Loading examples/USER/misc/bond_react/tiny_epoxy/in.tiny_epoxy.stabilized 0 → 100644 +49 −0 Original line number Diff line number Diff line # 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 velocity all create 300.0 4928459 dist gaussian molecule mol1 rxn1_stp1_pre.data_template molecule mol2 rxn1_stp1_post.data_template molecule mol3 rxn1_stp2_post.data_template molecule mol4 rxn2_stp1_pre.data_template molecule mol5 rxn2_stp1_post.data_template molecule mol6 rxn2_stp2_post.data_template 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 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 # write_restart restart_longrun # write_data restart_longrun.data nofix examples/USER/misc/bond_react/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 0 → 100644 +172 −0 Original line number Diff line number Diff line LAMMPS (20 Nov 2019) WARNING-WARNING-WARNING-WARNING-WARNING This LAMMPS executable was compiled using C++98 compatibility. Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 GNU C++ 4.8.5 WARNING-WARNING-WARNING-WARNING-WARNING Reading data file ... orthogonal box = (10 -10 -15) to (30 20 10) 1 by 1 by 1 MPI processor grid reading atoms ... 118 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 123 bonds reading angles ... 221 angles reading dihedrals ... 302 dihedrals reading impropers ... 115 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 10 = max # of 1-3 neighbors 19 = max # of 1-4 neighbors 22 = max # of special neighbors special bonds CPU = 0.000286808 secs read_data CPU = 0.00724107 secs Read molecule mol1: 31 atoms with max type 10 30 bonds with max type 15 53 angles with max type 29 66 dihedrals with max type 39 31 impropers with max type 5 Read molecule mol2: 31 atoms with max type 10 30 bonds with max type 17 55 angles with max type 36 75 dihedrals with max type 51 34 impropers with max type 5 Read molecule mol3: 31 atoms with max type 11 30 bonds with max type 18 53 angles with max type 37 72 dihedrals with max type 53 31 impropers with max type 5 Read molecule mol4: 42 atoms with max type 11 41 bonds with max type 18 73 angles with max type 41 96 dihedrals with max type 54 43 impropers with max type 5 Read molecule mol5: 42 atoms with max type 11 41 bonds with max type 18 75 angles with max type 37 108 dihedrals with max type 53 46 impropers with max type 5 Read molecule mol6: 42 atoms with max type 11 41 bonds with max type 19 73 angles with max type 50 102 dihedrals with max type 66 43 impropers with max type 22 dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10 ghost atom cutoff = 10 binsize = 5, bins = 4 6 5 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) fix bond/react, occasional, copy from (1) attributes: half, newton on 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) = 17.28 | 17.28 | 17.28 Mbytes Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] 0 300 0 0 0 0 50 391.52956 1 0 0 0 100 475.26826 1 1 0 0 150 605.26215 1 1 1 0 200 545.7485 1 1 1 0 250 461.64929 1 1 1 1 300 452.10611 1 1 1 1 350 379.61671 1 1 1 1 400 331.22444 1 1 1 1 450 275.63969 1 1 1 1 500 316.63407 1 1 1 1 550 261.39841 1 1 1 1 600 313.70928 1 1 1 1 650 294.24011 1 1 1 1 700 285.81736 1 1 1 1 750 340.37496 1 1 1 1 800 333.2496 1 1 1 1 850 307.40826 1 1 1 1 900 304.68718 1 1 1 1 950 328.0289 1 1 1 1 1000 290.22808 1 1 1 1 1050 272.78518 1 1 1 1 1100 291.30546 1 1 1 1 1150 320.33992 1 1 1 1 1200 330.57057 1 1 