forked from lijiext/lammps
147 lines
4.8 KiB
Groff
147 lines
4.8 KiB
Groff
LAMMPS (15 Jun 2020)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate SNAP W 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 3.1803
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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 3.1803
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Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
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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 (12.7212 12.7212 12.7212)
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1 by 1 by 1 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 W_2940_2017_2.snap
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# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
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#
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# Definition of SNAP+ZBL potential.
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 74
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# Specify hybrid with SNAP and ZBL
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pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
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pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
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pair_style hybrid/overlay zbl 4 4.8 snap
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pair_coeff 1 1 zbl ${zblz} ${zblz}
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pair_coeff 1 1 zbl 74 ${zblz}
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pair_coeff 1 1 zbl 74 74
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pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W
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Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
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SNAP Element = W, Radius 0.5, Weight 1
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Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
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SNAP keyword rcutfac 4.73442
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SNAP keyword twojmax 8
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0
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SNAP keyword bzeroflag 0
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SNAP keyword quadraticflag 0
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#Nomenclature on the snap files are Element_DakotaID_Year_Month
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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 = 5.8
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ghost atom cutoff = 5.8
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binsize = 2.9, bins = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair zbl, perpetual, half/full from (2)
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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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(2) 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) = 4.268 | 4.268 | 4.268 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -11.028325 0 -10.98985 3010.497
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10 293.10848 -11.027441 0 -10.989849 3259.9445
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20 273.14727 -11.024881 0 -10.989849 3979.8968
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30 242.20285 -11.020912 0 -10.989849 5089.0797
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40 203.51992 -11.01595 0 -10.989849 6462.9419
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50 161.14556 -11.010515 0 -10.989848 7948.1798
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60 119.47232 -11.00517 0 -10.989848 9380.8543
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70 82.729175 -11.000458 0 -10.989848 10606.025
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80 54.483648 -10.996835 0 -10.989848 11496.424
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90 37.225263 -10.994622 0 -10.989847 11967.579
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100 32.094224 -10.993964 0 -10.989847 11987.181
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Loop time of 2.29953 on 1 procs for 100 steps with 128 atoms
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Performance: 1.879 ns/day, 12.775 hours/ns, 43.487 timesteps/s
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99.7% CPU use with 1 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 | 2.2988 | 2.2988 | 2.2988 | 0.0 | 99.97
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.01
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Output | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.01
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Modify | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.00
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Other | | 0.0001643 | | | 0.01
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Nlocal: 128 ave 128 max 128 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 727 ave 727 max 727 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3712 ave 3712 max 3712 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 7424 ave 7424 max 7424 min
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Histogram: 1 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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