forked from lijiext/lammps
127 lines
4.2 KiB
Groff
127 lines
4.2 KiB
Groff
LAMMPS (15 Jun 2020)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate SNAP Mo potential
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# Initialize simulation
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variable nsteps index 100
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variable nrep equal 4
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variable a equal 3.160
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable nx equal 4
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variable ny equal ${nrep}
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variable ny equal 4
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variable nz equal ${nrep}
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variable nz equal 4
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boundary p p p
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lattice bcc $a
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lattice bcc 3.16
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Lattice spacing in x,y,z = 3.16 3.16 3.16
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 4 0 ${ny} 0 ${nz}
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region box block 0 4 0 4 0 ${nz}
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region box block 0 4 0 4 0 4
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create_box 1 box
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Created orthogonal box = (0.0 0.0 0.0) to (12.64 12.64 12.64)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 128 atoms
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create_atoms CPU = 0.000 seconds
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mass 1 183.84
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# choose potential
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include Mo_Chen_PRM2017.snap
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# DATE: 2017-09-18 UNITS: metal CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
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# Generated by Materials Virtual Lab
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# Definition of SNAP potential.
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pair_style snap
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pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo
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Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
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SNAP Element = Mo, Radius 0.5, Weight 1
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Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
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SNAP keyword rcutfac 4.615858
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SNAP keyword twojmax 6
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# Setup output
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thermo 10
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thermo_modify norm yes
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# Set up NVE run
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timestep 0.5e-3
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neighbor 1.0 bin
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neigh_modify once no every 1 delay 0 check yes
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# Run MD
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velocity all create 300.0 4928459 loop geom
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fix 1 all nve
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run ${nsteps}
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run 100
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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 = 5.61586
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ghost atom cutoff = 5.61586
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binsize = 2.80793, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair snap, 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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Per MPI rank memory allocation (min/avg/max) = 3.271 | 3.271 | 3.271 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -22.405975 0 -22.3675 2575.7657
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10 294.8148 -22.40531 0 -22.3675 2762.0942
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20 279.68628 -22.40337 0 -22.3675 3306.7656
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30 255.84798 -22.400312 0 -22.3675 4168.2979
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40 225.22346 -22.396384 0 -22.367499 5281.9537
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50 190.25143 -22.391899 0 -22.367499 6565.6626
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60 153.66642 -22.387207 0 -22.367499 7927.3186
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70 118.25575 -22.382665 0 -22.367499 9271.9554
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80 86.616338 -22.378607 0 -22.367499 10510.959
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90 60.935787 -22.375314 0 -22.367498 11568.261
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100 42.815823 -22.37299 0 -22.367498 12385.433
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Loop time of 0.260783 on 4 procs for 100 steps with 128 atoms
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Performance: 16.566 ns/day, 1.449 hours/ns, 383.461 timesteps/s
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97.1% 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 | 0.23045 | 0.23744 | 0.24455 | 1.2 | 91.05
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.014524 | 0.021267 | 0.027713 | 3.7 | 8.15
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Output | 0.00014997 | 0.00040495 | 0.0011623 | 0.0 | 0.16
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Modify | 4.2439e-05 | 4.6909e-05 | 5.0068e-05 | 0.0 | 0.02
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Other | | 0.00162 | | | 0.62
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Nlocal: 32 ave 32 max 32 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 431 ave 431 max 431 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 1856 ave 1856 max 1856 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 7424
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Ave neighs/atom = 58
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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