diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt index 3982da799d..6fbf46f844 100644 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt @@ -18,14 +18,19 @@ dihedral_style class2 improper_style class2 -read_data large_nylon_melt.data.gz +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 velocity all create 800.0 4928459 dist gaussian -molecule mol1 rxn1_stp1_unreacted.data_template -molecule mol2 rxn1_stp1_reacted.data_template -molecule mol3 rxn1_stp2_unreacted.data_template -molecule mol4 rxn1_stp2_reacted.data_template +molecule mol1 rxn1_stp1_unreacted.molecule_template +molecule mol2 rxn1_stp1_reacted.molecule_template +molecule mol3 rxn1_stp2_unreacted.molecule_template +molecule mol4 rxn1_stp2_reacted.molecule_template thermo 50 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz index c620b879a8..e1ec3079f7 100644 Binary files a/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz and b/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz differ diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 deleted file mode 100644 index 653c7582f8..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 +++ /dev/null @@ -1,175 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 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 - orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 35200 atoms - reading velocities ... - 35200 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 31 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 33600 bonds - reading angles ... - 59200 angles - reading dihedrals ... - 80000 dihedrals - reading impropers ... - 35200 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 800.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 12 - 25 angles with max type 24 - 23 dihedrals with max type 33 - 14 impropers with max type 9 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 11 - 31 angles with max type 23 - 39 dihedrals with max type 30 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 11 - 25 angles with max type 23 - 30 dihedrals with max type 30 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 13 - 19 angles with max type 25 - 16 dihedrals with max type 29 - 10 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: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -# stable at 800K -fix 1 statted_grp 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 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.20765 - grid = 18 18 18 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0333156 - estimated relative force accuracy = 0.000100329 - using double precision FFTs - 3d grid and FFT values/proc = 12167 5832 -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 = 15 15 15 - 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 -Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 800 3666.3948 0.80366765 0 0 - 50 673.95238 -9670.9169 0.80366765 31 0 - 100 697.22819 -4624.0512 0.80366765 57 22 - 150 723.60507 -17175.571 0.80366765 76 48 - 200 736.71277 -12961.963 0.80366765 84 64 -Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms - -Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 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 | 27.193 | 27.193 | 27.193 | 0.0 | 26.45 -Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01 -Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07 -Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22 -Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40 -Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00 -Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81 -Other | | 0.04545 | | | 0.04 - -Nlocal: 35200 ave 35200 max 35200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 38403 ave 38403 max 38403 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 6928101 -Ave neighs/atom = 196.821 -Ave special neighs/atom = 9.83727 -Neighbor list builds = 200 -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: 0:01:43 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 deleted file mode 100644 index cc0dda60c7..