forked from lijiext/lammps
156 lines
5.2 KiB
Groff
156 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 W-Be 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 0.0 0.0) to (12.7212 12.7212 12.7212)
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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 1 183.84
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mass 2 9.012182
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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/fractiongroup tungsten type 1
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123 atoms in group tungsten
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group beryllium type 2
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5 atoms in group beryllium
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# choose potential
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include WBe_Wood_PRB2019.snap
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# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
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# Definition of SNAP+ZBL potential.
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz1 equal 74
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variable zblz2 equal 4
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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 4.8 snap
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pair_coeff 1 1 zbl ${zblz1} ${zblz1}
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pair_coeff 1 1 zbl 74 ${zblz1}
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pair_coeff 1 1 zbl 74 74
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pair_coeff 1 2 zbl ${zblz1} ${zblz2}
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pair_coeff 1 2 zbl 74 ${zblz2}
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pair_coeff 1 2 zbl 74 4
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pair_coeff 2 2 zbl ${zblz2} ${zblz2}
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pair_coeff 2 2 zbl 4 ${zblz2}
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pair_coeff 2 2 zbl 4 4
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pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be
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SNAP Element = W, Radius 0.5, Weight 1
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SNAP Element = Be, Radius 0.417932, Weight 0.959049
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SNAP keyword rcutfac 4.8123
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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 bzeroflag 1
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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 = 5.8123
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ghost atom cutoff = 5.8123
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binsize = 2.90615, 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) = 4.268 | 4.268 | 4.268 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -8.5980876 0 -8.5596125 -35284.855
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10 296.32664 -8.5976164 0 -8.5596124 -35188.339
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20 282.41417 -8.595832 0 -8.5596123 -34782.293
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30 259.69014 -8.5929175 0 -8.5596121 -34113.316
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40 230.50415 -8.5891741 0 -8.5596119 -33260.777
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50 197.88816 -8.5849908 0 -8.5596116 -32309.975
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60 165.27259 -8.5808076 0 -8.5596113 -31365.766
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70 136.15697 -8.5770733 0 -8.5596111 -30542.657
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80 113.58947 -8.5741788 0 -8.5596109 -29939.23
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90 99.477916 -8.572369 0 -8.5596109 -29619.939
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100 94.121939 -8.5716822 0 -8.559611 -29598.002
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Loop time of 2.26616 on 1 procs for 100 steps with 128 atoms
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Performance: 1.906 ns/day, 12.590 hours/ns, 44.128 timesteps/s
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99.3% 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 | 2.2531 | 2.2531 | 2.2531 | 0.0 | 99.42
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 0.01
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Output | 0.012544 | 0.012544 | 0.012544 | 0.0 | 0.55
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Modify | 0.00010347 | 0.00010347 | 0.00010347 | 0.0 | 0.00
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Other | | 0.0001583 | | | 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: 0:00:02
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