forked from lijiext/lammps
149 lines
4.6 KiB
Groff
149 lines
4.6 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 3.316
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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) 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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Time spent = 0.000350714 secs
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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 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 Ta 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 diagonalstyle 3
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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
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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) = 4.138 | 4.138 | 4.138 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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10 295.96579 -11.851053 0 -11.813095 2696.1559
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20 284.32535 -11.84956 0 -11.813095 2301.3713
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30 266.04602 -11.847215 0 -11.813095 1832.1745
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40 242.2862 -11.844168 0 -11.813095 1492.6765
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50 214.48968 -11.840603 0 -11.813094 1312.8908
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60 184.32523 -11.836734 0 -11.813094 1284.582
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70 153.58055 -11.832791 0 -11.813094 1374.4457
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80 124.04276 -11.829003 0 -11.813094 1537.703
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90 97.37622 -11.825582 0 -11.813094 1734.9662
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100 75.007873 -11.822714 0 -11.813094 1930.8005
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Loop time of 5.03244 on 1 procs for 100 steps with 128 atoms
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Performance: 0.858 ns/day, 27.958 hours/ns, 19.871 timesteps/s
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98.9% 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 | 5.0308 | 5.0308 | 5.0308 | 0.0 | 99.97
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00070858 | 0.00070858 | 0.00070858 | 0.0 | 0.01
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Output | 0.00024676 | 0.00024676 | 0.00024676 | 0.0 | 0.00
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Modify | 0.0002749 | 0.0002749 | 0.0002749 | 0.0 | 0.01
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Other | | 0.0004299 | | | 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: 0:00:05
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