removing example script from nylon melt and adding to tiny nylon
This commit is contained in:
wverestek
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# 35,000 atom nylon melt example
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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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read_data large_nylon_melt.data.gz
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variable runsteps equal 200
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varaible prob equal step/v_runsteps
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velocity all create 800.0 4928459 dist gaussian
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molecule mol1 rxn1_stp1_unreacted.data_template
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molecule mol2 rxn1_stp1_reacted.data_template
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molecule mol3 rxn1_stp2_unreacted.data_template
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molecule mol4 rxn1_stp2_reacted.data_template
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thermo 50
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# dump 1 all xyz 100 test_vis.xyz
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fix myrxns all bond/react stabilization yes statted_grp .03 &
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react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
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react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
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# stable at 800K
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fix 1 statted_grp_REACT nvt temp 800 800 100
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# in order to customize behavior of reacting atoms,
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# you can use the internally created 'bond_react_MASTER_group', like so:
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# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
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thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
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# restart 100 restart1 restart2
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run 200
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# write_restart restart_longrun
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# write_data restart_longrun.data
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@ -0,0 +1,56 @@
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# 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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read_data tiny_nylon.data
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variable runsteps equal 1000
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variable prob1 equal step/v_runsteps*2
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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.data_template
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molecule mol2 rxn1_stp1_reacted.data_template
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molecule mol3 rxn1_stp2_unreacted.data_template
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molecule mol4 rxn1_stp2_reacted.data_template
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thermo 50
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# dump 1 all xyz 1 test_vis.xyz
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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
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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[1] f_myrxns[2]
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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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@ -0,0 +1,199 @@
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LAMMPS (15 Apr 2020)
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# 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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read_data tiny_nylon.data
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orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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44 atoms
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reading velocities ...
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44 velocities
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scanning bonds ...
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9 = max bonds/atom
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scanning angles ...
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21 = max angles/atom
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scanning dihedrals ...
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29 = max dihedrals/atom
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scanning impropers ...
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29 = max impropers/atom
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reading bonds ...
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42 bonds
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reading angles ...
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74 angles
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reading dihedrals ...
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100 dihedrals
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reading impropers ...
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44 impropers
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4 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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12 = max # of 1-4 neighbors
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41 = max # of special neighbors
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special bonds CPU = 0.000278722 secs
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read_data CPU = 0.0146239 secs
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variable runsteps equal 1000
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variable prob1 equal step/v_runsteps*2
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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.data_template
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Read molecule template mol1:
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1 molecules
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18 atoms with max type 8
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16 bonds with max type 14
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25 angles with max type 28
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23 dihedrals with max type 36
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14 impropers with max type 11
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molecule mol2 rxn1_stp1_reacted.data_template
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Read molecule template mol2:
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1 molecules
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18 atoms with max type 9
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17 bonds with max type 13
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31 angles with max type 27
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39 dihedrals with max type 33
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20 impropers with max type 1
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molecule mol3 rxn1_stp2_unreacted.data_template
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Read molecule template mol3:
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1 molecules
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15 atoms with max type 9
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14 bonds with max type 13
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25 angles with max type 27
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30 dihedrals with max type 33
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16 impropers with max type 1
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molecule mol4 rxn1_stp2_reacted.data_template
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Read molecule template mol4:
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1 molecules
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15 atoms with max type 11
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13 bonds with max type 15
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19 angles with max type 29
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16 dihedrals with max type 32
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10 impropers with max type 13
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thermo 50
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dump 1 all xyz 1 test_vis.xyz
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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
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WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:2052)
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WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:2052)
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dynamic group bond_react_MASTER_group defined
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dynamic group statted_grp_REACT defined
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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[1] f_myrxns[2]
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# restart 100 restart1 restart2
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run ${runsteps}
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run 1000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:332)
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G vector (1/distance) = 0.0534597
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grid = 2 2 2
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0402256
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estimated relative force accuracy = 0.000121138
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using double precision KISS FFT
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3d grid and FFT values/proc = 343 8
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.5
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ghost atom cutoff = 10.5
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binsize = 5.25, bins = 10 10 10
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair lj/class2/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) fix bond/react, occasional, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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WARNING: Inconsistent image flags (../domain.cpp:812)
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Per MPI rank memory allocation (min/avg/max) = 34.78 | 34.78 | 34.78 Mbytes
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Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
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0 300 346.78165 0.0034851739 0 0 0 0
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50 262.63913 -492.10749 0.0034851739 0.1 0 1 0
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100 766.52962 -29.714349 0.0034851739 0.2 0 1 0
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150 503.86837 50.220304 0.0034851739 0.3 0 1 0
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200 456.51295 12.312892 0.0034851739 0.4 0 1 0
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250 391.54928 9.2335844 0.0034851739 0.5 0 1 0
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300 336.6988 -47.193937 0.0034851739 0.6 0 1 0
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350 254.06985 -9.2867898 0.0034851739 0.7 0 1 0
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400 259.41098 -25.657321 0.0034851739 0.8 0 1 0
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450 258.10364 22.5086 0.0034851739 0.9 0 1 0
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500 272.13412 -6.5391448 0.0034851739 1 0 1 0
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550 202.75504 54.658731 0.0034851739 1.1 1 1 1
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600 344.79887 23.798478 0.0034851739 1.2 1 1 1
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650 328.44488 -29.908484 0.0034851739 1.3 1 1 1
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700 280.13593 -8.3223255 0.0034851739 1.4 1 1 1
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750 300.67624 1.0632669 0.0034851739 1.5 1 1 1
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800 376.64234 12.488392 0.0034851739 1.6 1 1 1
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850 321.07642 19.814074 0.0034851739 1.7 1 1 1
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900 332.23751 30.814079 0.0034851739 1.8 1 1 1
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950 311.14029 5.7853136 0.0034851739 1.9 1 1 1
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1000 253.14634 -37.560642 0.0034851739 2 1 1 1
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Loop time of 0.580684 on 1 procs for 1000 steps with 44 atoms
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Performance: 148.790 ns/day, 0.161 hours/ns, 1722.106 timesteps/s
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95.0% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.090707 | 0.090707 | 0.090707 | 0.0 | 15.62
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Bond | 0.18541 | 0.18541 | 0.18541 | 0.0 | 31.93
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Kspace | 0.065715 | 0.065715 | 0.065715 | 0.0 | 11.32
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Neigh | 0.085003 | 0.085003 | 0.085003 | 0.0 | 14.64
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Comm | 0.0068229 | 0.0068229 | 0.0068229 | 0.0 | 1.17
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Output | 0.096583 | 0.096583 | 0.096583 | 0.0 | 16.63
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Modify | 0.047377 | 0.047377 | 0.047377 | 0.0 | 8.16
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Other | | 0.00307 | | | 0.53
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Nlocal: 44 ave 44 max 44 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3 ave 3 max 3 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 722 ave 722 max 722 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 722
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Ave neighs/atom = 16.4091
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Ave special neighs/atom = 9.77273
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Neighbor list builds = 1000
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Dangerous builds = 0
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# write_restart restart_longrun
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# write_data restart_longrun.data
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:00
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Reference in New Issue
Block a user