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type labels for tiny_nylon example

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This commit is contained in:
Jacob Gissinger
2022-12-15 13:08:25 -05:00
parent 983401b015
commit b5eb64cc0c
24 changed files with 2559 additions and 1651 deletions
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15
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized
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@ -19,14 +19,19 @@ dihedral_style class2
improper_style class2
read_data tiny_nylon.data
read_data tiny_nylon.data &
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 300.0 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

15
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
View File

@ -19,7 +19,12 @@ dihedral_style class2
improper_style class2
read_data tiny_nylon.data
read_data tiny_nylon.data &
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
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2+0.1
@ -27,10 +32,10 @@ variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 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

16
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized
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@ -19,14 +19,20 @@ dihedral_style class2
improper_style class2
read_data tiny_nylon.data
read_data tiny_nylon.data &
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 300.0 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

201
examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1
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@ -1,201 +0,0 @@
LAMMPS (15 Apr 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# 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 = 0.000385045 secs
read_data CPU = 0.013443 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 (src/REACTION/fix_bond_react.cpp:2051)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051)
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 (src/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 FFTW3
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 (src/domain.cpp:812)
Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 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 0.379454 on 1 procs for 1000 steps with 44 atoms
Performance: 227.696 ns/day, 0.105 hours/ns, 2635.368 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.069723 | 0.069723 | 0.069723 | 0.0 | 18.37
Bond | 0.14802 | 0.14802 | 0.14802 | 0.0 | 39.01
Kspace | 0.044252 | 0.044252 | 0.044252 | 0.0 | 11.66
Neigh | 0.072359 | 0.072359 | 0.072359 | 0.0 | 19.07
Comm | 0.0044748 | 0.0044748 | 0.0044748 | 0.0 | 1.18
Output | 0.0022775 | 0.0022775 | 0.0022775 | 0.0 | 0.60
Modify | 0.036509 | 0.036509 | 0.036509 | 0.0 | 9.62
Other | | 0.00184 | | | 0.48
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

201
examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4
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@ -1,201 +0,0 @@
LAMMPS (15 Apr 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# 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 2 by 2 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 = 0.000431282 secs
read_data CPU = 0.0129571 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 (src/REACTION/fix_bond_react.cpp:2051)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051)
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 (src/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 FFTW3
3d grid and FFT values/proc = 252 2
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 (src/domain.cpp:812)
Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 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
50 266.5092 -90.813802 0.0034851739 0.1 0 1 0
100 559.41271 -53.23688 0.0034851739 0.2 0 1 0
150 489.90516 31.555817 0.0034851739 0.3 0 1 0
200 326.18391 7.7889992 0.0034851739 0.4 0 1 0
250 339.78203 2.3919541 0.0034851739 0.5 0 1 0
300 370.90263 -32.01673 0.0034851739 0.6 0 1 0
350 294.07547 -5.4019813 0.0034851739 0.7 0 1 0
400 287.76477 12.254133 0.0034851739 0.8 0 1 0
450 293.36482 66.372956 0.0034851739 0.9 0 1 0
500 246.84496 26.132317 0.0034851739 1 0 1 0
550 253.08778 -15.350262 0.0034851739 1.1 1 1 1
600 358.83641 25.007371 0.0034851739 1.2 1 1 1
650 320.51492 -32.34823 0.0034851739 1.3 1 1 1
700 310.87976 -8.2306669 0.0034851739 1.4 1 1 1
750 307.54142 12.025818 0.0034851739 1.5 1 1 1
800 272.51724 -22.92823 0.0034851739 1.6 1 1 1
850 268.66181 10.069534 0.0034851739 1.7 1 1 1
900 265.5531 -10.471377 0.0034851739 1.8 1 1 1
950 259.43086 9.4546712 0.0034851739 1.9 1 1 1
1000 247.14622 20.250308 0.0034851739 2 1 1 1
Loop time of 0.357762 on 4 procs for 1000 steps with 44 atoms
Performance: 241.502 ns/day, 0.099 hours/ns, 2795.157 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0003917 | 0.015545 | 0.033317 | 11.9 | 4.35
Bond | 0.0010131 | 0.030153 | 0.076975 | 18.2 | 8.43
Kspace | 0.092857 | 0.1462 | 0.18688 | 10.7 | 40.87
Neigh | 0.043786 | 0.044014 | 0.044189 | 0.1 | 12.30
Comm | 0.03636 | 0.038345 | 0.040538 | 0.8 | 10.72
Output | 0.00091578 | 0.0012541 | 0.0020923 | 1.4 | 0.35
Modify | 0.075379 | 0.080791 | 0.086052 | 1.8 | 22.58
Other | | 0.00146 | | | 0.41
Nlocal: 11 ave 32 max 0 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 40 ave 51 max 19 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 191 ave 529 max 0 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 764
Ave neighs/atom = 17.3636
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

