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Merge branch 'master' of github.com:lammps/lammps into pair-style-nnp

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This commit is contained in:
Andreas Singraber
2021-02-24 23:37:21 +01:00
parent 037441b502 e916c5d852
commit 992d0e13aa
79 changed files with 5000 additions and 2694 deletions
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2
examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
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@ -22,7 +22,7 @@ improper_style class2
read_data tiny_nylon.data
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2
variable prob1 equal step/v_runsteps*2+0.1
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian

42
examples/kim/in.kim-ex.melt
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@ -1,35 +1,35 @@
# 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
# 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 x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init LennardJones_Ar real
kim init LennardJones_Ar real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Ar
kim interactions Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
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
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

58
examples/kim/in.kim-pm-property
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@ -1,34 +1,34 @@
# kim-property example
# kim property example
#
# For detailed information of this example please refer to:
# https://openkim.org/doc/evaluation/tutorial-lammps/
# `https://openkim.org/doc/evaluation/tutorial-lammps/`
#
# Description:
#
# This example is designed to calculate the cohesive energy corresponding to
# the equilibrium FCC lattice constant for
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# https://openkim.org/doc/schema/properties-framework/ and
# https://lammps.sandia.gov/doc/kim_commands.html for further details).
# Then the created property instance is written to a file named results.edn
# using the `kim_property dump` commands.
# This example is designed to calculate the cohesive energy corresponding to
# the equilibrium FCC lattice constant for
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
# is installed. This can be done with the command
# `kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
# is installed. This can be done with the command
# kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
# 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)
@ -38,14 +38,14 @@
# 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.
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
# Initialize interatomic potential (KIM model) and units
atom_style atomic
# Set the OpenKIM model that will be used
kim_init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
kim init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
# the equilibrium lattice constant for the fcc structure
variable lattice_constant equal 5.248509056866169
@ -55,14 +55,14 @@ boundary p p p
# Create an FCC lattice with the lattice spacing
# using a single conventional (orthogonal) unit cell
lattice fcc ${lattice_constant}
region box block 0 1 0 1 0 1 units lattice
create_box 1 box
lattice fcc ${lattice_constant}
region box block 0 1 0 1 0 1 units lattice
create_box 1 box
create_atoms 1 box
mass 1 39.948
mass 1 39.948
# Specify the KIM interactions
kim_interactions Ar
kim interactions Ar
# Compute energy
run 0
@ -72,10 +72,10 @@ variable natoms equal "count(all)"
variable ecohesive equal "-pe/v_natoms"
# Create a property instance
kim_property create 1 cohesive-potential-energy-cubic-crystal
kim property create 1 cohesive-potential-energy-cubic-crystal
# Set all the key-value pairs for this property instance
kim_property modify 1 key short-name source-value 1 fcc &
kim property modify 1 key short-name source-value 1 fcc &
key species source-value 1 Ar &
key a source-value ${lattice_constant} &
source-unit angstrom &
@ -88,4 +88,4 @@ kim_property modify 1 key short-name source-value 1 fcc
source-unit eV
# Dump the results in a file
kim_property dump "results.edn"
kim property dump "results.edn"

44
examples/kim/in.kim-pm-query.melt
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@ -1,7 +1,7 @@
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# `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.
@ -13,34 +13,34 @@
# 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.
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
kim query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
lattice fcc ${a0}
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc ${a0}
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Si
kim interactions Si
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
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
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

42
examples/kim/in.kim-pm.melt
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@ -1,7 +1,7 @@
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# `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.
@ -13,33 +13,33 @@
# 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.
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Si
kim interactions Si
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
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
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

76
examples/kim/in.kim-query Normal file
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@ -0,0 +1,76 @@
# kim query example
#
# Requirement:
#
# This example requires LAMMPS is built with KIM package. A requirement for
# the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further
# details
#
# This example requires that the KIM Models
# `EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`
# and
# `EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000`
# are installed.
#
# This can be done with the commands
# `kim-api-collections-management install user `EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`
# `kim-api-collections-management install user `EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000`
#
# If these commands do 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.
#
# -----------------------------------------------
# Get an equilibrium fcc crystal lattice constant
# -----------------------------------------------
kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom]
print "FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = ${latconst_1}"
# Get the lattice contant from a different model
kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
print "FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = ${latconst_2}"
clear
# -----------------------------------------------
# Get an equilibrium fcc crystal lattice constant
# -----------------------------------------------
kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]
kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
print "FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = ${latconst_1}"
print "FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = ${latconst_2}"
clear
# -----------------------------------------------
# Get an equilibrium hcp crystal lattice constant
# -----------------------------------------------
kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal
kim query latconst split get_lattice_constant_hexagonal crystal=["hcp"] species=["Zr"] units=["angstrom"]
print "HCP lattice constants = ${latconst_1}, ${latconst_2}"
clear
# -----------------------------------------------
# Query for KIM models from openkim.org
# Get all the EAM models that support Al
# -----------------------------------------------
kim query model index get_available_models species=[Al] potential_type=[eam]
label model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
print "FCC lattice constant (${model}) = ${latconst}"
next model
jump SELF model_loop
clear

44
examples/kim/in.kim-sm.melt
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@ -1,8 +1,8 @@
# 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
# `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
@ -13,33 +13,33 @@
# 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.
# See `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions O
kim interactions O
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
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
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

44
examples/kim/in.lammps.melt
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@ -1,33 +1,33 @@
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units real
units real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
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
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

