330 lines
17 KiB
Groff
330 lines
17 KiB
Groff
LAMMPS (4 Nov 2022)
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# 20 styrene molecules
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# three reactions defined
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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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variable T equal 530
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read_data tiny_polystyrene.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
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Reading data file ...
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orthogonal box = (1.7426663 1.7426663 1.7426663) to (18.257334 18.257334 18.257334)
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1 by 2 by 2 MPI processor grid
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reading atom labelmap ...
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reading bond labelmap ...
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reading angle labelmap ...
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reading dihedral labelmap ...
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reading improper labelmap ...
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reading atoms ...
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320 atoms
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reading velocities ...
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320 velocities
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scanning bonds ...
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8 = max bonds/atom
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scanning angles ...
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18 = max angles/atom
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scanning dihedrals ...
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22 = max dihedrals/atom
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scanning impropers ...
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26 = max impropers/atom
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reading bonds ...
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320 bonds
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reading angles ...
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480 angles
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reading dihedrals ...
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640 dihedrals
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reading impropers ...
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160 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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3 = 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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39 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.018 seconds
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molecule mol1 2styrene_unreacted.molecule_template
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Read molecule template mol1:
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1 molecules
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0 fragments
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32 atoms with max type 4
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32 bonds with max type 11
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48 angles with max type 19
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64 dihedrals with max type 21
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16 impropers with max type 8
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molecule mol2 2styrene_reacted.molecule_template
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Read molecule template mol2:
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1 molecules
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0 fragments
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32 atoms with max type 6
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33 bonds with max type 13
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54 angles with max type 22
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79 dihedrals with max type 19
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14 impropers with max type 7
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molecule mol3 chain_plus_styrene_unreacted.molecule_template
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Read molecule template mol3:
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1 molecules
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0 fragments
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46 atoms with max type 6
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47 bonds with max type 13
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75 angles with max type 22
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105 dihedrals with max type 21
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21 impropers with max type 8
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molecule mol4 chain_plus_styrene_reacted.molecule_template
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Read molecule template mol4:
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1 molecules
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0 fragments
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46 atoms with max type 6
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48 bonds with max type 13
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81 angles with max type 22
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121 dihedrals with max type 19
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19 impropers with max type 7
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molecule mol5 chain_chain_unreacted.molecule_template
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Read molecule template mol5:
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1 molecules
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0 fragments
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50 atoms with max type 6
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51 bonds with max type 13
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84 angles with max type 22
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118 dihedrals with max type 19
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20 impropers with max type 7
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molecule mol6 chain_chain_reacted.molecule_template
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Read molecule template mol6:
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1 molecules
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0 fragments
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50 atoms with max type 6
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52 bonds with max type 13
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90 angles with max type 22
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135 dihedrals with max type 19
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18 impropers with max type 2
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thermo 100
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# dump 1 all xyz 5 test_vis.xyz
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fix rxn1 all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100
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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 $T $T 100
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fix 1 statted_grp_REACT nvt temp 530 $T 100
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fix 1 statted_grp_REACT nvt temp 530 530 100
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fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
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fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
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fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
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thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]
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run 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
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@Article{Gissinger17,
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author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
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title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
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journal = {Polymer},
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year = 2017,
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volume = 128,
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pages = {211--217}
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}
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@Article{Gissinger20,
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author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
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title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
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journal = {Macromolecules},
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year = 2020,
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volume = 53,
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number = 22,
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pages = {9953--9961}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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PPPM initialization ...
