forked from lijiext/lammps
158 lines
5.2 KiB
Groff
158 lines
5.2 KiB
Groff
LAMMPS (15 Jun 2020)
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using 1 OpenMP thread(s) per MPI task
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# Demonstrate SNAP InP 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 5.83
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units metal
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# generate the box and atom positions using a FCC 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 diamond $a
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lattice diamond 5.83
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Lattice spacing in x,y,z = 5.83 5.83 5.83
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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 2 box
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Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
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Created 512 atoms
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create_atoms CPU = 0.000 seconds
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mass 1 114.76
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mass 2 30.98
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# choose potential
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include InP_JCPA2020.snap
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# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
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# Definition of SNAP+ZBL potential.
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variable zblcutinner index 4
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variable zblcutouter index 4.2
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variable zblz1 index 49
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variable zblz2 index 15
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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 4.2 snap
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pair_coeff 1 1 zbl ${zblz1} ${zblz1}
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pair_coeff 1 1 zbl 49 ${zblz1}
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pair_coeff 1 1 zbl 49 49
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pair_coeff 1 2 zbl ${zblz1} ${zblz2}
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pair_coeff 1 2 zbl 49 ${zblz2}
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pair_coeff 1 2 zbl 49 15
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pair_coeff 2 2 zbl ${zblz2} ${zblz2}
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pair_coeff 2 2 zbl 15 ${zblz2}
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pair_coeff 2 2 zbl 15 15
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pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P
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Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01
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SNAP Element = In, Radius 3.81205, Weight 1
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SNAP Element = P, Radius 3.82945, Weight 0.929316
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Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01
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SNAP keyword rcutfac 1.0
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SNAP keyword twojmax 6
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0.0
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SNAP keyword bzeroflag 1
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SNAP keyword quadraticflag 0
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SNAP keyword wselfallflag 1
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SNAP keyword chemflag 1
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SNAP keyword bnormflag 1
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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 = 8.6589
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ghost atom cutoff = 8.6589
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binsize = 4.32945, bins = 6 6 6
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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) = 4.587 | 4.587 | 4.587 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -3.4805794 0 -3.4418771 1353.5968
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10 285.84677 -3.4787531 0 -3.4418766 1611.7131
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20 248.14649 -3.4738884 0 -3.4418756 2312.0308
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30 198.94136 -3.4675394 0 -3.4418744 3168.1543
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40 152.74831 -3.4615791 0 -3.4418734 3903.5749
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50 121.9796 -3.4576091 0 -3.4418728 4387.1254
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60 113.27555 -3.4564863 0 -3.4418729 4556.3003
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70 125.68089 -3.4580873 0 -3.4418735 4431.2083
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80 151.47475 -3.4614159 0 -3.4418745 4107.2369
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90 179.18708 -3.4649919 0 -3.4418754 3739.5881
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100 197.50662 -3.4673559 0 -3.441876 3492.7778
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Loop time of 3.73974 on 4 procs for 100 steps with 512 atoms
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Performance: 1.155 ns/day, 20.776 hours/ns, 26.740 timesteps/s
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98.3% 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 | 3.4687 | 3.5182 | 3.5985 | 2.7 | 94.07
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.13897 | 0.21952 | 0.26888 | 10.7 | 5.87
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Output | 0.00018191 | 0.00047094 | 0.0012944 | 0.0 | 0.01
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Modify | 0.00013065 | 0.00013524 | 0.00014186 | 0.0 | 0.00
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Other | | 0.001456 | | | 0.04
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Nlocal: 128 ave 128 max 128 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 1099 ave 1099 max 1099 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 7808 ave 7808 max 7808 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 15616 ave 15616 max 15616 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 62464
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Ave neighs/atom = 122
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:03
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