107
examples/kim/log.10Feb21.in.kim-ex.melt.clang.1 Normal file
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@ -0,0 +1,107 @@
LAMMPS (10 Feb 2021)
# 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
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has No mutable parameters.
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
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 = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.003 seconds
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1139)
WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1145)
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 8.450000000000001
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
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 2.8463 on 1 procs for 100 steps with 32000 atoms
Performance: 3.036 ns/day, 7.906 hours/ns, 35.133 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5046 | 2.5046 | 2.5046 | 0.0 | 88.00
Neigh | 0.29437 | 0.29437 | 0.29437 | 0.0 | 10.34
Comm | 0.01182 | 0.01182 | 0.01182 | 0.0 | 0.42
Output | 7e-05 | 7e-05 | 7e-05 | 0.0 | 0.00
Modify | 0.024522 | 0.024522 | 0.024522 | 0.0 | 0.86
Other | | 0.01091 | | | 0.38
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911.0 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 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 = 132.92969
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:02

107
examples/kim/log.10Feb21.in.kim-ex.melt.clang.4 Normal file
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@ -0,0 +1,107 @@
LAMMPS (10 Feb 2021)
# 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
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has No mutable parameters.
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
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 = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1139)
WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1145)
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 8.450000000000001
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
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 0.857614 on 4 procs for 100 steps with 32000 atoms
Performance: 10.074 ns/day, 2.382 hours/ns, 116.603 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 | 0.73048 | 0.73398 | 0.73855 | 0.3 | 85.58
Neigh | 0.083739 | 0.083964 | 0.084335 | 0.1 | 9.79
Comm | 0.017996 | 0.022912 | 0.026515 | 2.1 | 2.67
Output | 2.7e-05 | 3.5e-05 | 4.5e-05 | 0.0 | 0.00
Modify | 0.010073 | 0.010158 | 0.010271 | 0.1 | 1.18
Other | | 0.006571 | | | 0.77
Nlocal: 8000.00 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131.00 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0.00000 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 = 132.92969
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (10 Feb 2021)
# kim property example
#
# For detailed information of this example please refer to:
# `https://openkim.org/doc/evaluation/tutorial-lammps/`
#
# Description:
#
# This example is designed to calculate the cohesive energy corresponding to
# the equilibrium FCC lattice constant for
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
# is installed. This can be done with the command
# kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
# 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.
#
# Initialize interatomic potential (KIM model) and units
atom_style atomic
# Set the OpenKIM model that will be used
kim init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
#=== BEGIN kim init ==========================================
units metal
neighbor 2.0 bin # Angstroms
timestep 1.0e-3 # picoseconds
This model has 3 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | cutoff | "Double" | 1
2 | epsilon | "Double" | 1
3 | sigma | "Double" | 1
#=== END kim init ============================================
# the equilibrium lattice constant for the fcc structure
variable lattice_constant equal 5.248509056866169
# Periodic boundary conditions along all three dimensions
boundary p p p
# Create an FCC lattice with the lattice spacing
# using a single conventional (orthogonal) unit cell
lattice fcc ${lattice_constant}
lattice fcc 5.24850905686617
Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091
region box block 0 1 0 1 0 1 units lattice
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.2485091 5.2485091 5.2485091)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4 atoms
create_atoms CPU = 0.000 seconds
mass 1 39.948
# Specify the KIM interactions
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
pair_coeff * * Ar
#=== END kim interactions ====================================
# Compute energy
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_126566794224_004a} is archived in OpenKIM~\cite{MO_126566794224_004, MD_498634107543_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_126566794224_004.bib}
\end{document}
}
@Misc{MO_126566794224_004,
author = {Ellad Tadmor},
title = {{L}ennard-{J}ones model (shifted) for {A}r with parameters from {B}ernardes (1958) (medium precision cutoff) v004},
doi = {10.25950/9f98b989},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
keywords = {OpenKIM, Model, MO_126566794224_004},
publisher = {OpenKIM},
year = 2020,
}
@Misc{MD_498634107543_004,
author = {Ellad Tadmor},
title = {{D}river for the {L}ennard-{J}ones model uniformly shifted to have zero energy at the cutoff radius v004},
doi = {10.25950/bdffd6a6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
keywords = {OpenKIM, Model Driver, MD_498634107543_004},
publisher = {OpenKIM},
year = 2020,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_126566794224_004a,
author = {Newton Bernardes},
doi = {10.1103/PhysRev.112.1534},
issue = {5},
journal = {Physical Review},
pages = {1534--1539},
publisher = {American Physical Society},
title = {Theory of Solid {N}e, {A}, {K}r, and {X}e at 0{K}},
volume = {112},
year = {1958},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.5
ghost atom cutoff = 15.5
binsize = 7.75, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 15.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.119 | 3.119 | 3.119 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -0.34602203 0 -0.34602203 0.00061471244
Loop time of 0 on 1 procs for 0 steps with 4 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0 | | | 0.00
Nlocal: 4.00000 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1094.00 ave 1094 max 1094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1712.00 ave 1712 max 1712 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1712
Ave neighs/atom = 428.00000
Neighbor list builds = 0
Dangerous builds = 0
# Get cohesive energy
variable natoms equal "count(all)"
variable ecohesive equal "-pe/v_natoms"
# Create a property instance
kim property create 1 cohesive-potential-energy-cubic-crystal
#=== kim property ===========================================
# Set all the key-value pairs for this property instance
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value ${lattice_constant} source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value 0.0865055084950546 source-unit eV
#=== kim property ===========================================
# Dump the results in a file
kim property dump "results.edn"
#=== kim property ===========================================
Total wall time: 0:00:00