412
examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.1 Normal file
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@ -0,0 +1,412 @@
LAMMPS (4 Nov 2022)
# 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 extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
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 ...
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
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 = 0.000 seconds
read_data CPU = 0.007 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 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 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
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 f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
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
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 343 8
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 = 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
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:819)
Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 283.51963 -47.16359 0.0034851739 1 0
100 256.04648 21.778898 0.0034851739 1 1
150 450.78138 -11.7887 0.0034851739 1 1
200 400.15754 49.489858 0.0034851739 1 1
250 347.06066 68.952063 0.0034851739 1 1
300 291.89228 -1.5986302 0.0034851739 1 1
350 290.25995 17.634558 0.0034851739 1 1
400 234.89168 26.36452 0.0034851739 1 1
450 305.80709 -28.923896 0.0034851739 1 1
500 375.19218 -37.024375 0.0034851739 1 1
550 321.86944 -4.6961825 0.0034851739 1 1
600 307.2639 -31.393161 0.0034851739 1 1
650 255.95833 8.4995589 0.0034851739 1 1
700 294.54665 -17.06105 0.0034851739 1 1
750 273.08231 -10.7175 0.0034851739 1 1
800 249.69175 9.9777683 0.0034851739 1 1
850 307.71806 -6.9950048 0.0034851739 1 1
900 367.39855 9.9874985 0.0034851739 1 1
950 327.57334 -4.7029779 0.0034851739 1 1
1000 348.85247 15.763492 0.0034851739 1 1
1050 328.94435 -35.031279 0.0034851739 1 1
1100 283.23971 -16.937443 0.0034851739 1 1
1150 266.69676 42.308482 0.0034851739 1 1
1200 244.61493 -8.291143 0.0034851739 1 1
1250 206.68495 6.6280168 0.0034851739 1 1
1300 257.83339 -7.0826267 0.0034851739 1 1
1350 358.0875 -7.6024741 0.0034851739 1 1
1400 353.66614 18.091914 0.0034851739 1 1
1450 302.27969 13.828755 0.0034851739 1 1
1500 262.57851 9.256794 0.0034851739 1 1
1550 252.39493 1.2438641 0.0034851739 1 1
1600 247.18352 10.008173 0.0034851739 1 1
1650 290.30112 -2.1829035 0.0034851739 1 1
1700 272.78999 -57.305766 0.0034851739 1 1
1750 253.35258 24.729795 0.0034851739 1 1
1800 278.67831 -0.95016566 0.0034851739 1 1
1850 302.04743 16.002867 0.0034851739 1 1
1900 330.67188 -22.034206 0.0034851739 1 1
1950 342.64206 8.0076017 0.0034851739 1 1
2000 348.74388 -12.159887 0.0034851739 1 1
2050 300.48093 36.01054 0.0034851739 1 1
2100 275.01699 8.7612261 0.0034851739 1 1
2150 303.92758 10.317056 0.0034851739 1 1
2200 308.89457 33.245018 0.0034851739 1 1
2250 265.74177 35.857118 0.0034851739 1 1
2300 273.40088 53.001593 0.0034851739 1 1
2350 287.74746 -0.14590128 0.0034851739 1 1
2400 278.76055 -8.2080851 0.0034851739 1 1
2450 331.88978 39.025208 0.0034851739 1 1
2500 280.04045 -21.423616 0.0034851739 1 1
2550 388.81531 -12.350023 0.0034851739 1 1
2600 311.13452 -13.287102 0.0034851739 1 1
2650 325.07681 88.710878 0.0034851739 1 1
2700 319.08502 14.118057 0.0034851739 1 1
2750 261.72066 26.051675 0.0034851739 1 1
2800 281.03508 -21.200833 0.0034851739 1 1
2850 312.27359 4.3892078 0.0034851739 1 1
2900 274.81147 -12.738114 0.0034851739 1 1
2950 281.76969 11.198451 0.0034851739 1 1
3000 291.83918 48.595884 0.0034851739 1 1
3050 297.40189 -24.91102 0.0034851739 1 1
3100 341.47331 13.82699 0.0034851739 1 1
3150 347.51825 -10.458257 0.0034851739 1 1
3200 301.24666 26.550464 0.0034851739 1 1
3250 281.3679 -23.02985 0.0034851739 1 1
3300 279.8332 -53.222264 0.0034851739 1 1
3350 289.41496 -8.793156 0.0034851739 1 1
3400 288.5722 -25.441134 0.0034851739 1 1
3450 259.59524 77.884773 0.0034851739 1 1
3500 296.00389 30.3654 0.0034851739 1 1
3550 302.14443 -5.1101538 0.0034851739 1 1
3600 288.98098 -12.688781 0.0034851739 1 1
3650 333.83238 -33.121195 0.0034851739 1 1
3700 347.7556 -24.693995 0.0034851739 1 1
3750 354.42689 6.7030374 0.0034851739 1 1
3800 341.24011 -18.775449 0.0034851739 1 1
3850 320.50998 35.492418 0.0034851739 1 1
3900 326.81918 -49.073015 0.0034851739 1 1
3950 299.55145 -19.487946 0.0034851739 1 1
4000 308.81019 30.579971 0.0034851739 1 1
4050 251.83279 -17.500379 0.0034851739 1 1
4100 242.0783 21.228088 0.0034851739 1 1
4150 265.59921 -3.9446469 0.0034851739 1 1
4200 369.32464 -14.626205 0.0034851739 1 1
4250 346.22904 -32.749662 0.0034851739 1 1
4300 369.43175 11.916047 0.0034851739 1 1
4350 321.17007 -9.3009147 0.0034851739 1 1
4400 312.41821 -31.360537 0.0034851739 1 1
4450 281.59211 40.338618 0.0034851739 1 1
4500 289.10806 -4.2135222 0.0034851739 1 1
4550 317.55705 -4.3727576 0.0034851739 1 1
4600 310.64469 -14.403478 0.0034851739 1 1
4650 284.43433 37.416848 0.0034851739 1 1
4700 353.88469 7.7633789 0.0034851739 1 1
4750 328.48834 -60.780145 0.0034851739 1 1
4800 390.23986 4.2691385 0.0034851739 1 1
4850 364.06188 40.18245 0.0034851739 1 1
4900 304.64696 6.3557092 0.0034851739 1 1
4950 309.12139 -16.598924 0.0034851739 1 1
5000 311.03552 14.748037 0.0034851739 1 1
5050 320.97847 -26.733755 0.0034851739 1 1
5100 275.1237 -29.734972 0.0034851739 1 1
5150 287.76954 -2.5726321 0.0034851739 1 1
5200 267.72493 -6.6677739 0.0034851739 1 1
5250 290.63862 29.209807 0.0034851739 1 1
5300 276.51052 -19.746615 0.0034851739 1 1
5350 255.69196 25.130356 0.0034851739 1 1
5400 313.43108 -18.556701 0.0034851739 1 1
5450 327.91785 -16.08265 0.0034851739 1 1
5500 342.03301 33.271603 0.0034851739 1 1
5550 272.96564 -5.0247163 0.0034851739 1 1
5600 315.93807 -16.793394 0.0034851739 1 1
5650 294.66353 19.720691 0.0034851739 1 1
5700 283.4631 -6.5193772 0.0034851739 1 1
5750 261.06436 12.755679 0.0034851739 1 1
5800 274.15767 -9.6693117 0.0034851739 1 1
5850 271.1371 18.441828 0.0034851739 1 1
5900 283.39277 -4.6324708 0.0034851739 1 1
5950 326.30497 12.106133 0.0034851739 1 1
6000 316.91847 -32.864812 0.0034851739 1 1
6050 344.86369 21.226768 0.0034851739 1 1
6100 295.85211 -7.3603837 0.0034851739 1 1
6150 256.72292 4.6010174 0.0034851739 1 1
6200 248.33379 -20.795929 0.0034851739 1 1
6250 259.4054 63.590928 0.0034851739 1 1
6300 264.16648 2.6570242 0.0034851739 1 1
6350 243.22677 -18.621317 0.0034851739 1 1
6400 269.96092 53.832036 0.0034851739 1 1
6450 252.06358 -26.231052 0.0034851739 1 1
6500 275.4825 25.577441 0.0034851739 1 1
6550 298.27441 11.17373 0.0034851739 1 1
6600 297.29358 -21.382334 0.0034851739 1 1
6650 334.78542 38.892678 0.0034851739 1 1
6700 299.48699 -20.336163 0.0034851739 1 1
6750 315.01936 21.000444 0.0034851739 1 1
6800 244.68344 -6.3625659 0.0034851739 1 1
6850 251.56543 27.857872 0.0034851739 1 1
6900 280.81518 -12.494398 0.0034851739 1 1
6950 273.87437 -34.211085 0.0034851739 1 1
7000 274.91068 33.483158 0.0034851739 1 1
7050 298.56432 -61.821668 0.0034851739 1 1
7100 299.08395 10.365875 0.0034851739 1 1
7150 317.38233 29.049831 0.0034851739 1 1
7200 317.24932 -27.515026 0.0034851739 1 1
7250 305.63931 12.732123 0.0034851739 1 1
7300 309.44007 -53.922033 0.0034851739 1 1
7350 280.35029 45.495031 0.0034851739 1 1
7400 228.60929 1.7072084 0.0034851739 1 1
7450 276.206 -19.170327 0.0034851739 1 1
7500 257.9851 77.105642 0.0034851739 1 1
7550 306.46848 -29.189265 0.0034851739 1 1
7600 296.84522 -20.83365 0.0034851739 1 1
7650 296.5965 -14.890206 0.0034851739 1 1
7700 322.80474 44.883023 0.0034851739 1 1
7750 293.7355 -48.487658 0.0034851739 1 1
7800 358.41838 13.156339 0.0034851739 1 1
7850 293.81457 -19.50566 0.0034851739 1 1
7900 309.49618 -28.562417 0.0034851739 1 1
7950 285.6339 -22.488886 0.0034851739 1 1
8000 262.85312 57.125049 0.0034851739 1 1
8050 243.28673 -28.082125 0.0034851739 1 1
8100 279.71604 10.011975 0.0034851739 1 1
8150 344.77027 -56.89744 0.0034851739 1 1
8200 366.36063 21.02453 0.0034851739 1 1
8250 347.07209 2.7752885 0.0034851739 1 1
8300 337.74753 -10.957676 0.0034851739 1 1
8350 300.41188 -22.840776 0.0034851739 1 1
8400 282.27447 0.32063982 0.0034851739 1 1
8450 285.40722 -3.7167264 0.0034851739 1 1
8500 321.32722 -21.308158 0.0034851739 1 1
8550 293.65903 15.681219 0.0034851739 1 1
8600 293.38929 37.727045 0.0034851739 1 1
8650 299.55185 -15.004573 0.0034851739 1 1
8700 270.7608 14.615287 0.0034851739 1 1
8750 306.46813 67.018302 0.0034851739 1 1
8800 308.35025 -91.212286 0.0034851739 1 1
8850 349.40419 31.906004 0.0034851739 1 1
8900 351.32706 -24.901778 0.0034851739 1 1
8950 320.84369 18.380221 0.0034851739 1 1
9000 289.2862 9.981138 0.0034851739 1 1
9050 270.53883 12.028672 0.0034851739 1 1
9100 270.63206 -0.87842772 0.0034851739 1 1
9150 274.30671 -4.1228725 0.0034851739 1 1
9200 343.78546 20.427647 0.0034851739 1 1
9250 348.1019 13.339075 0.0034851739 1 1
9300 345.11791 -32.515359 0.0034851739 1 1
9350 329.8365 12.644587 0.0034851739 1 1
9400 286.41337 -28.79111 0.0034851739 1 1
9450 321.92318 32.154255 0.0034851739 1 1
9500 302.68527 -42.576022 0.0034851739 1 1
9550 335.24034 26.675219 0.0034851739 1 1
9600 270.62012 17.230138 0.0034851739 1 1
9650 273.71088 35.651219 0.0034851739 1 1
9700 286.2141 -26.15835 0.0034851739 1 1
9750 262.25352 -4.1954047 0.0034851739 1 1
9800 314.29455 23.252049 0.0034851739 1 1
9850 273.71272 -29.586039 0.0034851739 1 1
9900 300.63743 42.595289 0.0034851739 1 1
9950 367.68979 -64.582508 0.0034851739 1 1
10000 357.17941 31.607766 0.0034851739 1 1
Loop time of 1.82433 on 1 procs for 10000 steps with 44 atoms
Performance: 473.599 ns/day, 0.051 hours/ns, 5481.467 timesteps/s, 241.185 katom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.25039 | 0.25039 | 0.25039 | 0.0 | 13.72
Bond | 1.0461 | 1.0461 | 1.0461 | 0.0 | 57.34
Kspace | 0.34339 | 0.34339 | 0.34339 | 0.0 | 18.82
Neigh | 0.0097352 | 0.0097352 | 0.0097352 | 0.0 | 0.53
Comm | 0.0047764 | 0.0047764 | 0.0047764 | 0.0 | 0.26
Output | 0.0030537 | 0.0030537 | 0.0030537 | 0.0 | 0.17
Modify | 0.15534 | 0.15534 | 0.15534 | 0.0 | 8.51
Other | | 0.01155 | | | 0.63
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 823 ave 823 max 823 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 823
Ave neighs/atom = 18.704545
Ave special neighs/atom = 9.9090909
Neighbor list builds = 221
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:01

