forked from lijiext/lammps
114 lines
4.1 KiB
Groff
114 lines
4.1 KiB
Groff
LAMMPS (7 Aug 2019)
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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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kim_init LennardJones_Ar real
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#=== BEGIN kim-init ==========================================
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units real
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#=== END kim-init ============================================
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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 = 0.000989 secs
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kim_interactions Ar
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#=== BEGIN kim_interactions ==================================
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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 (../pair_kim.cpp:974)
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WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
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pair_coeff * * Ar
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WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
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WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
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#=== END kim_interactions ====================================
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mass 1 39.95
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velocity all create 200.0 232345 loop geom
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WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
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WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
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WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
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WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
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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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Setting up Verlet run ...
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Unit style : real
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Current step : 0
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Time step : 1
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Per MPI rank memory allocation (min/avg/max) = 9.791 | 9.791 | 9.791 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 145069.63 0 164146.22 128015.94
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100 95.179703 154939.42 0 164017.94 131602.75
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Loop time of 0.924494 on 4 procs for 100 steps with 32000 atoms
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Performance: 9.346 ns/day, 2.568 hours/ns, 108.167 timesteps/s
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99.6% 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 | 0.76434 | 0.76847 | 0.77207 | 0.3 | 83.12
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Neigh | 0.09089 | 0.094446 | 0.099911 | 1.1 | 10.22
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Comm | 0.038599 | 0.044759 | 0.051381 | 2.1 | 4.84
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Output | 3.5e-05 | 4e-05 | 4.9e-05 | 0.0 | 0.00
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Modify | 0.009396 | 0.009685 | 0.009941 | 0.2 | 1.05
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Other | | 0.00709 | | | 0.77
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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: 0:00:00
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