Loading examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.unstabilized.g++deleted 100644 → 0 +0 −199 Original line number Diff line number Diff line LAMMPS (15 Apr 2020) # two monomer nylon example # reaction produces a condensed water molecule 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 tiny_nylon.data orthogonal box = (-25 -25 -25) to (25 25 25) 1 by 1 by 1 MPI processor grid reading atoms ... 44 atoms reading velocities ... 44 velocities scanning bonds ... 9 = max bonds/atom scanning angles ... 21 = max angles/atom scanning dihedrals ... 29 = max dihedrals/atom scanning impropers ... 29 = max impropers/atom reading bonds ... 42 bonds reading angles ... 74 angles reading dihedrals ... 100 dihedrals reading impropers ... 44 impropers 4 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 12 = max # of 1-4 neighbors 41 = max # of special neighbors special bonds CPU = 0.000278722 secs read_data CPU = 0.0146239 secs variable runsteps equal 1000 variable prob1 equal step/v_runsteps*2 variable prob2 equal (step/v_runsteps)>0.5 velocity all create 300.0 4928459 dist gaussian molecule mol1 rxn1_stp1_unreacted.data_template Read molecule template mol1: 1 molecules 18 atoms with max type 8 16 bonds with max type 14 25 angles with max type 28 23 dihedrals with max type 36 14 impropers with max type 11 molecule mol2 rxn1_stp1_reacted.data_template Read molecule template mol2: 1 molecules 18 atoms with max type 9 17 bonds with max type 13 31 angles with max type 27 39 dihedrals with max type 33 20 impropers with max type 1 molecule mol3 rxn1_stp2_unreacted.data_template Read molecule template mol3: 1 molecules 15 atoms with max type 9 14 bonds with max type 13 25 angles with max type 27 30 dihedrals with max type 33 16 impropers with max type 1 molecule mol4 rxn1_stp2_reacted.data_template Read molecule template mol4: 1 molecules 15 atoms with max type 11 13 bonds with max type 15 19 angles with max type 29 16 dihedrals with max type 32 10 impropers with max type 13 thermo 50 dump 1 all xyz 1 test_vis.xyz fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:2052) WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:2052) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined fix 1 statted_grp_REACT nvt temp 300 300 100 # optionally, you can customize behavior of reacting atoms, # by using the internally-created 'bond_react_MASTER_group', like so: fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] # restart 100 restart1 restart2 run ${runsteps} run 1000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:332) G vector (1/distance) = 0.0534597 grid = 2 2 2 stencil order = 5 estimated absolute RMS force accuracy = 0.0402256 estimated relative force accuracy = 0.000121138 using double precision KISS FFT 3d grid and FFT values/proc = 343 8 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 10 10 10 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2/coul/long, 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 WARNING: Inconsistent image flags (../domain.cpp:812) Per MPI rank memory allocation (min/avg/max) = 34.78 | 34.78 | 34.78 Mbytes Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] 0 300 346.78165 0.0034851739 0 0 0 0 50 262.63913 -492.10749 0.0034851739 0.1 0 1 0 100 766.52962 -29.714349 0.0034851739 0.2 0 1 0 150 503.86837 50.220304 0.0034851739 0.3 0 1 0 200 456.51295 12.312892 0.0034851739 0.4 0 1 0 250 391.54928 9.2335844 0.0034851739 0.5 0 1 0 300 336.6988 -47.193937 0.0034851739 0.6 0 1 0 350 254.06985 -9.2867898 0.0034851739 0.7 0 1 0 400 259.41098 -25.657321 0.0034851739 0.8 0 1 0 450 258.10364 22.5086 0.0034851739 0.9 0 1 0 500 272.13412 -6.5391448 0.0034851739 1 0 1 0 550 202.75504 54.658731 0.0034851739 1.1 1 1 1 600 344.79887 23.798478 0.0034851739 1.2 1 1 1 650 328.44488 -29.908484 0.0034851739 1.3 1 1 1 700 280.13593 -8.3223255 0.0034851739 1.4 1 1 1 750 300.67624 1.0632669 0.0034851739 1.5 1 1 1 800 376.64234 12.488392 0.0034851739 1.6 1 1 1 850 321.07642 19.814074 0.0034851739 1.7 1 1 1 900 332.23751 30.814079 0.0034851739 1.8 1 1 1 950 311.14029 5.7853136 0.0034851739 1.9 1 1 1 1000 253.14634 -37.560642 0.0034851739 2 1 1 1 Loop time of 0.580684 on 1 procs for 1000 steps with 44 atoms Performance: 148.790 ns/day, 0.161 hours/ns, 1722.106 timesteps/s 95.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090707 | 0.090707 | 0.090707 | 0.0 | 15.62 Bond | 0.18541 | 0.18541 | 0.18541 | 0.0 | 31.93 Kspace | 0.065715 | 0.065715 | 0.065715 | 0.0 | 11.32 Neigh | 0.085003 | 0.085003 | 0.085003 | 0.0 | 14.64 Comm | 0.0068229 | 0.0068229 | 0.0068229 | 0.0 | 1.17 Output | 0.096583 | 0.096583 | 0.096583 | 0.0 | 16.63 Modify | 0.047377 | 0.047377 | 0.047377 | 0.0 | 8.16 Other | | 0.00307 | | | 0.53 Nlocal: 44 ave 44 max 44 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 722 ave 722 max 722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 722 Ave neighs/atom = 16.4091 Ave special neighs/atom = 9.77273 Neighbor list builds = 1000 Dangerous builds = 0 # write_restart restart_longrun # write_data restart_longrun.data Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:00 Loading
