66 lines
1.6 KiB
Plaintext
66 lines
1.6 KiB
Plaintext
# two monomer nylon example
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# reaction produces a condensed water molecule
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units real
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boundary p p p
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atom_style full
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kspace_style pppm 1.0e-4
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pair_style lj/class2/coul/long 8.5
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angle_style class2
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bond_style class2
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dihedral_style class2
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improper_style class2
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special_bonds lj/coul 0 0 1
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pair_modify tail yes mix sixthpower
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read_data tiny_nylon.data &
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extra/bond/per/atom 5 &
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extra/angle/per/atom 15 &
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extra/dihedral/per/atom 15 &
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extra/improper/per/atom 25 &
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extra/special/per/atom 25
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variable runsteps equal 1000
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variable prob1 equal step/v_runsteps*2+0.1
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variable prob2 equal (step/v_runsteps)>0.5
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velocity all create 300.0 4928459 dist gaussian
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molecule mol1 rxn1_stp1_unreacted.molecule_template
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molecule mol2 rxn1_stp1_reacted.molecule_template
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molecule mol3 rxn1_stp2_unreacted.molecule_template
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molecule mol4 rxn1_stp2_reacted.molecule_template
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thermo 50
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# dump 1 all xyz 1 test_vis.xyz
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# dump_modify 1 types labels
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fix myrxns all bond/react stabilization yes statted_grp .03 &
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react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 &
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react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 rescale_charges yes
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fix 1 statted_grp_REACT nvt temp 300 300 100
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# optionally, you can customize behavior of reacting atoms,
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# by using the internally-created 'bond_react_MASTER_group', like so:
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fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
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thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[*]
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# restart 100 restart1 restart2
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run ${runsteps}
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# write_restart restart_longrun
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# write_data restart_longrun.data
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