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 +++ /dev/null @@ -1,175 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 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 - orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 35200 atoms - reading velocities ... - 35200 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 31 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 33600 bonds - reading angles ... - 59200 angles - reading dihedrals ... - 80000 dihedrals - reading impropers ... - 35200 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 800.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 12 - 25 angles with max type 24 - 23 dihedrals with max type 33 - 14 impropers with max type 9 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 11 - 31 angles with max type 23 - 39 dihedrals with max type 30 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 11 - 25 angles with max type 23 - 30 dihedrals with max type 30 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 13 - 19 angles with max type 25 - 16 dihedrals with max type 29 - 10 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: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -# stable at 800K -fix 1 statted_grp 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 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.20765 - grid = 18 18 18 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0333156 - estimated relative force accuracy = 0.000100329 - using double precision FFTs - 3d grid and FFT values/proc = 4508 1620 -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 = 15 15 15 - 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 -Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 800 3666.3948 0.80366765 0 0 - 50 673.95238 -9670.9169 0.80366765 31 0 - 100 697.22819 -4624.0512 0.80366765 57 22 - 150 724.40407 -17166.729 0.80366765 76 49 - 200 737.28582 -12968.224 0.80366765 84 65 -Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms - -Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 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 | 12.926 | 13.247 | 13.493 | 6.7 | 25.89 -Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31 -Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19 -Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68 -Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47 -Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00 -Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39 -Other | | 0.03995 | | | 0.08 - -Nlocal: 8800 ave 8913 max 8652 min -Histogram: 1 0 0 0 1 0 0 0 1 1 -Nghost: 18366 ave 18461 max 18190 min -Histogram: 1 0 0 0 0 0 0 1 1 1 -Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min -Histogram: 1 0 1 0 0 0 0 0 0 2 - -Total # of neighbors = 6928132 -Ave neighs/atom = 196.822 -Ave special neighs/atom = 9.83608 -Neighbor list builds = 200 -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: 0:00:52 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 new file mode 100644 index 0000000000..26c11bd020 --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 @@ -0,0 +1,150 @@ +LAMMPS (4 Nov 2022) +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 + reading atom labelmap ... + reading bond labelmap ... + reading angle labelmap ... + reading dihedral labelmap ... + reading improper labelmap ... + reading atoms ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.026 seconds + read_data CPU = 0.937 seconds +Read molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 2 impropers with max type 9 +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 0 impropers with max type 0 +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 0 impropers with max type 0 +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 2 impropers with max type 11 +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 + +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. + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.20765034 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.033315619 + estimated relative force accuracy = 0.000100329 + using double precision KISS FFT + 3d grid and FFT values/proc = 12167 5832 +Generated 55 of 55 mixed pair_coeff terms from sixthpower/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 = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 15 15 15 + 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 + 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) = 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 + 50 673.94821 -9679.5038 0.80366765 31 0 + 100 694.45718 -2104.8514 0.80366765 57 22 + 150 716.53915 -12356.83 0.80366765 77 50 + 200 723.33218 -1319.9666 0.80366765 84 67 +Loop time of 87.9809 on 1 procs for 200 steps with 35200 atoms + +Performance: 0.196 ns/day, 122.196 hours/ns, 2.273 timesteps/s, 80.017 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 25.691 | 25.691 | 25.691 | 0.0 | 29.20 +Bond | 15.772 | 15.772 | 15.772 | 0.0 | 17.93 +Kspace | 4.611 | 4.611 | 4.611 | 0.0 | 5.24 +Neigh | 35.616 | 35.616 | 35.616 | 0.0 | 40.48 +Comm | 0.24971 | 0.24971 | 0.24971 | 0.0 | 0.28 +Output | 0.00098602 | 0.00098602 | 0.00098602 | 0.0 | 0.00 +Modify | 5.9596 | 5.9596 | 5.9596 | 0.0 | 6.77 +Other | | 0.08051 | | | 0.09 + +Nlocal: 35200 ave 35200 max 35200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 38403 ave 38403 max 38403 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 6.92764e+06 ave 6.92764e+06 max 6.92764e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6927635 +Ave neighs/atom = 196.80781 +Ave special neighs/atom = 9.8480114 +Neighbor list builds = 128 +Dangerous builds = 0 +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 new file mode 100644 index 0000000000..69a663c59c --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 @@ -0,0 +1,151 @@ +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) +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 + reading atom labelmap ... + reading bond labelmap ... + reading angle labelmap ... + reading dihedral labelmap ... + reading improper labelmap ... + reading atoms ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 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 + 6 = max # of 1-3 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 molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 2 impropers with max type 9 +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 0 impropers with max type 0 +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 0 impropers with max type 0 +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 2 impropers with max type 11 +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 + +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. + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.20765034 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.033315619 + estimated relative force accuracy = 0.000100329 + using double precision KISS FFT + 3d grid and FFT values/proc = 4508 1620 +Generated 55 of 55 mixed pair_coeff terms from sixthpower/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 = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 15 15 15 + 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 + 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) = 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 + 50 673.94821 -9679.5038 0.80366765 31 0 + 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 + +Performance: 0.749 ns/day, 32.042 hours/ns, 8.669 timesteps/s, 305.154 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 + +Nlocal: 8800 ave 8911 max 8662 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 18358.5 ave 18438 max 18183 min +Histogram: 1 0 0 0 0 0 0 0 1 2 +Neighs: 1.73191e+06 ave 1.77313e+06 max 1.68375e+06 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 6927655 +Ave neighs/atom = 196.80838 +Ave special neighs/atom = 9.8480114 +Neighbor list builds = 128 +Dangerous builds = 0 +Total wall time: 0:00:24 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template deleted file mode 100644 index 61c0408ce3..