1 1 1250 300.51008 1 1 1 1 1300 293.6209 1 1 1 1 1350 324.36604 1 1 1 1 1400 331.15408 1 1 1 1 1450 302.23396 1 1 1 1 1500 297.55562 1 1 1 1 1550 277.3187 1 1 1 1 1600 289.66052 1 1 1 1 1650 281.85404 1 1 1 1 1700 293.4999 1 1 1 1 1750 306.21866 1 1 1 1 1800 283.22696 1 1 1 1 1850 295.10473 1 1 1 1 1900 317.3843 1 1 1 1 1950 305.14825 1 1 1 1 2000 289.00911 1 1 1 1 Loop time of 1.87066 on 1 procs for 2000 steps with 118 atoms Performance: 92.374 ns/day, 0.260 hours/ns, 1069.141 timesteps/s 98.4% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12832 | 0.12832 | 0.12832 | 0.0 | 6.86 Bond | 0.77458 | 0.77458 | 0.77458 | 0.0 | 41.41 Neigh | 0.45068 | 0.45068 | 0.45068 | 0.0 | 24.09 Comm | 0.029785 | 0.029785 | 0.029785 | 0.0 | 1.59 Output | 0.31635 | 0.31635 | 0.31635 | 0.0 | 16.91 Modify | 0.16657 | 0.16657 | 0.16657 | 0.0 | 8.90 Other | | 0.004368 | | | 0.23 Nlocal: 118 ave 118 max 118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 332 ave 332 max 332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4338 ave 4338 max 4338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4338 Ave neighs/atom = 36.7627 Ave special neighs/atom = 10.5763 Neighbor list builds = 2000 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:02 examples/USER/misc/bond_react/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 0 → 100644 +172 −0 Original line number Diff line number Diff line LAMMPS (20 Nov 2019) WARNING-WARNING-WARNING-WARNING-WARNING This LAMMPS executable was compiled using C++98 compatibility. Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 GNU C++ 4.8.5 WARNING-WARNING-WARNING-WARNING-WARNING Reading data file ... orthogonal box = (10 -10 -15) to (30 20 10) 1 by 2 by 2 MPI processor grid reading atoms ... 118 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 123 bonds reading angles ... 221 angles reading dihedrals ... 302 dihedrals reading impropers ... 115 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 10 = max # of 1-3 neighbors 19 = max # of 1-4 neighbors 22 = max # of special neighbors special bonds CPU = 0.000239905 secs read_data CPU = 0.0080783 secs Read molecule mol1: 31 atoms with max type 10 30 bonds with max type 15 53 angles with max type 29 66 dihedrals with max type 39 31 impropers with max type 5 Read molecule mol2: 31 atoms with max type 10 30 bonds with max type 17 55 angles with max type 36 75 dihedrals with max type 51 34 impropers with max type 5 Read molecule mol3: 31 atoms with max type 11 30 bonds with max type 18 53 angles with max type 37 72 dihedrals with max type 53 31 impropers with max type 5 Read molecule mol4: 42 atoms with max type 11 41 bonds with max type 18 73 angles with max type 41 96 dihedrals with max type 54 43 impropers with max type 5 Read molecule mol5: 42 atoms with max type 11 41 bonds with max type 18 75 angles with max type 37 108 dihedrals with max type 53 46 impropers with max type 5 Read molecule mol6: 42 atoms with max type 11 41 bonds with max type 19 73 angles with max type 50 102 dihedrals with max type 66 43 impropers with max type 22 dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10 ghost atom cutoff = 10 binsize = 5, bins = 4 6 5 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) fix bond/react, occasional, copy from (1) attributes: half, newton on 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) = 16.26 | 16.45 | 16.63 Mbytes Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] 