forked from lijiext/lammps
Added logs for examples/kim
This commit is contained in:
Ryan S. Elliott
parent
d08d6b5fb0
commit
8619462b3b
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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 1 by 1 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 = 0.004321 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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#=== 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 = 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) = 28.12 | 28.12 | 28.12 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 3.48256 on 1 procs for 100 steps with 32000 atoms
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Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s
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98.3% CPU use with 1 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 | 3.0502 | 3.0502 | 3.0502 | 0.0 | 87.59
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Neigh | 0.3646 | 0.3646 | 0.3646 | 0.0 | 10.47
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Comm | 0.01783 | 0.01783 | 0.01783 | 0.0 | 0.51
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Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00
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Modify | 0.034349 | 0.034349 | 0.034349 | 0.0 | 0.99
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Other | | 0.01547 | | | 0.44
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 19911 ave 19911 max 19911 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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: 0:00:03
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@ -0,0 +1,113 @@
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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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@ -0,0 +1,124 @@
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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 1 by 1 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 = 0.005415 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) = 10.36 | 10.36 | 10.36 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 74.6055 on 1 procs for 100 steps with 32000 atoms
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Performance: 0.116 ns/day, 207.238 hours/ns, 1.340 timesteps/s
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98.6% CPU use with 1 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 | 74.446 | 74.446 | 74.446 | 0.0 | 99.79
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Neigh | 0.096611 | 0.096611 | 0.096611 | 0.0 | 0.13
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Comm | 0.014594 | 0.014594 | 0.014594 | 0.0 | 0.02
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Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00
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Modify | 0.03454 | 0.03454 | 0.03454 | 0.0 | 0.05
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Other | | 0.01396 | | | 0.02
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 9667 ave 9667 max 9667 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 450192 ave 450192 max 450192 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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: 0:01:16
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@ -0,0 +1,124 @@
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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
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 41 41 41
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -126084.25 0 -107007.66 1528.8768
|
||||
100 94.450495 -116016.03 0 -107007.07 2282.2685
|
||||
Loop time of 19.0792 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.453 ns/day, 52.998 hours/ns, 5.241 timesteps/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.78 | 18.855 | 18.937 | 1.5 | 98.83
|
||||
Neigh | 0.026047 | 0.026274 | 0.0266 | 0.1 | 0.14
|
||||
Comm | 0.09039 | 0.17196 | 0.24675 | 15.9 | 0.90
|
||||
Output | 3.9e-05 | 4.975e-05 | 6.1e-05 | 0.0 | 0.00
|
||||
Modify | 0.015667 | 0.015819 | 0.016008 | 0.1 | 0.08
|
||||
Other | | 0.01008 | | | 0.05
|
||||
|
||||
Nlocal: 8000 ave 8029 max 7968 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 4259 ave 4303 max 4202 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 112548 ave 113091 max 111995 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 450192
|
||||
Ave neighs/atom = 14.0685
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:20
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.003591 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 44 44 44
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -85249.847 0 -66173.259 -33302.387
|
||||
100 253.43357 -90346.68 0 -66173.441 -14888.698
|
||||
Loop time of 74.248 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.116 ns/day, 206.244 hours/ns, 1.347 timesteps/s
|
||||
98.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 74.118 | 74.118 | 74.118 | 0.0 | 99.83
|
||||
Neigh | 0.069623 | 0.069623 | 0.069623 | 0.0 | 0.09
|
||||
Comm | 0.0137 | 0.0137 | 0.0137 | 0.0 | 0.02
|
||||
Output | 7.6e-05 | 7.6e-05 | 7.6e-05 | 0.0 | 0.00
|
||||
Modify | 0.031883 | 0.031883 | 0.031883 | 0.0 | 0.04
|
||||
Other | | 0.01433 | | | 0.02
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7760 ave 7760 max 7760 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 402352 ave 402352 max 402352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 402352
|
||||
Ave neighs/atom = 12.5735
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:14
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Portable Model (PM)
|
||||
# SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
units real
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.000997 secs
|
||||
|
||||
kim_interactions Si
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
||||
pair_coeff * * Si
|
||||
#=== END kim_interactions ====================================
|
||||
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.07118
|
||||
ghost atom cutoff = 4.07118
|
||||
binsize = 2.03559, bins = 44 44 44
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 4.07118
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.517 | 3.517 | 3.517 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -85249.847 0 -66173.259 -33302.387
|
||||
100 253.43357 -90346.68 0 -66173.441 -14888.698
|
||||
Loop time of 19.0287 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 0.454 ns/day, 52.857 hours/ns, 5.255 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.81 | 18.838 | 18.883 | 0.6 | 99.00
|
||||
Neigh | 0.018598 | 0.01914 | 0.020732 | 0.7 | 0.10
|
||||
Comm | 0.10341 | 0.1475 | 0.17393 | 7.1 | 0.78
|
||||
Output | 6e-05 | 6.225e-05 | 6.7e-05 | 0.0 | 0.00
|
||||
Modify | 0.014839 | 0.014925 | 0.015047 | 0.1 | 0.08
|
||||
Other | | 0.008997 | | | 0.05
|
||||
|
||||
Nlocal: 8000 ave 8014 max 7988 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 3374.75 ave 3389 max 3361 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 100588 ave 100856 max 100392 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 402352
|
||||
Ave neighs/atom = 12.5735
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:19
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Simulator Model (PM)
|
||||
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# See https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# For Simulator : LAMMPS 28 Feb 2019
|
||||
# Running on : LAMMPS 7 Aug 2019
|
||||
#
|
||||
units real
|
||||
atom_style charge
|
||||
neigh_modify one 4000
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.003447 secs
|
||||
|
||||
kim_interactions O
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
|
||||
ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
|
||||
Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
|
||||
--------------------------------------------------------------------------
|
||||
Primary job terminated normally, but 1 process returned
|
||||
a non-zero exit code. Per user-direction, the job has been aborted.