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template +++ /dev/null @@ -1,189 +0,0 @@ -this is a molecule template for: initial nylon crosslink, post-reacting - -18 atoms -17 bonds -31 angles -39 dihedrals -20 impropers - -Types - -1 9 -2 1 -3 1 -4 4 -5 4 -6 3 -7 3 -8 1 -9 1 -10 5 -11 8 -12 6 -13 3 -14 3 -15 7 -16 1 -17 3 -18 3 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.000000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 0.000000 -16 0.000000 -17 0.000000 -18 0.000000 - -Coords - -1 -5.522237 -0.752722 1.631158 -2 -5.170398 -0.545733 0.178130 -3 -6.469695 -0.553072 -0.648889 -4 -6.052076 -1.721152 1.744648 -5 -6.183059 0.071387 1.971497 -6 -4.489340 -1.389197 -0.173156 -7 -4.637591 0.453703 0.051252 -8 -5.618658 0.138919 4.386107 -9 -4.669492 -0.989819 3.943591 -10 -4.270194 -0.766405 2.474102 -11 -3.348470 -1.875393 2.024289 -12 -3.569794 0.564183 2.345995 -13 -5.201079 -1.993301 4.044219 -14 -3.736682 -0.984819 4.598305 -15 -4.255402 1.370923 2.679069 -16 -6.136394 -0.339866 -2.136775 -17 -6.996331 -1.555519 -0.517408 -18 -7.153308 0.284949 -0.289930 - -Bonds - -1 9 1 2 -2 10 1 4 -3 10 1 5 -4 11 1 10 -5 1 2 3 -6 2 2 6 -7 2 2 7 -8 1 3 16 -9 2 3 17 -10 2 3 18 -11 1 8 9 -12 6 9 10 -13 2 9 13 -14 2 9 14 -15 7 10 11 -16 5 10 12 -17 8 12 15 - -Angles - -1 14 2 1 4 -2 14 2 1 5 -3 15 2 1 10 -4 16 4 1 5 -5 17 4 1 10 -6 17 5 1 10 -7 18 1 2 3 -8 19 1 2 6 -9 19 1 2 7 -10 1 3 2 6 -11 1 3 2 7 -12 3 6 2 7 -13 2 2 3 16 -14 1 2 3 17 -15 1 2 3 18 -16 1 16 3 17 -17 1 16 3 18 -18 3 17 3 18 -19 12 8 9 10 -20 1 8 9 13 -21 1 8 9 14 -22 13 13 9 10 -23 13 14 9 10 -24 3 13 9 14 -25 10 9 10 11 -26 8 9 10 12 -27 20 1 10 9 -28 21 11 10 12 -29 22 1 10 11 -30 23 1 10 12 -31 11 10 12 15 - -Dihedrals - -1 16 4 1 2 3 -2 17 4 1 2 6 -3 17 4 1 2 7 -4 16 5 1 2 3 -5 17 5 1 2 6 -6 17 5 1 2 7 -7 18 10 1 2 3 -8 19 10 1 2 6 -9 19 10 1 2 7 -10 20 2 1 10 9 -11 21 2 1 10 11 -12 22 2 1 10 12 -13 23 4 1 10 9 -14 24 4 1 10 11 -15 25 4 1 10 12 -16 23 5 1 10 9 -17 24 5 1 10 11 -18 25 5 1 10 12 -19 26 1 2 3 16 -20 27 1 2 3 17 -21 27 1 2 3 18 -22 4 16 3 2 6 -23 2 6 2 3 17 -24 2 6 2 3 18 -25 4 16 3 2 7 -26 2 7 2 3 17 -27 2 7 2 3 18 -28 14 8 9 10 11 -29 12 8 9 10 12 -30 28 8 9 10 1 -31 15 13 9 10 11 -32 13 13 9 10 12 -33 29 13 9 10 1 -34 15 14 9 10 11 -35 13 14 9 10 12 -36 29 14 9 10 1 -37 10 9 10 12 15 -38 11 11 10 12 15 -39 30 1 10 12 15 - -Impropers - -1 1 2 1 4 5 -2 1 2 1 4 10 -3 1 2 1 5 10 -4 1 4 1 5 10 -5 1 1 2 3 6 -6 1 1 2 3 7 -7 1 1 2 6 7 -8 1 3 2 6 7 -9 1 2 3 16 17 -10 1 2 3 16 18 -11 1 2 3 17 18 -12 1 16 3 17 18 -13 1 8 9 13 10 -14 1 8 9 14 10 -15 1 8 9 13 14 -16 1 13 9 14 10 -17 1 9 10 11 12 -18 1 1 10 9 11 -19 1 1 10 9 12 -20 1 1 10 11 12 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.molecule_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.molecule_template new file mode 100644 index 0000000000..40f3aa8276 --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.molecule_template @@ -0,0 +1,187 @@ +this is a molecule template for: initial nylon crosslink, post-reacting + + 18 atoms + 17 bonds + 31 angles + 39 dihedrals + 0 impropers + +Coords + + 1 -5.522237178 -0.752722499 1.631158408 + 2 -5.170398325 -0.545733378 0.178129978 + 3 -6.469694974 -0.553071841 -0.648889109 + 4 -6.052075697 -1.721152483 1.744647858 + 5 -6.183058842 0.071386755 1.971497329 + 6 -4.489339595 -1.389196844 -0.173156276 + 7 -4.637590712 0.453703382 0.051251954 + 8 -5.618657658 0.138918810 4.386106928 + 9 -4.669491736 -0.989818781 3.943591338 + 10 -4.270193542 -0.766405234 2.474102239 + 11 -3.348470373 -1.875393291 2.024289246 + 12 -3.569793683 0.564183226 2.345995471 + 13 -5.201078949 -1.993301389 4.044218837 + 14 -3.736681607 -0.984819193 4.598304847 + 15 -4.255401979 1.370923174 