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update create atoms example

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This commit is contained in:
Jacob Gissinger
2021-02-04 20:20:18 -05:00
parent c129259854
commit bd1cc91bdd
5 changed files with 23 additions and 29 deletions
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12
examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms
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@ -1,18 +1,18 @@
this is a map file
map file: styrene growth
1 edgeIDs
30 equivalences
16 createIDs
EdgeIDs
30
BondingIDs
InitiatorIDs
4
13
EdgeIDs
30
CreateIDs
1

4
examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template
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@ -1,4 +1,4 @@
LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for chain_plus_styrene_reacted
molecule template: end of chain plus polymerized styrene
46 atoms
48 bonds
@ -9,7 +9,7 @@ LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for chain_plus_styrene_re
Fragments
create_fit 34 44
create_fit 34 44
Types

4
examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template
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@ -1,4 +1,4 @@
LAMMPS data file via write_data, version 18 Sep 2020, timestep = 0
molecule template: end of styrene chain
30 atoms
31 bonds
@ -69,7 +69,7 @@ Coords
26 53.86061213540014 61.09506223825291 58.69441939855832
27 55.94906007539648 61.56969281804616 59.039933529456256
28 56.2513193202326 60.54265974655139 59.15389588713244
29 58.35468332440925 64.79274880895268 59.64495986218142
29 58.35468332440925 64.79274880895268 59.64495986218142
30 57.07961929431883 66.29987186904283 58.394030287459465
Charges

30
examples/USER/reaction/create_atoms_polystyrene/infromdata.class2
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@ -1,4 +1,4 @@
# Jake practice run
# use bond/react 'create atoms' feature to add 50 new styrene monomers to chain
units real
@ -20,30 +20,24 @@ improper_style class2
variable T equal 530
read_data trimer.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
read_data trimer.data
molecule mol3 chain_plus_styrene_unreacted_create_atoms.data_template
molecule mol4 chain_plus_styrene_reacted.data_template
molecule mol1 grow_styrene_pre.data_template
molecule mol2 grow_styrene_post.data_template
fix rxn1 all bond/react stabilization yes statted_grp .03 &
react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map_create_atoms &
modify_create fit create_fit near 2.0 stabilize_steps 100 max_rxn 50
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
modify_create fit create_fit overlap 2.0 &
stabilize_steps 100 max_rxn 50
fix 1 statted_grp_REACT nvt temp $T $T 100 #iso 1 1 1000
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_rxn1[1]
thermo_style custom step temp press density f_myrxns[1]
#restart 1 restart1 restart2
thermo 2
thermo 100
run 8000
write_data restart_longrun.data nofix
# write_data final.data nofix

2
examples/USER/reaction/create_atoms_polystyrene/trimer.data
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@ -1,4 +1,4 @@
LAMMPS data file via write_data, version 15 May 2019, timestep = 500
polystyrene trimer
48 atoms
7 atom types