128 lines
4.3 KiB
Groff
128 lines
4.3 KiB
Groff
LAMMPS (10 Feb 2021)
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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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neighbor 2.0 bin # Angstroms
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timestep 1.0 # femtoseconds
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This model has No mutable parameters.
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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 = 4.4300000 4.4300000 4.4300000
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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 = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
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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 = 0.001 seconds
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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 (src/KIM/pair_kim.cpp:1153)
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WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1159)
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pair_coeff * * Ar
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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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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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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
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@Article{tadmor:elliott:2011,
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author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
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title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
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journal = {{JOM}},
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year = 2011,
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volume = 63,
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number = 17,
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pages = {17},
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doi = {10.1007/s11837-011-0102-6}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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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 8.450000000000001
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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) = 9.791 | 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 0.843382 on 4 procs for 100 steps with 32000 atoms
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Performance: 10.244 ns/day, 2.343 hours/ns, 118.570 timesteps/s
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99.8% 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 | 0.71505 | 0.71942 | 0.72345 | 0.4 | 85.30
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Neigh | 0.089886 | 0.090153 | 0.090611 | 0.1 | 10.69
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Comm | 0.016342 | 0.020141 | 0.024546 | 2.5 | 2.39
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Output | 2.4e-05 | 2.625e-05 | 3.2e-05 | 0.0 | 0.00
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Modify | 0.008197 | 0.0083267 | 0.008504 | 0.1 | 0.99
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Other | | 0.005318 | | | 0.63
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Nlocal: 8000.00 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: 9131.00 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: 0.00000 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: 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 = 132.92969
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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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