diff --git a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms index a90f1528bb..88d282690c 100644 --- a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms +++ b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_map_create_atoms @@ -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 diff --git a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template index 83f04899b1..de0c2383bb 100755 --- a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template +++ b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_reacted.data_template @@ -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 diff --git a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template index f85b928f1e..d04fefccf5 100644 --- a/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template +++ b/examples/USER/reaction/create_atoms_polystyrene/chain_plus_styrene_unreacted_create_atoms.data_template @@ -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 diff --git a/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 b/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 index b6e63d5365..4331bf60b7 100755 --- a/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 +++ b/examples/USER/reaction/create_atoms_polystyrene/infromdata.class2 @@ -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 diff --git a/examples/USER/reaction/create_atoms_polystyrene/trimer.data b/examples/USER/reaction/create_atoms_polystyrene/trimer.data index 8bd81f0600..b3ad132f03 100644 --- a/examples/USER/reaction/create_atoms_polystyrene/trimer.data +++ b/examples/USER/reaction/create_atoms_polystyrene/trimer.data @@ -1,4 +1,4 @@ -LAMMPS data file via write_data, version 15 May 2019, timestep = 500 +polystyrene trimer 48 atoms 7 atom types