223
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LAMMPS (10 Feb 2021)
# kim property example
#
# For detailed information of this example please refer to:
# `https://openkim.org/doc/evaluation/tutorial-lammps/`
#
# Description:
#
# This example is designed to calculate the cohesive energy corresponding to
# the equilibrium FCC lattice constant for
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
# is installed. This can be done with the command
# kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
# 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.
#
# Initialize interatomic potential (KIM model) and units
atom_style atomic
# Set the OpenKIM model that will be used
kim init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
#=== BEGIN kim init ==========================================
units metal
neighbor 2.0 bin # Angstroms
timestep 1.0e-3 # picoseconds
This model has 3 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | cutoff | "Double" | 1
2 | epsilon | "Double" | 1
3 | sigma | "Double" | 1
#=== END kim init ============================================
# the equilibrium lattice constant for the fcc structure
variable lattice_constant equal 5.248509056866169
# Periodic boundary conditions along all three dimensions
boundary p p p
# Create an FCC lattice with the lattice spacing
# using a single conventional (orthogonal) unit cell
lattice fcc ${lattice_constant}
lattice fcc 5.24850905686617
Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091
region box block 0 1 0 1 0 1 units lattice
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.2485091 5.2485091 5.2485091)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4 atoms
create_atoms CPU = 0.000 seconds
mass 1 39.948
# Specify the KIM interactions
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
pair_coeff * * Ar
#=== END kim interactions ====================================
# Compute energy
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_126566794224_004a} is archived in OpenKIM~\cite{MO_126566794224_004, MD_498634107543_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_126566794224_004.bib}
\end{document}
}
@Misc{MO_126566794224_004,
author = {Ellad Tadmor},
title = {{L}ennard-{J}ones model (shifted) for {A}r with parameters from {B}ernardes (1958) (medium precision cutoff) v004},
doi = {10.25950/9f98b989},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
keywords = {OpenKIM, Model, MO_126566794224_004},
publisher = {OpenKIM},
year = 2020,
}
@Misc{MD_498634107543_004,
author = {Ellad Tadmor},
title = {{D}river for the {L}ennard-{J}ones model uniformly shifted to have zero energy at the cutoff radius v004},
doi = {10.25950/bdffd6a6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
keywords = {OpenKIM, Model Driver, MD_498634107543_004},
publisher = {OpenKIM},
year = 2020,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_126566794224_004a,
author = {Newton Bernardes},
doi = {10.1103/PhysRev.112.1534},
issue = {5},
journal = {Physical Review},
pages = {1534--1539},
publisher = {American Physical Society},
title = {Theory of Solid {N}e, {A}, {K}r, and {X}e at 0{K}},
volume = {112},
year = {1958},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.5
ghost atom cutoff = 15.5
binsize = 7.75, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 15.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.165 | 3.165 | 3.165 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -0.34602203 0 -0.34602203 0.00061471244
Loop time of 1.5e-06 on 4 procs for 0 steps with 4 atoms
100.0% 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 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.5e-06 | | |100.00
Nlocal: 1.00000 ave 1 max 1 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 935.000 ave 935 max 935 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 428.000 ave 428 max 428 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1712
Ave neighs/atom = 428.00000
Neighbor list builds = 0
Dangerous builds = 0
# Get cohesive energy
variable natoms equal "count(all)"
variable ecohesive equal "-pe/v_natoms"
# Create a property instance
kim property create 1 cohesive-potential-energy-cubic-crystal
#=== kim property ===========================================
# Set all the key-value pairs for this property instance
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value ${lattice_constant} source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value 0.0865055084950538 source-unit eV
#=== kim property ===========================================
# Dump the results in a file
kim property dump "results.edn"
#=== kim property ===========================================
Total wall time: 0:00:00

210
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@ -0,0 +1,210 @@
LAMMPS (10 Feb 2021)
# 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
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has 9 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | A | "Double" | 1
2 | B | "Double" | 1
3 | p | "Double" | 1
4 | q | "Double" | 1
5 | sigma | "Double" | 1
6 | gamma | "Double" | 1
7 | cutoff | "Double" | 1
8 | lambda | "Double" | 1
9 | costheta0 | "Double" | 1
#=== 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 = 4.1465819 4.1465819 4.1465819
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 = (0.0000000 0.0000000 0.0000000) to (82.931639 82.931639 82.931639)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.004 seconds
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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_405512056662_005.bib}
\end{document}
}
@Misc{MO_405512056662_005,
author = {Amit K Singh},
title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
doi = {10.25950/c74b293f},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model, MO_405512056662_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_335816936951_004,
author = {Mingjian Wen},
title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
doi = {10.25950/f3abd2d6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model Driver, MD_335816936951_004},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_405512056662_005a,
author = {Stillinger, Frank H. and Weber, Thomas A.},
doi = {10.1103/PhysRevB.31.5262},
issue = {8},
journal = {Physical Review B},
month = {Apr},
pages = {5262--5271},
publisher = {American Physical Society},
title = {Computer simulation of local order in condensed phases of silicon},
volume = {31},
year = {1985},
}
@Book{MO_405512056662_005b,
author = {Tadmor, Ellad B. and Miller, Ronald E.},
doi = {10.1017/CBO9781139003582},
publisher = {Cambridge University Press},
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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
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 18.2886 on 1 procs for 100 steps with 32000 atoms
Performance: 0.472 ns/day, 50.802 hours/ns, 5.468 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.155 | 18.155 | 18.155 | 0.0 | 99.27
Neigh | 0.087194 | 0.087194 | 0.087194 | 0.0 | 0.48
Comm | 0.009477 | 0.009477 | 0.009477 | 0.0 | 0.05
Output | 6.7e-05 | 6.7e-05 | 6.7e-05 | 0.0 | 0.00
Modify | 0.02616 | 0.02616 | 0.02616 | 0.0 | 0.14
Other | | 0.0111 | | | 0.06
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9667.00 ave 9667 max 9667 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 450192.0 ave 450192 max 450192 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 450192
Ave neighs/atom = 14.068500
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:21

