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 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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create_atoms CPU = 0.000317097 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) = 4.167 | 4.167 | 4.167 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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10 296.24946 -8.5976065 0 -8.5596124 -35140.29
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20 282.27904 -8.5958147 0 -8.5596123 -34710.3
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30 259.54978 -8.5928995 0 -8.5596121 -34060.43
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40 230.41412 -8.5891626 0 -8.5596119 -33258.275
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50 197.85135 -8.5849861 0 -8.5596116 -32389.527
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60 165.21732 -8.5808005 0 -8.5596113 -31550.426
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70 135.94024 -8.5770455 0 -8.5596111 -30839.006
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80 113.06617 -8.5741117 0 -8.5596109 -30339.177
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90 98.542347 -8.572249 0 -8.5596109 -30094.29
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100 92.524343 -8.5714774 0 -8.5596111 -30091.988
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Loop time of 0.813674 on 4 procs for 100 steps with 128 atoms
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Performance: 5.309 ns/day, 4.520 hours/ns, 122.899 timesteps/s
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99.7% 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 | 0.79079 | 0.79788 | 0.80888 | 0.8 | 98.06
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Neigh | 7.1049e-05 | 8.0049e-05 | 9.2983e-05 | 0.0 | 0.01
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Comm | 0.0041246 | 0.01515 | 0.022235 | 5.5 | 1.86
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Output | 0.000144 | 0.00017095 | 0.00024796 | 0.0 | 0.02
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Modify | 4.4823e-05 | 5.8889e-05 | 7.2718e-05 | 0.0 | 0.01
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Other | | 0.000338 | | | 0.04
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Nlocal: 32 ave 37 max 28 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Nghost: 431 ave 435 max 426 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Neighs: 927 ave 1071 max 821 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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FullNghs: 1854 ave 2144 max 1624 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Total # of neighbors = 7416
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Ave neighs/atom = 57.9375
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Neighbor list builds = 1
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Dangerous builds = 0
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Total wall time: 0:00:00
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