2.679069013 + 16 -6.136393628 -0.339866195 -2.136774990 + 17 -6.996331494 -1.555519161 -0.517408063 + 18 -7.153308038 0.284949373 -0.289930394 + +Types + + 1 n + 2 c2 + 3 c2 + 4 hn + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o + 13 hc + 14 hc + 15 ho + 16 c2 + 17 hc + 18 hc + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 0.000000 + 13 0.000000 + 14 0.000000 + 15 0.000000 + 16 0.000000 + 17 0.000000 + 18 0.000000 + +Molecules + + 1 1 + 2 1 + 3 1 + 4 1 + 5 1 + 6 1 + 7 1 + 8 1 + 9 1 + 10 1 + 11 1 + 12 1 + 13 1 + 14 1 + 15 1 + 16 1 + 17 1 + 18 1 + +Bonds + + 1 n-c2 1 2 + 2 n-hn 1 4 + 3 n-hn 1 5 + 4 n-c_1 1 10 + 5 c2-c2 2 3 + 6 c2-hc 2 6 + 7 c2-hc 2 7 + 8 c2-c2 3 16 + 9 c2-hc 3 17 + 10 c2-hc 3 18 + 11 c2-c2 8 9 + 12 c2-c_1 9 10 + 13 c2-hc 9 13 + 14 c2-hc 9 14 + 15 c_1-o_1 10 11 + 16 c_1-o 10 12 + 17 o-ho 12 15 + +Angles + + 1 c2-n-hn 2 1 4 + 2 c2-n-hn 2 1 5 + 3 c2-n-c_1 2 1 10 + 4 hn-n-hn 4 1 5 + 5 hn-n-c_1 4 1 10 + 6 hn-n-c_1 5 1 10 + 7 n-c2-c2 1 2 3 + 8 n-c2-hc 1 2 6 + 9 n-c2-hc 1 2 7 + 10 c2-c2-hc 3 2 6 + 11 c2-c2-hc 3 2 7 + 12 hc-c2-hc 6 2 7 + 13 c2-c2-c2 2 3 16 + 14 c2-c2-hc 2 3 17 + 15 c2-c2-hc 2 3 18 + 16 c2-c2-hc 16 3 17 + 17 c2-c2-hc 16 3 18 + 18 hc-c2-hc 17 3 18 + 19 c2-c2-c_1 8 9 10 + 20 c2-c2-hc 8 9 13 + 21 c2-c2-hc 8 9 14 + 22 hc-c2-c_1 13 9 10 + 23 hc-c2-c_1 14 9 10 + 24 hc-c2-hc 13 9 14 + 25 c2-c_1-o_1 9 10 11 + 26 c2-c_1-o 9 10 12 + 27 n-c_1-c2 1 10 9 + 28 o_1-c_1-o 11 10 12 + 29 n-c_1-o_1 1 10 11 + 30 n-c_1-o 1 10 12 + 31 c_1-o-ho 10 12 15 + +Dihedrals + + 1 hn-n-c2-c2 4 1 2 3 + 2 hn-n-c2-hc 4 1 2 6 + 3 hn-n-c2-hc 4 1 2 7 + 4 hn-n-c2-c2 5 1 2 3 + 5 hn-n-c2-hc 5 1 2 6 + 6 hn-n-c2-hc 5 1 2 7 + 7 c_1-n-c2-c2 10 1 2 3 + 8 c_1-n-c2-hc 10 1 2 6 + 9 c_1-n-c2-hc 10 1 2 7 + 10 c2-n-c_1-c2 2 1 10 9 + 11 c2-n-c_1-o_1 2 1 10 11 + 12 c2-n-c_1-o 2 1 10 12 + 13 hn-n-c_1-c2 4 1 10 9 + 14 hn-n-c_1-o_1 4 1 10 11 + 15 hn-n-c_1-o 4 1 10 12 + 16 hn-n-c_1-c2 5 1 10 9 + 17 hn-n-c_1-o_1 5 1 10 11 + 18 hn-n-c_1-o 5 1 10 12 + 19 n-c2-c2-c2 1 2 3 16 + 20 n-c2-c2-hc 1 2 3 17 + 21 n-c2-c2-hc 1 2 3 18 + 22 c2-c2-c2-hc 16 3 2 6 + 23 hc-c2-c2-hc 6 2 3 17 + 24 hc-c2-c2-hc 6 2 3 18 + 25 c2-c2-c2-hc 16 3 2 7 + 26 hc-c2-c2-hc 7 2 3 17 + 27 hc-c2-c2-hc 7 2 3 18 + 28 c2-c2-c_1-o_1 8 9 10 11 + 29 c2-c2-c_1-o 8 9 10 12 + 30 c2-c2-c_1-n 8 9 10 1 + 31 hc-c2-c_1-o_1 13 9 10 11 + 32 hc-c2-c_1-o 13 9 10 12 + 33 hc-c2-c_1-n 13 9 10 1 + 34 hc-c2-c_1-o_1 14 9 10 11 + 35 hc-c2-c_1-o 14 9 10 12 + 36 hc-c2-c_1-n 14 9 10 1 + 37 c2-c_1-o-ho 9 10 12 15 + 38 o_1-c_1-o-ho 11 10 12 15 + 39 n-c_1-o-ho 1 10 12 15 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template deleted file mode 100644 index 944d6918c5..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template +++ /dev/null @@ -1,160 +0,0 @@ -this is a molecule template for: initial nylon crosslink, pre-reacting - -18 atoms -16 bonds -25 angles -23 dihedrals -14 impropers - -Types - -1 2 -2 1 -3 1 -4 4 -5 4 -6 3 -7 3 -8 1 -9 1 -10 5 -11 8 -12 6 -13 3 -14 3 -15 7 -16 1 -17 3 -18 3 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.000000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 0.000000 -16 0.000000 -17 0.000000 -18 0.000000 - -Coords - -1 -4.922858 -0.946982 1.146055 -2 -5.047195 -0.935267 -0.358173 -3 -6.526281 -0.755366 -0.743523 -4 -5.282604 0.020447 1.552710 -5 -3.860697 -1.095850 1.428305 -6 -4.662382 -1.920900 -0.781524 -7 -4.433977 -0.072765 -0.784071 -8 -5.506279 0.202610 4.825816 -9 -4.449177 -0.844592 4.423366 -10 -4.103916 -0.749629 2.925195 -11 -3.376249 -1.886171 2.245643 -12 -4.493235 0.477214 2.137199 -13 -4.849053 -1.888877 4.663994 -14 -3.491823 -0.662913 5.018510 -15 -5.020777 1.189745 2.805427 -16 -3.964987 2.900602 -1.551341 -17 -4.460694 2.836102 0.668882 -18 -4.828494 3.219656 -0.122111 - -Bonds - -1 12 1 2 -2 4 1 4 -3 4 1 5 -4 1 2 3 -5 2 2 6 -6 2 2 7 -7 1 3 16 -8 2 3 17 -9 2 3 18 -10 1 8 9 -11 6 9 10 -12 2 9 13 -13 2 9 14 -14 7 10 11 -15 5 10 12 -16 8 12 15 - -Angles - -1 6 2 1 4 -2 6 2 1 5 -3 7 4 1 