134 lines
4.6 KiB
Groff
134 lines
4.6 KiB
Groff
LAMMPS (27 May 2021)
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# Demonstrate MLIAP interface to SNAP nn Cu 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 3.621262
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units metal
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# generate the box and atom positions using a FCC 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 fcc $a
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lattice fcc 3.621262
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Lattice spacing in x,y,z = 3.6212620 3.6212620 3.6212620
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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 = (0.0000000 0.0000000 0.0000000) to (14.485048 14.485048 14.485048)
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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 256 atoms
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create_atoms CPU = 0.000 seconds
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mass 1 63.546
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# choose potential
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pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor
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Reading potential file Cu.nn.mliap.model with DATE: 2021-03-03
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Reading potential file Cu.snap.mliap.descriptor with DATE: 2021-03-03
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SNAP keyword rcutfac 5.0
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SNAP keyword twojmax 6
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SNAP keyword nelems 1
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SNAP keyword elems Cu
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SNAP keyword radelems 0.5
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SNAP keyword welems 1.0
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0
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SNAP keyword bzeroflag 0
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SNAP keyword switchflag 1
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pair_coeff * * Cu
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# Setup output
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compute eatom all pe/atom
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compute energy all reduce sum c_eatom
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compute satom all stress/atom NULL
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compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
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variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
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thermo_style custom step temp epair c_energy etotal press v_press
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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 = 6
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ghost atom cutoff = 6
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binsize = 3, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair mliap, 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) = 30.85 | 30.85 | 30.85 Mbytes
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Step Temp E_pair c_energy TotEng Press v_press
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0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505
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10 294.11049 -4.0927998 -4.0927998 -4.0549315 -2654.7826 2654.7826
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20 276.89115 -4.0905826 -4.0905826 -4.0549314 -1879.2872 1879.2872
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30 249.71134 -4.0870829 -4.0870829 -4.0549312 -627.47006 627.47006
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40 214.92415 -4.0826036 -4.0826036 -4.054931 995.44801 -995.44801
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50 175.86879 -4.0775747 -4.0775747 -4.0549307 2811.6019 -2811.6019
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60 136.62706 -4.0725218 -4.0725218 -4.0549303 4640.4144 -4640.4144
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70 101.48566 -4.0679968 -4.0679968 -4.05493 6313.5871 -6313.5871
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80 74.248664 -4.0644897 -4.0644897 -4.0549298 7644.1364 -7644.1364
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90 57.500423 -4.0623332 -4.0623332 -4.0549297 8514.2222 -8514.2222
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100 52.104609 -4.0616385 -4.0616385 -4.0549298 8870.8923 -8870.8923
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Loop time of 1.25021 on 4 procs for 100 steps with 256 atoms
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Performance: 3.455 ns/day, 6.946 hours/ns, 79.987 timesteps/s
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100.0% 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 | 1.2256 | 1.2347 | 1.2415 | 0.5 | 98.76
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0074687 | 0.014311 | 0.023481 | 4.8 | 1.14
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Output | 0.00060678 | 0.00062859 | 0.00066781 | 0.0 | 0.05
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Modify | 8.7976e-05 | 9.7811e-05 | 0.00010943 | 0.0 | 0.01
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Other | | 0.0004484 | | | 0.04
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Nlocal: 64.0000 ave 64 max 64 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 843.000 ave 843 max 843 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 4992.00 ave 4992 max 4992 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 19968
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Ave neighs/atom = 78.000000
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:01
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