210
examples/kim/log.10Feb21.in.kim-pm-query.melt.clang.4 Normal file
View File

@ -0,0 +1,210 @@
LAMMPS (10 Feb 2021)
# 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
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has 9 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | A | "Double" | 1
2 | B | "Double" | 1
3 | p | "Double" | 1
4 | q | "Double" | 1
5 | sigma | "Double" | 1
6 | gamma | "Double" | 1
7 | cutoff | "Double" | 1
8 | lambda | "Double" | 1
9 | costheta0 | "Double" | 1
#=== 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 = 4.1465819 4.1465819 4.1465819
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 = (0.0000000 0.0000000 0.0000000) to (82.931639 82.931639 82.931639)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_405512056662_005.bib}
\end{document}
}
@Misc{MO_405512056662_005,
author = {Amit K Singh},
title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
doi = {10.25950/c74b293f},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model, MO_405512056662_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_335816936951_004,
author = {Mingjian Wen},
title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
doi = {10.25950/f3abd2d6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model Driver, MD_335816936951_004},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_405512056662_005a,
author = {Stillinger, Frank H. and Weber, Thomas A.},
doi = {10.1103/PhysRevB.31.5262},
issue = {8},
journal = {Physical Review B},
month = {Apr},
pages = {5262--5271},
publisher = {American Physical Society},
title = {Computer simulation of local order in condensed phases of silicon},
volume = {31},
year = {1985},
}
@Book{MO_405512056662_005b,
author = {Tadmor, Ellad B. and Miller, Ronald E.},
doi = {10.1017/CBO9781139003582},
publisher = {Cambridge University Press},
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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
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 5.00432 on 4 procs for 100 steps with 32000 atoms
Performance: 1.727 ns/day, 13.901 hours/ns, 19.983 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.9281 | 4.9366 | 4.9447 | 0.3 | 98.65
Neigh | 0.02399 | 0.024135 | 0.024318 | 0.1 | 0.48
Comm | 0.020646 | 0.029014 | 0.037515 | 4.3 | 0.58
Output | 2.9e-05 | 3.325e-05 | 4.2e-05 | 0.0 | 0.00
Modify | 0.008808 | 0.0088445 | 0.00888 | 0.0 | 0.18
Other | | 0.005691 | | | 0.11
Nlocal: 8000.00 ave 8029 max 7968 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 4259.00 ave 4303 max 4202 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 112548.0 ave 113091 max 111995 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 450192
Ave neighs/atom = 14.068500
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:07

204
examples/kim/log.10Feb21.in.kim-pm.melt.clang.1 Normal file
View File

@ -0,0 +1,204 @@
LAMMPS (10 Feb 2021)
# 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
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has 9 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | A | "Double" | 1
2 | B | "Double" | 1
3 | p | "Double" | 1
4 | q | "Double" | 1
5 | sigma | "Double" | 1
6 | gamma | "Double" | 1
7 | cutoff | "Double" | 1
8 | lambda | "Double" | 1
9 | costheta0 | "Double" | 1
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
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 = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.002 seconds
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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_405512056662_005.bib}
\end{document}
}
@Misc{MO_405512056662_005,
author = {Amit K Singh},
title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
doi = {10.25950/c74b293f},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model, MO_405512056662_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_335816936951_004,
author = {Mingjian Wen},
title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
doi = {10.25950/f3abd2d6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model Driver, MD_335816936951_004},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_405512056662_005a,
author = {Stillinger, Frank H. and Weber, Thomas A.},
doi = {10.1103/PhysRevB.31.5262},
issue = {8},
journal = {Physical Review B},
month = {Apr},
pages = {5262--5271},
publisher = {American Physical Society},
title = {Computer simulation of local order in condensed phases of silicon},
volume = {31},
year = {1985},
}
@Book{MO_405512056662_005b,
author = {Tadmor, Ellad B. and Miller, Ronald E.},
doi = {10.1017/CBO9781139003582},
publisher = {Cambridge University Press},
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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
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 17.7449 on 1 procs for 100 steps with 32000 atoms
Performance: 0.487 ns/day, 49.291 hours/ns, 5.635 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.64 | 17.64 | 17.64 | 0.0 | 99.41
Neigh | 0.060149 | 0.060149 | 0.060149 | 0.0 | 0.34
Comm | 0.008585 | 0.008585 | 0.008585 | 0.0 | 0.05
Output | 6.3e-05 | 6.3e-05 | 6.3e-05 | 0.0 | 0.00
Modify | 0.025324 | 0.025324 | 0.025324 | 0.0 | 0.14
Other | | 0.01057 | | | 0.06
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7760.00 ave 7760 max 7760 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 402352.0 ave 402352 max 402352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 402352
Ave neighs/atom = 12.573500
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:17

