From f0af982d09c323b0d40128c83355e18ecda7fe32 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Thu, 15 Dec 2022 13:22:15 -0500 Subject: [PATCH] tiny_epoxy: actually use log files --- .../log.4Nov2022.tiny_epoxy.stabilized.g++.1 | 92 ++++++++++++++---- .../log.4Nov2022.tiny_epoxy.stabilized.g++.4 | 93 +++++++++++++++---- 2 files changed, 152 insertions(+), 33 deletions(-) diff --git a/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1 index b5eb8c4157..24b8fb0987 100644 --- a/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1 +++ b/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1 @@ -1,4 +1,24 @@ LAMMPS (4 Nov 2022) +# two molecules DGEBA (diepoxy) and one DETA (linker) +# two crosslinking reactions + +units real + +boundary p p p + +atom_style full + +pair_style lj/class2 8 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_epoxy.data Reading data file ... orthogonal box = (10 -10 -15) to (30 20 10) 1 by 1 by 1 MPI processor grid @@ -33,7 +53,11 @@ Finding 1-2 1-3 1-4 neighbors ... 19 = max # of 1-4 neighbors 22 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.022 seconds + read_data CPU = 0.015 seconds + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_pre.molecule_template Read molecule template mol1: 1 molecules 0 fragments @@ -42,6 +66,7 @@ Read molecule template mol1: 53 angles with max type 29 66 dihedrals with max type 39 3 impropers with max type 5 +molecule mol2 rxn1_stp1_post.molecule_template Read molecule template mol2: 1 molecules 0 fragments @@ -50,6 +75,7 @@ Read molecule template mol2: 55 angles with max type 36 75 dihedrals with max type 51 2 impropers with max type 5 +molecule mol3 rxn1_stp2_post.molecule_template Read molecule template mol3: 1 molecules 0 fragments @@ -58,6 +84,7 @@ Read molecule template mol3: 53 angles with max type 37 72 dihedrals with max type 53 3 impropers with max type 5 +molecule mol4 rxn2_stp1_pre.molecule_template Read molecule template mol4: 1 molecules 0 fragments @@ -66,6 +93,7 @@ Read molecule template mol4: 73 angles with max type 41 96 dihedrals with max type 54 3 impropers with max type 5 +molecule mol5 rxn2_stp1_post.molecule_template Read molecule template mol5: 1 molecules 0 fragments @@ -74,6 +102,7 @@ Read molecule template mol5: 75 angles with max type 37 108 dihedrals with max type 53 2 impropers with max type 5 +molecule mol6 rxn2_stp2_post.molecule_template Read molecule template mol6: 1 molecules 0 fragments @@ -82,14 +111,46 @@ Read molecule template mol6: 73 angles with max type 50 102 dihedrals with max type 66 3 impropers with max type 22 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix rxns all bond/react stabilization yes statted_grp .03 react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined + +fix 1 statted_grp_REACT nvt temp 300 300 100 + +thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] + +run 2000 + CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: + - fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012 -The log file lists these citations in BibTeX format. + +@Article{Gissinger17, + author = {J. R. Gissinger and B. D. Jensen and K. E. Wise}, + title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations}, + journal = {Polymer}, + year = 2017, + volume = 128, + pages = {211--217} +} + +@Article{Gissinger20, + author = {J. R. Gissinger, B. D. Jensen, K. E. Wise}, + title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics}, + journal = {Macromolecules}, + year = 2020, + volume = 53, + number = 22, + pages = {9953--9961} +} CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE @@ -111,10 +172,6 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.64 | 16.64 | 16.64 Mbytes Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] 0 300 0 0 0 0 @@ -158,21 +215,21 @@ Per MPI rank memory allocation (min/avg/max) = 16.64 | 16.64 | 16.64 Mbytes 1900 315.3756 1 1 1 1 1950 260.65335 1 1 1 1 2000 354.03612 1 1 1 1 -Loop time of 0.909774 on 1 procs for 2000 steps with 118 atoms +Loop time of 0.910097 on 1 procs for 2000 steps with 118 atoms -Performance: 189.937 ns/day, 0.126 hours/ns, 2198.347 timesteps/s, 259.405 katom-step/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 189.870 ns/day, 0.126 hours/ns, 2197.568 timesteps/s, 259.313 katom-step/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.10261 | 0.10261 | 0.10261 | 0.0 | 11.28 -Bond | 0.63695 | 0.63695 | 0.63695 | 0.0 | 70.01 -Neigh | 0.013916 | 0.013916 | 0.013916 | 0.0 | 1.53 -Comm | 0.0057214 | 0.0057214 | 0.0057214 | 0.0 | 0.63 -Output | 0.0005856 | 0.0005856 | 0.0005856 | 0.0 | 0.06 -Modify | 0.14641 | 0.14641 | 0.14641 | 0.0 | 16.09 -Other | | 0.003576 | | | 0.39 +Pair | 0.10286 | 0.10286 | 0.10286 | 0.0 | 11.30 +Bond | 0.63714 | 0.63714 | 0.63714 | 0.0 | 70.01 +Neigh | 0.013949 | 0.013949 | 0.013949 | 0.0 | 1.53 +Comm | 0.0056606 | 0.0056606 | 0.0056606 | 0.0 | 0.62 +Output | 0.00055825 | 0.00055825 | 0.00055825 | 0.0 | 0.06 +Modify | 0.14629 | 0.14629 | 0.14629 | 0.0 | 16.07 +Other | | 0.003637 | | | 0.40 Nlocal: 118 ave 118 max 118 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -186,4 +243,7 @@ Ave neighs/atom = 29.550847 Ave special