0 300 0 0 0 0 50 391.52956 1 0 0 0 100 475.26826 1 1 0 0 150 605.26215 1 1 1 0 200 545.7485 1 1 1 0 250 461.64929 1 1 1 1 300 452.10611 1 1 1 1 350 379.61671 1 1 1 1 400 331.22444 1 1 1 1 450 275.63969 1 1 1 1 500 316.63407 1 1 1 1 550 261.39841 1 1 1 1 600 313.70928 1 1 1 1 650 294.24011 1 1 1 1 700 285.81736 1 1 1 1 750 340.37496 1 1 1 1 800 333.2496 1 1 1 1 850 307.40826 1 1 1 1 900 304.68718 1 1 1 1 950 328.0289 1 1 1 1 1000 290.22808 1 1 1 1 1050 272.78518 1 1 1 1 1100 291.30546 1 1 1 1 1150 320.33992 1 1 1 1 1200 330.57057 1 1 1 1 1250 300.51008 1 1 1 1 1300 293.6209 1 1 1 1 1350 324.36604 1 1 1 1 1400 331.15408 1 1 1 1 1450 302.23396 1 1 1 1 1500 297.55562 1 1 1 1 1550 277.3187 1 1 1 1 1600 289.66052 1 1 1 1 1650 281.85404 1 1 1 1 1700 293.4999 1 1 1 1 1750 306.21866 1 1 1 1 1800 283.22695 1 1 1 1 1850 295.10472 1 1 1 1 1900 317.38431 1 1 1 1 1950 305.14824 1 1 1 1 2000 289.00909 1 1 1 1 Loop time of 0.689125 on 4 procs for 2000 steps with 118 atoms Performance: 250.753 ns/day, 0.096 hours/ns, 2902.231 timesteps/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 | 0.02002 | 0.030617 | 0.053133 | 7.7 | 4.44 Bond | 0.10356 | 0.18908 | 0.22691 | 11.6 | 27.44 Neigh | 0.16721 | 0.17002 | 0.17247 | 0.5 | 24.67 Comm | 0.057286 | 0.12002 | 0.21612 | 17.0 | 17.42 Output | 0.00028991 | 0.00034121 | 0.00049323 | 0.0 | 0.05 Modify | 0.17626 | 0.17675 | 0.17721 | 0.1 | 25.65 Other | | 0.002287 | | | 0.33 Nlocal: 29.5 ave 41 max 18 min Histogram: 1 0 0 1 0 0 1 0 0 1 Nghost: 306 ave 349 max 269 min Histogram: 1 1 0 0 0 0 1 0 0 1 Neighs: 1084.5 ave 2154 max 397 min Histogram: 1 0 1 1 0 0 0 0 0 1 Total # of neighbors = 4338 Ave neighs/atom = 36.7627 Ave special neighs/atom = 10.5763 Neighbor list builds = 2000 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:01 examples/USER/misc/bond_react/tiny_epoxy/rxn1_stp1.map 0 → 100644 +47 −0 Original line number Diff line number Diff line this is a map file 1 edgeIDs 31 equivalences BondingIDs 15 1 EdgeIDs 5 Equivalences 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 14 15 15 16 16 17 17 18 18 19 19 20 20 21 21 22 22 23 23 24 24 25 25 26 26 27 27 28 28 29 29 30 30 31 31 examples/USER/misc/bond_react/tiny_epoxy/rxn1_stp1_post.data_template 0 → 100644 +315 −0 Original line number Diff line number Diff line rxn1_stp1_post 31 atoms 30 bonds 55 angles 75 dihedrals 34 impropers Types 1 1 2 6 3 1 4 7 5 4 6 7 7 8 8 8 9 8 10 8 11 8 12 9 13 1 14 1 15 9 16 9 17 1 18 1 19 10 20 8 21 8 22 8 23 8 24 10 25 10 26 10 27 10 28 8 29 8 30 8 31 8 Charges 1 0.000000 2 0.000000 3 0.000000 4 0.100000 5 0.000000 6 0.000000 7 0.000000 8 0.000000 9 0.000000 10 0.000000 11 0.000000 12 0.000000 13 0.000000 14 0.000000 15 -0.025000 16 -0.025000 17 0.000000 18 0.000000 19 0.000000 20 0.000000 21 0.000000 22 0.000000 23 0.000000 24 0.000000 25 0.000000 26 0.000000 27 0.000000 28 0.000000 29 0.000000 30 0.000000 31 0.000000 Coords 1 22.582573 10.988183 -5.014054 2 23.904713 10.750493 -4.202215 3 23.989172 9.487042 -3.323374 4 24.067001 11.723383 -4.037435 5 24.627851 7.325302 -3.319944 6 24.554632 8.418972 -4.080365 7 22.667763 11.445703 -5.999605 8 21.787441 10.247643 -4.916974 9 24.964962 10.712683 -4.449374 10 24.616703 9.689913 -2.456034 11 22.989313 9.208153 -2.991455 12 18.808882 13.758042 -3.958724 13 19.293213 12.549683 -3.196594 14 20.810543 12.417832 -3.417504 15 21.090193 12.251203 -4.891234 