204
examples/kim/log.10Feb21.in.kim-pm.melt.clang.4 Normal file
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@ -0,0 +1,204 @@
LAMMPS (10 Feb 2021)
# 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
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has 9 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | A | "Double" | 1
2 | B | "Double" | 1
3 | p | "Double" | 1
4 | q | "Double" | 1
5 | sigma | "Double" | 1
6 | gamma | "Double" | 1
7 | cutoff | "Double" | 1
8 | lambda | "Double" | 1
9 | costheta0 | "Double" | 1
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
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 = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_405512056662_005.bib}
\end{document}
}
@Misc{MO_405512056662_005,
author = {Amit K Singh},
title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
doi = {10.25950/c74b293f},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model, MO_405512056662_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_335816936951_004,
author = {Mingjian Wen},
title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
doi = {10.25950/f3abd2d6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model Driver, MD_335816936951_004},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_405512056662_005a,
author = {Stillinger, Frank H. and Weber, Thomas A.},
doi = {10.1103/PhysRevB.31.5262},
issue = {8},
journal = {Physical Review B},
month = {Apr},
pages = {5262--5271},
publisher = {American Physical Society},
title = {Computer simulation of local order in condensed phases of silicon},
volume = {31},
year = {1985},
}
@Book{MO_405512056662_005b,
author = {Tadmor, Ellad B. and Miller, Ronald E.},
doi = {10.1017/CBO9781139003582},
publisher = {Cambridge University Press},
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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
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 4.87378 on 4 procs for 100 steps with 32000 atoms
Performance: 1.773 ns/day, 13.538 hours/ns, 20.518 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8075 | 4.816 | 4.8244 | 0.3 | 98.81
Neigh | 0.015902 | 0.015996 | 0.016077 | 0.1 | 0.33
Comm | 0.018078 | 0.026375 | 0.034752 | 4.2 | 0.54
Output | 3e-05 | 3.5e-05 | 4.4e-05 | 0.0 | 0.00
Modify | 0.009331 | 0.0094922 | 0.009588 | 0.1 | 0.19
Other | | 0.005919 | | | 0.12
Nlocal: 8000.00 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: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 100588.0 ave 100856 max 100392 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 402352
Ave neighs/atom = 12.573500
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (10 Feb 2021)
# kim query example
#
# Requirement:
#
# This example requires LAMMPS is built with KIM package. A requirement for
# the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further
# details
#
# This example requires that the KIM Models
# `EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`
# and
# `EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000`
# are installed.
#
# This can be done with the commands
# `kim-api-collections-management install user `EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`
# `kim-api-collections-management install user `EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000`
#
# If these commands do 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.
#
# -----------------------------------------------
# Get an equilibrium fcc crystal lattice constant
# -----------------------------------------------
kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
#=== BEGIN kim init ==========================================
units metal
neighbor 2.0 bin # Angstroms
timestep 1.0e-3 # picoseconds
This model has 6 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | cutoff | "Double" | 1
2 | deltaRho | "Double" | 1
3 | deltaR | "Double" | 1
4 | embeddingData | "Double" | 500
5 | rPhiData | "Double" | 500
6 | densityData | "Double" | 500
#=== END kim init ============================================
kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom]
#=== BEGIN kim-query =========================================
variable latconst_1 string "4.032082033157349"
#=== END kim-query ===========================================
print "FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = ${latconst_1}"
FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = 4.032082033157349
# Get the lattice contant from a different model
kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
#=== BEGIN kim-query =========================================
variable latconst_2 string "4.024845376610756"
#=== END kim-query ===========================================
print "FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = ${latconst_2}"
FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = 4.024845376610756
clear
# -----------------------------------------------
# Get an equilibrium fcc crystal lattice constant
# -----------------------------------------------
kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]
#=== BEGIN kim-query =========================================
variable latconst_1 string "4.032082033157349"
#=== END kim-query ===========================================
kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
#=== BEGIN kim-query =========================================
variable latconst_2 string "4.024845376610756"
#=== END kim-query ===========================================
print "FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = ${latconst_1}"
FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = 4.032082033157349
print "FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = ${latconst_2}"
FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = 4.024845376610756
clear
# -----------------------------------------------
# Get an equilibrium hcp crystal lattice constant
# -----------------------------------------------
kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal
#=== BEGIN kim init ==========================================
units metal
neighbor 2.0 bin # Angstroms
timestep 1.0e-3 # picoseconds
This model has 6 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | cutoff | "Double" | 1
2 | deltaRho | "Double" | 1
3 | deltaR | "Double" | 1
4 | embeddingData | "Double" | 10000
5 | rPhiData | "Double" | 10000
6 | densityData | "Double" | 10000
#=== END kim init ============================================
kim query latconst split get_lattice_constant_hexagonal crystal=["hcp"] species=["Zr"] units=["angstrom"]
#=== BEGIN kim-query =========================================
variable latconst_1 string 3.234055244384789
variable latconst_2 string 5.167650199630013
#=== END kim-query ===========================================
print "HCP lattice constants = ${latconst_1}, ${latconst_2}"
HCP lattice constants = 3.234055244384789, 5.167650199630013
clear
# -----------------------------------------------
# Query for KIM models from openkim.org
# Get all the EAM models that support Al
# -----------------------------------------------
kim query model index get_available_models species=[Al] potential_type=[eam]
#=== BEGIN kim-query =========================================
variable model index "EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_002" "EAM_Dynamo_AngeloMoodyBaskes_1995_NiAlH__MO_418978237058_005" "EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_005" "EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005" "EAM_Dynamo_FarkasJones_1996_NbTiAl__MO_042691367780_000" "EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000" "EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_005" "EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_000" "EAM_Dynamo_LiuErcolessiAdams_2004_Al__MO_051157671505_000" "EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_000" "EAM_Dynamo_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000" "EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_005" "EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_000" "EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_005" "EAM_Dynamo_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_005" "EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_005" "EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_005" "EAM_Dynamo_Mishin_2004_NiAl__MO_101214310689_005" "EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_005" "EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_000" "EAM_Dynamo_PunYamakovMishin_2013_NiAlCo__MO_826591359508_000" "EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_000" "EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_005" "EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_005" "EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005" "EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000" "EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Al__MO_060567868558_000" "EAM_Dynamo_ZhouJohnsonWadley_2004_Al__MO_131650261510_005" "EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_000" "EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_005" "EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005" "EAM_ErcolessiAdams_1994_Al__MO_324507536345_003" "EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_003" "EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003" "EAM_IMD_SchopfBrommerFrigan_2012_AlMnPd__MO_878712978062_003" "EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002" "EAM_QuinticHermiteSpline_ErcolessiAdams_1994_Al__MO_781138671863_002" "EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001" "EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001"
#=== END kim-query ===========================================
label model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_002]
#=== BEGIN kim-query =========================================
variable latconst string "4.032082748413087"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_002) = 4.032082748413087
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_AngeloMoodyBaskes_1995_NiAlH__MO_418978237058_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050000071525574"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_AngeloMoodyBaskes_1995_NiAlH__MO_418978237058_005) = 4.050000071525574
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.049763545393944"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_005) = 4.049763545393944
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.032082033157349"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = 4.032082033157349
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_FarkasJones_1996_NbTiAl__MO_042691367780_000]
#=== BEGIN kim-query =========================================
variable latconst string "3.869337007403374"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_FarkasJones_1996_NbTiAl__MO_042691367780_000) = 3.869337007403374
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000]
#=== BEGIN kim-query =========================================
variable latconst string "3.987558534741402"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000) = 3.987558534741402
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.031036108732224"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_005) = 4.031036108732224
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.03203821182251"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_000) = 4.03203821182251
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LiuErcolessiAdams_2004_Al__MO_051157671505_000]
#=== BEGIN kim-query =========================================
variable latconst string "9.5"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LiuErcolessiAdams_2004_Al__MO_051157671505_000) = 9.5
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.032073378562927"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_000) = 4.032073378562927
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000]
#=== BEGIN kim-query =========================================
variable latconst string "8.5"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000) = 8.5
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.045270472764969"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_005) = 4.045270472764969
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.040926471352577"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_000) = 4.040926471352577
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.045259781181811"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_005) = 4.045259781181811
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.03330184519291"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_005) = 4.03330184519291
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050004702806472"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_005) = 4.050004702806472
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.051526293158533"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_005) = 4.051526293158533
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_Mishin_2004_NiAl__MO_101214310689_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.049999862909317"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_Mishin_2004_NiAl__MO_101214310689_005) = 4.049999862909317
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050000071525574"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_005) = 4.050000071525574
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.05000014603138"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_000) = 4.05000014603138
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_PunYamakovMishin_2013_NiAlCo__MO_826591359508_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.05000014603138"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_PunYamakovMishin_2013_NiAlCo__MO_826591359508_000) = 4.05000014603138
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.210718545317654"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_000) = 4.210718545317654
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050010219216347"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_005) = 4.050010219216347
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.049696564674378"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_005) = 4.049696564674378
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.024845376610756"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = 4.024845376610756
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.031999975442885"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000) = 4.031999975442885
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Al__MO_060567868558_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.050199627876282"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Al__MO_060567868558_000) = 4.050199627876282
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZhouJohnsonWadley_2004_Al__MO_131650261510_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050180745124819"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZhouJohnsonWadley_2004_Al__MO_131650261510_005) = 4.050180745124819
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.081654928624631"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_000) = 4.081654928624631
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050000011920929"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_005) = 4.050000011920929
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.049999445676804"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005) = 4.049999445676804
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_ErcolessiAdams_1994_Al__MO_324507536345_003]
#=== BEGIN kim-query =========================================
variable latconst string "4.032082714140415"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_ErcolessiAdams_1994_Al__MO_324507536345_003) = 4.032082714140415
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_003]
#=== BEGIN kim-query =========================================
variable latconst string "4.128871455788613"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_003) = 4.128871455788613
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003]
#=== BEGIN kim-query =========================================
variable latconst string "4.073718130588532"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003) = 4.073718130588532
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_IMD_SchopfBrommerFrigan_2012_AlMnPd__MO_878712978062_003]
#=== BEGIN kim-query =========================================
variable latconst string "4.210700303316115"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_IMD_SchopfBrommerFrigan_2012_AlMnPd__MO_878712978062_003) = 4.210700303316115
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002]
#=== BEGIN kim-query =========================================
variable latconst string "4.032082897424699"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002) = 4.032082897424699
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_QuinticHermiteSpline_ErcolessiAdams_1994_Al__MO_781138671863_002]
#=== BEGIN kim-query =========================================
variable latconst string "4.03208246231079"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_QuinticHermiteSpline_ErcolessiAdams_1994_Al__MO_781138671863_002) = 4.03208246231079
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001]
#=== BEGIN kim-query =========================================
variable latconst string "3.994616635143757"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001) = 3.994616635143757
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001]
#=== BEGIN kim-query =========================================
variable latconst string "3.994608342647553"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001) = 3.994608342647553
next model
jump SELF model_loop
clear
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_123629422045_005a} is archived in OpenKIM~\cite{MO_123629422045_005, MD_120291908751_005, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_123629422045_005.bib}
\end{document}
}
@Misc{MO_123629422045_005,
author = {Ryan S. Elliott},
title = {{EAM} potential ({LAMMPS} cubic hermite tabulation) for {A}l developed by {E}rcolessi and {A}dams (1994) v005},
doi = {10.25950/7cd2a6ab},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7cd2a6ab}},
keywords = {OpenKIM, Model, MO_123629422045_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_120291908751_005,
author = {Ryan S. Elliott},
title = {{EAM} {M}odel {D}river for tabulated potentials with cubic {H}ermite spline interpolation as used in {LAMMPS} v005},
doi = {10.25950/68defa36},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7cd2a6ab}},
keywords = {OpenKIM, Model Driver, MD_120291908751_005},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_123629422045_005a,
author = {F. Ercolessi and J. B. Adams},
doi = {10.1209/0295-5075/26/8/005},
journal = {Europhysics Letters},
number = {8},
pages = {583},
title = {Interatomic Potentials from First-Principles Calculations: {T}he Force-Matching Method},
volume = {26},
year = {1994},
}
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_004835508849_000a} is archived in OpenKIM~\cite{MO_004835508849_000, MD_120291908751_005, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_004835508849_000.bib}
\end{document}
}
@Misc{MO_004835508849_000,
author = {Ellad Tadmor},
title = {{F}innis-{S}inclair potential ({LAMMPS} cubic hermite tabulation) for {Z}r developed by {M}endelev and {A}ckland (2007); version 3 refitted for radiation studies v000},
doi = {10.25950/7b7b5ab5},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7b7b5ab5}},
keywords = {OpenKIM, Model, MO_004835508849_000},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_120291908751_005,
author = {Ryan S. Elliott},
title = {{EAM} {M}odel {D}river for tabulated potentials with cubic {H}ermite spline interpolation as used in {LAMMPS} v005},
doi = {10.25950/68defa36},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7b7b5ab5}},
keywords = {OpenKIM, Model Driver, MD_120291908751_005},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_004835508849_000a,
author = {Mendelev, M. I. and Ackland, G. J.},
doi = {10.1080/09500830701191393},
journal = {Philosophical Magazine Letters},
number = {5},
pages = {349-359},
title = {Development of an interatomic potential for the simulation of phase transformations in zirconium},
volume = {87},
year = {2007},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Total wall time: 0:01:58