412
examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.4 Normal file
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@ -0,0 +1,412 @@
LAMMPS (4 Nov 2022)
# 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 extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
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
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 = 0.000 seconds
read_data CPU = 0.008 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 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 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
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 f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
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
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 252 2
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 = 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
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:819)
Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 283.51963 -47.16359 0.0034851739 1 0
100 256.04648 21.778898 0.0034851739 1 1
150 450.78138 -11.7887 0.0034851739 1 1
200 400.15754 49.489858 0.0034851739 1 1
250 347.06066 68.952063 0.0034851739 1 1
300 291.89228 -1.5986302 0.0034851739 1 1
350 290.25995 17.634558 0.0034851739 1 1
400 234.89168 26.36452 0.0034851739 1 1
450 305.80709 -28.923896 0.0034851739 1 1
500 375.19218 -37.024375 0.0034851739 1 1
550 321.86944 -4.6961825 0.0034851739 1 1
600 307.2639 -31.393161 0.0034851739 1 1
650 255.95833 8.4995589 0.0034851739 1 1
700 294.54665 -17.06105 0.0034851739 1 1
750 273.08231 -10.7175 0.0034851739 1 1
800 249.69175 9.9777684 0.0034851739 1 1
850 307.71806 -6.9950047 0.0034851739 1 1
900 367.39855 9.9874984 0.0034851739 1 1
950 327.57334 -4.702978 0.0034851739 1 1
1000 348.85247 15.763492 0.0034851739 1 1
1050 328.94435 -35.031279 0.0034851739 1 1
1100 283.23971 -16.937443 0.0034851739 1 1
1150 266.69676 42.308482 0.0034851739 1 1
1200 244.61493 -8.2911432 0.0034851739 1 1
1250 206.68495 6.6280166 0.0034851739 1 1
1300 257.83339 -7.0826264 0.0034851739 1 1
1350 358.0875 -7.602474 0.0034851739 1 1
1400 353.66614 18.091914 0.0034851739 1 1
1450 302.27969 13.828755 0.0034851739 1 1
1500 262.57851 9.2567956 0.0034851739 1 1
1550 252.39492 1.2438631 0.0034851739 1 1
1600 247.18352 10.008173 0.0034851739 1 1
1650 290.30112 -2.1829055 0.0034851739 1 1
1700 272.78999 -57.305766 0.0034851739 1 1
1750 253.35258 24.729797 0.0034851739 1 1
1800 278.67832 -0.95017071 0.0034851739 1 1
1850 302.04743 16.002872 0.0034851739 1 1
1900 330.67188 -22.034206 0.0034851739 1 1
1950 342.64206 8.0075967 0.0034851739 1 1
2000 348.74388 -12.159899 0.0034851739 1 1
2050 300.48095 36.010534 0.0034851739 1 1
2100 275.017 8.7612294 0.0034851739 1 1
2150 303.92758 10.317032 0.0034851739 1 1
2200 308.89452 33.245012 0.0034851739 1 1
2250 265.74176 35.857111 0.0034851739 1 1
2300 273.40086 53.001626 0.0034851739 1 1
2350 287.74753 -0.14586562 0.0034851739 1 1
2400 278.7606 -8.20812 0.0034851739 1 1
2450 331.88979 39.02519 0.0034851739 1 1
2500 280.04041 -21.423589 0.0034851739 1 1
2550 388.81536 -12.350053 0.0034851739 1 1
2600 311.13468 -13.286785 0.0034851739 1 1
2650 325.07686 88.710881 0.0034851739 1 1
2700 319.08471 14.118288 0.0034851739 1 1
2750 261.72067 26.051439 0.0034851739 1 1
2800 281.03459 -21.201297 0.0034851739 1 1
2850 312.27342 4.3904047 0.0034851739 1 1
2900 274.81152 -12.739138 0.0034851739 1 1
2950 281.76873 11.199981 0.0034851739 1 1
3000 291.8377 48.595661 0.0034851739 1 1
3050 297.40212 -24.911752 0.0034851739 1 1
3100 341.48252 13.825136 0.0034851739 1 1
3150 347.5099 -10.452847 0.0034851739 1 1
3200 301.24901 26.553909 0.0034851739 1 1
3250 281.35392 -23.028031 0.0034851739 1 1
3300 279.82881 -53.225332 0.0034851739 1 1
3350 289.41016 -8.7866567 0.0034851739 1 1
3400 288.56923 -25.445059 0.0034851739 1 1
3450 259.59956 77.88466 0.0034851739 1 1
3500 295.99591 30.357393 0.0034851739 1 1
3550 302.1675 -5.103997 0.0034851739 1 1
3600 289.00244 -12.687621 0.0034851739 1 1
3650 333.89968 -33.124064 0.0034851739 1 1
3700 347.82328 -24.745583 0.0034851739 1 1
3750 354.51391 6.7131611 0.0034851739 1 1
3800 341.31124 -18.777474 0.0034851739 1 1
3850 320.48132 35.547595 0.0034851739 1 1
3900 326.8911 -49.153151 0.0034851739 1 1
3950 299.65543 -19.443322 0.0034851739 1 1
4000 308.97943 30.368402 0.0034851739 1 1
4050 251.46183 -17.518988 0.0034851739 1 1
4100 241.50223 22.103347 0.0034851739 1 1
4150 265.01178 -4.4952098 0.0034851739 1 1
4200 369.78569 -14.603579 0.0034851739 1 1
4250 348.20071 -33.060693 0.0034851739 1 1
4300 368.11836 11.897676 0.0034851739 1 1
4350 321.1145 -9.3124104 0.0034851739 1 1
4400 313.95395 -31.940883 0.0034851739 1 1
4450 280.50985 41.398853 0.0034851739 1 1
4500 289.36914 -2.3915112 0.0034851739 1 1
4550 318.52735 -5.0086703 0.0034851739 1 1
4600 308.68169 -13.642004 0.0034851739 1 1
4650 285.24153 35.314806 0.0034851739 1 1
4700 357.15021 8.8271927 0.0034851739 1 1
4750 359.11051 -59.672314 0.0034851739 1 1
4800 453.11584 0.54316266 0.0034851739 1 1
4850 392.52232 46.350736 0.0034851739 1 1
4900 310.42864 5.9002223 0.0034851739 1 1
4950 285.97355 -19.321724 0.0034851739 1 1
5000 309.41828 18.331381 0.0034851739 1 1
5050 324.96434 -27.143631 0.0034851739 1 1
5100 266.49422 -26.977074 0.0034851739 1 1
5150 295.35576 -14.271299 0.0034851739 1 1
5200 275.8961 14.057873 0.0034851739 1 1
5250 332.75955 26.04747 0.0034851739 1 1
5300 296.57102 -20.904181 0.0034851739 1 1
5350 264.68808 29.533914 0.0034851739 1 1
5400 293.373 -13.579532 0.0034851739 1 1
5450 290.55933 9.3458628 0.0034851739 1 1
5500 340.54834 8.8308229 0.0034851739 1 1
5550 336.08713 -6.9696582 0.0034851739 1 1
5600 331.77668 -7.9756709 0.0034851739 1 1
5650 307.8419 -10.263349 0.0034851739 1 1
5700 262.70119 78.855544 0.0034851739 1 1
5750 285.37985 -15.4042 0.0034851739 1 1
5800 267.44612 -30.053955 0.0034851739 1 1
5850 241.52125 3.2904907 0.0034851739 1 1
5900 265.13367 27.69901 0.0034851739 1 1
5950 277.95155 18.419031 0.0034851739 1 1
6000 309.62777 -20.054029 0.0034851739 1 1
6050 363.41588 16.435337 0.0034851739 1 1
6100 348.85793 -14.513241 0.0034851739 1 1
6150 323.73745 56.990265 0.0034851739 1 1
6200 338.66823 -19.93498 0.0034851739 1 1
6250 325.41329 -13.824943 0.0034851739 1 1
6300 279.82345 -9.0557197 0.0034851739 1 1
6350 285.90705 52.434161 0.0034851739 1 1
6400 260.34102 -15.766595 0.0034851739 1 1
6450 304.65686 7.5058044 0.0034851739 1 1
6500 265.02097 1.7203356 0.0034851739 1 1
6550 293.35057 1.8896974 0.0034851739 1 1
6600 284.06837 -9.3674953 0.0034851739 1 1
6650 307.29863 -2.3882614 0.0034851739 1 1
6700 336.20676 43.913926 0.0034851739 1 1
6750 291.53938 -16.749433 0.0034851739 1 1
6800 298.4418 -13.340335 0.0034851739 1 1
6850 264.13368 -11.219357 0.0034851739 1 1
6900 273.63109 -15.897238 0.0034851739 1 1
6950 282.64715 6.8275423 0.0034851739 1 1
7000 277.4091 -25.381099 0.0034851739 1 1
7050 278.07001 63.552969 0.0034851739 1 1
7100 293.33358 22.103462 0.0034851739 1 1
7150 308.36447 -27.212203 0.0034851739 1 1
7200 251.45077 -40.385347 0.0034851739 1 1
7250 317.57808 1.0302048 0.0034851739 1 1
7300 348.52627 48.392457 0.0034851739 1 1
7350 356.5821 27.933626 0.0034851739 1 1
7400 311.29835 -18.899768 0.0034851739 1 1
7450 274.24476 -19.41577 0.0034851739 1 1
7500 261.38075 1.2110527 0.0034851739 1 1
7550 299.78907 -17.64954 0.0034851739 1 1
7600 271.36191 25.99439 0.0034851739 1 1
7650 287.51241 1.532789 0.0034851739 1 1
7700 280.87778 -31.828432 0.0034851739 1 1
7750 312.22588 45.320976 0.0034851739 1 1
7800 312.73849 4.1022573 0.0034851739 1 1
7850 299.18742 50.272069 0.0034851739 1 1
7900 312.4916 -34.425195 0.0034851739 1 1
7950 284.5205 15.716375 0.0034851739 1 1
8000 248.39764 -7.1922339 0.0034851739 1 1
8050 242.65659 -32.701773 0.0034851739 1 1
8100 228.76112 54.351 0.0034851739 1 1
8150 308.67672 -15.835344 0.0034851739 1 1
8200 304.26746 -11.106867 0.0034851739 1 1
8250 338.67601 44.199636 0.0034851739 1 1
8300 308.59612 -9.6487546 0.0034851739 1 1
8350 287.08027 11.036122 0.0034851739 1 1
8400 319.79578 -78.918735 0.0034851739 1 1
8450 320.78978 57.275745 0.0034851739 1 1
8500 282.90803 33.716746 0.0034851739 1 1
8550 235.23686 -44.587941 0.0034851739 1 1
8600 265.62925 45.976855 0.0034851739 1 1
8650 260.35429 -9.3951434 0.0034851739 1 1
8700 236.16314 19.504695 0.0034851739 1 1
8750 291.51087 -13.996885 0.0034851739 1 1
8800 357.00246 -26.674845 0.0034851739 1 1
8850 327.72543 15.954838 0.0034851739 1 1
8900 321.17809 -14.794959 0.0034851739 1 1
8950 357.51102 39.861567 0.0034851739 1 1
9000 286.68385 -52.799636 0.0034851739 1 1
9050 283.96224 13.044025 0.0034851739 1 1
9100 304.04431 25.510777 0.0034851739 1 1
9150 261.33631 -18.611794 0.0034851739 1 1
9200 297.50501 25.733551 0.0034851739 1 1
9250 279.85018 -26.91045 0.0034851739 1 1
9300 336.07358 35.385228 0.0034851739 1 1
9350 326.27961 -36.941794 0.0034851739 1 1
9400 400.42857 7.5301492 0.0034851739 1 1
9450 296.80174 11.898673 0.0034851739 1 1
9500 275.98796 41.303486 0.0034851739 1 1
9550 278.56924 31.033397 0.0034851739 1 1
9600 260.24476 -11.416595 0.0034851739 1 1
9650 281.86065 12.60709 0.0034851739 1 1
9700 287.26789 -29.086626 0.0034851739 1 1
9750 290.82789 3.2830325 0.0034851739 1 1
9800 270.99421 -25.824595 0.0034851739 1 1
9850 385.1884 4.1048816 0.0034851739 1 1
9900 363.1711 18.815879 0.0034851739 1 1
9950 344.93572 17.375158 0.0034851739 1 1
10000 335.65852 -0.84087429 0.0034851739 1 1
Loop time of 1.78856 on 4 procs for 10000 steps with 44 atoms
Performance: 483.070 ns/day, 0.050 hours/ns, 5591.087 timesteps/s, 246.008 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 | 0.0021174 | 0.066025 | 0.20024 | 31.5 | 3.69
Bond | 0.0035593 | 0.2715 | 0.74757 | 58.6 | 15.18
Kspace | 0.50386 | 1.0492 | 1.3455 | 33.6 | 58.66
Neigh | 0.0079056 | 0.0079463 | 0.0079766 | 0.0 | 0.44
Comm | 0.044284 | 0.08173 | 0.10388 | 8.1 | 4.57
Output | 0.0021661 | 0.0024497 | 0.0031314 | 0.8 | 0.14
Modify | 0.2648 | 0.29459 | 0.33479 | 5.5 | 16.47
Other | | 0.01514 | | | 0.85
Nlocal: 11 ave 41 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 27.5 ave 41 max 0 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 205.75 ave 820 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 823
Ave neighs/atom = 18.704545
Ave special neighs/atom = 9.9090909
Neighbor list builds = 225
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:01

