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type labels for nylon_melt example

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This commit is contained in:
Jacob Gissinger
2022-12-13 00:37:09 -05:00
parent 0375a7569e
commit 983401b015
14 changed files with 965 additions and 993 deletions
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15
examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt
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@ -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

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examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz
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examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
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@ -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

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examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
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@ -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

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examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 Normal file
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@ -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

151
examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 Normal file
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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

189
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template
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@ -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

187
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.molecule_template Normal file
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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

160
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template
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@ -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

169
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.molecule_template Normal file
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@ -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

131
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template
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@ -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

141
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.molecule_template Normal file
View File

@ -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

158
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template
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@ -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

157
examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.molecule_template Normal file
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@ -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 -5.020776528 1.189745133 2.805427194
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
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
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 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 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 c_1-o 10 12
14 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-c_1 8 9 10
14 c2-c2-hc 8 9 13
15 c2-c2-hc 8 9 14
16 hc-c2-c_1 13 9 10
17 hc-c2-c_1 14 9 10
18 hc-c2-hc 13 9 14
19 c2-c_1-o_1 9 10 11
20 c2-c_1-o 9 10 12
21 n-c_1-c2 1 10 9
22 o_1-c_1-o 11 10 12
23 n-c_1-o_1 1 10 11
24 n-c_1-o 1 10 12
25 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 c2-c2-c_1-o_1 8 9 10 11
20 c2-c2-c_1-o 8 9 10 12
21 c2-c2-c_1-n 8 9 10 1
22 hc-c2-c_1-o_1 13 9 10 11
23 hc-c2-c_1-o 13 9 10 12
24 hc-c2-c_1-n 13 9 10 1
25 hc-c2-c_1-o_1 14 9 10 11
26 hc-c2-c_1-o 14 9 10 12
27 hc-c2-c_1-n 14 9 10 1
28 c2-c_1-o-ho 9 10 12 15
29 o_1-c_1-o-ho 11 10 12 15
30 n-c_1-o-ho 1 10 12 15