105 lines
3.3 KiB
Groff
105 lines
3.3 KiB
Groff
LAMMPS (30 Apr 2019)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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#
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# This example requires that the example models provided with
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# the kim-api package are installed. see the ./lib/kim/README or
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# ./lib/kim/Install.py files for details on how to install these
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# example models.
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#
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable xx equal 20*1
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variable yy equal 20*$y
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variable yy equal 20*1
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variable zz equal 20*$z
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variable zz equal 20*1
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units metal
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atom_style atomic
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newton on
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kim_style init LennardJones_Ar
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lattice fcc 4.4300
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Lattice spacing in x,y,z = 4.43 4.43 4.43
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 20 0 ${yy} 0 ${zz}
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region box block 0 20 0 20 0 ${zz}
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region box block 0 20 0 20 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
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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 32000 atoms
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create_atoms CPU = 0.0979962 secs
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#pair_style lj/cut 8.1500
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#pair_coeff 1 1 0.0104 3.4000
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kim_style define Ar
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pair_style kim LennardJones_Ar
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WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:980)
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WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:985)
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pair_coeff * * Ar
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mass 1 39.95
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velocity all create 200.0 232345 loop geom
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 all nve
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#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
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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 = 8.45
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ghost atom cutoff = 8.45
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binsize = 4.225, bins = 21 21 21
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair kim, perpetual
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attributes: full, newton off, cut 8.45
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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) = 9.789 | 9.789 | 9.789 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 6290.8194 0 7118.0584 129712.25
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100 95.179725 6718.814 0 7112.496 133346.59
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Loop time of 6.29539 on 4 procs for 100 steps with 32000 atoms
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Performance: 1.372 ns/day, 17.487 hours/ns, 15.885 timesteps/s
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48.4% 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 | 1.9399 | 2.079 | 2.2181 | 9.1 | 33.02
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Neigh | 0.25924 | 0.26632 | 0.2692 | 0.8 | 4.23
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Comm | 2.5011 | 2.6605 | 2.751 | 5.9 | 42.26
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Output | 0.069904 | 0.07097 | 0.071545 | 0.3 | 1.13
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Modify | 0.011383 | 0.012206 | 0.01419 | 1.0 | 0.19
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Other | | 1.206 | | | 19.16
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Nlocal: 8000 ave 8018 max 7967 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 9131 ave 9164 max 9113 min
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Histogram: 2 0 0 1 0 0 0 0 0 1
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Neighs: 0 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: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Total # of neighbors = 4253750
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Ave neighs/atom = 132.93
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Neighbor list builds = 3
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Dangerous builds = 0
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Total wall time: 0:00:07
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