16 17.657042 16.437199 -3.985224 17 19.126713 16.210239 -4.245154 18 19.589151 14.957593 -3.479565 19 19.000433 13.609432 -5.041715 20 18.761223 11.614392 -3.573184 21 19.082903 12.688992 -2.085145 22 21.202852 11.511562 -2.848624 23 21.328482 13.360252 -3.038924 24 19.949852 12.199403 -5.680355 25 21.477343 13.247442 -5.445915 26 17.080341 15.555528 -4.334374 27 17.319832 17.341927 -4.532204 28 19.720472 17.115158 -3.887564 29 19.298622 16.058659 -5.361685 30 19.410772 15.105113 -2.363724 31 20.700163 14.782252 -3.666344 Bonds 1 1 1 8 2 16 1 2 3 1 1 7 4 13 1 15 5 16 3 2 6 12 2 9 7 17 2 4 8 3 3 6 9 1 3 10 10 1 3 11 11 8 6 5 12 13 13 12 13 13 18 12 14 14 12 19 15 15 13 14 16 1 13 20 17 1 13 21 18 13 14 15 19 1 14 22 20 1 14 23 21 14 15 24 22 14 15 25 23 13 17 16 24 14 16 26 25 14 16 27 26 15 17 18 27 1 17 28 28 1 17 29 29 1 18 30 30 1 18 31 Angles 1 30 2 1 8 2 2 8 1 7 3 26 8 1 15 4 30 2 1 7 5 31 2 1 15 6 26 7 1 15 7 32 1 2 3 8 33 1 2 9 9 34 1 2 4 10 33 3 2 9 11 34 3 2 4 12 35 4 2 9 13 36 2 3 6 14 30 2 3 10 15 30 2 3 11 16 3 6 3 10 17 3 6 3 11 18 2 10 3 11 19 22 3 6 5 20 23 13 12 18 21 24 13 12 19 22 24 18 12 19 23 25 14 13 12 24 26 20 13 12 25 26 21 13 12 26 27 14 13 20 27 27 14 13 21 28 2 20 13 21 29 25 13 14 15 30 27 13 14 22 31 27 13 14 23 32 26 22 14 15 33 26 23 14 15 34 2 22 14 23 35 23 1 15 14 36 24 1 15 24 37 24 1 15 25 38 24 14 15 24 39 24 14 15 25 40 28 24 15 25 41 24 17 16 26 42 24 17 16 27 43 28 26 16 27 44 25 18 17 16 45 26 28 17 16 46 26 29 17 16 47 27 18 17 28 48 27 18 17 29 49 2 28 17 29 50 25 17 18 12 51 26 30 18 12 52 26 31 18 12 53 27 17 18 30 54 27 17 18 31 55 2 30 18 31 Dihedrals 1 40 8 1 2 3 2 41 8 1 2 9 3 42 8 1 2 4 4 40 7 1 2 3 5 41 7 1 2 9 6 42 7 1 2 4 7 43 15 1 2 3 8 44 15 1 2 9 9 45 15 1 2 4 10 28 8 1 15 14 11 30 8 1 15 24 12 30 8 1 15 25 13 46 2 1 15 14 14 47 2 1 15 24 15 47 2 1 15 25 16 28 7 1 15 14 17 30 7 1 15 24 18 30 7 1 15 25 19 48 6 3 2 1 20 40 10 3 2 1 21 40 11 3 2 1 22 49 6 3 2 9 23 41 10 3 2 9 24 41 11 3 2 9 25 50 6 3 2 4 26 42 10 3 2 4 27 42 11 3 2 4 28 51 2 3 6 5 29 7 10 3 6 5 30 7 11 3 6 5 31 27 14 13 12 18 32 28 20 13 12 18 33 28 21 13 12 18 34 29 14 13 12 19 35 30 20 13 12 19 36 30 21 13 12 19 37 27 17 18 12 13 38 28 30 18 12 13 39 28 31 18 12 13 40 29 17 18 12 19 41 30 30 18 12 19 42 30 31 18 12 19 43 31 12 13 14 15 44 32 22 14 13 12 45 32 23 14 13 12 46 32 20 13 14 15 47 33 20 13 14 22 48 33 20 13 14 23 49 32 21 13 14 15 50 33 21 13 14 22 51 33 21 13 14 23 52 27 13 14 15 1 53 29 13 14 15 24 54 29 13 14 15 25 55 28 22 14 15 1 56 30 22 14 15 24 57 30 22 14 15 25 58 28 23 14 15 1 59 30 23 14 15 24 60 30 23 14 15 25 61 29 18 17 16 26 62 30 28 17 16 26 63 30 29 17 16 26 64 29 18 17 16 27 65 30 28 17 16 27 66 30 29 17 16 27 67 31 16 17 18 12 68 32 30 18 17 16 69 32 31 18 17 16 70 32 28 17 18 12 71 33 28 17 18 30 72 33 28 17 18 31 73 32 29 17 18 12 74 33 29 17 18 30 75 33 29 17 18 31 Impropers 1 4 13 12 18 19 2 5 17 16 26 27 3 1 2 1 8 7 4 1 2 1 8 15 5 1 8 1 7 15 6 1 2 1 7 15 7 1 1 2 3 9 8 1 1 2 3 4 9 1 1 2 4 9 10 1 3 2 4 9 11 1 2 3 6 10 12 1 2 3 6 11 13 1 2 3 10 11 14 1 6 3 10 11 15 1 14 13 20 12 16 1 14 13 21 12 17 1 20 13 21 12 18 1 14 13 20 21 19 1 13 14 22 15 20 1 13 14 23 15 21 1 13 14 22 23 22 1 22 14 23 15 23 1 1 15 14 24 24 1 1 15 14 25 25 1 1 15 24 25 26 1 14 15 24 25 27 1 18 17 28 16 28 1 18 17 29 16 29 1 28 17 29 16 30 1 18 17 28 29 31 1 17 18 30 12 32 1 17 18 31 12 33 1 30 18 31 12 34 1 17 18 30 31 Loading