neighs/atom = 10.576271 Neighbor list builds = 68 Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data nofix Total wall time: 0:00:01 diff --git a/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4 index 5d6ac8ab21..5d1a80405a 100644 --- a/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4 +++ b/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4 @@ -1,5 +1,24 @@ LAMMPS (4 Nov 2022) -WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:529) +# two molecules DGEBA (diepoxy) and one DETA (linker) +# two crosslinking reactions + +units real + +boundary p p p + +atom_style full + +pair_style lj/class2 8 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_epoxy.data Reading data file ... orthogonal box = (10 -10 -15) to (30 20 10) 1 by 2 by 2 MPI processor grid @@ -34,7 +53,11 @@ Finding 1-2 1-3 1-4 neighbors ... 19 = max # of 1-4 neighbors 22 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.009 seconds + read_data CPU = 0.013 seconds + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_pre.molecule_template Read molecule template mol1: 1 molecules 0 fragments @@ -43,6 +66,7 @@ Read molecule template mol1: 53 angles with max type 29 66 dihedrals with max type 39 3 impropers with max type 5 +molecule mol2 rxn1_stp1_post.molecule_template Read molecule template mol2: 1 molecules 0 fragments @@ -51,6 +75,7 @@ Read molecule template mol2: 55 angles with max type 36 75 dihedrals with max type 51 2 impropers with max type 5 +molecule mol3 rxn1_stp2_post.molecule_template Read molecule template mol3: 1 molecules 0 fragments @@ -59,6 +84,7 @@ Read molecule template mol3: 53 angles with max type 37 72 dihedrals with max type 53 3 impropers with max type 5 +molecule mol4 rxn2_stp1_pre.molecule_template Read molecule template mol4: 1 molecules 0 fragments @@ -67,6 +93,7 @@ Read molecule template mol4: 73 angles with max type 41 96 dihedrals with max type 54 3 impropers with max type 5 +molecule mol5 rxn2_stp1_post.molecule_template Read molecule template mol5: 1 molecules 0 fragments @@ -75,6 +102,7 @@ Read molecule template mol5: 75 angles with max type 37 108 dihedrals with max type 53 2 impropers with max type 5 +molecule mol6 rxn2_stp2_post.molecule_template Read molecule template mol6: 1 molecules 0 fragments @@ -83,14 +111,46 @@ Read molecule template mol6: 73 angles with max type 50 102 dihedrals with max type 66 3 impropers with max type 22 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix rxns all bond/react stabilization yes statted_grp .03 react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined + +fix 1 statted_grp_REACT nvt temp 300 300 100 + +thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] + +run 2000 + CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: + - fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012 -The log file lists these citations in BibTeX format. + +@Article{Gissinger17, + author = {J. R. Gissinger and B. D. Jensen and K. E. Wise}, + title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations}, + journal = {Polymer}, + year = 2017, + volume = 128, + pages = {211--217} +} + +@Article{Gissinger20, + author = {J. R. Gissinger, B. D. Jensen, K. E. Wise}, + title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics}, + journal = {Macromolecules}, + year = 2020, + volume = 53, + number = 22, + pages = {9953--9961} +} CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE @@ -112,10 +172,6 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 1 Per MPI rank memory allocation (min/avg/max) = 16.63 | 16.63 | 16.64 Mbytes Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] 0 300 0 0 0 0 @@ -159,21 +215,21 @@ Per MPI rank memory allocation (min/avg/max) = 16.63 | 16.63 | 16.64 Mbytes 1900 315.3756 1 1 1 1 1950 260.65334 1 1 1 1 2000 354.03612 1 1 1 1 -Loop time of 0.473184 on 4 procs for 2000 steps with 118 atoms +Loop time of 0.47159 on 4 procs for 2000 steps with 118 atoms -Performance: 365.186 ns/day, 0.066 hours/ns, 4226.686 timesteps/s, 498.749 katom-step/s -100.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 366.420 ns/day, 0.065 hours/ns, 4240.970 timesteps/s, 500.434 katom-step/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.01651 | 0.024868 | 0.039209 | 5.4 | 5.26 -Bond | 0.072805 | 0.16458 | 0.21783 | 13.9 | 34.78 -Neigh | 0.0056701 | 0.0057265 | 0.0057792 | 0.1 | 1.21 -Comm | 0.028105 | 0.095922 | 0.19546 | 20.3 | 20.27 -Output | 0.00034311 | 0.00041507 | 0.0006278 | 0.0 | 0.09 -Modify | 0.17725 | 0.17761 | 0.17826 | 0.1 | 37.54 -Other | | 0.004064 | | | 0.86 +Pair | 0.016546 | 0.024458 | 0.038858 | 5.5 | 5.19 +Bond | 0.072622 | 0.16458 | 0.21778 | 13.9 | 34.90 +Neigh | 0.0056307 | 0.0056812 | 0.0057292 | 0.1 | 1.20 +Comm | 0.028022 | 0.095922 | 0.19526 | 20.3 | 20.34 +Output | 0.00034591 | 0.00041633 | 0.00062378 | 0.0 | 0.09 +Modify | 0.17613 | 0.17649 | 0.17711 | 0.1 | 37.43 +Other | | 0.00404 | | | 0.86 Nlocal: 29.5 ave 45 max 7 min Histogram: 1 0 0 0 0 0 1 1 0 1 @@ -187,4 +243,7 @@ Ave neighs/atom = 29.550847 Ave special neighs/atom = 10.576271 Neighbor list builds = 68 Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data nofix Total wall time: 0:00:00