forked from lijiext/lammps
127 lines
4.1 KiB
Groff
127 lines
4.1 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate SNAP Ta 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) 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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Time spent = 0.000289917 secs
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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 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 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
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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) = 3.486 | 3.486 | 3.486 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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10 294.63153 -22.405286 0 -22.3675 2753.4662
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20 278.98535 -22.40328 0 -22.3675 3272.416
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30 254.38916 -22.400125 0 -22.3675 4091.8933
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40 222.91191 -22.396088 0 -22.367499 5148.5505
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50 187.16984 -22.391504 0 -22.367499 6362.2454
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60 150.08253 -22.386747 0 -22.367499 7643.2732
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70 114.60307 -22.382197 0 -22.367499 8900.2448
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80 83.449257 -22.378201 0 -22.367499 10047.619
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90 58.862643 -22.375048 0 -22.367498 11012.233
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100 42.41931 -22.372939 0 -22.367498 11740.641
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Loop time of 2.15419 on 4 procs for 100 steps with 128 atoms
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Performance: 2.005 ns/day, 11.968 hours/ns, 46.421 timesteps/s
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92.0% 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 | 1.7677 | 1.9028 | 1.9897 | 6.2 | 88.33
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.15367 | 0.24295 | 0.38029 | 17.6 | 11.28
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Output | 0.00034404 | 0.0012512 | 0.0017219 | 1.6 | 0.06
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Modify | 0.00018859 | 0.00021273 | 0.00023699 | 0.0 | 0.01
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Other | | 0.007011 | | | 0.33
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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: 0:00:02
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