examples/USER/misc/bond_react/tiny_epoxy/in.tiny_epoxy.stabilized 0 → 100644 +49 −0 Original line number Diff line number Diff line # 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 velocity all create 300.0 4928459 dist gaussian molecule mol1 rxn1_stp1_pre.data_template molecule mol2 rxn1_stp1_post.data_template molecule mol3 rxn1_stp2_post.data_template molecule mol4 rxn2_stp1_pre.data_template molecule mol5 rxn2_stp1_post.data_template molecule mol6 rxn2_stp2_post.data_template 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 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 # write_restart restart_longrun # write_data restart_longrun.data nofix
examples/USER/misc/bond_react/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 0 → 100644 +172 −0 Original line number Diff line number Diff line LAMMPS (20 Nov 2019) WARNING-WARNING-WARNING-WARNING-WARNING This LAMMPS executable was compiled using C++98 compatibility. Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 GNU C++ 4.8.5 WARNING-WARNING-WARNING-WARNING-WARNING Reading data file ... orthogonal box = (10 -10 -15) to (30 20 10) 1 by 1 by 1 MPI processor grid reading atoms ... 118 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 123 bonds reading angles ... 221 angles reading dihedrals ... 302 dihedrals reading impropers ... 115 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 10 = max # of 1-3 neighbors 19 = max # of 1-4 neighbors 22 = max # of special neighbors special bonds CPU = 0.000286808 secs read_data CPU = 0.00724107 secs Read molecule mol1: 31 atoms with max type 10 30 bonds with max type 15 53 angles with max type 29 66 dihedrals with max type 39 31 impropers with max type 5 Read molecule mol2: 31 atoms with max type 10 30 bonds with max type 17 55 angles with max type 36 75 dihedrals with max type 51 34 impropers with max type 5 Read molecule mol3: 31 atoms with max type 11 30 bonds with max type 18 53 angles with max type 37 72 dihedrals with max type 53 31 impropers with max type 5 Read molecule mol4: 42 atoms with max type 11 41 bonds with max type 18 73 angles with max type 41 96 dihedrals with max type 54 43 impropers with max type 5 Read molecule mol5: 42 atoms with max type 11 41 bonds with max type 18 75 angles with max type 37 108 dihedrals with max type 53 46 impropers with max type 5 Read molecule mol6: 42 atoms with max type 11 41 bonds with max type 19 73 angles with max type 50 102 dihedrals with max type 66 43 impropers with max type 22 dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10 ghost atom cutoff = 10 binsize = 5, bins = 4 6 5 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) fix bond/react, occasional, copy from (1) attributes: half, newton on 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) = 17.28 | 17.28 | 17.28 Mbytes Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] 0 300 0 0 0 0 50 391.52956 1 0 0 0 100 475.26826 1 1 0 0 150 605.26215 1 1 1 0 200 545.7485 1 1 1 0 250 461.64929 1 1 1 1 300 452.10611 1 1 1 1 350 379.61671 1 1 1 1 400 331.22444 1 1 1 1 450 275.63969 1 1 1 1 500 316.63407 1 1 1 1 550 261.39841 1 1 1 1 600 313.70928 1 1 1 1 650 294.24011 1 1 1 1 700 285.81736 1 1 1 1 750 340.37496 1 1 1 1 800 333.2496 1 1 1 1 850 307.40826 1 1 1 1 900 304.68718 1 1 1 1 950 328.0289 1 1 1 1 1000 290.22808 1 1 1 1 1050 272.78518 1 1 1 1 1100 291.30546 1 1 1 1 1150 320.33992 1 1 1 1 1200 330.57057 1 1 1 