From 21745538a76b2e421c4229503bd22539c5389816 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 2 Apr 2024 23:02:04 -0400 Subject: [PATCH] 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 examples/rigid/log.20Mar22.rigid.poems.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.poems2.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.poems2.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.poems3.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.poems3.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.poems4.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.poems4.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.poems5.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.poems5.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.small.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.small.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.small.infile.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.small.infile.g++.4 delete mode 100644 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examples/rigid/log.25Mar24.rigid.small.g++.1 delete mode 100644 examples/rigid/log.25Mar24.rigid.small.g++.4 delete mode 100644 examples/rigid/log.25Mar24.rigid.small.infile.g++.1 delete mode 100644 examples/rigid/log.25Mar24.rigid.small.infile.g++.4 delete mode 100644 examples/rigid/log.25Mar24.rigid.tnr.g++.1 delete mode 100644 examples/rigid/log.25Mar24.rigid.tnr.g++.4 create mode 100644 examples/rigid/log.27Nov18.rigid.atomfile.g++.1 create mode 100644 examples/rigid/log.27Nov18.rigid.atomfile.g++.4 create mode 100644 examples/rigid/log.27Nov18.rigid.atomvar.g++.1 create mode 100644 examples/rigid/log.27Nov18.rigid.atomvar.g++.4 create mode 100644 examples/rigid/log.27Nov18.rigid.early.g++.1 create mode 100644 examples/rigid/log.27Nov18.rigid.early.g++.4 create mode 100644 examples/rigid/log.27Nov18.rigid.g++.1 create mode 100644 examples/rigid/log.27Nov18.rigid.g++.4 create mode 100644 examples/rigid/log.27Nov18.rigid.nve.early.g++.1 create mode 100644 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 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 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 -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 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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 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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 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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 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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 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 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 + 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 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 + 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 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 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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 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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 -0.00076532811 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 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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 -7.9722832e-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 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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 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 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 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 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 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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 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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 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 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 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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 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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 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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 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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 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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 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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 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 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-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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-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 1.4878541800989344e+00 -1.2440909745469027e+00 - 5 -8.7601967096385724e-01 9.3417436540614585e-01 4.0272031680429610e-01 - 6 3.0755837780630380e-01 2.2629147986222176e-01 -1.2791162680674191e+00 - 7 3.5322094628027934e-01 -1.0043890952942114e-02 -2.4548503163675806e+00 - 8 1.1736205127908210e+00 -4.8269091330536096e-01 -6.7273784266496328e-01 - 9 1.3865071239753313e+00 -2.5278331076580596e-01 2.6996653369765600e-01 - 10 2.0239883243193466e+00 -1.4252201368163044e+00 -9.6228264545858089e-01 - 11 1.7991233925767878e+00 -1.9828365722521095e+00 -1.8762366544350000e+00 - 12 3.0044710092991682e+00 -4.8928363303924272e-01 -1.6126944183953009e+00 - 13 4.0415308387391402e+00 -9.0061411581958151e-01 -1.6321139880365303e+00 - 14 2.6064005411335902e+00 -4.0859653026938592e-01 -2.6465043951813936e+00 - 15 2.9775904824773161e+00 5.6065407887862850e-01 -1.2391617757509259e+00 - 16 2.6542663248059526e+00 -2.3895844048753085e+00 3.5746598094734239e-02 - 17 2.2355490747049700e+00 -2.0962135127172692e+00 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-3.9329047688996304e+00 1.5399898445636406e+00 + 29 -1.2195954744860957e+00 -3.5211468177700818e+00 2.2116264666073615e+00 run_vel: ! |2 - 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 + 1 1.2393084479630034e-03 7.0215195817155049e-04 -1.1910956210640397e-03 + 2 1.3060936199988536e-03 2.5041119719347224e-04 -1.4496302699051125e-03 + 3 8.7069732478159932e-04 6.1866591813748923e-04 -6.2317312592554579e-04 + 4 8.8100215742025064e-04 5.8380213791516000e-04 -6.5145037264846529e-04 + 5 8.7979303397991678e-04 1.1152950208762130e-03 -4.7231382224758212e-04 + 6 5.3965146863311727e-04 6.8643008418757634e-05 -2.7149223435848658e-04 + 7 3.7117679682181569e-04 -4.5322194777211656e-04 -1.7317402888851005e-04 + 8 4.0378854177636284e-04 9.9015358993666757e-05 -4.1783685861269460e-05 + 9 5.4970639315540500e-04 4.5048022318729304e-04 -1.6045108899919851e-04 + 10 1.2521448037945991e-04 -2.5472783650533836e-04 2.9052485920877619e-04 + 11 -1.0599027352488127e-04 -5.9051612835384309e-04 5.5226010155799178e-04 + 12 3.1798607399623040e-04 -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 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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-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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-8.9434512967440649e-01 9.3651699743494377e-01 4.0191726558257690e-01 + 6 2.9454439634452678e-01 2.2724545792543693e-01 -1.2845195053960459e+00 + 7 3.4049112903278234e-01 -9.4655678321664549e-03 -2.4634480020857370e+00 + 8 1.1644354555804921e+00 -4.8367776650962330e-01 -6.7663643940738027e-01 + 9 1.3781717822695918e+00 -2.5332509530017322e-01 2.6864954436590494e-01 + 10 2.0186368606042460e+00 -1.4285861423625348e+00 -9.6712491252784183e-01 + 11 1.7929137227578726e+00 -1.9875455388406436e+00 -1.8836565352267429e+00 + 12 3.0032775230400142e+00 -4.8983022415161337e-01 -1.6190248017342870e+00 + 13 4.0448964162126639e+00 -9.0213155122374034e-01 -1.6385398399478515e+00 + 14 2.6035151245016883e+00 -4.0874995493201027e-01 -2.6555999074785985e+00 + 15 2.9761196776172243e+00 5.6287237454118566e-01 -1.2442626196081918e+00 + 16 2.6517373021566577e+00 -2.3957035508393689e+00 3.3389262100618433e-02 + 17 2.2311114924744668e+00 -2.1018393228799419e+00 1.1496088522376777e+00 + 18 2.1390642573199212e+00 3.0164773560692755e+00 -3.5143984803853900e+00 + 19 1.5353246655143720e+00 2.6305911186314508e+00 -4.2455871034736816e+00 + 20 2.7649421538935122e+00 3.6818603528430254e+00 -3.9364115785985936e+00 + 21 4.9043112657301942e+00 -4.0774268210396798e+00 -3.6200836396129796e+00 + 22 4.3665322424286144e+00 -4.2075138112953070e+00 -4.4636587264885614e+00 + 23 5.7355405581987764e+00 -3.5789558641907195e+00 -3.8805763324090350e+00 + 24 2.0692780332810026e+00 3.1504920436416008e+00 3.1571131300668833e+00 + 25 1.3007297593168636e+00 3.2745259354178766e+00 2.5110163874103986e+00 + 26 2.5819416446099002e+00 4.0104903120757012e+00 3.2150249624525742e+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 4.7093289825842481e-04 2.6351122778449815e-04 -4.4905093064115029e-04 - 2 4.9594625316470614e-04 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-2.4875318161051720e-04 - 16 -9.0958138549606716e-06 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 + 1 4.7093289825841293e-04 2.6351122778450888e-04 -4.4905093064113717e-04 + 2 4.9594625316469964e-04 9.4561370489668111e-05 -5.4581359894048111e-04 + 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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 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 + 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 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 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 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);