208
examples/kim/log.10Feb21.in.kim-sm.melt.clang.1 Normal file
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@ -0,0 +1,208 @@
LAMMPS (10 Feb 2021)
# 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 10 Feb 2021
#
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
atom_style charge
neigh_modify one 4000
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
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 = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.003 seconds
kim interactions O
#=== BEGIN kim interactions ==================================
variable kim_periodic equal 1
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-pgBW45WFK0TI/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-pgBW45WFK0TI/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-pgBW45WFK0TI/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-pgBW45WFK0TI/param.qeq
#=== 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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Simulator Model originally published in \cite{SM_107643900657_000a} is archived in OpenKIM~\cite{SM_107643900657_000, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-SM_107643900657_000.bib}
\end{document}
}
@Misc{SM_107643900657_000,
author = {Ellad Tadmor},
title = {{LAMMPS} {R}eax{FF} potential for {RDX} ({C}-{H}-{N}-{O}) systems developed by {S}trachan et al. (2003) v000},
doi = {10.25950/acd3fc89},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/acd3fc89}},
keywords = {OpenKIM, Simulator Model, SM_107643900657_000},
publisher = {OpenKIM},
year = 2019,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{SM_107643900657_000a,
author = {Strachan, Alejandro and van Duin, Adri C. T. and Chakraborty, Debashis and Dasgupta, Siddharth and Goddard, William A.},
doi = {10.1103/PhysRevLett.91.098301},
issue = {9},
journal = {Physical Review Letters},
month = {Aug},
numpages = {4},
pages = {098301},
publisher = {American Physical Society},
title = {Shock Waves in High-Energy Materials: {T}he Initial Chemical Events in Nitramine {RDX}},
volume = {91},
year = {2003},
}
- pair reax/c command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reax command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 4000, page size: 100000
master list distance cutoff = 10.3
ghost atom cutoff = 10.3
binsize = 5.15, bins = 18 18 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 1803.0 | 1803.0 | 1803.0 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -39091.147 0 -20014.559 19501.107
100 63.198252 -26042.062 0 -20014.027 21497.661
Loop time of 40.2545 on 1 procs for 100 steps with 32000 atoms
Performance: 0.215 ns/day, 111.818 hours/ns, 2.484 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 24.364 | 24.364 | 24.364 | 0.0 | 60.52
Neigh | 0.4185 | 0.4185 | 0.4185 | 0.0 | 1.04
Comm | 0.022045 | 0.022045 | 0.022045 | 0.0 | 0.05
Output | 6.6e-05 | 6.6e-05 | 6.6e-05 | 0.0 | 0.00
Modify | 15.438 | 15.438 | 15.438 | 0.0 | 38.35
Other | | 0.01285 | | | 0.03
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26825.0 ave 26825 max 26825 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3.73924e+06 ave 3.73924e+06 max 3.73924e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3739236
Ave neighs/atom = 116.85112
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:41