1 1250 300.51008 1 1 1 1 1300 293.6209 1 1 1 1 1350 324.36604 1 1 1 1 1400 331.15408 1 1 1 1 1450 302.23396 1 1 1 1 1500 297.55562 1 1 1 1 1550 277.3187 1 1 1 1 1600 289.66052 1 1 1 1 1650 281.85404 1 1 1 1 1700 293.4999 1 1 1 1 1750 306.21866 1 1 1 1 1800 283.22696 1 1 1 1 1850 295.10473 1 1 1 1 1900 317.3843 1 1 1 1 1950 305.14825 1 1 1 1 2000 289.00911 1 1 1 1 Loop time of 1.87066 on 1 procs for 2000 steps with 118 atoms Performance: 92.374 ns/day, 0.260 hours/ns, 1069.141 timesteps/s 98.4% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12832 | 0.12832 | 0.12832 | 0.0 | 6.86 Bond | 0.77458 | 0.77458 | 0.77458 | 0.0 | 41.41 Neigh | 0.45068 | 0.45068 | 0.45068 | 0.0 | 24.09 Comm | 0.029785 | 0.029785 | 0.029785 | 0.0 | 1.59 Output | 0.31635 | 0.31635 | 0.31635 | 0.0 | 16.91 Modify | 0.16657 | 0.16657 | 0.16657 | 0.0 | 8.90 Other | | 0.004368 | | | 0.23 Nlocal: 118 ave 118 max 118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 332 ave 332 max 332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4338 ave 4338 max 4338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4338 Ave neighs/atom = 36.7627 Ave special neighs/atom = 10.5763 Neighbor list builds = 2000 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:02
examples/USER/misc/bond_react/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 0 → 100644 +172 −0 Original line number Diff line number Diff line LAMMPS (20 Nov 2019) WARNING-WARNING-WARNING-WARNING-WARNING This LAMMPS executable was compiled using C++98 compatibility. Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 GNU C++ 4.8.5 WARNING-WARNING-WARNING-WARNING-WARNING Reading data file ... orthogonal box = (10 -10 -15) to (30 20 10) 1 by 2 by 2 MPI processor grid reading atoms ... 118 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 123 bonds reading angles ... 221 angles reading dihedrals ... 302 dihedrals reading impropers ... 115 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 10 = max # of 1-3 neighbors 19 = max # of 1-4 neighbors 22 = max # of special neighbors special bonds CPU = 0.000239905 secs read_data CPU = 0.0080783 secs Read molecule mol1: 31 atoms with max type 10 30 bonds with max type 15 53 angles with max type 29 66 dihedrals with max type 39 31 impropers with max type 5 Read molecule mol2: 31 atoms with max type 10 30 bonds with max type 17 55 angles with max type 36 75 dihedrals with max type 51 34 impropers with max type 5 Read molecule mol3: 31 atoms with max type 11 30 bonds with max type 18 53 angles with max type 37 72 dihedrals with max type 53 31 impropers with max type 5 Read molecule mol4: 42 atoms with max type 11 41 bonds with max type 18 73 angles with max type 41 96 dihedrals with max type 54 43 impropers with max type 5 Read molecule mol5: 42 atoms with max type 11 41 bonds with max type 18 75 angles with max type 37 108 dihedrals with max type 53 46 impropers with max type 5 Read molecule mol6: 42 atoms with max type 11 41 bonds with max type 19 73 angles with max type 50 102 dihedrals with max type 66 43 impropers with max type 22 dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10 ghost atom cutoff = 10 binsize = 5, bins = 4 6 5 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) fix bond/react, occasional, copy from (1) attributes: half, newton on 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) = 16.26 | 16.45 | 16.63 Mbytes Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] 