Renamed InP potential files and create standard log files
This commit is contained in:
Aidan Thompson
155
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1
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155
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1
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LAMMPS (2 Jun 2020)
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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 1 by 1 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 equal 4
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variable zblcutouter equal 4.2
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variable zblz1 equal 49
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variable zblz2 equal 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 alloyflag 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
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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) = 6.027 | 6.027 | 6.027 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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10 286.42264 -3.4788274 0 -3.4418767 1586.4881
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20 250.14148 -3.4741459 0 -3.4418757 2219.0344
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30 202.52417 -3.4680017 0 -3.4418745 2982.7272
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40 157.39113 -3.4621782 0 -3.4418735 3631.0936
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50 126.7004 -3.4582183 0 -3.441873 4053.7725
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60 117.00722 -3.4569679 0 -3.441873 4204.9542
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70 127.65968 -3.4583427 0 -3.4418736 4106.3112
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80 151.50217 -3.4614195 0 -3.4418745 3840.7205
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90 177.67607 -3.464797 0 -3.4418754 3527.9794
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100 195.30359 -3.4670717 0 -3.4418761 3300.3795
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Loop time of 18.1983 on 1 procs for 100 steps with 512 atoms
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Performance: 0.237 ns/day, 101.102 hours/ns, 5.495 timesteps/s
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99.8% CPU use with 1 MPI tasks x no 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 | 18.196 | 18.196 | 18.196 | 0.0 | 99.99
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00104 | 0.00104 | 0.00104 | 0.0 | 0.01
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Output | 0.000262 | 0.000262 | 0.000262 | 0.0 | 0.00
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Modify | 0.000576 | 0.000576 | 0.000576 | 0.0 | 0.00
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Other | | 0.000486 | | | 0.00
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Nlocal: 512 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1959 ave 1959 max 1959 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 31232 ave 31232 max 31232 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 62464 ave 62464 max 62464 min
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Histogram: 1 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: 0:00:18
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155
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4
Normal file
155
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4
Normal file
@ -0,0 +1,155 @@
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LAMMPS (2 Jun 2020)
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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 = 0.001 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 equal 4
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variable zblcutouter equal 4.2
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variable zblz1 equal 49
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variable zblz2 equal 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 alloyflag 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
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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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10 286.58246 -3.478848 0 -3.4418767 1582.995
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20 250.70996 -3.4742192 0 -3.4418757 2207.7507
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30 203.58199 -3.4681382 0 -3.4418746 2968.5206
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40 158.84622 -3.462366 0 -3.4418736 3619.0285
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50 128.30488 -3.4584254 0 -3.4418731 4047.173
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60 118.40349 -3.4571481 0 -3.4418731 4203.3421
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70 128.48973 -3.4584499 0 -3.4418737 4109.0296
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80 151.54241 -3.4614247 0 -3.4418746 3847.4617
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90 176.92084 -3.4646996 0 -3.4418755 3548.7811
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100 193.9555 -3.4668978 0 -3.4418761 3342.8083
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Loop time of 5.73708 on 4 procs for 100 steps with 512 atoms
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Performance: 0.753 ns/day, 31.873 hours/ns, 17.430 timesteps/s
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99.3% CPU use with 4 MPI tasks x no 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 | 5.5736 | 5.5812 | 5.591 | 0.3 | 97.28
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.14432 | 0.15366 | 0.16168 | 1.6 | 2.68
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Output | 0.000187 | 0.00024775 | 0.000419 | 0.0 | 0.00
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Modify | 0.000293 | 0.00038075 | 0.000582 | 0.0 | 0.01
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Other | | 0.00161 | | | 0.03
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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: 0:00:05
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