5 -4 24 1 2 3 -5 5 1 2 6 -6 5 1 2 7 -7 1 3 2 6 -8 1 3 2 7 -9 3 6 2 7 -10 2 2 3 16 -11 1 2 3 17 -12 1 2 3 18 -13 1 16 3 17 -14 1 16 3 18 -15 3 17 3 18 -16 12 8 9 10 -17 1 8 9 13 -18 1 8 9 14 -19 13 13 9 10 -20 13 14 9 10 -21 3 13 9 14 -22 10 9 10 11 -23 8 9 10 12 -24 21 11 10 12 -25 11 10 12 15 - -Dihedrals - -1 31 4 1 2 3 -2 32 4 1 2 6 -3 32 4 1 2 7 -4 31 5 1 2 3 -5 32 5 1 2 6 -6 32 5 1 2 7 -7 33 1 2 3 16 -8 1 1 2 3 17 -9 1 1 2 3 18 -10 4 16 3 2 6 -11 2 6 2 3 17 -12 2 6 2 3 18 -13 4 16 3 2 7 -14 2 7 2 3 17 -15 2 7 2 3 18 -16 14 8 9 10 11 -17 12 8 9 10 12 -18 15 13 9 10 11 -19 13 13 9 10 12 -20 15 14 9 10 11 -21 13 14 9 10 12 -22 10 9 10 12 15 -23 11 11 10 12 15 - -Impropers - -1 1 2 1 4 5 -2 9 9 10 11 12 -3 1 1 2 3 6 -4 1 1 2 3 7 -5 1 1 2 6 7 -6 1 3 2 6 7 -7 1 2 3 16 17 -8 1 2 3 16 18 -9 1 2 3 17 18 -10 1 16 3 17 18 -11 1 8 9 13 10 -12 1 8 9 14 10 -13 1 8 9 13 14 -14 1 13 9 14 10 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.molecule_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.molecule_template new file mode 100644 index 0000000000..7de7512f1c --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.molecule_template @@ -0,0 +1,169 @@ +this is a molecule template for: initial nylon crosslink, pre-reacting + + 18 atoms + 16 bonds + 25 angles + 23 dihedrals + 2 impropers + +Coords + + 1 -4.922858499 -0.946981747 1.146055346 + 2 -5.047194816 -0.935266843 -0.358172771 + 3 -6.526281447 -0.755365854 -0.743523227 + 4 -5.282604074 0.020446894 1.552710361 + 5 -3.860696509 -1.095850190 1.428304925 + 6 -4.662381862 -1.920899862 -0.781524026 + 7 -4.433976540 -0.072765142 -0.784070641 + 8 -5.506279186 0.202610302 4.825815562 + 9 -4.449176624 -0.844592213 4.423366146 + 10 -4.103915981 -0.749628655 2.925195217 + 11 -3.376248536 -1.886171498 2.245643443 + 12 -4.493235430 0.477213651 2.137199034 + 13 -4.849052953 -1.888876753 4.663993750 + 14 -3.491822950 -0.662913310 5.018510248 + 15 -5.020776528 1.189745133 2.805427194 + 16 -3.964987378 2.900602044 -1.551341170 + 17 -4.460693773 2.836101897 0.668881952 + 18 -4.828494000 3.219655862 -0.122111278 + +Types + + 1 na + 2 c2 + 3 c2 + 4 hn + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o + 13 hc + 14 hc + 15 ho + 16 c2 + 17 hc + 18 hc + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 0.000000 + 13 0.000000 + 14 0.000000 + 15 0.000000 + 16 0.000000 + 17 0.000000 + 18 0.000000 + +Molecules + + 1 1 + 2 1 + 3 1 + 4 1 + 5 1 + 6 1 + 7 1 + 8 1 + 9 1 + 10 1 + 11 1 + 12 1 + 13 1 + 14 1 + 15 1 + 16 1 + 17 1 + 18 1 + +Bonds + + 1 na-c2 1 2 + 2 na-hn 1 4 + 3 na-hn 1 5 + 4 c2-c2 2 3 + 5 c2-hc 2 6 + 6 c2-hc 2 7 + 7 c2-c2 3 16 + 8 c2-hc 3 17 + 9 c2-hc 3 18 + 10 c2-c2 8 9 + 11 c2-c_1 9 10 + 12 c2-hc 9 13 + 13 c2-hc 9 14 + 14 c_1-o_1 10 11 + 15 c_1-o 10 12 + 16 o-ho 12 15 + +Angles + + 1 c2-na-hn 2 1 4 + 2 c2-na-hn 2 1 5 + 3 hn-na-hn 4 1 5 + 4 na-c2-c2 1 2 3 + 5 na-c2-hc 1 2 6 + 6 na-c2-hc 1 2 7 + 7 c2-c2-hc 3 2 6 + 8 c2-c2-hc 3 2 7 + 9 hc-c2-hc 6 2 7 + 10 c2-c2-c2 2 3 16 + 11 c2-c2-hc 2 3 17 + 12 c2-c2-hc 2 3 18 + 13 c2-c2-hc 16 3 17 + 14 c2-c2-hc 16 3 18 + 15 hc-c2-hc 17 3 18 + 16 c2-c2-c_1 8 9 10 + 17 c2-c2-hc 8 9 13 + 18 c2-c2-hc 8 9 14 + 19 hc-c2-c_1 13 9 10 + 20 hc-c2-c_1 14 9 10 + 21 hc-c2-hc 13 9 14 + 22 c2-c_1-o_1 9 10 11 + 23 c2-c_1-o 9 10 12 + 24 o_1-c_1-o 11 10 12 + 25 c_1-o-ho 10 12 15 + +Dihedrals + + 1 hn-na-c2-c2 4 1 2 3 + 2 hn-na-c2-hc 4 1 2 6 + 3 hn-na-c2-hc 4 1 2 7 + 4 hn-na-c2-c2 5 1 2 3 + 5 hn-na-c2-hc 5 1 2 6 + 6 hn-na-c2-hc 5 1 2 7 + 7 na-c2-c2-c2 1 2 3 16 + 8 na-c2-c2-hc 1 2 3 17 + 9 na-c2-c2-hc 1 2 3 18 + 10 c2-c2-c2-hc 16 3 2 6 + 11 hc-c2-c2-hc 6 2 3 17 + 12 hc-c2-c2-hc 6 2 3 18 + 13 c2-c2-c2-hc 16 3 2 7 + 14 hc-c2-c2-hc 7 2 3 17 + 15 hc-c2-c2-hc 7 2 3 18 + 16 c2-c2-c_1-o_1 8 9 10 11 + 17 c2-c2-c_1-o 8 9 10 12 + 18 hc-c2-c_1-o_1 13 9 10 11 + 19 hc-c2-c_1-o 13 9 10 12 + 20 hc-c2-c_1-o_1 14 9 10 11 + 21 hc-c2-c_1-o 14 9 10 12 + 22 c2-c_1-o-ho 9 10 12 15 + 23 o_1-c_1-o-ho 11 10 12 15 + +Impropers + + 1 c2-na-hn-hn 2 1 4 5 + 2 c2-c_1-o_1-o 9 10 11 12 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template deleted file mode 100644 index ffd3ef733c..