0 300 0 0 0 0 50 391.52956 1 0 0 0 100 475.26826 1 1 0 0 150 605.26215 1 1 1 0 200 545.7485 1 1 1 0 250 461.64929 1 1 1 1 300 452.10611 1 1 1 1 350 379.61671 1 1 1 1 400 331.22444 1 1 1 1 450 275.63969 1 1 1 1 500 316.63407 1 1 1 1 550 261.39841 1 1 1 1 600 313.70928 1 1 1 1 650 294.24011 1 1 1 1 700 285.81736 1 1 1 1 750 340.37496 1 1 1 1 800 333.2496 1 1 1 1 850 307.40826 1 1 1 1 900 304.68718 1 1 1 1 950 328.0289 1 1 1 1 1000 290.22808 1 1 1 1 1050 272.78518 1 1 1 1 1100 291.30546 1 1 1 1 1150 320.33992 1 1 1 1 1200 330.57057 1 1 1 1 1250 300.51008 1 1 1 1 1300 293.6209 1 1 1 1 1350 324.36604 1 1 1 1 1400 331.15408 1 1 1 1 1450 302.23396 1 1 1 1 1500 297.55562 1 1 1 1 1550 277.3187 1 1 1 1 1600 289.66052 1 1 1 1 1650 281.85404 1 1 1 1 1700 293.4999 1 1 1 1 1750 306.21866 1 1 1 1 1800 283.22695 1 1 1 1 1850 295.10472 1 1 1 1 1900 317.38431 1 1 1 1 1950 305.14824 1 1 1 1 2000 289.00909 1 1 1 1 Loop time of 0.689125 on 4 procs for 2000 steps with 118 atoms Performance: 250.753 ns/day, 0.096 hours/ns, 2902.231 timesteps/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 | 0.02002 | 0.030617 | 0.053133 | 7.7 | 4.44 Bond | 0.10356 | 0.18908 | 0.22691 | 11.6 | 27.44 Neigh | 0.16721 | 0.17002 | 0.17247 | 0.5 | 24.67 Comm | 0.057286 | 0.12002 | 0.21612 | 17.0 | 17.42 Output | 0.00028991 | 0.00034121 | 0.00049323 | 0.0 | 0.05 Modify | 0.17626 | 0.17675 | 0.17721 | 0.1 | 25.65 Other | | 0.002287 | | | 0.33 Nlocal: 29.5 ave 41 max 18 min Histogram: 1 0 0 1 0 0 1 0 0 1 Nghost: 306 ave 349 max 269 min Histogram: 1 1 0 0 0 0 1 0 0 1 Neighs: 1084.5 ave 2154 max 397 min Histogram: 1 0 1 1 0 0 0 0 0 1 Total # of neighbors = 4338 Ave neighs/atom = 36.7627 Ave special neighs/atom = 10.5763 Neighbor list builds = 2000 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:01
examples/USER/misc/bond_react/tiny_epoxy/rxn1_stp1.map 0 → 100644 +47 −0 Original line number Diff line number Diff line this is a map file 1 edgeIDs 31 equivalences BondingIDs 15 1 EdgeIDs 5 Equivalences 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13 14 14 15 15 16 16 17 17 18 18 19 19 20 20 21 21 22 22 23 23 24 24 25 25 26 26 27 27 28 28 29 29 30 30 31 31
examples/USER/misc/bond_react/tiny_epoxy/rxn1_stp1_post.data_template 0 → 100644 +315 −0 Original line number Diff line number Diff line rxn1_stp1_post 31 atoms 30 bonds 55 angles 75 dihedrals 34 impropers Types 1 1 2 6 3 1 4 7 5 4 6 7 7 8 8 8 9 8 10 8 11 8 12 9 13 1 14 1 15 9 16 9 17 1 18 1 19 10 20 8 21 8 22 8 23 8 24 10 25 10 26 10 27 10 28 8 29 8 30 8 31 8 Charges 1 0.000000 2 0.000000 3 0.000000 4 0.100000 5 0.000000 6 0.000000 7 0.000000 8 0.000000 9 0.000000 10 0.000000 11 0.000000 12 0.000000 13 0.000000 14 0.000000 15 -0.025000 16 -0.025000 17 0.000000 18 0.000000 19 0.000000 20 0.000000 21 0.000000 22 0.000000 23 0.000000 24 0.000000 25 0.000000 26 0.000000 27 0.000000 28 0.000000 29 0.000000 30 0.000000 31 0.000000 Coords 1 22.582573 10.988183 -5.014054 2 23.904713 10.750493 -4.202215 3 23.989172 9.487042 -3.323374 4 24.067001 11.723383 -4.037435 5 24.627851 7.325302 -3.319944 6 24.554632 8.418972 -4.080365 7 22.667763 11.445703 -5.999605 8 21.787441 10.247643 -4.916974 9 24.964962 10.712683 -4.449374 10 24.616703 9.689913 -2.456034 11 22.989313 9.208153 -2.991455 12 18.808882 13.758042 -3.958724 13 19.293213 12.549683 -3.196594 14 20.810543 12.417832 -3.417504 15 21.090193 12.251203 -4.891234 