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WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:327)
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using 12-bit tables for long-range coulomb (../kspace.cpp:342)
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G vector (1/distance) = 0.25561147
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grid = 6 6 6
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0097469157
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estimated relative force accuracy = 2.9352547e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 704 72
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Generated 21 of 21 mixed pair_coeff terms from sixthpower/geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 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 = 4 4 4
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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
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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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Per MPI rank memory allocation (min/avg/max) = 31.03 | 31.05 | 31.06 Mbytes
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Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3]
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0 320.13638 -376.0844 0.76796752 0 0 0
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100 342.22237 -3489.4495 0.76796752 0 0 0
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200 412.23828 -1367.104 0.76796752 0 0 0
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300 467.98145 4841.002 0.76796752 0 0 0
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400 505.39864 2213.0509 0.76796752 1 0 0
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500 519.63371 -28223.513 0.76796752 2 0 0
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600 526.40655 8701.2728 0.76796752 2 0 0
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700 579.91953 2507.5868 0.76796752 2 0 0
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800 517.29593 5558.2895 0.76796752 2 0 0
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900 503.38392 -5027.1154 0.76796752 2 0 0
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1000 509.30767 3979.0529 0.76796752 2 0 0
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1100 551.34763 5119.0848 0.76796752 2 0 0
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1200 562.5176 -2867.8688 0.76796752 2 0 0
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1300 552.90918 2090.7508 0.76796752 2 0 0
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1400 516.10716 3374.2169 0.76796752 2 0 0
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1500 518.70418 471.99711 0.76796752 2 0 0
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1600 559.49915 5450.8774 0.76796752 2 0 0
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1700 531.50638 4525.5892 0.76796752 2 0 0
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1800 529.18331 -3566.9245 0.76796752 2 0 0
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1900 517.79846 -2364.8287 0.76796752 2 0 0
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2000 495.0983 -488.99696 0.76796752 2 0 0
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2100 567.80521 2050.9596 0.76796752 3 0 0
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2200 553.24434 5665.0753 0.76796752 3 0 0
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2300 561.08278 2879.1572 0.76796752 3 0 0
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2400 461.3712 3185.6091 0.76796752 3 0 0
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2500 500.95595 565.81792 0.76796752 4 0 0
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2600 538.3865 463.58228 0.76796752 4 0 0
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2700 525.95739 2011.1914 0.76796752 4 0 0
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2800 533.4197 157.38106 0.76796752 4 0 0
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2900 526.27036 1331.5115 0.76796752 5 1 0
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3000 502.65015 -93.915921 0.76796752 5 1 0
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3100 505.4224 -1314.224 0.76796752 5 1 0
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3200 538.52692 10420.644 0.76796752 5 1 0
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3300 518.32801 5933.553 0.76796752 5 2 0
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3400 540.04815 741.54438 0.76796752 6 2 1
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3500 554.07567 5778.8913 0.76796752 6 2 1
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3600 546.90828 4751.5437 0.76796752 6 2 1
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3700 529.75739 432.20829 0.76796752 6 2 1
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3800 542.806 -380.00399 0.76796752 6 2 1
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3900 521.55789 -1224.1912 0.76796752 6 2 2
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4000 519.73935 2792.996 0.76796752 6 2 2
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4100 535.06314 -1926.8692 0.76796752 6 2 2
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4200 549.75482 2852.5521 0.76796752 6 2 2
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4300 510.71949 6581.1729 0.76796752 7 2 2
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4400 485.93403 -695.24007 0.76796752 7 2 2
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4500 535.3677 2519.2711 0.76796752 7 2 2
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4600 504.87216 533.16619 0.76796752 7 2 2
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4700 495.68939 5502.1672 0.76796752 7 2 2
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4800 534.13893 -1187.1228 0.76796752 7 2 2
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4900 512.56394 1731.3856 0.76796752 7 2 2
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5000 508.63054 2467.0387 0.76796752 7 2 2
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5100 501.65027 3403.8111 0.76796752 7 2 2
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5200 556.68281 4310.0492 0.76796752 7 2 2
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5300 506.86652 -773630.77 0.76796752 7 2 3
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5400 570.01783 11663.867 0.76796752 7 2 3
