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clean up tiny_nylon example

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This commit is contained in:
Jacob Gissinger
2024-08-25 14:19:17 -04:00
parent 6514dbb4b6
commit e94d32e7d3
6 changed files with 605 additions and 714 deletions
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1
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized
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@ -44,6 +44,7 @@ thermo 50
fix myrxns all bond/react stabilization yes statted_grp .03 & fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & 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 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
fix 1 statted_grp_REACT nvt temp 300 300 100 fix 1 statted_grp_REACT nvt temp 300 300 100

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
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@ -47,7 +47,7 @@ thermo 50
fix myrxns all bond/react stabilization yes statted_grp .03 & 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 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 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 rescale_charges yes
fix 1 statted_grp_REACT nvt temp 300 300 100 fix 1 statted_grp_REACT nvt temp 300 300 100

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized
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@ -44,7 +44,7 @@ thermo 50
fix myrxns all bond/react stabilization no & fix myrxns all bond/react stabilization no &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & 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 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
fix 1 all nve/limit .03 fix 1 all nve/limit .03

21
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template
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@ -48,27 +48,6 @@ Types
17 hc 17 hc
18 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 Molecules
1 1 1 1

30
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template
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@ -44,21 +44,21 @@ Types
Charges Charges
1 -0.300000 1 -0.60533
2 0.000000 2 -0.01149
3 0.000000 3 -0.76306
4 0.410000 4 0.38
5 0.000000 5 0.29346
6 0.000000 6 0.18360
7 0.000000 7 0.15396
8 0.000000 8 -0.72636
9 0.000000 9 -0.27437
10 0.300000 10 0.40603
11 0.000000 11 -0.65530
12 -0.820000 12 -0.76
13 0.000000 13 0.21423
14 0.000000 14 0.18949
15 0.410000 15 0.38
Molecules Molecules

1263
examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data
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