forked from lijiext/lammps
155 lines
4.8 KiB
Groff
155 lines
4.8 KiB
Groff
LAMMPS (7 Aug 2019)
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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) 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 = 0.000234842 secs
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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/fraction
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group 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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# 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
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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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10 299.29029 -8.5979965 0 -8.5596125 -35299.259
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20 288.99334 -8.5966759 0 -8.5596124 -35004.093
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30 269.91027 -8.5942284 0 -8.5596123 -34447.077
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40 243.57361 -8.5908505 0 -8.5596121 -33687.105
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50 212.21385 -8.5868284 0 -8.5596119 -32821.864
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60 178.77144 -8.5825391 0 -8.5596116 -31971.17
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70 146.71854 -8.578428 0 -8.5596113 -31245.51
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80 119.50956 -8.5749383 0 -8.5596111 -30724.137
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90 99.872785 -8.5724197 0 -8.559611 -30440.244
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100 89.604584 -8.5711027 0 -8.5596109 -30392.805
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Loop time of 3.16831 on 1 procs for 100 steps with 128 atoms
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Performance: 1.364 ns/day, 17.602 hours/ns, 31.563 timesteps/s
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199.5% 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 | 3.1672 | 3.1672 | 3.1672 | 0.0 | 99.97
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Neigh | 0.00030208 | 0.00030208 | 0.00030208 | 0.0 | 0.01
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Comm | 0.00029612 | 0.00029612 | 0.00029612 | 0.0 | 0.01
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Output | 0.00019813 | 0.00019813 | 0.00019813 | 0.0 | 0.01
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Modify | 0.00014448 | 0.00014448 | 0.00014448 | 0.0 | 0.00
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Other | | 0.0001433 | | | 0.00
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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: 3710 ave 3710 max 3710 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 7420 ave 7420 max 7420 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 7420
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Ave neighs/atom = 57.9688
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Neighbor list builds = 1
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Dangerous builds = 0
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Total wall time: 0:00:03
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