237
examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.1 Normal file
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@ -0,0 +1,237 @@
LAMMPS (4 Nov 2022)
# 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 extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
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 ...
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
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 = 0.000 seconds
read_data CPU = 0.007 seconds
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2+0.1
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 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: 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
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
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
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 343 8
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 = 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
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:819)
Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes
Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0.1 0 0 0
50 265.51039 -67.489756 0.0034851739 0.2 0 1 0
100 596.03388 -27.815189 0.0034851739 0.3 0 1 0
150 500.05269 2.9684972 0.0034851739 0.4 0 1 0
200 511.40295 56.791868 0.0034851739 0.5 0 1 0
250 375.95679 -4.0587677 0.0034851739 0.6 0 1 0
300 371.1629 -60.689059 0.0034851739 0.7 0 1 0
350 336.06545 8.6411023 0.0034851739 0.8 0 1 0
400 301.41962 50.628044 0.0034851739 0.9 0 1 0
450 281.08727 -15.590922 0.0034851739 1 0 1 0
500 297.35323 -9.5761786 0.0034851739 1.1 0 1 0
550 197.45298 3.6867353 0.0034851739 1.2 1 1 1
600 240.1748 -19.889198 0.0034851739 1.3 1 1 1
650 231.57018 -13.078808 0.0034851739 1.4 1 1 1
700 296.00816 -18.772183 0.0034851739 1.5 1 1 1
750 294.94016 15.43915 0.0034851739 1.6 1 1 1
800 316.51231 12.070563 0.0034851739 1.7 1 1 1
850 348.59373 9.0940092 0.0034851739 1.8 1 1 1
900 330.5264 -3.4868175 0.0034851739 1.9 1 1 1
950 307.02461 34.643373 0.0034851739 2 1 1 1
1000 250.06536 5.8440413 0.0034851739 2.1 1 1 1
Loop time of 0.202863 on 1 procs for 1000 steps with 44 atoms
Performance: 425.903 ns/day, 0.056 hours/ns, 4929.437 timesteps/s, 216.895 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 | 0.025759 | 0.025759 | 0.025759 | 0.0 | 12.70
Bond | 0.11024 | 0.11024 | 0.11024 | 0.0 | 54.34
Kspace | 0.034344 | 0.034344 | 0.034344 | 0.0 | 16.93
Neigh | 0.0015719 | 0.0015719 | 0.0015719 | 0.0 | 0.77
Comm | 0.00045259 | 0.00045259 | 0.00045259 | 0.0 | 0.22
Output | 0.0004759 | 0.0004759 | 0.0004759 | 0.0 | 0.23
Modify | 0.028713 | 0.028713 | 0.028713 | 0.0 | 14.15
Other | | 0.001307 | | | 0.64
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: 802 ave 802 max 802 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 802
Ave neighs/atom = 18.227273
Ave special neighs/atom = 9.9090909
Neighbor list builds = 32
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00

