125 lines
4.4 KiB
Groff
125 lines
4.4 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 KIM Portable Model (PM)
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# SW_StillingerWeber_1985_Si__MO_405512056662_005
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# is installed. This can be done with the command
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# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
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# If this command does not work, you may need to setup your PATH to find the utility.
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# If you installed the kim-api using the LAMMPS CMake build, you can do the following
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# (where the current working directory is assumed to be the LAMMPS build directory)
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# source ./kim_build-prefix/bin/kim-api-activate
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# If you installed the kim-api using the LAMMPS Make build, you can do the following
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# (where the current working directory is assumed to be the LAMMPS src directory)
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# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
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# (where you should relplace X.Y.Z with the appropriate kim-api version number).
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#
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# Or, see https://openkim.org/doc/obtaining-models for alternative options.
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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 SW_StillingerWeber_1985_Si__MO_405512056662_005 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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kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
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#=== BEGIN kim-query =========================================
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variable a0 string 4.146581932902336
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#=== END kim-query ===========================================
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lattice fcc ${a0}
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lattice fcc 4.146581932902336
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Lattice spacing in x,y,z = 4.14658 4.14658 4.14658
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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 (82.9316 82.9316 82.9316)
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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 = 0.000946 secs
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kim_interactions Si
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#=== BEGIN kim_interactions ==================================
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pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
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pair_coeff * * Si
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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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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 = 4.07118
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ghost atom cutoff = 4.07118
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binsize = 2.03559, bins = 41 41 41
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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 4.07118
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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) = 3.489 | 3.489 | 3.489 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 200 -126084.25 0 -107007.66 1528.8768
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100 94.450495 -116016.03 0 -107007.07 2282.2685
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Loop time of 19.0792 on 4 procs for 100 steps with 32000 atoms
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Performance: 0.453 ns/day, 52.998 hours/ns, 5.241 timesteps/s
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99.4% 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 | 18.78 | 18.855 | 18.937 | 1.5 | 98.83
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Neigh | 0.026047 | 0.026274 | 0.0266 | 0.1 | 0.14
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Comm | 0.09039 | 0.17196 | 0.24675 | 15.9 | 0.90
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Output | 3.9e-05 | 4.975e-05 | 6.1e-05 | 0.0 | 0.00
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Modify | 0.015667 | 0.015819 | 0.016008 | 0.1 | 0.08
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Other | | 0.01008 | | | 0.05
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Nlocal: 8000 ave 8029 max 7968 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 4259 ave 4303 max 4202 min
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Histogram: 1 0 0 0 0 0 2 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: 112548 ave 113091 max 111995 min
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Histogram: 1 0 0 1 0 0 0 1 0 1
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Total # of neighbors = 450192
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Ave neighs/atom = 14.0685
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Neighbor list builds = 3
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:20
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