208
examples/kim/log.10Feb21.in.kim-sm.melt.clang.4 Normal file
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@ -0,0 +1,208 @@
LAMMPS (10 Feb 2021)
# 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 10 Feb 2021
#
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
atom_style charge
neigh_modify one 4000
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
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 = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
kim interactions O
#=== BEGIN kim interactions ==================================
variable kim_periodic equal 1
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-zYQfH0ms5WSw/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-zYQfH0ms5WSw/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-zYQfH0ms5WSw/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-zYQfH0ms5WSw/param.qeq
#=== 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
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- @Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Simulator Model originally published in \cite{SM_107643900657_000a} is archived in OpenKIM~\cite{SM_107643900657_000, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-SM_107643900657_000.bib}
\end{document}
}
@Misc{SM_107643900657_000,
author = {Ellad Tadmor},
title = {{LAMMPS} {R}eax{FF} potential for {RDX} ({C}-{H}-{N}-{O}) systems developed by {S}trachan et al. (2003) v000},
doi = {10.25950/acd3fc89},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/acd3fc89}},
keywords = {OpenKIM, Simulator Model, SM_107643900657_000},
publisher = {OpenKIM},
year = 2019,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{SM_107643900657_000a,
author = {Strachan, Alejandro and van Duin, Adri C. T. and Chakraborty, Debashis and Dasgupta, Siddharth and Goddard, William A.},
doi = {10.1103/PhysRevLett.91.098301},
issue = {9},
journal = {Physical Review Letters},
month = {Aug},
numpages = {4},
pages = {098301},
publisher = {American Physical Society},
title = {Shock Waves in High-Energy Materials: {T}he Initial Chemical Events in Nitramine {RDX}},
volume = {91},
year = {2003},
}
- pair reax/c command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reax command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 4000, page size: 100000
master list distance cutoff = 10.3
ghost atom cutoff = 10.3
binsize = 5.15, bins = 18 18 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 630.2 | 630.2 | 630.2 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -39091.147 0 -20014.559 19501.107
100 63.198252 -26042.062 0 -20014.027 21497.661
Loop time of 15.049 on 4 procs for 100 steps with 32000 atoms
Performance: 0.574 ns/day, 41.803 hours/ns, 6.645 timesteps/s
99.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.8158 | 9.8159 | 9.8161 | 0.0 | 65.23
Neigh | 0.17685 | 0.17759 | 0.17832 | 0.1 | 1.18
Comm | 0.028692 | 0.028847 | 0.028942 | 0.1 | 0.19
Output | 2.5e-05 | 3.575e-05 | 4.6e-05 | 0.0 | 0.00
Modify | 5.0171 | 5.0179 | 5.0186 | 0.0 | 33.34
Other | | 0.008715 | | | 0.06
Nlocal: 8000.00 ave 8010 max 7993 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 12605.0 ave 12612 max 12595 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1.00097e+06 ave 1.00187e+06 max 1.0006e+06 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 4003876
Ave neighs/atom = 125.12113
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:15