|
||||
--------------------------------------------------------------------------
|
||||
--------------------------------------------------------------------------
|
||||
mpirun detected that one or more processes exited with non-zero status, thus causing
|
||||
the job to be terminated. The first process to do so was:
|
||||
|
||||
Process name: [[33054,1],0]
|
||||
Exit code: 1
|
||||
--------------------------------------------------------------------------
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the KIM Simulator Model (PM)
|
||||
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# is installed. This can be done with the command
|
||||
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# If this command does not work, you may need to setup your PATH to find the utility.
|
||||
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS build directory)
|
||||
# source ./kim_build-prefix/bin/kim-api-activate
|
||||
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
||||
# (where the current working directory is assumed to be the LAMMPS src directory)
|
||||
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
||||
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
||||
#
|
||||
# See https://openkim.org/doc/obtaining-models for alternative options.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
|
||||
#=== BEGIN kim-init ==========================================
|
||||
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
|
||||
# For Simulator : LAMMPS 28 Feb 2019
|
||||
# Running on : LAMMPS 7 Aug 2019
|
||||
#
|
||||
units real
|
||||
atom_style charge
|
||||
neigh_modify one 4000
|
||||
#=== END kim-init ============================================
|
||||
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.001307 secs
|
||||
|
||||
kim_interactions O
|
||||
#=== BEGIN kim_interactions ==================================
|
||||
pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100
|
||||
ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
|
||||
Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100
|
||||
|
|
@ -0,0 +1,92 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units real
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.003037 secs
|
||||
|
||||
pair_style lj/cut 8.1500
|
||||
pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
#pair_style kim LennardJones_Ar
|
||||
#pair_coeff * * Ar
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 25367.408 6750.7421
|
||||
100 98.747096 15900.676 0 25319.465 10184.453
|
||||
Loop time of 2.43768 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 3.544 ns/day, 6.771 hours/ns, 41.023 timesteps/s
|
||||
97.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1895 | 2.1895 | 2.1895 | 0.0 | 89.82
|
||||
Neigh | 0.17546 | 0.17546 | 0.17546 | 0.0 | 7.20
|
||||
Comm | 0.021001 | 0.021001 | 0.021001 | 0.0 | 0.86
|
||||
Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00
|
||||
Modify | 0.034253 | 0.034253 | 0.034253 | 0.0 | 1.41
|
||||
Other | | 0.01735 | | | 0.71
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.96027e+06 ave 1.96027e+06 max 1.96027e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1960266
|
||||
Ave neighs/atom = 61.2583
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,92 @@
|
|||
LAMMPS (7 Aug 2019)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*1
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*1
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*1
|
||||
|
||||
units real
|
||||
|
||||
lattice fcc 4.4300
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 ${yy} 0 ${zz}
|
||||
region box block 0 20 0 20 0 ${zz}
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.001194 secs
|
||||
|
||||
pair_style lj/cut 8.1500
|
||||
pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
#pair_style kim LennardJones_Ar
|
||||
#pair_coeff * * Ar
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.633 | 7.633 | 7.633 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 25367.408 6750.7421
|
||||
100 98.747096 15900.676 0 25319.465 10184.453
|
||||
Loop time of 0.726239 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 11.897 ns/day, 2.017 hours/ns, 137.696 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.57617 | 0.5835 | 0.59084 | 0.9 | 80.34
|
||||
Neigh | 0.046682 | 0.047783 | 0.048641 | 0.3 | 6.58
|
||||
Comm | 0.065469 | 0.071509 | 0.07899 | 2.3 | 9.85
|
||||
Output | 3.9e-05 | 4.6e-05 | 6.1e-05 | 0.0 | 0.01
|
||||
Modify | 0.013205 | 0.01363 | 0.014044 | 0.3 | 1.88
|
||||
Other | | 0.009775 | | | 1.35
|
||||
|
||||
Nlocal: 8000 ave 8012 max 7989 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 9131 ave 9142 max 9119 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 490066 ave 491443 max 489273 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1960266
|
||||
Ave neighs/atom = 61.2583
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
Loading…
Reference in New Issue