Loading examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 0 → 100644 +107 −0 Original line number Diff line number Diff line LAMMPS (7 Aug 2019) # 3d Lennard-Jones melt # # This example requires that the example models provided with # the kim-api package are installed. see the ./lib/kim/README or # ./lib/kim/Install.py files for details on how to install these # example models. # 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 LennardJones_Ar 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 = 0.004321 secs kim_interactions Ar #=== BEGIN kim_interactions ================================== pair_style kim LennardJones_Ar WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) pair_coeff * * Ar #=== 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 = 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 kim, perpetual attributes: full, newton off, cut 8.45 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) = 28.12 | 28.12 | 28.12 Mbytes Step Temp E_pair E_mol TotEng Press 0 200 145069.63 0 164146.22 128015.94 100 95.179703 154939.42 0 164017.94 131602.75 Loop time of 3.48256 on 1 procs for 100 steps with 32000 atoms Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s 98.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0502 | 3.0502 | 3.0502 | 0.0 | 87.59 Neigh | 0.3646 | 0.3646 | 0.3646 | 0.0 | 10.47 Comm | 0.01783 | 0.01783 | 0.01783 | 0.0 | 0.51 Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00 Modify | 0.034349 | 0.034349 | 0.034349 | 0.0 | 0.99 Other | | 0.01547 | | | 0.44 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: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4253750 Ave neighs/atom = 132.93 Neighbor list builds = 3 Dangerous builds = 0 Total wall time: 0:00:03 examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 0 → 100644 +113 −0 Original line number Diff line number Diff line LAMMPS (7 Aug 2019) # 3d Lennard-Jones melt # # This example requires that the example models provided with # the kim-api package are installed. see the ./lib/kim/README or # ./lib/kim/Install.py files for details on how to install these # example models. # 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 LennardJones_Ar 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 = 0.000989 secs kim_interactions Ar #=== BEGIN kim_interactions ================================== pair_style kim LennardJones_Ar WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) pair_coeff * * Ar WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) #=== END kim_interactions ==================================== mass 1 39.95 velocity all create 200.0 232345 loop geom WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) 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 kim, perpetual attributes: full, newton off, cut 8.45 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) = 9.791 | 9.791 | 9.791 Mbytes Step Temp E_pair E_mol TotEng Press 0 200 145069.63 0 164146.22 128015.94 100 95.179703 154939.42 0 164017.94 131602.75 Loop time of 0.924494 on 4 procs for 100 steps with 32000 atoms Performance: 9.346 ns/day, 2.568 hours/ns, 108.167 timesteps/s 99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76434 | 0.76847 | 0.77207 | 0.3 | 83.12 Neigh | 0.09089 | 0.094446 | 0.099911 | 1.1 | 10.22 Comm | 0.038599 | 0.044759 | 0.051381 | 2.1 | 4.84 Output | 3.5e-05 | 4e-05 | 4.9e-05 | 0.0 | 0.00 Modify | 0.009396 | 0.009685 | 0.009941 | 0.2 | 1.05 Other | | 0.00709 | | | 0.77 Nlocal: 8000 ave 8018 max 7967 min Histogram: 1 0 0 0 0 0 1 0 0 2 Nghost: 9131 ave 9164 max 9113 min Histogram: 2 0 0 1 0 0 0 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min Histogram: 1 0 0 0 0 0 1 0 0 2 Total # of neighbors = 4253750 Ave neighs/atom = 132.93 Neighbor list builds = 3 Dangerous builds = 0 Total wall time: 0:00:00 examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 0 → 100644 +124 −0 Original line number Diff line number Diff line 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 ============================================ kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] #=== BEGIN kim-query ========================================= variable a0 string 4.146581932902336 #=== END kim-query =========================================== lattice fcc ${a0} lattice fcc 4.146581932902336 Lattice spacing in x,y,z = 4.14658 4.14658 4.14658 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 (82.9316 82.9316 82.9316) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.005415 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 = 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) = 10.36 | 10.36 | 10.36 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 74.6055 on 1 procs for 100 steps with 32000 atoms Performance: 0.116 ns/day, 207.238 hours/ns, 1.340 timesteps/s 98.6% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 74.446 | 74.446 | 74.446 | 0.0 | 99.79 Neigh | 0.096611 | 0.096611 | 0.096611 | 0.0 | 0.13 Comm | 0.014594 | 0.014594 | 0.014594 | 0.0 | 0.02 Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00 Modify | 0.03454 | 0.03454 | 0.03454 | 0.0 | 0.05 Other | | 0.01396 | | | 0.02 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9667 ave 9667 max 9667 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: 450192 ave 450192 max 450192 min Histogram: 1 0 0 0 0 0 0 0 0 0 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: 0:01:16 examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 0 → 100644 +124 −0 Original line number Diff line number Diff line 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 ============================================ kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] #=== BEGIN kim-query ========================================= variable a0 string 4.146581932902336 #=== END kim-query =========================================== lattice fcc ${a0} lattice fcc 4.146581932902336 Lattice spacing in x,y,z = 4.14658 4.14658 4.14658 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 (82.9316 82.9316 82.9316) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.000946 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 = 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 examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 0 → 100644 +118 −0 Original line number Diff line number Diff line 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 Loading
examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 0 → 100644 +107 −0 Original line number Diff line number Diff line LAMMPS (7 Aug 2019) # 3d Lennard-Jones melt # # This example requires that the example models provided with # the kim-api package are installed. see the ./lib/kim/README or # ./lib/kim/Install.py files for details on how to install these # example models. # 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 LennardJones_Ar 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 = 0.004321 secs kim_interactions Ar #=== BEGIN kim_interactions ================================== pair_style kim LennardJones_Ar WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) pair_coeff * * Ar #=== 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 = 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 kim, perpetual attributes: full, newton off, cut 8.45 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) = 28.12 | 28.12 | 28.12 Mbytes Step Temp E_pair E_mol TotEng Press 0 200 145069.63 0 164146.22 128015.94 100 95.179703 154939.42 0 164017.94 131602.75 Loop time of 3.48256 on 1 procs for 100 steps with 32000 atoms Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s 98.3% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0502 | 3.0502 | 3.0502 | 0.0 | 87.59 Neigh | 0.3646 | 0.3646 | 0.3646 | 0.0 | 10.47 Comm | 0.01783 | 0.01783 | 0.01783 | 0.0 | 0.51 Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00 Modify | 0.034349 | 0.034349 | 0.034349 | 0.0 | 0.99 Other | | 0.01547 | | | 0.44 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: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4253750 Ave neighs/atom = 132.93 Neighbor list builds = 3 Dangerous builds = 0 Total wall time: 0:00:03
examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 0 → 100644 +113 −0 Original line number Diff line number Diff line LAMMPS (7 Aug 2019) # 3d Lennard-Jones melt # # This example requires that the example models provided with # the kim-api package are installed. see the ./lib/kim/README or # ./lib/kim/Install.py files for details on how to install these # example models. # 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 LennardJones_Ar 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 = 0.000989 secs kim_interactions Ar #=== BEGIN kim_interactions ================================== pair_style kim LennardJones_Ar WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) pair_coeff * * Ar WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) #=== END kim_interactions ==================================== mass 1 39.95 velocity all create 200.0 232345 loop geom WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974) WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979) 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 kim, perpetual attributes: full, newton off, cut 8.45 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) = 9.791 | 9.791 | 9.791 Mbytes Step Temp E_pair E_mol TotEng Press 0 200 145069.63 0 164146.22 128015.94 100 95.179703 154939.42 0 164017.94 131602.75 Loop time of 0.924494 on 4 procs for 100 steps with 32000 atoms Performance: 9.346 ns/day, 2.568 hours/ns, 108.167 timesteps/s 99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76434 | 0.76847 | 0.77207 | 0.3 | 83.12 Neigh | 0.09089 | 0.094446 | 0.099911 | 1.1 | 10.22 Comm | 0.038599 | 0.044759 | 0.051381 | 2.1 | 4.84 Output | 3.5e-05 | 4e-05 | 4.9e-05 | 0.0 | 0.00 Modify | 0.009396 | 0.009685 | 0.009941 | 0.2 | 1.05 Other | | 0.00709 | | | 0.77 Nlocal: 8000 ave 8018 max 7967 min Histogram: 1 0 0 0 0 0 1 0 0 2 Nghost: 9131 ave 9164 max 9113 min Histogram: 2 0 0 1 0 0 0 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min Histogram: 1 0 0 0 0 0 1 0 0 2 Total # of neighbors = 4253750 Ave neighs/atom = 132.93 Neighbor list builds = 3 Dangerous builds = 0 Total wall time: 0:00:00
examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 0 → 100644 +124 −0 Original line number Diff line number Diff line 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 ============================================ kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] #=== BEGIN kim-query ========================================= variable a0 string 4.146581932902336 #=== END kim-query =========================================== lattice fcc ${a0} lattice fcc 4.146581932902336 Lattice spacing in x,y,z = 4.14658 4.14658 4.14658 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 (82.9316 82.9316 82.9316) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.005415 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 = 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) = 10.36 | 10.36 | 10.36 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 74.6055 on 1 procs for 100 steps with 32000 atoms Performance: 0.116 ns/day, 207.238 hours/ns, 1.340 timesteps/s 98.6% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 74.446 | 74.446 | 74.446 | 0.0 | 99.79 Neigh | 0.096611 | 0.096611 | 0.096611 | 0.0 | 0.13 Comm | 0.014594 | 0.014594 | 0.014594 | 0.0 | 0.02 Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00 Modify | 0.03454 | 0.03454 | 0.03454 | 0.0 | 0.05 Other | | 0.01396 | | | 0.02 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9667 ave 9667 max 9667 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: 450192 ave 450192 max 450192 min Histogram: 1 0 0 0 0 0 0 0 0 0 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: 0:01:16
examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 0 → 100644 +124 −0 Original line number Diff line number Diff line 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 ============================================ kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"] #=== BEGIN kim-query ========================================= variable a0 string 4.146581932902336 #=== END kim-query =========================================== lattice fcc ${a0} lattice fcc 4.146581932902336 Lattice spacing in x,y,z = 4.14658 4.14658 4.14658 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 (82.9316 82.9316 82.9316) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.000946 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 = 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
examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 0 → 100644 +118 −0 Original line number Diff line number Diff line 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