88
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LAMMPS (10 Feb 2021)
# 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 = 4.4300000 4.4300000 4.4300000
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 = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.002 seconds
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
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 1.92822 on 1 procs for 100 steps with 32000 atoms
Performance: 4.481 ns/day, 5.356 hours/ns, 51.861 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7377 | 1.7377 | 1.7377 | 0.0 | 90.12
Neigh | 0.14234 | 0.14234 | 0.14234 | 0.0 | 7.38
Comm | 0.011694 | 0.011694 | 0.011694 | 0.0 | 0.61
Output | 6.7e-05 | 6.7e-05 | 6.7e-05 | 0.0 | 0.00
Modify | 0.02476 | 0.02476 | 0.02476 | 0.0 | 1.28
Other | | 0.01163 | | | 0.60
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911.0 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 = 61.258313
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:01

88
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LAMMPS (10 Feb 2021)
# 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 = 4.4300000 4.4300000 4.4300000
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 = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
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
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 0.561006 on 4 procs for 100 steps with 32000 atoms
Performance: 15.401 ns/day, 1.558 hours/ns, 178.251 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 | 0.48486 | 0.48676 | 0.48817 | 0.2 | 86.77
Neigh | 0.040698 | 0.04091 | 0.041066 | 0.1 | 7.29
Comm | 0.016616 | 0.01811 | 0.0202 | 1.1 | 3.23
Output | 3e-05 | 3.575e-05 | 4.7e-05 | 0.0 | 0.01
Modify | 0.008934 | 0.009025 | 0.009142 | 0.1 | 1.61
Other | | 0.006161 | | | 1.10
Nlocal: 8000.00 ave 8012 max 7989 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 9131.00 ave 9142 max 9119 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 490066.0 ave 491443 max 489273 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 1960266
Ave neighs/atom = 61.258313
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

107
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@ -1,107 +0,0 @@
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

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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

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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

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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

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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

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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

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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
--------------------------------------------------------------------------

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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

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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

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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