237
examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.4 Normal file
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@ -0,0 +1,237 @@
LAMMPS (4 Nov 2022)
# 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 extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
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
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 = 0.000 seconds
read_data CPU = 0.008 seconds
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2+0.1
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 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: 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
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
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
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 252 2
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 = 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
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:819)
Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes
Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0.1 0 0 0
50 275.80938 -29.158908 0.0034851739 0.2 0 1 0
100 751.80013 8.8967942 0.0034851739 0.3 0 1 0
150 412.82804 61.44542 0.0034851739 0.4 0 1 0
200 432.95275 81.052275 0.0034851739 0.5 0 1 0
250 338.65702 -39.770422 0.0034851739 0.6 0 1 0
300 326.15993 -46.690912 0.0034851739 0.7 0 1 0
350 286.66126 51.986782 0.0034851739 0.8 0 1 0
400 244.24575 25.460254 0.0034851739 0.9 0 1 0
450 294.06274 5.0448726 0.0034851739 1 0 1 0
500 280.71089 0.86710712 0.0034851739 1.1 0 1 0
550 241.94123 -5.7812057 0.0034851739 1.2 1 1 1
600 235.1535 61.669814 0.0034851739 1.3 1 1 1
650 359.33618 -22.053171 0.0034851739 1.4 1 1 1
700 329.37555 -4.7839581 0.0034851739 1.5 1 1 1
750 285.76974 11.553815 0.0034851739 1.6 1 1 1
800 303.29561 16.017529 0.0034851739 1.7 1 1 1
850 256.86479 8.7487305 0.0034851739 1.8 1 1 1
900 292.29316 -11.376211 0.0034851739 1.9 1 1 1
950 293.47531 -2.7153276 0.0034851739 2 1 1 1
1000 303.66454 -4.8603249 0.0034851739 2.1 1 1 1
Loop time of 0.195512 on 4 procs for 1000 steps with 44 atoms
Performance: 441.916 ns/day, 0.054 hours/ns, 5114.771 timesteps/s, 225.050 katom-step/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.000163 | 0.0068784 | 0.016583 | 8.5 | 3.52
Bond | 0.00040383 | 0.028615 | 0.083462 | 20.0 | 14.64
Kspace | 0.043566 | 0.10199 | 0.13314 | 11.4 | 52.16
Neigh | 0.00096634 | 0.00097064 | 0.00097509 | 0.0 | 0.50
Comm | 0.0052532 | 0.0093802 | 0.014076 | 3.2 | 4.80
Output | 0.00039802 | 0.00043637 | 0.00050031 | 0.0 | 0.22
Modify | 0.043549 | 0.045538 | 0.049781 | 1.2 | 23.29
Other | | 0.001708 | | | 0.87
Nlocal: 11 ave 29 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 32.5 ave 45 max 16 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 196.25 ave 448 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 785
Ave neighs/atom = 17.840909
Ave special neighs/atom = 9.9090909
Neighbor list builds = 27
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00