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template +++ /dev/null @@ -1,131 +0,0 @@ -this is a molecule template for: water condensation, post-reacting - -15 atoms -13 bonds -19 angles -16 dihedrals -10 impropers - -Types - -1 9 -2 1 -3 1 -4 10 -5 4 -6 3 -7 3 -8 1 -9 1 -10 5 -11 8 -12 11 -13 3 -14 3 -15 10 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.410000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 -0.820000 -13 0.000000 -14 0.000000 -15 0.410000 - -Coords - -1 -4.856280 -1.050468 1.432625 -2 -5.047195 -0.935267 -0.358173 -3 -6.526281 -0.755366 -0.743523 -4 -5.282604 0.020447 1.552710 -5 -3.860697 -1.095850 1.428305 -6 -4.662382 -1.920900 -0.781524 -7 -4.433977 -0.072765 -0.784071 -8 -5.506279 0.202610 4.825816 -9 -4.449177 -0.844592 4.423366 -10 -4.103916 -0.749629 2.925195 -11 -3.376249 -1.886171 2.245643 -12 -4.493235 0.477214 2.137199 -13 -4.849053 -1.888877 4.663994 -14 -3.491823 -0.662913 5.018510 -15 -5.020777 1.189745 2.805427 - -Bonds - -1 9 1 2 -2 10 1 5 -3 11 1 10 -4 1 2 3 -5 2 2 6 -6 2 2 7 -7 13 4 12 -8 1 8 9 -9 6 9 10 -10 2 9 13 -11 2 9 14 -12 7 10 11 -13 13 15 12 - -Angles - -1 14 2 1 5 -2 15 2 1 10 -3 17 5 1 10 -4 18 1 2 3 -5 19 1 2 6 -6 19 1 2 7 -7 1 3 2 6 -8 1 3 2 7 -9 3 6 2 7 -10 12 8 9 10 -11 1 8 9 13 -12 1 8 9 14 -13 13 13 9 10 -14 13 14 9 10 -15 3 13 9 14 -16 10 9 10 11 -17 20 1 10 9 -18 22 1 10 11 -19 25 15 12 4 - -Dihedrals - -1 16 5 1 2 3 -2 17 5 1 2 6 -3 17 5 1 2 7 -4 18 10 1 2 3 -5 19 10 1 2 6 -6 19 10 1 2 7 -7 20 2 1 10 9 -8 21 2 1 10 11 -9 23 5 1 10 9 -10 24 5 1 10 11 -11 14 8 9 10 11 -12 28 8 9 10 1 -13 15 13 9 10 11 -14 29 13 9 10 1 -15 15 14 9 10 11 -16 29 14 9 10 1 - -Impropers - -1 10 2 1 5 10 -2 11 1 10 9 11 -3 1 1 2 3 6 -4 1 1 2 3 7 -5 1 1 2 6 7 -6 1 3 2 6 7 -7 1 8 9 13 10 -8 1 8 9 14 10 -9 1 8 9 13 14 -10 1 13 9 14 10 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.molecule_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.molecule_template new file mode 100644 index 0000000000..2e91261468 --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.molecule_template @@ -0,0 +1,141 @@ +this is a molecule template for: water condensation, post-reacting + + 15 atoms + 13 bonds + 19 angles + 16 dihedrals + 2 impropers + +Coords + + 1 -4.856280281 -1.050467974 1.432625159 + 2 -5.047194816 -0.935266843 -0.358172771 + 3 -6.526281447 -0.755365854 -0.743523227 + 4 -5.282604074 0.020446894 1.552710361 + 5 -3.860696509 -1.095850190 1.428304925 + 6 -4.662381862 -1.920899862 -0.781524026 + 7 -4.433976540 -0.072765142 -0.784070641 + 8 -5.506279186 0.202610302 4.825815562 + 9 -4.449176624 -0.844592213 4.423366146 + 10 -4.103915981 -0.749628655 2.925195217 + 11 -3.376248536 -1.886171498 2.245643443 + 12 -4.493235430 0.477213651 2.137199034 + 13 -4.849052953 -1.888876753 4.663993750 + 14 -3.491822950 -0.662913310 5.018510248 + 15 -5.020776528 1.189745133 2.805427194 + +Types + + 1 n + 2 c2 + 3 c2 + 4 hw + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o* + 13 hc + 14 hc + 15 hw + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.410000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 -0.820000 + 13 0.000000 + 14 0.000000 + 15 0.410000 + +Molecules + + 1 1 + 2 1 + 3 1 + 4 1 + 5 1 + 6 1 + 7 1 + 8 1 + 9 1 + 10 1 + 11 1 + 12 1 + 13 1 + 14 1 + 15 1 + +Bonds + + 1 n-c2 1 2 + 2 n-hn 1 5 + 3 n-c_1 1 10 + 4 c2-c2 2 3 + 5 c2-hc 2 6 + 6 c2-hc 2 7 + 7 hw-o* 4 12 + 8 c2-c2 8 9 + 9 c2-c_1 9 10 + 10 c2-hc 9 13 + 11 c2-hc 9 14 + 12 c_1-o_1 10 11 + 13 hw-o* 15 12 + +Angles + + 1 c2-n-hn 2 1 5 + 2 c2-n-c_1 2 1 10 + 3 hn-n-c_1 5 1 10 + 4 n-c2-c2 1 2 3 + 5 n-c2-hc 1 2 6 + 6 n-c2-hc 1 2 7 + 7 c2-c2-hc 3 2 6 + 8 c2-c2-hc 3 2 7 + 9 hc-c2-hc 6 2 7 + 10 c2-c2-c_1 8 9 10 + 11 c2-c2-hc 8 9 13 + 12 c2-c2-hc 8 9 14 + 13 hc-c2-c_1 13 9 10 + 14 hc-c2-c_1 14 9 10 + 15 hc-c2-hc 13 9 14 + 16 c2-c_1-o_1 