examples/USER/reaction/tiny_nylon/log.22Apr20.tiny_nylon.unstabilized.g++deleted 100644 → 0 +0 −199 Original line number Diff line number Diff line LAMMPS (15 Apr 2020) # two monomer nylon example # reaction produces a condensed water molecule 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 tiny_nylon.data orthogonal box = (-25 -25 -25) to (25 25 25) 1 by 1 by 1 MPI processor grid reading atoms ... 44 atoms reading velocities ... 44 velocities scanning bonds ... 9 = max bonds/atom scanning angles ... 21 = max angles/atom scanning dihedrals ... 29 = max dihedrals/atom scanning impropers ... 29 = max impropers/atom reading bonds ... 42 bonds reading angles ... 74 angles reading dihedrals ... 100 dihedrals reading impropers ... 44 impropers 4 = max # of 1-2 neighbors 6 = max # of 1-3 neighbors 12 = max # of 1-4 neighbors 41 = max # of special neighbors special bonds CPU = 0.000278722 secs read_data CPU = 0.0146239 secs variable runsteps equal 1000 variable prob1 equal step/v_runsteps*2 variable prob2 equal (step/v_runsteps)>0.5 velocity all create 300.0 4928459 dist gaussian molecule mol1 rxn1_stp1_unreacted.data_template Read molecule template mol1: 1 molecules 18 atoms with max type 8 16 bonds with max type 14 25 angles with max type 28 23 dihedrals with max type 36 14 impropers with max type 11 molecule mol2 rxn1_stp1_reacted.data_template Read molecule template mol2: 1 molecules 18 atoms with max type 9 17 bonds with max type 13 31 angles with max type 27 39 dihedrals with max type 33 20 impropers with max type 1 molecule mol3 rxn1_stp2_unreacted.data_template Read molecule template mol3: 1 molecules 15 atoms with max type 9 14 bonds with max type 13 25 angles with max type 27 30 dihedrals with max type 33 16 impropers with max type 1 molecule mol4 rxn1_stp2_reacted.data_template Read molecule template mol4: 1 molecules 15 atoms with max type 11 13 bonds with max type 15 19 angles with max type 29 16 dihedrals with max type 32 10 impropers with max type 13 thermo 50 dump 1 all xyz 1 test_vis.xyz fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:2052) WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:2052) dynamic group bond_react_MASTER_group defined dynamic group statted_grp_REACT defined fix 1 statted_grp_REACT nvt temp 300 300 100 # optionally, you can customize behavior of reacting atoms, # by using the internally-created 'bond_react_MASTER_group', like so: fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] # restart 100 restart1 restart2 run ${runsteps} run 1000 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:332) G vector (1/distance) = 0.0534597 grid = 2 2 2 stencil order = 5 estimated absolute RMS force accuracy = 0.0402256 estimated relative force accuracy = 0.000121138 using double precision KISS FFT 3d grid and FFT values/proc = 343 8 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 10 10 10 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2/coul/long, 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 WARNING: Inconsistent image flags (../domain.cpp:812) Per MPI rank memory allocation (min/avg/max) = 34.78 | 34.78 | 34.78 Mbytes Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] 0 300 346.78165 0.0034851739 0 0 0 0 50 262.63913 -492.10749 0.0034851739 0.1 0 1 0 100 766.52962 -29.714349 0.0034851739 0.2 0 1 0 150 503.86837 50.220304 0.0034851739 0.3 0 1 0 200 456.51295 12.312892 0.0034851739 0.4 0 1 0 250 391.54928 9.2335844 0.0034851739 0.5 0 1 0 300 336.6988 -47.193937 0.0034851739 0.6 0 1 0 350 254.06985 -9.2867898 0.0034851739 0.7 0 1 0 400 259.41098 -25.657321 0.0034851739 0.8 0 1 0 450 258.10364 22.5086 0.0034851739 0.9 0 1 0 500 272.13412 -6.5391448 0.0034851739 1 0 1 0 550 202.75504 54.658731 0.0034851739 1.1 1 1 1 600 344.79887 23.798478 0.0034851739 1.2 1 1 1 650 328.44488 -29.908484 0.0034851739 1.3 1 1 1 700 280.13593 -8.3223255 0.0034851739 1.4 1 1 1 750 300.67624 1.0632669 0.0034851739 1.5 1 1 1 800 376.64234 12.488392 0.0034851739 1.6 1 1 1 850 321.07642 19.814074 0.0034851739 1.7 1 1 1 900 332.23751 30.814079 0.0034851739 1.8 1 1 1 950 311.14029 5.7853136 0.0034851739 1.9 1 1 1 1000 253.14634 -37.560642 0.0034851739 2 1 1 1 Loop time of 0.580684 on 1 procs for 1000 steps with 44 atoms Performance: 148.790 ns/day, 0.161 hours/ns, 1722.106 timesteps/s 95.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090707 | 0.090707 | 0.090707 | 0.0 | 15.62 Bond | 0.18541 | 0.18541 | 0.18541 | 0.0 | 31.93 Kspace | 0.065715 | 0.065715 | 0.065715 | 0.0 | 11.32 Neigh | 0.085003 | 0.085003 | 0.085003 | 0.0 | 14.64 Comm | 0.0068229 | 0.0068229 | 0.0068229 | 0.0 | 1.17 Output | 0.096583 | 0.096583 | 0.096583 | 0.0 | 16.63 Modify | 0.047377 | 0.047377 | 0.047377 | 0.0 | 8.16 Other | | 0.00307 | | | 0.53 Nlocal: 44 ave 44 max 44 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 722 ave 722 max 722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 722 Ave neighs/atom = 16.4091 Ave special neighs/atom = 9.77273 Neighbor list builds = 1000 Dangerous builds = 0 # write_restart restart_longrun # write_data restart_longrun.data Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:00