228
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LAMMPS (4 Nov 2022)
# 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 extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
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 ...
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
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 = 0.000 seconds
read_data CPU = 0.008 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization no react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 1000
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
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 343 8
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 = 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
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:819)
Per MPI rank memory allocation (min/avg/max) = 33.72 | 33.72 | 33.72 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 530.51001 -15.418012 0.0034851739 1 0
100 677.21327 16.545108 0.0034851739 1 1
150 386.79268 -28.445486 0.0034851739 1 1
200 380.29074 1.8065066 0.0034851739 1 1
250 353.27609 -7.3505628 0.0034851739 1 1
300 357.84405 -7.0569 0.0034851739 1 1
350 337.65224 54.441683 0.0034851739 1 1
400 322.54035 20.338902 0.0034851739 1 1
450 316.91217 44.76973 0.0034851739 1 1
500 345.40444 -8.2133383 0.0034851739 1 1
550 296.22085 -30.331582 0.0034851739 1 1
600 263.8024 -36.834323 0.0034851739 1 1
650 284.05699 1.2532577 0.0034851739 1 1
700 274.86269 4.6881357 0.0034851739 1 1
750 298.72284 -18.225831 0.0034851739 1 1
800 292.72143 -5.1622029 0.0034851739 1 1
850 279.30224 -10.72513 0.0034851739 1 1
900 284.97331 30.268801 0.0034851739 1 1
950 262.46089 16.98134 0.0034851739 1 1
1000 297.55359 28.583097 0.0034851739 1 1
Loop time of 0.175951 on 1 procs for 1000 steps with 44 atoms
Performance: 491.045 ns/day, 0.049 hours/ns, 5683.388 timesteps/s, 250.069 katom-step/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.022992 | 0.022992 | 0.022992 | 0.0 | 13.07
Bond | 0.1045 | 0.1045 | 0.1045 | 0.0 | 59.39
Kspace | 0.034057 | 0.034057 | 0.034057 | 0.0 | 19.36
Neigh | 0.0013592 | 0.0013592 | 0.0013592 | 0.0 | 0.77
Comm | 0.00040677 | 0.00040677 | 0.00040677 | 0.0 | 0.23
Output | 0.00030929 | 0.00030929 | 0.00030929 | 0.0 | 0.18
Modify | 0.01121 | 0.01121 | 0.01121 | 0.0 | 6.37
Other | | 0.001118 | | | 0.64
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8 ave 8 max 8 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 810 ave 810 max 810 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810
Ave neighs/atom = 18.409091
Ave special neighs/atom = 9.9090909
Neighbor list builds = 28
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00

228
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@ -0,0 +1,228 @@
LAMMPS (4 Nov 2022)
# 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 extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
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
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 = 0.000 seconds
read_data CPU = 0.008 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
18 atoms with max type 8
16 bonds with max type 10
25 angles with max type 28
23 dihedrals with max type 36
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
2 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization no react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 1000
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
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.05345967
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.040225597
estimated relative force accuracy = 0.00012113819
using double precision KISS FFT
3d grid and FFT values/proc = 252 2
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 = 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
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:819)
Per MPI rank memory allocation (min/avg/max) = 33.59 | 33.82 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 530.51001 -15.418012 0.0034851739 1 0
100 677.21327 16.545108 0.0034851739 1 1
150 386.79268 -28.445486 0.0034851739 1 1
200 380.29074 1.8065066 0.0034851739 1 1
250 353.27609 -7.3505628 0.0034851739 1 1
300 357.84405 -7.0569 0.0034851739 1 1
350 337.65224 54.441683 0.0034851739 1 1
400 322.54035 20.338902 0.0034851739 1 1
450 316.91217 44.76973 0.0034851739 1 1
500 345.40444 -8.2133383 0.0034851739 1 1
550 296.22085 -30.331582 0.0034851739 1 1
600 263.8024 -36.834323 0.0034851739 1 1
650 284.05699 1.2532577 0.0034851739 1 1
700 274.86269 4.6881357 0.0034851739 1 1
750 298.72284 -18.225831 0.0034851739 1 1
800 292.72143 -5.1622029 0.0034851739 1 1
850 279.30224 -10.72513 0.0034851739 1 1
900 284.97331 30.268801 0.0034851739 1 1
950 262.46089 16.98134 0.0034851739 1 1
1000 297.55359 28.583097 0.0034851739 1 1
Loop time of 0.179911 on 4 procs for 1000 steps with 44 atoms
Performance: 480.238 ns/day, 0.050 hours/ns, 5558.315 timesteps/s, 244.566 katom-step/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0001131 | 0.0060483 | 0.016546 | 8.7 | 3.36
Bond | 0.00024262 | 0.027106 | 0.07455 | 18.6 | 15.07
Kspace | 0.059795 | 0.11105 | 0.13995 | 9.9 | 61.72
Neigh | 0.0012033 | 0.0012139 | 0.0012228 | 0.0 | 0.67
Comm | 0.0056243 | 0.0098345 | 0.013482 | 2.9 | 5.47
Output | 0.00025378 | 0.0002833 | 0.00034961 | 0.0 | 0.16
Modify | 0.020145 | 0.02287 | 0.027899 | 2.1 | 12.71
Other | | 0.001506 | | | 0.84
Nlocal: 11 ave 41 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 34.5 ave 46 max 8 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 202.5 ave 807 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 810
Ave neighs/atom = 18.409091
Ave special neighs/atom = 9.9090909
Neighbor list builds = 28
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00

