forked from lijiext/lammps
184 lines
6.4 KiB
Groff
184 lines
6.4 KiB
Groff
LAMMPS (20 Apr 2018)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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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 3.1803
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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 2 box
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Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 128 atoms
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Time spent = 0.000274658 secs
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mass 1 183.84
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mass 2 4.0026
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set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
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5 settings made for type/fraction
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group tungsten type 1
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123 atoms in group tungsten
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group helium type 2
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5 atoms in group helium
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# choose potential
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include W_2940_2017_2_He_JW2013.snap
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# DATE: 2017-02-20 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+Tabulated 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 table spline 10000 table spline 10000
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pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
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pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
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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 W_2940_2017_2.snapparam W NULL
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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 diagonalstyle 3
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SNAP keyword bzeroflag 0
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SNAP keyword quadraticflag 0
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pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
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Reading potential file He_He_JW2013.table with DATE: 2017-02-20
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WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
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Should only be flagged at inflection points (../pair_table.cpp:481)
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pair_coeff 1 2 table 2 W_He_JW2013.table WHe
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Reading potential file W_He_JW2013.table with DATE: 2017-02-20
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WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
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Should only be flagged at inflection points (../pair_table.cpp:481)
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#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
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#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
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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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6 neighbor lists, perpetual/occasional/extra = 6 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/skip
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stencil: none
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bin: none
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(2) pair snap, perpetual, skip from (6)
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attributes: full, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) pair table, perpetual, skip from (5)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(4) pair table, perpetual, skip from (5)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(5) neighbor class addition, perpetual, half/full from (6)
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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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(6) neighbor class addition, 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) = 7.656 | 7.656 | 7.656 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -10.438105 0 -10.39963 -5445.2808
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10 292.13979 -10.437097 0 -10.39963 -5516.3963
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20 272.55728 -10.434585 0 -10.399629 -5460.4268
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30 245.06559 -10.431059 0 -10.399629 -5016.6351
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40 212.79459 -10.42692 0 -10.399629 -3924.2175
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50 178.03903 -10.422462 0 -10.399629 -2354.5485
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60 141.62155 -10.417791 0 -10.399628 -595.41345
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70 107.24843 -10.413383 0 -10.399628 1138.4107
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80 79.985938 -10.409886 0 -10.399628 2392.1106
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90 62.568933 -10.407652 0 -10.399628 3141.7027
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100 56.697933 -10.406899 0 -10.399628 3583.9538
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Loop time of 4.82103 on 4 procs for 100 steps with 128 atoms
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Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 timesteps/s
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99.0% 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 | 4.4837 | 4.6734 | 4.7605 | 5.2 | 96.94
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.057389 | 0.14453 | 0.33421 | 29.4 | 3.00
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Output | 0.00038719 | 0.00073916 | 0.0017841 | 0.0 | 0.02
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Modify | 0.00018716 | 0.00022203 | 0.00026417 | 0.0 | 0.00
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Other | | 0.002119 | | | 0.04
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Nlocal: 32 ave 32 max 32 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 431 ave 431 max 431 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 856.25 ave 885 max 818 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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FullNghs: 1712.5 ave 1738 max 1658 min
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Histogram: 1 0 0 0 0 0 0 0 2 1
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Total # of neighbors = 6850
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Ave neighs/atom = 53.5156
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:04
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