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 1 by 1 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 = 0.015 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 = 1331 216
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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) = 31.51 | 31.51 | 31.51 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 5558.2894 0.76796752 2 0 0
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900 503.38392 -5027.1155 0.76796752 2 0 0
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1000 509.30766 3979.0526 0.76796752 2 0 0
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1100 551.34763 5119.0854 0.76796752 2 0 0
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1200 562.51766 -2867.8721 0.76796752 2 0 0
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1300 552.90947 2090.7196 0.76796752 2 0 0
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1400 516.10667 3374.3471 0.76796752 2 0 0
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1500 518.70363 472.0237 0.76796752 2 0 0
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1600 559.50145 5451.1908 0.76796752 2 0 0
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1700 531.49515 4526.9547 0.76796752 2 0 0
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1800 529.18545 -3566.8838 0.76796752 2 0 0
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1900 517.52577 -2390.6662 0.76796752 2 0 0
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2000 495.24246 -485.62368 0.76796752 2 0 0
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2100 567.90338 2009.3507 0.76796752 3 0 0
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2200 553.05006 5694.0307 0.76796752 3 0 0
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2300 561.22521 2944.2766 0.76796752 3 0 0
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2400 460.05535 3058.3944 0.76796752 3 0 0
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2500 501.01426 365.04418 0.76796752 4 0 0
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2600 543.94728 267.33298 0.76796752 4 0 0
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2700 539.40536 4258.9345 0.76796752 4 0 0
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2800 557.67853 -2732.3135 0.76796752 4 0 0
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2900 539.85456 3987.7331 0.76796752 4 1 0
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3000 501.3125 3280.3821 0.76796752 4 1 0
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3100 537.77092 -5290.371 0.76796752 4 1 0
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3200 528.20744 11690.902 0.76796752 4 1 0
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3300 548.56721 2464.6039 0.76796752 4 1 0
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3400 542.73725 -27951.173 0.76796752 4 1 1
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3500 547.63988 7925.1202 0.76796752 4 1 1
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3600 502.69726 7875.8308 0.76796752 4 1 1
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3700 495.26614 -1907.7215 0.76796752 4 1 1
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3800 526.91826 -4267.1784 0.76796752 4 1 1
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3900 538.8248 6811.7446 0.76796752 4 1 1
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4000 531.42158 5031.2992 0.76796752 4 1 1
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4100 539.69772 6278.9861 0.76796752 4 1 1
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4200 519.11497 9206.6513 0.76796752 4 1 1
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4300 518.08237 -63.769046 0.76796752 4 1 1
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4400 582.43352 4189.0234 0.76796752 4 1 1
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4500 541.87979 -2072.4133 0.76796752 4 1 1
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4600 514.7508 7502.1057 0.76796752 4 1 1
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4700 530.22173 51.50674 0.76796752 4 1 1
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4800 507.14885 5148.7797 0.76796752 4 1 1
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4900 516.05055 9110.3072 0.76796752 4 1 1
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5000 552.55865 7310.0399 0.76796752 4 1 1
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5100 581.79588 3282.8939 0.76796752 4 1 1
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5200 523.07607 -1312.6111 0.76796752 4 1 1
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5300 528.44235 -2242.0268 0.76796752 4 1 1
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5400 537.63408 4599.5474 0.76796752 4 1 1
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5500 526.75093 5551.7841 0.76796752 4 1 1
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5600 562.74766 2764.4556 0.76796752 4 1 1
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5700 545.12259 -3139.3468 0.76796752 4 1 1
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5800 563.77404 4261.7786 0.76796752 4 1 1
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5900 514.07804 4057.43 0.76796752 4 1 1
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6000 548.42605 -2814.3308 0.76796752 4 1 1
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6100 525.16391 -2902.5409 0.76796752 4 1 1
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6200 504.92542 -706.19923 0.76796752 4 1 2
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6300 531.55271 1217.7795 0.76796752 4 1 2
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6400 537.29797 264.24006 0.76796752 4 1 2
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6500 581.8752 2228.1037 0.76796752 4 1 2
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6600 536.95487 -10318.365 0.76796752 4 2 2
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6700 498.26961 5005.4587 0.76796752 5 2 2
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6800 526.00873 -2678.0327 0.76796752 5 2 2
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6900 542.74619 -1567.8558 0.76796752 5 2 2
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7000 549.02037 8321.4935 0.76796752 5 2 2
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7100 542.28295 -1513.6114 0.76796752 5 2 2
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7200 474.70347 2120.9699 0.76796752 5 2 2
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7300 506.58637 2588.8837 0.76796752 5 2 2
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7400 512.45393 -2101371.7 0.76796752 5 2 3
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7500 546.20285 -2458.3002 0.76796752 5 2 3
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7600 551.57132 3148.9131 0.76796752 5 2 3
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7700 544.3684 -775.59686 0.76796752 5 2 3
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7800 511.32529 2353.0343 0.76796752 5 2 3
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7900 520.30502 10726.007 0.76796752 5 2 3
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8000 561.81009 12476.296 0.76796752 5 2 3
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8100 588.85859 5905.4979 0.76796752 5 2 3
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8200 490.1071 1132.5027 0.76796752 5 2 3
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8300 537.65085 -1445.0979 0.76796752 5 2 3
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8400 523.60343 -589.18012 0.76796752 5 2 3
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8500 538.90848 -300.32152 0.76796752 5 2 3
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8600 573.63835 5912.9027 0.76796752 5 2 3
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8700 557.82593 2585.6634 0.76796752 5 2 3
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8800 562.5277 -1843272.8 0.76796752 5 2 4
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8900 564.26894 -1396.8521 0.76796752 5 2 4
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9000 576.4382 5029.6995 0.76796752 5 2 4
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9100 514.83258 -935.9015 0.76796752 5 2 4
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9200 536.33755 -1671.9254 0.76796752 5 2 4
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9300 494.49553 582.08687 0.76796752 5 2 4
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9400 532.12156 -6991.3223 0.76796752 6 2 4
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9500 528.87489 4587.7048 0.76796752 6 2 4
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9600 555.92299 -3688.5966 0.76796752 6 2 4
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9700 510.09341 1545.1276 0.76796752 6 2 4
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9800 505.94984 -4677.2879 0.76796752 6 2 4
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9900 531.38104 4891.0352 0.76796752 6 2 4
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10000 517.59995 4299.0553 0.76796752 6 2 4
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Loop time of 29.4182 on 1 procs for 10000 steps with 320 atoms
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Performance: 29.370 ns/day, 0.817 hours/ns, 339.926 timesteps/s, 108.776 katom-step/s
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100.0% 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 | 10.883 | 10.883 | 10.883 | 0.0 | 36.99
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Bond | 8.0953 | 8.0953 | 8.0953 | 0.0 | 27.52
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Kspace | 2.6136 | 2.6136 | 2.6136 | 0.0 | 8.88
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Neigh | 1.0863 | 1.0863 | 1.0863 | 0.0 | 3.69
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Comm | 0.2095 | 0.2095 | 0.2095 | 0.0 | 0.71
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Output | 0.0019263 | 0.0019263 | 0.0019263 | 0.0 | 0.01
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Modify | 6.4695 | 6.4695 | 6.4695 | 0.0 | 21.99
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Other | | 0.05924 | | | 0.20
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Nlocal: 320 ave 320 max 320 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3425 ave 3425 max 3425 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 54783 ave 54783 max 54783 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 54783
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Ave neighs/atom = 171.19688
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Ave special neighs/atom = 10.3375
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Neighbor list builds = 460
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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: 0:00:29
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