187 lines
8.4 KiB
Groff
187 lines
8.4 KiB
Groff
LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-269-g5a12c762f3-modified)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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#CTIP potential for NiO
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#Contributing author: Gabriel Plummer (NASA)
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#Initialize
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units metal
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atom_style charge
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dimension 3
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boundary p p p
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#Create Structure
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read_data data.ctip
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Reading data file ...
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orthogonal box = (0 0 0) to (24.719478 24.719478 24.719478)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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1728 atoms
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read_data CPU = 0.007 seconds
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#Define Charges
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group type1 type 1
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864 atoms in group type1
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compute charge1 type1 property/atom q
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compute q1 type1 reduce ave c_charge1
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group type2 type 2
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864 atoms in group type2
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compute charge2 type2 property/atom q
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compute q2 type2 reduce ave c_charge2
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#Define Potential
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pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
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pair_coeff * * eam/fs NiO.eam.fs Ni O
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Reading eam/fs potential file NiO.eam.fs with DATE: 2024-04-29
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pair_coeff * * coul/ctip NiO.ctip Ni O
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Reading coul/ctip potential file NiO.ctip with DATE: 2024-09-11
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fix qeq all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
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#Setup
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timestep 0.001
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thermo 100
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thermo_style custom step temp pe lx ly lz pxx pyy pzz c_q1 c_q2
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#Minimization
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fix relax all box/relax iso 0
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minimize 1e-10 1e-10 100000 100000
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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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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 = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 4 4 4
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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair eam/fs, perpetual, trim from (2)
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attributes: half, newton on, cut 8
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pair build: trim
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stencil: none
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bin: none
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(2) pair coul/ctip, perpetual, half/full from (3)
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attributes: half, newton on
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pair build: halffull/newton
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stencil: none
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bin: none
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(3) fix qeq/ctip, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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WARNING: Energy due to 1 extra global DOFs will be included in minimizer energies
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(src/min.cpp:219)
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Per MPI rank memory allocation (min/avg/max) = 19.71 | 19.71 | 19.71 Mbytes
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Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
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0 0 -9633.183 24.719478 24.719478 24.719478 -1491.273 -1491.273 -1491.273 1.2374666 -1.2374666
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6 0 -9633.1929 24.707505 24.707505 24.707505 0.0050498849 0.0050498856 0.0050498855 1.2410908 -1.2410908
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Loop time of 0.288818 on 4 procs for 6 steps with 1728 atoms
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99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-9633.18301849946 -9633.19294329957 -9633.19294333066
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Force two-norm initial, final = 42.177998 0.00014286398
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Force max component initial, final = 42.177998 0.00014268867
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Final line search alpha, max atom move = 0.0079490643 1.1342414e-06
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Iterations, force evaluations = 6 8
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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 | 0.09401 | 0.095886 | 0.097631 | 0.4 | 33.20
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0024298 | 0.004185 | 0.0060676 | 2.1 | 1.45
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0.18779 | 0.1878 | 0.18781 | 0.0 | 65.02
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Other | | 0.000945 | | | 0.33
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Nlocal: 432 ave 432 max 432 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 8593 ave 8593 max 8593 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 54000 ave 54000 max 54000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 585792 ave 585792 max 585792 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2343168
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Ave neighs/atom = 1356
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Neighbor list builds = 0
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Dangerous builds = 0
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unfix relax
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#Dynamics
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reset_timestep 0
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variable T equal 1000
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variable rnd equal round(random(0,999,${T}))
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variable rnd equal round(random(0,999,1000))
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velocity all create ${T} ${rnd} mom yes rot yes
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velocity all create 1000 ${rnd} mom yes rot yes
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velocity all create 1000 233 mom yes rot yes
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fix npt all npt temp ${T} ${T} 0.1 iso 0 0 1
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fix npt all npt temp 1000 ${T} 0.1 iso 0 0 1
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fix npt all npt temp 1000 1000 0.1 iso 0 0 1
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run 1000
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Per MPI rank memory allocation (min/avg/max) = 18.83 | 18.83 | 18.83 Mbytes
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Step Temp PotEng Lx Ly Lz Pxx Pyy Pzz c_q1 c_q2
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0 1000 -9633.1929 24.707505 24.707505 24.707505 15934.991 15754.787 15735.602 1.2410908 -1.2410908
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100 600.77874 -9528.0602 24.816519 24.816519 24.816519 -16709.313 -15443.072 -17750.832 1.2181988 -1.2181988
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200 578.84295 -9490.9794 24.812627 24.812627 24.812627 -5879.8769 -4851.4601 -6722.107 1.2254363 -1.2254363
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300 694.7973 -9478.5512 24.764285 24.764285 24.764285 14639.415 13827.989 13766.766 1.2372201 -1.2372201
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400 803.93731 -9462.2542 24.866629 24.866629 24.866629 -4644.2853 -6017.2884 -7744.2567 1.2086229 -1.2086229
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500 893.70492 -9441.0072 24.891756 24.891756 24.891756 -5784.2232 -8219.1644 -4187.392 1.2001224 -1.2001224
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600 947.21728 -9416.7532 24.863623 24.863623 24.863623 11265.076 12952.469 11331.883 1.2115124 -1.2115124
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700 1040.4874 -9409.8397 24.933859 24.933859 24.933859 -6570.5926 -8532.7456 -3284.7317 1.1902794 -1.1902794
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800 1037.9366 -9398.4828 24.935138 24.935138 24.935138 -4681.8675 -2576.5001 -7160.5622 1.1880324 -1.1880324
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900 1049.4211 -9411.115 24.899733 24.899733 24.899733 3250.2695 8121.9274 5945.0541 1.2024086 -1.2024086
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1000 964.18789 -9412.4405 24.926442 24.926442 24.926442 -7652.603 -5142.926 -8351.8839 1.1908935 -1.1908935
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Loop time of 63.5378 on 4 procs for 1000 steps with 1728 atoms
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Performance: 1.360 ns/day, 17.649 hours/ns, 15.739 timesteps/s, 27.196 katom-step/s
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99.5% CPU use with 4 MPI tasks x 1 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 | 12.737 | 12.782 | 12.839 | 1.1 | 20.12
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Neigh | 0.082989 | 0.083627 | 0.084898 | 0.3 | 0.13
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Comm | 0.39773 | 0.45431 | 0.49896 | 5.5 | 0.72
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Output | 0.00038299 | 0.0004067 | 0.00047658 | 0.0 | 0.00
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Modify | 50.207 | 50.207 | 50.208 | 0.0 | 79.02
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Other | | 0.01047 | | | 0.02
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Nlocal: 432 ave 446 max 421 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Nghost: 8594.5 ave 8608 max 8579 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Neighs: 52597 ave 54466 max 51209 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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FullNghs: 558619 ave 576961 max 544134 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Total # of neighbors = 2234476
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Ave neighs/atom = 1293.0995
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Neighbor list builds = 5
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Dangerous builds = 0
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Total wall time: 0:01:04
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