994e-04 + 18 7.9277804690533363e-04 -1.5618239874416928e-03 2.1367192719678658e-03 + 19 5.6167660797890148e-04 -1.2371794194914493e-03 2.1562222137424727e-03 + 20 1.1137406410120911e-03 -1.8729421751419769e-03 2.1222207985341088e-03 + 21 -2.8426953558134235e-03 -2.9730185469789214e-03 1.8564402246258563e-03 + 22 -2.9480844379788334e-03 -2.6797216173776307e-03 1.8784164631755556e-03 + 23 -2.5997293519669897e-03 -3.3926375081639489e-03 1.8288830284142509e-03 + 24 1.1689404599044329e-03 -1.6701257754517325e-03 2.1428138286393884e-03 + 25 1.2027302640331447e-03 -1.2630861421197028e-03 2.1808987508669616e-03 + 26 1.6116362268908176e-03 -1.9337182438138503e-03 2.1377249582867175e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml index 3b13658e19..b7b074debd 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_npt_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:12 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -13,38 +14,38 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -8.7531774769722489e+01 5.5811525017966304e+00 -5.5468297744356747e+01 -1.5316306343483370e+02 1.4641268097314367e+02 1.7263710089631324e+01 -global_scalar: 77.78983430293286 + -8.7531774640811420e+01 5.5811525750281774e+00 -5.5468297761715007e+01 -1.5316306336726905e+02 1.4641268095299071e+02 1.7263710083146290e+01 +global_scalar: 77.78983430422252 run_pos: ! |2 - 1 -4.6333219629007161e-01 2.7511450055070625e+00 -1.2865946102806269e-01 - 2 1.7937148390204793e-01 3.2800405238539234e+00 -8.8510337855738808e-01 - 3 -9.2104620265671233e-01 1.3941717929286011e+00 -6.2603796687145774e-01 - 4 -1.8960869879711328e+00 1.6675144043869761e+00 -1.3178544214440926e+00 - 5 -1.1426748052069362e+00 1.0535885915279550e+00 5.0562616550054784e-01 - 6 1.7070712623541162e-01 2.7107933832755826e-01 -1.3571701846607374e+00 - 7 2.2159329060539701e-01 1.0068698962042433e-02 -2.6593507556860114e+00 - 8 1.1315940381701060e+00 -5.1414408469809381e-01 -6.8596713849763802e-01 - 9 1.3675404538221994e+00 -2.6001531899016506e-01 3.5817751536664133e-01 - 10 2.0752698846777218e+00 -1.5574812996955254e+00 -1.0070795245589492e+00 - 11 1.8261547470632067e+00 -2.1745615463231482e+00 -2.0195839000288469e+00 - 12 3.1626236108721066e+00 -5.2019677375525752e-01 -1.7266801053747978e+00 - 13 4.3131602274134853e+00 -9.7533717592326674e-01 -1.7483045222380902e+00 - 14 2.7211536303664605e+00 -4.3036348628163701e-01 -2.8715539682060491e+00 - 15 3.1323683805788374e+00 6.4234915962457073e-01 -1.3123899007466848e+00 - 16 2.7746546569032322e+00 -2.6258578189755974e+00 9.7666596945726880e-02 - 17 2.3099360535750506e+00 -2.3017831004883886e+00 1.3305794265747686e+00 - 18 2.2091748314094701e+00 3.3564440703097080e+00 -3.8370878208998480e+00 - 19 1.5986312961639815e+00 2.9614993054417287e+00 -4.5778944294436021e+00 - 20 2.8405364052167421e+00 4.0335971973474170e+00 -4.2659151034329339e+00 - 21 5.2651527410670678e+00 -4.4761614286515128e+00 -3.9518304737634447e+00 - 22 4.7192922284117014e+00 -4.6119045765637390e+00 -4.8062296930647124e+00 - 23 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1.0068698962099276e-02 -2.6593507556865532e+00 + 8 1.1315940381700180e+00 -5.1414408469817374e-01 -6.8596713849766644e-01 + 9 1.3675404538221745e+00 -2.6001531899018637e-01 3.5817751536688647e-01 + 10 2.0752698846778816e+00 -1.5574812996958780e+00 -1.0070795245590576e+00 + 11 1.8261547470632973e+00 -2.1745615463236652e+00 -2.0195839000292208e+00 + 12 3.1626236108725436e+00 -5.2019677375534190e-01 -1.7266801053750953e+00 + 13 4.3131602274142278e+00 -9.7533717592347013e-01 -1.7483045222383922e+00 + 14 2.7211536303667962e+00 -4.3036348628169740e-01 -2.8715539682066451e+00 + 15 3.1323683805792637e+00 6.4234915962478567e-01 -1.3123899007468758e+00 + 16 2.7746546569035768e+00 -2.6258578189762343e+00 9.7666596945902739e-02 + 17 2.3099360535752709e+00 -2.3017831004889393e+00 1.3305794265752642e+00 + 18 2.2091748313982826e+00 3.3564440703034535e+00 -3.8370878209026742e+00 + 19 1.5986312961681257e+00 2.9614993054929961e+00 -4.5778944294898185e+00 + 20 2.8405364052584243e+00 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-9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 7.2384391131466940e-04 -6.0015829212802722e-04 1.5957533238990559e-03 - 19 1.7583138222551384e-03 -3.0158245948490804e-03 2.0310435058142470e-03 - 20 -1.4153552732353322e-03 9.7835305930749246e-04 9.3881222516217474e-04 - 21 -2.7591188772323472e-03 -5.1180650802276303e-04 2.2758295071994400e-03 - 22 -3.2319732401280494e-03 -3.0809796427949646e-03 2.9861065768383484e-03 - 23 6.9767443123301817e-04 -8.1543313142268207e-03 -8.9929522742256325e-04 - 24 1.7345816999787505e-03 -1.8508160062822962e-03 1.0723416147087287e-03 - 25 3.2855417755407162e-03 -4.5284294762327620e-03 -1.2529299007822618e-03 - 26 -3.4004728795728936e-03 8.5952140737749613e-04 5.0505027847540665e-03 + 18 7.2384391137821785e-04 -6.0015829219183913e-04 1.5957533239005792e-03 + 19 1.7583138220942001e-03 -3.0158245949231362e-03 2.0310435058145879e-03 + 20 -1.4153552733289841e-03 9.7835305963750062e-04 9.3881222515317965e-04 + 21 -2.7591188784018856e-03 -5.1180651254767841e-04 2.2758295071625967e-03 + 22 -3.2319732438308327e-03 -3.0809796341686479e-03 2.9861065796802132e-03 + 23 6.9767443960831559e-04 -8.1543313047864312e-03 -8.9929523012053270e-04 + 24 1.7345816996818938e-03 -1.8508160077951139e-03 1.0723416139084840e-03 + 25 3.2855417748809557e-03 -4.5284294761711655e-03 -1.2529298997977286e-03 + 26 -3.4004728777299181e-03 8.5952141335802687e-04 5.0505027869618231e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml index b20d639fd4..0e8f18da7b 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_group.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:13 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,65 +15,65 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4245356938011610e+03 -1.4496493316650424e+03 -3.6144360982532016e+03 8.4840626794792252e+02 2.0318336802442886e+02 -6.0622397695978805e+02 -global_scalar: 15.711521423178128 + -1.4245356938011316e+03 -1.4496493316650758e+03 -3.6144360982530934e+03 8.4840626794790273e+02 2.0318336802433893e+02 -6.0622397695991208e+02 +global_scalar: 15.711521423178162 run_pos: ! |2 - 1 -2.7899546863905123e-01 2.4731857340327181e+00 -1.7290667740231969e-01 - 2 3.0296221610252227e-01 2.9517129916957194e+00 -8.5798904387756503e-01 - 3 -6.9368802364141247e-01 1.2445115421753310e+00 -6.2281111198650718e-01 - 4 -1.5764879647103560e+00 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2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml index 839ac060a5..b0e52d3fea 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_molecule.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:13 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00 -global_scalar: 18.340560167364448 + -4.9200114760030708e+01 -2.6907707699312748e+01 -6.0080872440179061e+00 -2.5620425767600064e+01 -1.3450222535184853e+01 -1.4947348700253382e+00 +global_scalar: 18.340560165889197 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588270928e+00 3.0171068018423082e+00 -3.5144628518853867e+00 - 19 1.5366124996934336e+00 2.6286809834236959e+00 -4.2452547844313493e+00 - 20 2.7628161763597592e+00 3.6842251687468450e+00 -3.9370881219419189e+00 - 21 4.9036621348471368e+00 -4.0757648444604762e+00 -3.6192617654906609e+00 - 22 4.3655322292129357e+00 -4.2084949964269480e+00 -4.4622011117992786e+00 - 23 5.7380414790507261e+00 -3.5841969189265162e+00 -3.8827839828320116e+00 - 24 2.0701314764933532e+00 3.1499370533556008e+00 3.1565324853054118e+00 - 25 1.3030170721038390e+00 3.2711173927738786e+00 2.5081940917867680e+00 - 26 2.5776230784374867e+00 4.0127347067334345e+00 3.2182355136150917e+00 + 18 2.1392027588241729e+00 3.0171068018404634e+00 -3.5144628518858858e+00 + 19 1.5366124996944652e+00 2.6286809834366300e+00 -4.2452547844429631e+00 + 20 2.7628161763703827e+00 3.6842251687412753e+00 -3.9370881219283147e+00 + 21 4.9036621349084646e+00 -4.0757648444931904e+00 -3.6192617654848509e+00 + 22 4.3655322292057255e+00 -4.2084949967079632e+00 -4.4622011117106153e+00 + 23 5.7380414788131207e+00 -3.5841969185149058e+00 -3.8827839829438688e+00 + 24 2.0701314764430685e+00 3.1499370533656190e+00 3.1565324853444698e+00 + 25 1.3030170721374645e+00 3.2711173928413317e+00 2.5081940917372791e+00 + 26 2.5776230786045939e+00 4.0127347066259897e+00 3.2182355135086644e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625094898067e-04 -3.1032459262177040e-04 8.1043030117471950e-04 - 19 8.5103884664914254e-04 -1.4572280597118469e-03 1.0163621287571445e-03 - 20 -6.5204659274939057e-04 4.3989037444674739e-04 4.9909839028631532e-04 - 21 -1.3888125888095134e-03 -3.1978049191290817e-04 1.1455681505629727e-03 - 22 -1.6084223473476296e-03 -1.5355394235202363e-03 1.4772010819351844e-03 - 23 2.6392672583440717e-04 -3.9375414417551127e-03 -3.6991583302200246e-04 - 24 8.6062827046548790e-04 -9.4179873487668705e-04 5.5396395555797203e-04 - 25 1.5933645478462865e-03 -2.2139156628290975e-03 -5.5078029723780941e-04 - 26 -1.5679561736454237e-03 3.5146224433513641e-04 2.4446924193838983e-03 + 18 3.6149625095571725e-04 -3.1032459263052550e-04 8.1043030117473349e-04 + 19 8.5103884662188244e-04 -1.4572280597071525e-03 1.0163621287543638e-03 + 20 -6.5204659274901945e-04 4.3989037447700791e-04 4.9909839028904252e-04 + 21 -1.3888125889514069e-03 -3.1978049248194420e-04 1.1455681505565557e-03 + 22 -1.6084223477996385e-03 -1.5355394224557757e-03 1.4772010822781041e-03 + 23 2.6392672685288674e-04 -3.9375414405480738e-03 -3.6991583333937880e-04 + 24 8.6062827042478370e-04 -9.4179873506334828e-04 5.5396395546095014e-04 + 25 1.5933645477524167e-03 -2.2139156628045932e-03 -5.5078029709943691e-04 + 26 -1.5679561733890424e-03 3.5146224505578228e-04 2.4446924196328459e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml index 854e8b4d45..0277d7991a 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_single.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:13 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,26 +15,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3754817467882767e+03 -1.4228425246441275e+03 -3.6087196200592489e+03 8.7407043142559303e+02 2.1665316510426268e+02 -6.0480791467747542e+02 -global_scalar: 4.531423038570333 + -1.3754817467882813e+03 -1.4228425246442055e+03 -3.6087196200592184e+03 8.7407043142559792e+02 2.1665316510417179e+02 -6.0480791467761571e+02 +global_scalar: 4.531423038570381 run_pos: ! |2 - 1 -2.7899546859706881e-01 2.4731857340427750e+00 -1.7290667720866193e-01 - 2 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-1.8836565351900401e+00 + 12 3.0032775230343471e+00 -4.8983022415926980e-01 -1.6190248016125621e+00 + 13 4.0448964161972807e+00 -9.0213155125594269e-01 -1.6385398398261892e+00 + 14 2.6035151245155976e+00 -4.0874995488530264e-01 -2.6555999073601715e+00 + 15 2.9761196776308503e+00 5.6287237451805949e-01 -1.2442626194416131e+00 + 16 2.6517373020764849e+00 -2.3957035509095892e+00 3.3389262134333686e-02 + 17 2.2311114923825035e+00 -2.1018393229879604e+00 1.1496088522769004e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -47,23 +48,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093296226164550e-04 2.6351124312060223e-04 -4.4905063547613568e-04 - 2 4.9594635271876775e-04 9.4561409237174846e-05 -5.4581325723053790e-04 - 3 3.3306088119081919e-04 2.3224949911015709e-04 -2.3659435306899653e-04 - 4 3.3692332940285361e-04 2.1926824120528752e-04 -2.4716611858555457e-04 - 5 3.3642541894622217e-04 4.1797578053944250e-04 -1.8011323945926332e-04 - 6 2.0926870695908031e-04 2.6449376032433555e-05 -1.0508922741401509e-04 - 7 1.4629046128363305e-04 -1.6873362379725323e-04 -6.8353900724087087e-05 - 8 1.5844098346817862e-04 3.7728756087615553e-05 -1.9162577392847385e-05 - 9 2.1299357198252531e-04 1.6917133003967874e-04 -6.3528006071188683e-05 - 10 5.4261569071251603e-05 -9.4655546204709643e-05 1.0511372702289179e-04 - 11 -3.2194218121513917e-05 -2.2025090185605342e-04 2.0300208519291412e-04 - 12 1.2640585449265036e-04 -2.9851081600945991e-04 -7.9476186245599681e-05 - 13 8.4523551795123310e-05 -4.0583140303606936e-04 -4.7550925831962545e-05 - 14 9.9954071734181717e-05 -4.2610809338914382e-04 -7.9255453072696249e-05 - 15 2.4417483202631243e-04 -2.3521005781666407e-04 -2.4875292755154228e-04 - 16 -9.0959360838797421e-06 3.7773746063106756e-06 2.4035204669042973e-04 - 17 5.7507084250803101e-05 2.2629200960629499e-04 2.0686926033796699e-04 + 1 4.7093296226165618e-04 2.6351124312058857e-04 -4.4905063547614403e-04 + 2 4.9594635271877252e-04 9.4561409237151983e-05 -5.4581325723054321e-04 + 3 3.3306088119082413e-04 2.3224949911015692e-04 -2.3659435306899455e-04 + 4 3.3692332940285378e-04 2.1926824120529077e-04 -2.4716611858554389e-04 + 5 3.3642541894623611e-04 4.1797578053944765e-04 -1.8011323945926958e-04 + 6 2.0926870695907706e-04 2.6449376032434591e-05 -1.0508922741400673e-04 + 7 1.4629046128361865e-04 -1.6873362379725188e-04 -6.8353900724066446e-05 + 8 