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tutorial 8 updates
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‎figures/REACTED_VMD.png‎

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‎files/tutorial8/mixing.log‎

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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-566-g224468d946-modified)
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# inserting styrene molecules around a periodic CNT
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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-5
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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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special_bonds lj/coul 0 0 1
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pair_modify tail yes mix sixthpower
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variable T equal 530
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read_data CNT.data extra/special/per/atom 20
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Reading data file ...
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orthogonal box = (-43.564937 -40 -40) to (43.564937 40 40)
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4 by 2 by 4 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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1056 atoms
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reading velocities ...
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1056 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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3 = max angles/atom
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scanning dihedrals ...
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12 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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orthogonal box = (-43.564937 -40 -40) to (43.564937 40 40)
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4 by 2 by 4 MPI processor grid
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reading bonds ...
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1584 bonds
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reading angles ...
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3168 angles
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reading dihedrals ...
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6336 dihedrals
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reading impropers ...
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1056 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 1
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special bond factors coul: 0 0 1
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3 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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29 = max # of special neighbors
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special bonds CPU = 0.002 seconds
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read_data CPU = 0.059 seconds
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#write_data CNT.data
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molecule styrene styrene.molecule_template
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Read molecule template styrene:
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styrene_molecule
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1 molecules
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0 fragments
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16 atoms with max type 4
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16 bonds with max type 11
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24 angles with max type 19
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32 dihedrals with max type 21
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8 impropers with max type 9
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create_atoms 0 random 1000 8305 NULL overlap 2.75 maxtry 500 mol styrene 7687
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WARNING: Only inserted 999 particles out of 1000 (../create_atoms.cpp:893)
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Created 15984 atoms
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using lattice units in orthogonal box = (-43.564937 -40 -40) to (43.564937 40 40)
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create_atoms CPU = 1.320 seconds
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thermo_style custom step density temp etotal press pxx pyy pzz lx ly lz
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minimize 1.0e-4 1.0e-6 100 1000
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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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- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
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@Article{Gissinger24,
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author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
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title = {Type Label Framework for Bonded Force Fields in LAMMPS},
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journal = {J. Phys. Chem. B},
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year = 2024,
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volume = 128,
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number = 13,
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pages = {3282--3297}
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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 = 211.0002 (../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) = 0.27506117
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grid = 36 36 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0034350933
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estimated relative force accuracy = 1.0344682e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 4508 2592
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Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower 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 = 17 16 16
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1 neighbor lists, perpetual/occasional/extra = 1 0 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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WARNING: Inconsistent image flags (../domain.cpp:1051)
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Per MPI rank memory allocation (min/avg/max) = 15.06 | 15.08 | 15.17 Mbytes
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Step Density Temp TotEng Press Pxx Pyy Pzz Lx Ly Lz
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0 0.34761281 17.644269 371476.17 4142.167 6150.893 6829.2787 -553.67091 87.129874 80 80
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100 0.34761281 17.644269 255469.33 -7589.6411 -1091.0191 -10825.649 -10852.255 87.129874 80 80
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Loop time of 0.541063 on 32 procs for 100 steps with 17040 atoms
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97.0% CPU use with 32 MPI tasks x no OpenMP threads
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Minimization stats:
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Stopping criterion = max iterations
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Energy initial, next-to-last, final =