9 10 11 + 17 n-c_1-c2 1 10 9 + 18 n-c_1-o_1 1 10 11 + 19 hw-o*-hw 15 12 4 + +Dihedrals + + 1 hn-n-c2-c2 5 1 2 3 + 2 hn-n-c2-hc 5 1 2 6 + 3 hn-n-c2-hc 5 1 2 7 + 4 c_1-n-c2-c2 10 1 2 3 + 5 c_1-n-c2-hc 10 1 2 6 + 6 c_1-n-c2-hc 10 1 2 7 + 7 c2-n-c_1-c2 2 1 10 9 + 8 c2-n-c_1-o_1 2 1 10 11 + 9 hn-n-c_1-c2 5 1 10 9 + 10 hn-n-c_1-o_1 5 1 10 11 + 11 c2-c2-c_1-o_1 8 9 10 11 + 12 c2-c2-c_1-n 8 9 10 1 + 13 hc-c2-c_1-o_1 13 9 10 11 + 14 hc-c2-c_1-n 13 9 10 1 + 15 hc-c2-c_1-o_1 14 9 10 11 + 16 hc-c2-c_1-n 14 9 10 1 + +Impropers + + 1 c2-n-hn-c_1 2 1 5 10 + 2 n-c_1-c2-o_1 1 10 9 11 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template deleted file mode 100644 index 7abe15ada8..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template +++ /dev/null @@ -1,158 +0,0 @@ -this is a molecule template for: water condensation, pre-reacting - -15 atoms -14 bonds -25 angles -30 dihedrals -16 impropers - -Types - -1 9 -2 1 -3 1 -4 4 -5 4 -6 3 -7 3 -8 1 -9 1 -10 5 -11 8 -12 6 -13 3 -14 3 -15 7 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.000000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 0.000000 - -Coords - -1 -4.922858 -0.946982 1.146055 -2 -5.047195 -0.935267 -0.358173 -3 -6.526281 -0.755366 -0.743523 -4 -5.282604 0.020447 1.552710 -5 -3.860697 -1.095850 1.428305 -6 -4.662382 -1.920900 -0.781524 -7 -4.433977 -0.072765 -0.784071 -8 -5.506279 0.202610 4.825816 -9 -4.449177 -0.844592 4.423366 -10 -4.103916 -0.749629 2.925195 -11 -3.376249 -1.886171 2.245643 -12 -4.493235 0.477214 2.137199 -13 -4.849053 -1.888877 4.663994 -14 -3.491823 -0.662913 5.018510 -15 -5.020777 1.189745 2.805427 - -Bonds - -1 9 1 2 -2 10 1 4 -3 10 1 5 -4 11 1 10 -5 1 2 3 -6 2 2 6 -7 2 2 7 -8 1 8 9 -9 6 9 10 -10 2 9 13 -11 2 9 14 -12 7 10 11 -13 5 10 12 -14 8 12 15 - -Angles - -1 14 2 1 4 -2 14 2 1 5 -3 15 2 1 10 -4 16 4 1 5 -5 17 4 1 10 -6 17 5 1 10 -7 18 1 2 3 -8 19 1 2 6 -9 19 1 2 7 -10 1 3 2 6 -11 1 3 2 7 -12 3 6 2 7 -13 12 8 9 10 -14 1 8 9 13 -15 1 8 9 14 -16 13 13 9 10 -17 13 14 9 10 -18 3 13 9 14 -19 10 9 10 11 -20 8 9 10 12 -21 20 1 10 9 -22 21 11 10 12 -23 22 1 10 11 -24 23 1 10 12 -25 11 10 12 15 - -Dihedrals - -1 16 4 1 2 3 -2 17 4 1 2 6 -3 17 4 1 2 7 -4 16 5 1 2 3 -5 17 5 1 2 6 -6 17 5 1 2 7 -7 18 10 1 2 3 -8 19 10 1 2 6 -9 19 10 1 2 7 -10 20 2 1 10 9 -11 21 2 1 10 11 -12 22 2 1 10 12 -13 23 4 1 10 9 -14 24 4 1 10 11 -15 25 4 1 10 12 -16 23 5 1 10 9 -17 24 5 1 10 11 -18 25 5 1 10 12 -19 14 8 9 10 11 -20 12 8 9 10 12 -21 28 8 9 10 1 -22 15 13 9 10 11 -23 13 13 9 10 12 -24 29 13 9 10 1 -25 15 14 9 10 11 -26 13 14 9 10 12 -27 29 14 9 10 1 -28 10 9 10 12 15 -29 11 11 10 12 15 -30 30 1 10 12 15 - -Impropers - -1 1 2 1 4 5 -2 1 2 1 4 10 -3 1 2 1 5 10 -4 1 4 1 5 10 -5 1 1 2 3 6 -6 1 1 2 3 7 -7 1 1 2 6 7 -8 1 3 2 6 7 -9 1 8 9 13 10 -10 1 8 9 14 10 -11 1 8 9 13 14 -12 1 13 9 14 10 -13 1 9 10 11 12 -14 1 1 10 9 11 -15 1 1 10 9 12 -16 1 1 10 11 12 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.molecule_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.molecule_template new file mode 100644 index 0000000000..86a772634d --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.molecule_template @@ -0,0 +1,157 @@ +this is a molecule template for: water condensation, pre-reacting + + 15 atoms + 14 bonds + 25 angles + 30 dihedrals + 0 impropers + +Coords + + 1 -4.922858499 -0.946981747 1.146055346 + 2 -5.047194816 -0.935266843 -0.358172771 + 3 -6.526281447 -0.755365854 -0.743523227 + 4 -5.282604074 0.020446894 1.552710361 + 5 -3.860696509 -1.095850190 1.428304925 + 6 -4.662381862 -1.920899862 -0.781524026 + 7 -4.433976540 -0.072765142 -0.784070641 + 8 -5.506279186 0.202610302 4.825815562 + 9 -4.449176624 -0.844592213 4.423366146 + 10 -4.103915981 -0.749628655 2.925195217 + 11 -3.376248536 -1.886171498 2.245643443 + 12 -4.493235430 0.477213651 2.137199034 + 13 -4.849052953 -1.888876753 4.663993750 + 14 -3.491822950 -0.662913310 5.018510248 + 15 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