1.5844098346817927e-04 3.7728756087617390e-05 -1.9162577392845779e-05 + 9 2.1299357198253474e-04 1.6917133003967807e-04 -6.3528006071197993e-05 + 10 5.4261569071247645e-05 -9.4655546204705848e-05 1.0511372702289633e-04 + 11 -3.2194218121526927e-05 -2.2025090185604412e-04 2.0300208519293052e-04 + 12 1.2640585449264128e-04 -2.9851081600947238e-04 -7.9476186245595616e-05 + 13 8.4523551795112752e-05 -4.0583140303608579e-04 -4.7550925831960783e-05 + 14 9.9954071734163598e-05 -4.2610809338915548e-04 -7.9255453072680826e-05 + 15 2.4417483202630842e-04 -2.3521005781668527e-04 -2.4875292755154548e-04 + 16 -9.0959360838764895e-06 3.7773746063197473e-06 2.4035204669042547e-04 + 17 5.7507084250817169e-05 2.2629200960630572e-04 2.0686926033795233e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml index 664921b147..1a017f0a6c 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nve_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:14 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200114774918006e+01 -2.6907707694141354e+01 -6.0080872444875970e+00 -2.5620425756344780e+01 -1.3450222538011893e+01 -1.4947348732785031e+00 -global_scalar: 0.5007318719663203 + -4.9200114760030708e+01 -2.6907707699312748e+01 -6.0080872440179061e+00 -2.5620425767600064e+01 -1.3450222535184853e+01 -1.4947348700253382e+00 +global_scalar: 0.5007318719399354 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -34,15 +35,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1392027588270928e+00 3.0171068018423082e+00 -3.5144628518853867e+00 - 19 1.5366124996934336e+00 2.6286809834236959e+00 -4.2452547844313493e+00 - 20 2.7628161763597592e+00 3.6842251687468450e+00 -3.9370881219419189e+00 - 21 4.9036621348471368e+00 -4.0757648444604762e+00 -3.6192617654906609e+00 - 22 4.3655322292129357e+00 -4.2084949964269480e+00 -4.4622011117992786e+00 - 23 5.7380414790507261e+00 -3.5841969189265162e+00 -3.8827839828320116e+00 - 24 2.0701314764933532e+00 3.1499370533556008e+00 3.1565324853054118e+00 - 25 1.3030170721038390e+00 3.2711173927738786e+00 2.5081940917867680e+00 - 26 2.5776230784374867e+00 4.0127347067334345e+00 3.2182355136150917e+00 + 18 2.1392027588241729e+00 3.0171068018404634e+00 -3.5144628518858858e+00 + 19 1.5366124996944652e+00 2.6286809834366300e+00 -4.2452547844429631e+00 + 20 2.7628161763703827e+00 3.6842251687412753e+00 -3.9370881219283147e+00 + 21 4.9036621349084646e+00 -4.0757648444931904e+00 -3.6192617654848509e+00 + 22 4.3655322292057255e+00 -4.2084949967079632e+00 -4.4622011117106153e+00 + 23 5.7380414788131207e+00 -3.5841969185149058e+00 -3.8827839829438688e+00 + 24 2.0701314764430685e+00 3.1499370533656190e+00 3.1565324853444698e+00 + 25 1.3030170721374645e+00 3.2711173928413317e+00 2.5081940917372791e+00 + 26 2.5776230786045939e+00 4.0127347066259897e+00 3.2182355135086644e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -64,15 +65,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 3.6149625094898067e-04 -3.1032459262177040e-04 8.1043030117471950e-04 - 19 8.5103884664914254e-04 -1.4572280597118469e-03 1.0163621287571445e-03 - 20 -6.5204659274939057e-04 4.3989037444674739e-04 4.9909839028631532e-04 - 21 -1.3888125888095134e-03 -3.1978049191290817e-04 1.1455681505629727e-03 - 22 -1.6084223473476296e-03 -1.5355394235202363e-03 1.4772010819351844e-03 - 23 2.6392672583440717e-04 -3.9375414417551127e-03 -3.6991583302200246e-04 - 24 8.6062827046548790e-04 -9.4179873487668705e-04 5.5396395555797203e-04 - 25 1.5933645478462865e-03 -2.2139156628290975e-03 -5.5078029723780941e-04 - 26 -1.5679561736454237e-03 3.5146224433513641e-04 2.4446924193838983e-03 + 18 3.6149625095571725e-04 -3.1032459263052550e-04 8.1043030117473349e-04 + 19 8.5103884662188244e-04 -1.4572280597071525e-03 1.0163621287543638e-03 + 20 -6.5204659274901945e-04 4.3989037447700791e-04 4.9909839028904252e-04 + 21 -1.3888125889514069e-03 -3.1978049248194420e-04 1.1455681505565557e-03 + 22 -1.6084223477996385e-03 -1.5355394224557757e-03 1.4772010822781041e-03 + 23 2.6392672685288674e-04 -3.9375414405480738e-03 -3.6991583333937880e-04 + 24 8.6062827042478370e-04 -9.4179873506334828e-04 5.5396395546095014e-04 + 25 1.5933645477524167e-03 -2.2139156628045932e-03 -5.5078029709943691e-04 + 26 -1.5679561733890424e-03 3.5146224505578228e-04 2.4446924196328459e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml index a49508ca15..f15e2a3c7f 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt.yaml @@ -1,7 +1,8 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 -epsilon: 5e-13 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:14 2024 +epsilon: 1e-12 skip_tests: prerequisites: ! | atom full @@ -13,26 +14,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3123962047757550e+03 -1.3675423591710460e+03 -3.5468492999583855e+03 7.8271738572396373e+02 2.6480486115495069e+02 -7.6950536863736306e+02 -global_scalar: 68.08659647423171 + -1.3123962047758187e+03 -1.3675423591720764e+03 -3.5468492999580299e+03 7.8271738572394452e+02 2.6480486115379637e+02 -7.6950536863892899e+02 +global_scalar: 68.08659647424867 run_pos: ! |2 - 1 -2.7802951913990959e-01 2.4737132264311215e+00 -1.7381271738602289e-01 - 2 3.0397800832473609e-01 2.9519031941431444e+00 -8.5908822750267100e-01 - 3 -6.9299720296404743e-01 1.2449766685866726e+00 -6.2329294828335358e-01 - 4 -1.5757894675975461e+00 1.4924105480974301e+00 -1.2497098747240374e+00 - 5 -8.9364750934418624e-01 9.3735293261000852e-01 4.0154813851989335e-01 - 6 2.9498813449175199e-01 2.2729986882976547e-01 -1.2847387164260673e+00 - 7 3.4080910885027837e-01 -9.8008218359699473e-03 -2.4635938021179546e+00 - 8 1.1647778042705452e+00 -4.8360070140706557e-01 -6.7668409924218165e-01 - 9 1.3786230528159027e+00 -2.5298559880150862e-01 2.6851325883861188e-01 - 10 2.0187712935465942e+00 -1.4287732348422091e+00 -9.6692440387148870e-01 - 11 1.7928755785831587e+00 -1.9879833661313322e+00 -1.8832605388690278e+00 - 12 3.0035558347419657e+00 -4.9042429038271507e-01 -1.6191927838346238e+00 - 13 4.0450911337530959e+00 -9.0293975523160919e-01 -1.6386440514135796e+00 - 14 2.6037405819194577e+00 -4.0959881564101863e-01 -2.6557674031621108e+00 - 15 2.9766330093335447e+00 5.6240461100771322e-01 -1.2447686007433758e+00 - 16 2.6517453810147344e+00 -2.3956939898026426e+00 3.3859750042781744e-02 - 17 2.2312525656149020e+00 -2.1013855689264771e+00 1.1500124166835219e+00 + 1 -2.7802951913978302e-01 2.4737132264315886e+00 -1.7381271738770820e-01 + 2 3.0397800832462774e-01 2.9519031941430738e+00 -8.5908822750493219e-01 + 3 -6.9299720296403144e-01 1.2449766685867643e+00 -6.2329294828390935e-01 + 4 -1.5757894675977402e+00 1.4924105480969891e+00 -1.2497098747245081e+00 + 5 -8.9364750934382919e-01 9.3735293261092456e-01 4.0154813851965188e-01 + 6 2.9498813449158368e-01 2.2729986882934847e-01 -1.2847387164261186e+00 + 7 3.4080910884973536e-01 -9.8008218373410172e-03 -2.4635938021178290e+00 + 8 1.1647778042705941e+00 -4.8360070140696521e-01 -6.7668409924193851e-01 + 9 1.3786230528162504e+00 -2.5298559880063631e-01 2.6851325883859889e-01 + 10 2.0187712935465760e+00 -1.4287732348423197e+00 -9.6692440387075651e-01 + 11 1.7928755785828601e+00 -1.9879833661321924e+00 -1.8832605388677695e+00 + 12 3.0035558347417104e+00 -4.9042429038332558e-01 -1.6191927838349707e+00 + 13 4.0450911337528455e+00 -9.0293975523220671e-01 -1.6386440514139291e+00 + 14 2.6037405819188639e+00 -4.0959881564248080e-01 -2.6557674031623937e+00 + 15 2.9766330093333795e+00 5.6240461100740513e-01 -1.2447686007445669e+00 + 16 2.6517453810150675e+00 -2.3956939898019254e+00 3.3859750044092363e-02 + 17 2.2312525656155877e+00 -2.1013855689248668e+00 1.1500124166847305e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -46,23 +47,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 1.8443993556501188e-03 1.0121779580014884e-03 -1.7361326034900006e-03 - 2 1.9401022924558343e-03 3.6428754787592733e-04 -2.1069540627804634e-03 - 3 1.3158623602983108e-03 8.9265747656461540e-04 -9.2144725682164657e-04 - 4 1.3306255280096089e-03 8.4281508655990054e-04 -9.6194026572564146e-04 - 5 1.3289682243410692e-03 1.6048237018834067e-03 -7.0511232123071470e-04 - 6 8.4113718611833661e-04 1.0389683283144290e-04 -4.1697370456873913e-04 - 7 5.9950574545626287e-04 -6.4437674895215604e-04 -2.7586696717582678e-04 - 8 6.4634547270651834e-04 1.4734228826522431e-04 -8.7540766366730972e-05 - 9 8.5561404484505246e-04 6.5123532540338036e-04 -2.5782947158524498e-04 - 10 2.4688038968480818e-04 -3.5995975344065565e-04 3.8912416843275122e-04 - 11 -8.4672359473208624e-05 -8.4134349031640394e-04 7.6463157764214873e-04 - 12 5.2321633256319569e-04 -1.1418047427480882e-03 -3.1842516233562688e-04 - 13 3.6258187754908603e-04 -1.5531581259494627e-03 -1.9590476904013767e-04 - 14 4.2166181631324117e-04 -1.6310415916630540e-03 -3.1740232809360453e-04 - 15 9.7471807923383321e-04 -8.9939841790992827e-04 -9.6757308853409824e-04 - 16 4.1534888649229478e-06 1.7705740202856454e-05 9.0753010117813394e-04 - 17 2.5969943716026096e-04 8.7075266710270492e-04 7.7887058799645239e-04 + 1 1.8443993556507550e-03 1.0121779580008364e-03 -1.7361326034906117e-03 + 2 1.9401022924561704e-03 3.6428754787474148e-04 -2.1069540627809144e-03 + 3 1.3158623602986111e-03 8.9265747656469769e-04 -9.2144725682167822e-04 + 4 1.3306255280096579e-03 8.4281508656016844e-04 -9.6194026572521364e-04 + 5 1.3289682243418409e-03 1.6048237018838117e-03 -7.0511232123120064e-04 + 6 8.4113718611817723e-04 1.0389683283156166e-04 -4.1697370456838980e-04 + 7 5.9950574545550414e-04 -6.4437674895204296e-04 -2.7586696717479603e-04 + 8 6.4634547270655271e-04 1.4734228826538870e-04 -8.7540766366732192e-05 + 9 8.5561404484556399e-04 6.5123532540342654e-04 -2.5782947158584915e-04 + 10 2.4688038968457540e-04 -3.5995975344040265e-04 3.8912416843293944e-04 + 11 -8.4672359473939376e-05 -8.4134349031586390e-04 7.6463157764299549e-04 + 12 5.2321633256271539e-04 -1.1418047427487572e-03 -3.1842516233546950e-04 + 13 3.6258187754852045e-04 -1.5531581259503574e-03 -1.9590476904008422e-04 + 14 4.2166181631227780e-04 -1.6310415916636891e-03 -3.1740232809282303e-04 + 15 9.7471807923364706e-04 -8.9939841791107037e-04 -9.6757308853435780e-04 + 16 4.1534888650543531e-06 1.7705740203412426e-05 9.0753010117785768e-04 + 17 2.5969943716097897e-04 8.7075266710338634e-04 7.7887058799558893e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml index 6068993094..dab3d52a04 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_nvt_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:15 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -13,8 +14,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.4827261116680472e+02 -1.8411194349753309e+01 -1.0752762859308649e+02 -2.1814511477016276e+02 1.7027764307147623e+02 2.1058942244057214e+01 -global_scalar: 0.9532609554739606 + -1.4827261099624999e+02 -1.8411194282828326e+01 -1.0752762861573947e+02 -2.1814511471949461e+02 1.7027764305079162e+02 2.1058942246396320e+01 +global_scalar: 0.9532609552151339 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 @@ -33,15 +34,15 @@ run_pos: ! |2 15 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 16 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 17 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 - 18 2.1395635672981443e+00 3.0168023048492310e+00 -3.5136606977867388e+00 - 19 1.5374727853253387e+00 2.6272080572819609e+00 -4.2442423140467360e+00 - 20 2.7621434607990372e+00 3.6846842324743214e+00 -3.9366036441030396e+00 - 21 4.9022821625125470e+00 -4.0760572704380627e+00 -3.6181235130909242e+00 - 22 4.3639257458824501e+00 -4.2100277325126187e+00 -4.4607219430080747e+00 - 23 5.7383384133351401e+00 -3.5881799317362106e+00 -3.8831848688588710e+00 - 24 2.0709922902331592e+00 3.1490053461169678e+00 3.1570777020268803e+00 - 25 1.3046262534530633e+00 3.2688902575528282e+00 2.5076144141701078e+00 - 26 2.5760050685080813e+00 4.0131166912605272e+00 3.2207051913215210e+00 + 18 2.1395635672857165e+00 3.0168023048413781e+00 -3.5136606977888540e+00 + 19 1.5374727853296883e+00 2.6272080573369379e+00 -4.2442423140961818e+00 + 20 2.7621434608442974e+00 3.6846842324506923e+00 -3.9366036440451500e+00 + 21 4.9022821627727593e+00 -4.0760572705753884e+00 -3.6181235130648650e+00 + 22 4.3639257458473608e+00 -4.2100277337137149e+00 -4.4607219426242057e+00 + 23 5.7383384123314833e+00 -3.5881799299869201e+00 -3.8831848693467652e+00 + 24 2.0709922900187268e+00 3.1490053461587983e+00 3.1570777021928031e+00 + 25 1.3046262535950772e+00 3.2688902578410239e+00 2.5076144139609013e+00 + 26 2.5760050692220648e+00 4.0131166908053464e+00 3.2207051908683750e+00 27 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 @@ -63,15 +64,15 @@ run_vel: ! |2 15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03 16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03 17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04 - 18 7.8522439440007537e-04 -6.6826115062653757e-04 1.7528441282153480e-03 - 19 1.8628941719211862e-03 -3.1840047051916367e-03 2.2062694140207390e-03 - 20 -1.4430972531298200e-03 