250 lines
9.6 KiB
Groff
250 lines
9.6 KiB
Groff
LAMMPS (4 Nov 2022)
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# two molecules DGEBA (diepoxy) and one DETA (linker)
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# two crosslinking reactions
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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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pair_style lj/class2 8
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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_epoxy.data
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Reading data file ...
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orthogonal box = (10 -10 -15) to (30 20 10)
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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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118 atoms
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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18 = max dihedrals/atom
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scanning impropers ...
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4 = max impropers/atom
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reading bonds ...
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123 bonds
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reading angles ...
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221 angles
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reading dihedrals ...
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302 dihedrals
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reading impropers ...
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115 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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4 = max # of 1-2 neighbors
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10 = max # of 1-3 neighbors
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19 = max # of 1-4 neighbors
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22 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.015 seconds
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velocity all create 300.0 4928459 dist gaussian
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molecule mol1 rxn1_stp1_pre.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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31 atoms with max type 10
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30 bonds with max type 15
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53 angles with max type 29
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66 dihedrals with max type 39
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3 impropers with max type 5
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molecule mol2 rxn1_stp1_post.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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31 atoms with max type 10
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30 bonds with max type 17
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55 angles with max type 36
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75 dihedrals with max type 51
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2 impropers with max type 5
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molecule mol3 rxn1_stp2_post.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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31 atoms with max type 11
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30 bonds with max type 18
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53 angles with max type 37
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72 dihedrals with max type 53
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3 impropers with max type 5
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molecule mol4 rxn2_stp1_pre.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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42 atoms with max type 11
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41 bonds with max type 18
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73 angles with max type 41
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96 dihedrals with max type 54
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3 impropers with max type 5
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molecule mol5 rxn2_stp1_post.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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42 atoms with max type 11
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41 bonds with max type 18
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75 angles with max type 37
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108 dihedrals with max type 53
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2 impropers with max type 5
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molecule mol6 rxn2_stp2_post.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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42 atoms with max type 11
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41 bonds with max type 19
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73 angles with max type 50
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102 dihedrals with max type 66
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3 impropers with max type 22
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thermo 50
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# dump 1 all xyz 1 test_vis.xyz
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fix rxns all bond/react stabilization yes statted_grp .03 react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map
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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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thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
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run 2000
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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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Generated 55 of 55 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
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ghost atom cutoff = 10
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binsize = 5, bins = 4 6 5
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) pair lj/class2, 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) = 16.64 | 16.64 | 16.64 Mbytes
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Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
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0 300 0 0 0 0
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50 378.29345 1 0 0 0
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100 471.04152 1 1 0 0
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150 583.79755 1 1 1 0
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200 526.00812 1 1 1 1
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250 429.56812 1 1 1 1
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300 512.54655 1 1 1 1
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350 461.18357 1 1 1 1
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400 379.38965 1 1 1 1
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450 424.89528 1 1 1 1
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500 324.72257 1 1 1 1
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550 302.91042 1 1 1 1
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600 253.80911 1 1 1 1
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650 252.90262 1 1 1 1
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700 270.62628 1 1 1 1
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750 311.64391 1 1 1 1
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800 318.9413 1 1 1 1
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850 354.20196 1 1 1 1
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900 302.19641 1 1 1 1
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950 316.97905 1 1 1 1
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1000 303.08194 1 1 1 1
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1050 317.51619 1 1 1 1
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1100 287.57204 1 1 1 1
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1150 226.72101 1 1 1 1
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1200 283.97519 1 1 1 1
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1250 287.0607 1 1 1 1
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1300 327.65278 1 1 1 1
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1350 316.06809 1 1 1 1
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1400 337.69947 1 1 1 1
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1450 326.12278 1 1 1 1
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1500 300.89265 1 1 1 1
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1550 325.2415 1 1 1 1
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1600 294.1844 1 1 1 1
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1650 293.98596 1 1 1 1
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1700 317.35477 1 1 1 1
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1750 296.97768 1 1 1 1
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1800 274.97297 1 1 1 1
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1850 335.36697 1 1 1 1
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1900 315.3756 1 1 1 1
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1950 260.65335 1 1 1 1
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2000 354.03612 1 1 1 1
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Loop time of 0.910097 on 1 procs for 2000 steps with 118 atoms
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Performance: 189.870 ns/day, 0.126 hours/ns, 2197.568 timesteps/s, 259.313 katom-step/s
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99.9% 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 | 0.10286 | 0.10286 | 0.10286 | 0.0 | 11.30
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Bond | 0.63714 | 0.63714 | 0.63714 | 0.0 | 70.01
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Neigh | 0.013949 | 0.013949 | 0.013949 | 0.0 | 1.53
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Comm | 0.0056606 | 0.0056606 | 0.0056606 | 0.0 | 0.62
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Output | 0.00055825 | 0.00055825 | 0.00055825 | 0.0 | 0.06
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Modify | 0.14629 | 0.14629 | 0.14629 | 0.0 | 16.07
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Other | | 0.003637 | | | 0.40
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Nlocal: 118 ave 118 max 118 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 372 ave 372 max 372 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3487 ave 3487 max 3487 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3487
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Ave neighs/atom = 29.550847
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Ave special neighs/atom = 10.576271
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Neighbor list builds = 68
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Dangerous builds = 0
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# write_restart restart_longrun
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# write_data restart_longrun.data nofix
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Total wall time: 0:00:01
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