16 17.657042 16.437199 -3.985224 17 19.126713 16.210239 -4.245154 18 19.589151 14.957593 -3.479565 19 19.000433 13.609432 -5.041715 20 18.761223 11.614392 -3.573184 21 19.082903 12.688992 -2.085145 22 21.202852 11.511562 -2.848624 23 21.328482 13.360252 -3.038924 24 19.949852 12.199403 -5.680355 25 21.477343 13.247442 -5.445915 26 17.080341 15.555528 -4.334374 27 17.319832 17.341927 -4.532204 28 19.720472 17.115158 -3.887564 29 19.298622 16.058659 -5.361685 30 19.410772 15.105113 -2.363724 31 20.700163 14.782252 -3.666344 Bonds 1 1 1 8 2 16 1 2 3 1 1 7 4 13 1 15 5 16 3 2 6 12 2 9 7 17 2 4 8 3 3 6 9 1 3 10 10 1 3 11 11 8 6 5 12 13 13 12 13 13 18 12 14 14 12 19 15 15 13 14 16 1 13 20 17 1 13 21 18 13 14 15 19 1 14 22 20 1 14 23 21 14 15 24 22 14 15 25 23 13 17 16 24 14 16 26 25 14 16 27 26 15 17 18 27 1 17 28 28 1 17 29 29 1 18 30 30 1 18 31 Angles 1 30 2 1 8 2 2 8 1 7 3 26 8 1 15 4 30 2 1 7 5 31 2 1 15 6 26 7 1 15 7 32 1 2 3 8 33 1 2 9 9 34 1 2 4 10 33 3 2 9 11 34 3 2 4 12 35 4 2 9 13 36 2 3 6 14 30 2 3 10 15 30 2 3 11 16 3 6 3 10 17 3 6 3 11 18 2 10 3 11 19 22 3 6 5 20 23 13 12 18 21 24 13 12 19 22 24 18 12 19 23 25 14 13 12 24 26 20 13 12 25 26 21 13 12 26 27 14 13 20 27 27 14 13 21 28 2 20 13 21 29 25 13 14 15 30 27 13 14 22 31 27 13 14 23 32 26 22 14 15 33 26 23 14 15 34 2 22 14 23 35 23 1 15 14 36 24 1 15 24 37 24 1 15 25 38 24 14 15 24 39 24 14 15 25 40 28 24 15 25 41 24 17 16 26 42 24 17 16 27 43 28 26 16 27 44 25 18 17 16 45 26 28 17 16 46 26 29 17 16 47 27 18 17 28 48 27 18 17 29 49 2 28 17 29 50 25 17 18 12 51 26 30 18 12 52 26 31 18 12 53 27 17 18 30 54 27 17 18 31 55 2 30 18 31 Dihedrals 1 40 8 1 2 3 2 41 8 1 2 9 3 42 8 1 2 4 4 40 7 1 2 3 5 41 7 1 2 9 6 42 7 1 2 4 7 43 15 1 2 3 8 44 15 1 2 9 9 45 15 1 2 4 10 28 8 1 15 14 11 30 8 1 15 24 12 30 8 1 15 25 13 46 2 1 15 14 14 47 2 1 15 24 15 47 2 1 15 25 16 28 7 1 15 14 17 30 7 1 15 24 18 30 7 1 15 25 19 48 6 3 2 1 20 40 10 3 2 1 21 40 11 3 2 1 22 49 6 3 2 9 23 41 10 3 2 9 24 41 11 3 2 9 25 50 6 3 2 4 26 42 10 3 2 4 27 42 11 3 2 4 28 51 2 3 6 5 29 7 10 3 6 5 30 7 11 3 6 5 31 27 14 13 12 18 32 28 20 13 12 18 33 28 21 13 12 18 34 29 14 13 12 19 35 30 20 13 12 19 36 30 21 13 12 19 37 27 17 18 12 13 38 28 30 18 12 13 39 28 31 18 12 13 40 29 17 18 12 19 41 30 30 18 12 19 42 30 31 18 12 19 43 31 12 13 14 15 44 32 22 14 13 12 45 32 23 14 13 12 46 32 20 13 14 15 47 33 20 13 14 22 48 33 20 13 14 23 49 32 21 13 14 15 50 33 21 13 14 22 51 33 21 13 14 23 52 27 13 14 15 1 53 29 13 14 15 24 54 29 13 14 15 25 55 28 22 14 15 1 56 30 22 14 15 24 57 30 22 14 15 25 58 28 23 14 15 1 59 30 23 14 15 24 60 30 23 14 15 25 61 29 18 17 16 26 62 30 28 17 16 26 63 30 29 17 16 26 64 29 18 17 16 27 65 30 28 17 16 27 66 30 29 17 16 27 67 31 16 17 18 12 68 32 30 18 17 16 69 32 31 18 17 16 70 32 28 17 18 12 71 33 28 17 18 30 72 33 28 17 18 31 73 32 29 17 18 12 74 33 29 17 18 30 75 33 29 17 18 31 Impropers 1 4 13 12 18 19 2 5 17 16 26 27 3 1 2 1 8 7 4 1 2 1 8 15 5 1 8 1 7 15 6 1 2 1 7 15 7 1 1 2 3 9 8 1 1 2 3 4 9 1 1 2 4 9 10 1 3 2 4 9 11 1 2 3 6 10 12 1 2 3 6 11 13 1 2 3 10 11 14 1 6 3 10 11 15 1 14 13 20 12 16 1 14 13 21 12 17 1 20 13 21 12 18 1 14 13 20 21 19 1 13 14 22 15 20 1 13 14 23 15 21 1 13 14 22 23 22 1 22 14 23 15 23 1 1 15 14 24 24 1 1 15 14 25 25 1 1 15 24 25 26 1 14 15 24 25 27 1 18 17 28 16 28 1 18 17 29 16 29 1 28 17 29 16 30 1 18 17 28 29 31 1 17 18 30 12 32 1 17 18 31 12 33 1 30 18 31 12 34 1 17 18 30 31