9.7564145841628493e-04 1.0686492192569898e-03 - 21 -3.0047717246574385e-03 -6.6139343888744974e-04 2.4784169377340712e-03 - 22 -3.4980341571643784e-03 -3.3380963325931002e-03 3.2191613979274040e-03 - 23 5.9333930569297746e-04 -8.6231086219834968e-03 -8.2692040355627789e-04 - 24 1.8727912311097641e-03 -2.0349136820274911e-03 1.1951471753018509e-03 - 25 3.4887365958745920e-03 -4.8232966889391266e-03 -1.2263764490291313e-03 - 26 -3.4770258010749858e-03 7.8662050223200905e-04 5.3381090661352298e-03 + 18 7.8522439447394326e-04 -6.6826115070004464e-04 1.7528441282176825e-03 + 19 1.8628941717384645e-03 -3.1840047052822556e-03 2.2062694140226819e-03 + 20 -1.4430972532419690e-03 9.7564145880034414e-04 1.0686492192457362e-03 + 21 -3.0047717260078453e-03 -6.6139344410253201e-04 2.4784169376928207e-03 + 22 -3.4980341614361554e-03 -3.3380963226435131e-03 3.2191614012082861e-03 + 23 5.9333931535562748e-04 -8.6231086111150188e-03 -8.2692040667271425e-04 + 24 1.8727912307694413e-03 -2.0349136837727452e-03 1.1951471743788897e-03 + 25 3.4887365951187166e-03 -4.8232966888750181e-03 -1.2263764478999317e-03 + 26 -3.4770257989604671e-03 7.8662050913487318e-04 5.3381090686904524e-03 27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04 28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03 29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml index 02acb437d9..5af45ebc1b 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_single.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_single.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:15 2024 epsilon: 7.5e-13 skip_tests: prerequisites: ! | @@ -14,26 +15,26 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -1.3754817466835989e+03 -1.4228425246166137e+03 -3.6087196201914348e+03 8.7407043149698916e+02 2.1665316519769885e+02 -6.0480791462033073e+02 -global_scalar: 4.531423038570297 + -1.3754817466835991e+03 -1.4228425246166084e+03 -3.6087196201914162e+03 8.7407043149699155e+02 2.1665316519769920e+02 -6.0480791462032153e+02 +global_scalar: 4.531423038570312 run_pos: ! |2 - 1 -2.7899546859693136e-01 2.4731857340428784e+00 -1.7290667720876285e-01 - 2 3.0296221616793728e-01 2.9517129917211546e+00 -8.5798904365355155e-01 - 3 -6.9368802362166204e-01 1.2445115422149751e+00 -6.2281111185285498e-01 - 4 -1.5764879646739487e+00 1.4919714416722010e+00 -1.2492069413381564e+00 - 5 -8.9434512967954416e-01 9.3651699743538730e-01 4.0191726569957442e-01 - 6 2.9454439635065910e-01 2.2724545796943096e-01 -1.2845195052894232e+00 - 7 3.4049112905311751e-01 -9.4655677385591108e-03 -2.4634480019885228e+00 - 8 1.1644354555589662e+00 -4.8367776651302724e-01 -6.7663643931660777e-01 - 9 1.3781717822376680e+00 -2.5332509534947545e-01 2.6864954447021416e-01 - 10 2.0186368605645764e+00 -1.4285861423742918e+00 -9.6712491246325605e-01 - 11 1.7929137227200918e+00 -1.9875455388074483e+00 -1.8836565351900385e+00 - 12 3.0032775230343125e+00 -4.8983022415935312e-01 -1.6190248016126132e+00 - 13 4.0448964161972283e+00 -9.0213155125606947e-01 -1.6385398398262669e+00 - 14 2.6035151245155355e+00 -4.0874995488538129e-01 -2.6555999073602123e+00 - 15 2.9761196776308694e+00 5.6287237451798222e-01 -1.2442626194416753e+00 - 16 2.6517373020764219e+00 -2.3957035509096407e+00 3.3389262134315700e-02 - 17 2.2311114923824857e+00 -2.1018393229879817e+00 1.1496088522768926e+00 + 1 -2.7899546859693225e-01 2.4731857340428771e+00 -1.7290667720876018e-01 + 2 3.0296221616793617e-01 2.9517129917211538e+00 -8.5798904365354822e-01 + 3 -6.9368802362166271e-01 1.2445115422149740e+00 -6.2281111185285387e-01 + 4 -1.5764879646739496e+00 1.4919714416722003e+00 -1.2492069413381550e+00 + 5 -8.9434512967954460e-01 9.3651699743538508e-01 4.0191726569957453e-01 + 6 2.9454439635065910e-01 2.2724545796943096e-01 -1.2845195052894227e+00 + 7 3.4049112905311785e-01 -9.4655677385578896e-03 -2.4634480019885232e+00 + 8 1.1644354555589664e+00 -4.8367776651302741e-01 -6.7663643931660822e-01 + 9 1.3781717822376678e+00 -2.5332509534947639e-01 2.6864954447021405e-01 + 10 2.0186368605645768e+00 -1.4285861423742912e+00 -9.6712491246325705e-01 + 11 1.7929137227200933e+00 -1.9875455388074468e+00 -1.8836565351900401e+00 + 12 3.0032775230343129e+00 -4.8983022415935129e-01 -1.6190248016126136e+00 + 13 4.0448964161972292e+00 -9.0213155125606781e-01 -1.6385398398262672e+00 + 14 