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5500 538.08785 6391.6546 0.76796752 7 2 3
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5600 502.48456 44.409604 0.76796752 7 2 3
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5700 545.75445 1558.6373 0.76796752 7 2 3
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5800 517.5076 -166.52488 0.76796752 7 2 3
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5900 558.64383 1528.1198 0.76796752 7 2 3
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6000 557.8358 442.21273 0.76796752 7 2 3
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6100 483.13771 5201.4489 0.76796752 8 2 3
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6200 533.42675 5112.0828 0.76796752 8 2 3
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6300 576.32772 269.77058 0.76796752 8 2 3
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6400 492.79331 565.35222 0.76796752 8 2 4
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6500 514.5727 6233.7568 0.76796752 8 2 4
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6600 509.86906 -943.58621 0.76796752 8 2 4
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6700 546.62752 -323284.04 0.76796752 8 2 5
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6800 541.19749 1306.3182 0.76796752 8 2 5
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6900 497.72333 -1792.483 0.76796752 8 2 5
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7000 516.02636 2028.3813 0.76796752 8 2 5
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7100 486.54013 6153.9142 0.76796752 8 2 5
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7200 553.33698 4352.3987 0.76796752 8 2 5
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7300 519.23896 6536.766 0.76796752 8 2 5
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7400 486.74787 -1744.8351 0.76796752 8 2 5
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7500 516.71935 -315.43649 0.76796752 8 2 5
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7600 513.62572 -1100.1363 0.76796752 8 2 5
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7700 531.11296 1727.7113 0.76796752 8 2 5
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7800 530.82809 9566.2386 0.76796752 8 2 5
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7900 513.09884 8545.6728 0.76796752 8 2 5
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8000 511.38714 2995.8438 0.76796752 8 2 5
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8100 527.76731 709.63649 0.76796752 8 2 5
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8200 514.09092 2103.8591 0.76796752 8 2 5
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8300 534.90612 7707.3378 0.76796752 8 2 5
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8400 547.40716 660.54641 0.76796752 8 2 5
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8500 518.75522 -872.69754 0.76796752 8 2 5
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8600 511.70922 6645.6264 0.76796752 8 2 5
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8700 480.70739 -640.57939 0.76796752 8 2 5
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8800 527.35475 6944.8472 0.76796752 8 2 5
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8900 554.26477 -2311.6153 0.76796752 8 2 5
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9000 520.48502 1469.4805 0.76796752 8 2 5
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9100 522.0619 -4159.697 0.76796752 8 2 5
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9200 501.34664 7486.8266 0.76796752 8 2 5
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9300 524.96422 6158.2524 0.76796752 8 2 5
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9400 564.30456 -2964.7187 0.76796752 8 2 6
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9500 569.02736 5765.8856 0.76796752 8 2 6
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9600 554.31532 2805.5671 0.76796752 8 2 6
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9700 521.3957 -924.74562 0.76796752 8 2 6
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9800 518.45356 -2440.5266 0.76796752 8 2 6
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9900 512.03787 -834.07647 0.76796752 8 2 6
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10000 573.10576 4372.5769 0.76796752 8 2 6
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Loop time of 11.2088 on 4 procs for 10000 steps with 320 atoms
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Performance: 77.082 ns/day, 0.311 hours/ns, 892.155 timesteps/s, 285.490 katom-step/s
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100.0% CPU use with 4 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 | 2.6217 | 2.8126 | 3.0128 | 9.5 | 25.09
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Bond | 2.0439 | 2.1734 | 2.3326 | 7.0 | 19.39
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Kspace | 1.4277 | 1.7772 | 2.0148 | 17.9 | 15.86
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Neigh | 0.32002 | 0.3201 | 0.3202 | 0.0 | 2.86
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Comm | 0.42382 | 0.43347 | 0.4412 | 1.1 | 3.87
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Output | 0.0013461 | 0.0015202 | 0.0020328 | 0.8 | 0.01
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Modify | 3.6386 | 3.6396 | 3.6408 | 0.0 | 32.47
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Other | | 0.05092 | | | 0.45
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Nlocal: 80 ave 93 max 71 min
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Histogram: 1 1 0 0 1 0 0 0 0 1
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Nghost: 2184.75 ave 2276 max 2092 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 13678.5 ave 15576 max 11682 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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Total # of neighbors = 54714
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Ave neighs/atom = 170.98125
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Ave special neighs/atom = 10.9125
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Neighbor list builds = 471
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Dangerous builds = 0
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# write_restart restart_longrun nofix
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# write_data restart_longrun.data
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Total wall time: 0:00:11
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