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370580.014860093 254601.075890351 254573.174228796
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Force two-norm initial, final = 29259.13 197.17728
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Force max component initial, final = 660.08646 15.936135
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Final line search alpha, max atom move = 0.0019101557 0.030440499
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Iterations, force evaluations = 100 187
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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 | 0.11933 | 0.14487 | 0.17858 | 3.5 | 26.77
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Bond | 0.11844 | 0.14206 | 0.1739 | 4.2 | 26.26
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Kspace | 0.13953 | 0.20545 | 0.25206 | 6.1 | 37.97
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Neigh | 0.012835 | 0.012881 | 0.012936 | 0.0 | 2.38
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Comm | 0.025827 | 0.027098 | 0.02801 | 0.3 | 5.01
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Output | 0.00012221 | 0.00012926 | 0.00014089 | 0.0 | 0.02
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.008579 | | | 1.59
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Nlocal: 532.5 ave 602 max 492 min
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Histogram: 5 5 4 6 3 4 2 2 0 1
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Nghost: 2763.97 ave 2958 max 2544 min
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Histogram: 2 2 4 4 0 6 3 6 3 2
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Neighs: 40020.2 ave 48477 max 32721 min
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Histogram: 1 3 5 4 7 3 3 3 1 2
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Total # of neighbors = 1280648
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Ave neighs/atom = 75.155399
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Ave special neighs/atom = 8.6482394
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Neighbor list builds = 7
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Dangerous builds = 0
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velocity all create 300.0 4928459 rot yes dist gaussian loop local
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thermo_style custom step density temp etotal press pxx pyy pzz lx ly lz
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fix 1 all nvt temp 300 300 100 #y 1 1 3000 z 1 1 3000
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fix 2 all deform 1 y erate -0.0001 z erate -0.0001
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variable density equal density
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fix 3 all halt 10 v_density > 0.9 error continue
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thermo 500
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dump myDump all xyz 100 test.xyz
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run 9000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:342)
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G vector (1/distance) = 0.27506117
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grid = 36 36 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0034350933
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estimated relative force accuracy = 1.0344682e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 4508 2592
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Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
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WARNING: Inconsistent image flags (../domain.cpp:1051)
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Per MPI rank memory allocation (min/avg/max) = 13.95 | 13.97 | 14.06 Mbytes
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Step Density Temp TotEng Press Pxx Pyy Pzz Lx Ly Lz
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100 0.34761281 300 269810.18 -6414.0378 83.373986 -9638.5794 -9686.9081 87.129874 80 80
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500 0.37718404 254.88444 268137.3 -8162.2858 -1776.5865 -11287.011 -11423.26 87.129874 76.8 76.8
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1000 0.41977154 314.28458 260818.95 -9444.8629 -3714.1682 -12166.147 -12454.273 87.129874 72.8 72.8
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1500 0.4700011 304.24881 249924.04 -10324.449 -5188.9787 -12829.622 -12954.747 87.129874 68.8 68.8
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2000 0.52981681 302.00448 238419.45 -12029.534 -7003.9724 -14794.4 -14290.231 87.129874 64.8 64.8
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2500 0.60182273 302.01293 227177.01 -14190.394 -10644.054 -15752.386 -16174.742 87.129874 60.8 60.8
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3000 0.68957114 300.00594 215282.94 -16502.603 -13771.089 -18400.99 -17335.73 87.129874 56.8 56.8
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3500 0.79800921 297.25631 202753.65 -18780.174 -18095.609 -18655.569 -19589.343 87.129874 52.8 52.8
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Fix halt condition for fix-id 3 met on step 3890 with value 0.9013896603771433 (../fix_halt.cpp:240)
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Loop time of 14.4437 on 32 procs for 3790 steps with 17040 atoms
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Performance: 22.671 ns/day, 1.059 hours/ns, 262.399 timesteps/s, 4.471 Matom-step/s
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98.1% CPU use with 32 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 | 2.4969 | 3.5937 | 4.9245 | 37.9 | 24.88
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Bond | 1.9804 | 2.6972 | 3.3912 | 26.3 | 18.67
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Kspace | 3.191 | 5.1013 | 6.8327 | 50.1 | 35.32
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Neigh | 0.82013 | 0.82391 | 0.82848 | 0.2 | 5.70
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Comm | 0.7503 | 0.77559 | 0.84476 | 2.5 | 5.37
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Output | 0.031092 | 0.051743 | 0.069465 | 4.9 | 0.36
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Modify | 0.67967 | 0.80461 | 1.2989 | 20.5 | 5.57
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Other | | 0.5957 | | | 4.12
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Nlocal: 532.5 ave 604 max 466 min
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Histogram: 1 2 4 8 1 3 5 7 0 1
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Nghost: 4664.62 ave 4780 max 4543 min
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Histogram: 5 1 2 5 4 0 4 5 2 4
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Neighs: 102963 ave 121341 max 82558 min
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Histogram: 1 2 4 6 3 2 3 5 4 2
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Total # of neighbors = 3294830
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Ave neighs/atom = 193.35857
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Ave special neighs/atom = 8.6482394
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Neighbor list builds = 258
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Dangerous builds = 0
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unfix 2
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unfix 3