2.6035151245155359e+00 -4.0874995488537874e-01 -2.6555999073602123e+00 + 15 2.9761196776308694e+00 5.6287237451798344e-01 -1.2442626194416739e+00 + 16 2.6517373020764223e+00 -2.3957035509096416e+00 3.3389262134313369e-02 + 17 2.2311114923824853e+00 -2.1018393229879830e+00 1.1496088522768906e+00 18 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 19 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 20 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 @@ -47,23 +48,23 @@ run_pos: ! |2 28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 run_vel: ! |2 - 1 4.7093296226165759e-04 2.6351124312057290e-04 -4.4905063547614669e-04 - 2 4.9594635271877263e-04 9.4561409237138512e-05 -5.4581325723053421e-04 - 3 3.3306088119083101e-04 2.3224949911015481e-04 -2.3659435306900835e-04 - 4 3.3692332940286717e-04 2.1926824120529722e-04 -2.4716611858556465e-04 - 5 3.3642541894624077e-04 4.1797578053943724e-04 -1.8011323945929064e-04 - 6 2.0926870695908283e-04 2.6449376032441855e-05 -1.0508922741401397e-04 - 7 1.4629046128362884e-04 -1.6873362379723068e-04 -6.8353900724071325e-05 - 8 1.5844098346817943e-04 3.7728756087619084e-05 -1.9162577392849316e-05 - 9 2.1299357198253002e-04 1.6917133003966749e-04 -6.3528006071200284e-05 - 10 5.4261569071245856e-05 -9.4655546204698666e-05 1.0511372702289738e-04 - 11 -3.2194218121523431e-05 -2.2025090185602293e-04 2.0300208519292805e-04 - 12 1.2640585449263546e-04 -2.9851081600946745e-04 -7.9476186245575585e-05 - 13 8.4523551795102263e-05 -4.0583140303608199e-04 -4.7550925831931374e-05 - 14 9.9954071734163435e-05 -4.2610809338913835e-04 -7.9255453072661880e-05 - 15 2.4417483202629980e-04 -2.3521005781669047e-04 -2.4875292755152005e-04 - 16 -9.0959360838836724e-06 3.7773746063194780e-06 2.4035204669042463e-04 - 17 5.7507084250807628e-05 2.2629200960629336e-04 2.0686926033794547e-04 + 1 4.7093296226165726e-04 2.6351124312057366e-04 -4.4905063547614750e-04 + 2 4.9594635271877263e-04 9.4561409237139244e-05 -5.4581325723053519e-04 + 3 3.3306088119083079e-04 2.3224949911015511e-04 -2.3659435306900900e-04 + 4 3.3692332940286722e-04 2.1926824120529738e-04 -2.4716611858556574e-04 + 5 3.3642541894624012e-04 4.1797578053943767e-04 -1.8011323945929113e-04 + 6 2.0926870695908297e-04 2.6449376032441903e-05 -1.0508922741401427e-04 + 7 1.4629046128362941e-04 -1.6873362379723111e-04 -6.8353900724071745e-05 + 8 1.5844098346817935e-04 3.7728756087619165e-05 -1.9162577392849147e-05 + 9 2.1299357198252962e-04 1.6917133003966793e-04 -6.3528006071199972e-05 + 10 5.4261569071245965e-05 -9.4655546204698774e-05 1.0511372702289789e-04 + 11 -3.2194218121522970e-05 -2.2025090185602350e-04 2.0300208519292848e-04 + 12 1.2640585449263589e-04 -2.9851081600946756e-04 -7.9476186245575178e-05 + 13 8.4523551795102697e-05 -4.0583140303608210e-04 -4.7550925831930561e-05 + 14 9.9954071734164248e-05 -4.2610809338913878e-04 -7.9255453072661758e-05 + 15 2.4417483202630007e-04 -2.3521005781669015e-04 -2.4875292755151984e-04 + 16 -9.0959360838839976e-06 3.7773746063194848e-06 2.4035204669042588e-04 + 17 5.7507084250806896e-05 2.2629200960629374e-04 2.0686926033794661e-04 18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04 19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03 20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03 diff --git a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml index 92754f85f5..ed92a4e5a8 100644 --- a/unittest/force-styles/tests/fix-timestep-rigid_small.yaml +++ b/unittest/force-styles/tests/fix-timestep-rigid_small.yaml @@ -1,6 +1,7 @@ --- -lammps_version: 17 Feb 2022 -date_generated: Fri Mar 18 22:18:00 2022 +lammps_version: 7 Feb 2024 +tags: +date_generated: Thu Apr 4 21:27:15 2024 epsilon: 5e-13 skip_tests: prerequisites: ! | @@ -14,8 +15,8 @@ post_commands: ! | input_file: in.fourmol natoms: 29 run_stress: ! |- - -4.9200116134789873e+01 -2.6907707565987707e+01 -6.0080860422278581e+00 -2.5620423972101300e+01 -1.3450224059983967e+01 -1.4947288487003760e+00 -global_scalar: 18.3405601674144 + -4.9200116134788615e+01 -2.6907707565987401e+01 -6.0080860422276308e+00 -2.5620423972100241e+01 -1.3450224059984270e+01 -1.4947288487006070e+00 +global_scalar: 18.340560167414402 run_pos: ! |2 1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 2 3.0197083955402204e-01 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