forked from lijiext/lammps
148 lines
4.7 KiB
Groff
148 lines
4.7 KiB
Groff
LAMMPS (15 Jun 2020)
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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 3.316
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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 3.316
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Lattice spacing in x,y,z = 3.316 3.316 3.316
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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 (13.264 13.264 13.264)
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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 1 180.88
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# choose potential
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include Ta06A.snap
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# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
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# Definition of SNAP potential Ta_Cand06A
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# Assumes 1 LAMMPS atom type
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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# Specify hybrid with SNAP, 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 73 ${zblz}
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pair_coeff 1 1 zbl 73 73
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pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
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Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
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SNAP Element = Ta, Radius 0.5, Weight 1
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Reading potential file Ta06A.snapparam with DATE: 2014-09-05
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SNAP keyword rcutfac 4.67637
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SNAP keyword twojmax 6
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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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# 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) = 3.967 | 3.967 | 3.967 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -11.85157 0 -11.813095 2717.1661
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10 296.01467 -11.851059 0 -11.813095 2697.4796
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20 284.53666 -11.849587 0 -11.813095 2289.1527
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30 266.51577 -11.847275 0 -11.813095 1851.7131
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40 243.05007 -11.844266 0 -11.813095 1570.684
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50 215.51032 -11.840734 0 -11.813094 1468.1899
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60 185.48331 -11.836883 0 -11.813094 1524.8757
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70 154.6736 -11.832931 0 -11.813094 1698.3351
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80 124.79303 -11.829099 0 -11.813094 1947.0715
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90 97.448054 -11.825592 0 -11.813094 2231.9563
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100 74.035418 -11.822589 0 -11.813094 2515.8526
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Loop time of 0.702618 on 1 procs for 100 steps with 128 atoms
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Performance: 6.148 ns/day, 3.903 hours/ns, 142.325 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 | 0.70188 | 0.70188 | 0.70188 | 0.0 | 99.90
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00025487 | 0.00025487 | 0.00025487 | 0.0 | 0.04
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Output | 0.00015402 | 0.00015402 | 0.00015402 | 0.0 | 0.02
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Modify | 0.00011039 | 0.00011039 | 0.00011039 | 0.0 | 0.02
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Other | | 0.000217 | | | 0.03
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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: 0:00:00
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