148
examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1
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@ -1,148 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
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
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 = 0.000181113 secs
read_data CPU = 0.0251833 secs
Read molecule mol1:
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
Read molecule mol2:
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
Read molecule mol3:
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
Read molecule mol4:
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
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
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 FFTs
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
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms
Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s
87.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13
Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01
Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70
Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60
Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74
Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80
Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64
Other | | 0.001306 | | | 0.38
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 740 ave 740 max 740 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

148
examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4
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@ -1,148 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 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
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 = 0.000178751 secs
read_data CPU = 0.0385782 secs
Read molecule mol1:
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
Read molecule mol2:
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
Read molecule mol3:
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
Read molecule mol4:
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
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
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 FFTs
3d grid and FFT values/proc = 252 2
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
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
98.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85
Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84
Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16
Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78
Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03
Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93
Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10
Other | | 0.0008281 | | | 0.31
Nlocal: 11 ave 21 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 32.5 ave 43 max 23 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 185 ave 376 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1
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@ -1,147 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
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
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 = 0.000217102 secs
read_data CPU = 0.00630778 secs
Read molecule mol1:
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
Read molecule mol2:
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
Read molecule mol3:
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
Read molecule mol4:
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
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
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 FFTs
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
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms
Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s
91.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17
Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42
Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78
Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61
Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74
Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98
Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91
Other | | 0.001336 | | | 0.38
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: 818 ave 818 max 818 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4
View File

@ -1,147 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 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
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 = 0.000163256 secs
read_data CPU = 0.0244579 secs
Read molecule mol1:
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
Read molecule mol2:
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
Read molecule mol3:
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
Read molecule mol4:
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
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
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 FFTs
3d grid and FFT values/proc = 252 2
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
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56
Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62
Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04
Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16
Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31
Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13
Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91
Other | | 0.0007123 | | | 0.28
Nlocal: 11 ave 29 max 0 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 25 ave 31 max 12 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 204.5 ave 443 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

189
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template
View File

@ -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 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
16 1
17 4
18 4
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 11 1 2
2 12 1 4
3 12 1 5
4 13 1 10
5 2 2 3
6 1 2 6
7 1 2 7
8 2 3 16
9 1 3 17
10 1 3 18
11 2 8 9
12 4 9 10
13 1 9 13
14 1 9 14
15 5 10 11
16 3 10 12
17 6 12 15
Angles
1 17 2 1 4
2 17 2 1 5
3 18 2 1 10
4 19 4 1 5
5 20 4 1 10
6 20 5 1 10
7 21 1 2 3
8 22 1 2 6
9 22 1 2 7
10 2 3 2 6
11 2 3 2 7
12 1 6 2 7
13 3 2 3 16
14 2 2 3 17
15 2 2 3 18
16 2 16 3 17
17 2 16 3 18
18 1 17 3 18
19 8 8 9 10
20 2 8 9 13
21 2 8 9 14
22 23 13 9 10
23 23 14 9 10
24 1 13 9 14
25 6 9 10 11
26 4 9 10 12
27 24 1 10 9
28 25 11 10 12
29 26 1 10 11
30 27 1 10 12
31 7 10 12 15
Dihedrals
1 19 4 1 2 3
2 20 4 1 2 6
3 20 4 1 2 7
4 19 5 1 2 3
5 20 5 1 2 6
6 20 5 1 2 7
7 21 10 1 2 3
8 22 10 1 2 6
9 22 10 1 2 7
10 23 2 1 10 9
11 24 2 1 10 11
12 25 2 1 10 12
13 26 4 1 10 9
14 27 4 1 10 11
15 28 4 1 10 12
16 26 5 1 10 9
17 27 5 1 10 11
18 28 5 1 10 12
19 29 1 2 3 16
20 30 1 2 3 17
21 30 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 10 8 9 10 11
29 8 8 9 10 12
30 31 8 9 10 1
31 11 13 9 10 11
32 9 13 9 10 12
33 32 13 9 10 1
34 11 14 9 10 11
35 9 14 9 10 12
36 32 14 9 10 1
37 6 9 10 12 15
38 7 11 10 12 15
39 33 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/tiny_nylon/rxn1_stp1_reacted.molecule_template Normal file
View File

@ -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

160
examples/PACKAGES/reaction/tiny_nylon/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 7
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
16 1
17 4
18 4
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 14 1 2
2 10 1 4
3 10 1 5
4 2 2 3
5 1 2 6
6 1 2 7
7 2 3 16
8 1 3 17
9 1 3 18
10 2 8 9
11 4 9 10
12 1 9 13
13 1 9 14
14 5 10 11
15 3 10 12
16 6 12 15
Angles
1 15 2 1 4
2 15 2 1 5
3 16 4 1 5
4 28 1 2 3
5 14 1 2 6
6 14 1 2 7
7 2 3 2 6
8 2 3 2 7
9 1 6 2 7
10 3 2 3 16
11 2 2 3 17
12 2 2 3 18
13 2 16 3 17
14 2 16 3 18
15 1 17 3 18
16 8 8 9 10
17 2 8 9 13
18 2 8 9 14
19 23 13 9 10
20 23 14 9 10
21 1 13 9 14
22 6 9 10 11
23 4 9 10 12
24 25 11 10 12
25 7 10 12 15
Dihedrals
1 34 4 1 2 3
2 35 4 1 2 6
3 35 4 1 2 7
4 34 5 1 2 3
5 35 5 1 2 6
6 35 5 1 2 7
7 36 1 2 3 16
8 12 1 2 3 17
9 12 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 10 8 9 10 11
17 8 8 9 10 12
18 11 13 9 10 11
19 9 13 9 10 12
20 11 14 9 10 11
21 9 14 9 10 12
22 6 9 10 12 15
23 7 11 10 12 15
Impropers
1 6 2 1 4 5
2 11 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/tiny_nylon/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/tiny_nylon/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 8
6 4
7 4
8 1
9 1
10 2
11 6
12 11
13 4
14 4
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 11 1 2
2 12 1 5
3 13 1 10
4 2 2 3
5 1 2 6
6 1 2 7
7 15 4 12
8 2 8 9
9 4 9 10
10 1 9 13
11 1 9 14
12 5 10 11
13 15 15 12
Angles
1 17 2 1 5
2 18 2 1 10
3 20 5 1 10
4 21 1 2 3
5 22 1 2 6
6 22 1 2 7
7 2 3 2 6
8 2 3 2 7
9 1 6 2 7
10 8 8 9 10
11 2 8 9 13
12 2 8 9 14
13 23 13 9 10
14 23 14 9 10
15 1 13 9 14
16 6 9 10 11
17 24 1 10 9
18 26 1 10 11
19 29 15 12 4
Dihedrals
1 19 5 1 2 3
2 20 5 1 2 6
3 20 5 1 2 7
4 21 10 1 2 3
5 22 10 1 2 6
6 22 10 1 2 7
7 23 2 1 10 9
8 24 2 1 10 11
9 26 5 1 10 9
10 27 5 1 10 11
11 10 8 9 10 11
12 31 8 9 10 1
13 11 13 9 10 11
14 32 13 9 10 1
15 11 14 9 10 11
16 32 14 9 10 1
Impropers
1 12 2 1 5 10
2 13 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/tiny_nylon/rxn1_stp2_reacted.molecule_template Normal file
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@ -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/tiny_nylon/rxn1_stp2_unreacted.data_template
View File

