diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 index 26c11bd020..440b2e5cf0 100644 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 @@ -1,4 +1,25 @@ LAMMPS (4 Nov 2022) +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25 Reading data file ... orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648) 1 by 1 by 1 MPI processor grid @@ -36,6 +57,10 @@ Finding 1-2 1-3 1-4 neighbors ... 41 = max # of special neighbors special bonds CPU = 0.026 seconds read_data CPU = 0.937 seconds + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template Read molecule template mol1: 1 molecules 0 fragments @@ -44,6 +69,7 @@ Read molecule template mol1: 25 angles with max type 24 23 dihedrals with max type 33 2 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.molecule_template Read molecule template mol2: 1 molecules 0 fragments @@ -52,6 +78,7 @@ Read molecule template mol2: 31 angles with max type 23 39 dihedrals with max type 30 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template Read molecule template mol3: 1 molecules 0 fragments @@ -60,6 +87,7 @@ Read molecule template mol3: 25 angles with max type 23 30 dihedrals with max type 30 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template Read molecule template mol4: 1 molecules 0 fragments @@ -68,15 +96,53 @@ Read molecule template mol4: 19 angles with max type 25 16 dihedrals with max type 29 2 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined +# stable at 800K +fix 1 statted_grp_REACT nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 + 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 @@ -107,10 +173,6 @@ 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) = 209.8 | 209.8 | 209.8 Mbytes Step Temp Press Density f_myrxns[1] f_myrxns[2] 0 800 3666.3948 0.80366765 0 0 @@ -147,4 +209,7 @@ Ave neighs/atom = 196.80781 Ave special neighs/atom = 9.8480114 Neighbor list builds = 128 Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data Total wall time: 0:01:29 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 index 69a663c59c..52b36325b8 100644 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 @@ -1,5 +1,25 @@ 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) +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25 Reading data file ... orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648) 2 by 1 by 2 MPI processor grid @@ -36,7 +56,11 @@ Finding 1-2 1-3 1-4 neighbors ... 12 = max # of 1-4 neighbors 41 = max # of special neighbors special bonds CPU = 0.007 seconds - read_data CPU = 0.853 seconds + read_data CPU = 0.854 seconds + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template Read molecule template mol1: 1 molecules 0 fragments @@ -45,6 +69,7 @@ Read molecule template mol1: 25 angles with max type 24 23 dihedrals with max type 33 2 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.molecule_template Read molecule template mol2: 1 molecules 0 fragments @@ -53,6 +78,7 @@ Read molecule template mol2: 31 angles with max type 23 39 dihedrals with max type 30 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template Read molecule template mol3: 1 molecules 0 fragments @@ -61,6 +87,7 @@ Read molecule template mol3: 25 angles with max type 23 30 dihedrals with max type 30 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template Read molecule template mol4: 1 molecules 0 fragments @@ -69,15 +96,53 @@ Read molecule template mol4: 19 angles with max type 25 16 dihedrals with max type 29 2 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined +# stable at 800K +fix 1 statted_grp_REACT nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 + 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 @@ -108,10 +173,6 @@ 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) = 81.39 | 81.41 | 81.43 Mbytes Step Temp Press Density f_myrxns[1] f_myrxns[2] 0 800 3666.3948 0.80366765 0 0 @@ -119,22 +180,22 @@ Per MPI rank memory allocation (min/avg/max) = 81.39 | 81.41 | 81.43 Mbytes 100 694.36354 -2108.4881 0.80366765 57 22 150 716.5075 -12356.04 0.80366765 77 50 200 722.97306 -1308.3439 0.80366765 84 67 -Loop time of 23.0703 on 4 procs for 200 steps with 35200 atoms +Loop time of 23.1041 on 4 procs for 200 steps with 35200 atoms -Performance: 0.749 ns/day, 32.042 hours/ns, 8.669 timesteps/s, 305.154 katom-step/s +Performance: 0.748 ns/day, 32.089 hours/ns, 8.656 timesteps/s, 304.708 katom-step/s 100.0% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.6778 | 6.8513 | 6.9896 | 5.2 | 29.70 -Bond | 3.8962 | 3.9719 | 4.0488 | 3.0 | 17.22 -Kspace | 1.1907 | 1.3846 | 1.6278 | 15.9 | 6.00 -Neigh | 8.7963 | 8.7965 | 8.7967 | 0.0 | 38.13 -Comm | 0.1468 | 0.15512 | 0.16131 | 1.6 | 0.67 -Output | 0.00035931 | 0.00037432 | 0.00041707 | 0.0 | 0.00 -Modify | 1.8808 | 1.8808 | 1.8809 | 0.0 | 8.15 -Other | | 0.02973 | | | 0.13 +Pair | 6.6935 | 6.8618 | 7.0049 | 5.1 | 29.70 +Bond | 3.8936 | 3.9807 | 4.0626 | 3.5 | 17.23 +Kspace | 1.1828 | 1.4033 | 1.6503 | 16.6 | 6.07 +Neigh | 8.7942 | 8.7945 | 8.7946 | 0.0 | 38.06 +Comm | 0.14682 | 0.15559 | 0.16441 | 1.8 | 0.67 +Output | 0.00035959 | 0.00037472 | 0.00041627 | 0.0 | 0.00 +Modify | 1.8787 | 1.8787 | 1.8788 | 0.0 | 8.13 +Other | | 0.02917 | | | 0.13 Nlocal: 8800 ave 8911 max 8662 min Histogram: 1 0 0 1 0 0 0 0 1 1 @@ -148,4 +209,7 @@ Ave neighs/atom = 196.80838 Ave special neighs/atom = 9.8480114 Neighbor list builds = 128 Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data Total wall time: 0:00:24