diff --git a/examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 new file mode 100644 index 0000000000..17fa1bc534 --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.1 @@ -0,0 +1,107 @@ +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 diff --git a/examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 new file mode 100644 index 0000000000..8e076815fc --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-ex.melt.clang.4 @@ -0,0 +1,113 @@ +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 diff --git a/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 new file mode 100644 index 0000000000..1ca44c98ef --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1 @@ -0,0 +1,124 @@ +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 diff --git a/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 new file mode 100644 index 0000000000..8c4148ce15 --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4 @@ -0,0 +1,124 @@ +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 diff --git a/examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 new file mode 100644 index 0000000000..f5845d7fc4 --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.1 @@ -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 diff --git a/examples/kim/log.7Aug19.in.kim-pm.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.4 new file mode 100644 index 0000000000..0b4632b999 --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-pm.melt.clang.4 @@ -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 diff --git a/examples/kim/log.7Aug19.in.kim-sm.melt.clang.1 b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.1 new file mode 100644 index 0000000000..1b77e58a3a --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.1 @@ -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 +-------------------------------------------------------------------------- diff --git a/examples/kim/log.7Aug19.in.kim-sm.melt.clang.4 b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.4 new file mode 100644 index 0000000000..72b62beffb --- /dev/null +++ b/examples/kim/log.7Aug19.in.kim-sm.melt.clang.4 @@ -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 ${zz} +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + create_atoms CPU = 0.001307 secs + +kim_interactions O +#=== BEGIN kim_interactions ================================== +pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100 +ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262) +Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100 diff --git a/examples/kim/log.7Aug19.in.lammps.melt.clang.1 b/examples/kim/log.7Aug19.in.lammps.melt.clang.1 new file mode 100644 index 0000000000..f697504777 --- /dev/null +++ b/examples/kim/log.7Aug19.in.lammps.melt.clang.1 @@ -0,0 +1,92 @@ +LAMMPS (7 Aug 2019) +# 3d Lennard-Jones melt + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$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 diff --git a/examples/kim/log.7Aug19.in.lammps.melt.clang.4 b/examples/kim/log.7Aug19.in.lammps.melt.clang.4 new file mode 100644 index 0000000000..2d25348b06 --- /dev/null +++ b/examples/kim/log.7Aug19.in.lammps.melt.clang.4 @@ -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