@ -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 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
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 11 1 2
2 12 1 4
3 12 1 5
4 13 1 10
5 2 2 3
6 1 2 6
7 1 2 7
8 2 8 9
9 4 9 10
10 1 9 13
11 1 9 14
12 5 10 11
13 3 10 12
14 6 12 15
Angles
1 17 2 1 4
2 17 2 1 5
3 18 2 1 10
4 19 4 1 5
5 20 4 1 10
6 20 5 1 10
7 21 1 2 3
8 22 1 2 6
9 22 1 2 7
10 2 3 2 6
11 2 3 2 7
12 1 6 2 7
13 8 8 9 10
14 2 8 9 13
15 2 8 9 14
16 23 13 9 10
17 23 14 9 10
18 1 13 9 14
19 6 9 10 11
20 4 9 10 12
21 24 1 10 9
22 25 11 10 12
23 26 1 10 11
24 27 1 10 12
25 7 10 12 15
Dihedrals
1 19 4 1 2 3
2 20 4 1 2 6
3 20 4 1 2 7
4 19 5 1 2 3
5 20 5 1 2 6
6 20 5 1 2 7
7 21 10 1 2 3
8 22 10 1 2 6
9 22 10 1 2 7
10 23 2 1 10 9
11 24 2 1 10 11
12 25 2 1 10 12
13 26 4 1 10 9
14 27 4 1 10 11
15 28 4 1 10 12
16 26 5 1 10 9
17 27 5 1 10 11
18 28 5 1 10 12
19 10 8 9 10 11
20 8 8 9 10 12
21 31 8 9 10 1
22 11 13 9 10 11
23 9 13 9 10 12
24 32 13 9 10 1
25 11 14 9 10 11
26 9 14 9 10 12
27 32 14 9 10 1
28 6 9 10 12 15
29 7 11 10 12 15
30 33 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/tiny_nylon/rxn1_stp2_unreacted.molecule_template Normal file
View File

@ -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

126
examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data
View File

@ -10,16 +10,130 @@ this is LAMMPS data file containing two nylon monomers
36 dihedral types
44 impropers
13 improper types
5 extra bond per atom
15 extra angle per atom
15 extra dihedral per atom
25 extra improper per atom
25 extra special per atom
-25 25 xlo xhi
-25 25 ylo yhi
-25 25 zlo zhi
Atom Type Labels
1 c2
2 c_1
3 o
4 hc
5 ho
6 o_1
7 na
8 hn
9 n
10 hw
11 o*
Bond Type Labels
1 c2-hc
2 c2-c2
3 c_1-o
4 c2-c_1
5 c_1-o_1
6 o-ho
7 c2-c2-repeat
8 c2-hc-repeat
9 na-c2
10 na-hn
11 n-c2
12 n-hn
13 n-c_1
14 c2-na
15 hw-o*
Angle Type Labels
1 hc-c2-hc
2 c2-c2-hc
3 c2-c2-c2
4 c2-c_1-o_1
5 o-c_1-o_1
6 c2-c_1-o
7 c_1-o-ho
8 c2-c2-c_1
9 c_1-c2-hc
10 c2-c2-hc-repeat
11 c2-c2-c2-repeat
12 hc-c2-hc-repeat
13 c2-c2-na
14 na-c2-hc
15 c2-na-hn
16 hn-na-hn
17 c2-n-hn
18 c2-n-c_1
19 hn-n-hn
20 hn-n-c_1
21 n-c2-c2
22 n-c2-hc
23 hc-c2-c_1
24 n-c_1-c2
25 o_1-c_1-o
26 n-c_1-o_1
27 n-c_1-o
28 na-c2-c2
29 hw-o*-hw
Dihedral Type Labels
1 c_1-c2-c2-hc
2 hc-c2-c2-hc
3 c2-c2-c2-c_1
4 c2-c2-c2-hc
5 c2-c2-c2-c2
6 c2-c_1-o-ho
7 o_1-c_1-o-ho
8 c2-c2-c_1-o
9 hc-c2-c_1-o
10 c2-c2-c_1-o_1
11 hc-c2-c_1-o_1
12 na-c2-c2-hc
13 hc-c2-c2-hc-repeat
14 c2-c2-c2-na
15 c2-c2-c2-hc-repeat
16 c2-c2-c2-c2-repeat
17 c2-c2-na-hn
18 hn-na-c2-hc
19 hn-n-c2-c2
20 hn-n-c2-hc
21 c_1-n-c2-c2
22 c_1-n-c2-hc
23 c2-n-c_1-c2
24 c2-n-c_1-o_1
25 c2-n-c_1-o
26 hn-n-c_1-c2
27 hn-n-c_1-o_1
28 hn-n-c_1-o
29 n-c2-c2-c2
30 n-c2-c2-hc
31 c2-c2-c_1-n
32 hc-c2-c_1-n
33 n-c_1-o-ho
34 hn-na-c2-c2
35 hc-c2-na-hn
36 na-c2-c2-c2
Improper Type Labels
1 c2-c_1-o-o_1
2 c2-na-hn-hn
3 c2-c_1-o_1-o
4 c2-n-hn-c_1
5 zero5
6 zero6
7 zero7
8 zero8
9 zero9
10 zero10
11 zero11
12 zero12
13 n-c_1-c2-o_1
Masses
1 12.0112
@ -94,7 +208,7 @@ Angle Coeffs # class2
24 116.926 39.4193 -10.9945 -8.7733
25 118.986 98.6813 -22.2485 10.3673
26 125.542 92.572 -34.48 -11.1871
27 0 0 0 0
27 125.542 92.572 -34.48 -11.1871
28 111.91 60.7147 -13.3366 -13.0785
29 103.7 49.84 -11.6 -8