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run 10000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:342)
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G vector (1/distance) = 0.28757057
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grid = 40 25 25
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0033264521
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estimated relative force accuracy = 1.0017512e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 3705 1120
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Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
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WARNING: Inconsistent image flags (../domain.cpp:1051)
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Per MPI rank memory allocation (min/avg/max) = 15.03 | 15.28 | 15.45 Mbytes
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Step Density Temp TotEng Press Pxx Pyy Pzz Lx Ly Lz
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3890 0.90138966 298.86743 193196.88 -20669.223 -21815.115 -20048.038 -20144.514 87.129874 49.68 49.68
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4000 0.90138966 298.35686 192919.69 -21294.809 -22512.317 -21433.658 -19938.451 87.129874 49.68 49.68
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4500 0.90138966 299.17881 193385.19 -22148.311 -23368.969 -21492.255 -21583.71 87.129874 49.68 49.68
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5000 0.90138966 305.64921 193747.89 -21660.18 -22803.68 -21890.785 -20286.074 87.129874 49.68 49.68
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5500 0.90138966 300.11618 193320.85 -22704.487 -23700.572 -21625.09 -22787.797 87.129874 49.68 49.68
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6000 0.90138966 299.03893 193676.83 -22661.805 -24031.414 -22233.014 -21720.986 87.129874 49.68 49.68
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6500 0.90138966 299.30614 193230.36 -23293.156 -24213.942 -22028.619 -23636.906 87.129874 49.68 49.68
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7000 0.90138966 300.34264 193396.5 -23185.053 -23842.691 -22906.747 -22805.72 87.129874 49.68 49.68
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7500 0.90138966 301.12174 193417.87 -22741.042 -23326.468 -22812.022 -22084.636 87.129874 49.68 49.68
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8000 0.90138966 299.03696 193392.17 -23878.853 -25399.951 -22812.512 -23424.096 87.129874 49.68 49.68
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8500 0.90138966 301.33078 193595.23 -23561.472 -24606.653 -23068.198 -23009.564 87.129874 49.68 49.68
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9000 0.90138966 300.3531 193576.8 -23753.7 -24070.154 -23487.747 -23703.201 87.129874 49.68 49.68
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9500 0.90138966 299.40771 193407.39 -22616.306 -23205.753 -22075.285 -22567.879 87.129874 49.68 49.68
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10000 0.90138966 300.95215 193402.63 -23254.076 -24612.302 -22350.311 -22799.616 87.129874 49.68 49.68
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10500 0.90138966 299.8429 193262.01 -23038.102 -23647.943 -22384.148 -23082.214 87.129874 49.68 49.68
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11000 0.90138966 300.65582 193453.24 -22850.106 -24288.251 -21977.677 -22284.388 87.129874 49.68 49.68
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11500 0.90138966 303.14713 193497.65 -23589.186 -25072.38 -22690.615 -23004.562 87.129874 49.68 49.68
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12000 0.90138966 295.06122 192956.77 -24822.216 -26014.559 -24240.401 -24211.687 87.129874 49.68 49.68
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12500 0.90138966 299.02027 193373.85 -23357.017 -24383.816 -23314.19 -22373.045 87.129874 49.68 49.68
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13000 0.90138966 299.17257 193336.43 -24012.72 -25194.899 -23448.731 -23394.53 87.129874 49.68 49.68
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13500 0.90138966 300.01369 193350.63 -24041.934 -24780.2 -23260.854 -24084.75 87.129874 49.68 49.68
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13890 0.90138966 298.73517 193191.99 -24165.823 -24911.557 -23636.331 -23949.581 87.129874 49.68 49.68
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Loop time of 36.3297 on 32 procs for 10000 steps with 17040 atoms
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Performance: 23.782 ns/day, 1.009 hours/ns, 275.257 timesteps/s, 4.690 Matom-step/s
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96.8% CPU use with 32 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 | 12.493 | 14.693 | 16.96 | 44.8 | 40.44
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Bond | 5.9522 | 7.1338 | 8.4755 | 38.4 | 19.64
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Kspace | 5.5716 | 9.0334 | 12.369 | 90.3 | 24.86
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Neigh | 2.001 | 2.0091 | 2.0178 | 0.3 | 5.53
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Comm | 2.6499 | 2.6903 | 2.7524 | 1.4 | 7.41
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Output | 0.080838 | 0.13288 | 0.18287 | 8.3 | 0.37
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Modify | 0.13989 | 0.16571 | 0.20131 | 5.5 | 0.46
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Other | | 0.4715 | | | 1.30
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Nlocal: 532.5 ave 594 max 459 min
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Histogram: 1 5 7 2 1 0 2 0 9 5
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Nghost: 4663.84 ave 4840 max 4504 min
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Histogram: 2 8 6 0 0 2 0 9 3 2
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Neighs: 103380 ave 121708 max 83146 min
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Histogram: 4 7 4 1 0 0 0 2 6 8
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Total # of neighbors = 3308147
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Ave neighs/atom = 194.14008
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Ave special neighs/atom = 8.6482394
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Neighbor list builds = 526
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Dangerous builds = 0
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#unfix 1
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#fix 1 all npt temp 300 300 100 y 1 1 3000 z 1 1 3000
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#run 10000
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write_data composite.data
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System init for write_data ...
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:342)
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G vector (1/distance) = 0.28757057
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grid = 40 25 25
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0033264521
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estimated relative force accuracy = 1.0017512e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 3705 1120
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Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
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Total wall time: 0:00:53

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