pair_style kim virialmode model
pair_style kim KIMvirial model_Ar_P_Morse pair_coeff * * Ar Ar
This pair style is a wrapper on the Knowledge Base for Interatomic Models (KIM) repository of interatomic potentials, so that they can be used by LAMMPS scripts.
In KIM lingo, a potential is a "model" and a model contains both the analytic formulas that define the potential as well as the parameters needed to run it for one or more materials, including coefficients and cutoffs.
The argument virialmode determines how the global virial is calculated. If KIMvirial is specified, the KIM model performs the global virial calculation. If LAMMPSvirial is specified, LAMMPS computes the global virial using its fdotr mechanism.
The argument model is the name of the KIM model for a specific potential as KIM defines it. In principle, LAMMPS can invoke any KIM model. You should get an error or warning message from either LAMMPS or KIM if there is an incompatibility.
Only a single pair_coeff command is used with the kim style which specifies the mapping of LAMMPS atom types to KIM elements. This is done by specifying N additional arguments after the * * in the pair_coeff command, where N is the number of LAMMPS atom types:
As an example, imagine the KIM model supports Si and C atoms. If your LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command:
pair_coeff * * Si Si Si C
The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to Si as defined within KIM. The final C argument maps LAMMPS atom type 4 to C as defined within KIM. If a mapping value is specified as NULL, the mapping is not performed. This can only be used when a kim potential is used as part of the hybrid pair style. The NULL values are placeholders for atom types that will be used with other potentials.
In addition to the usual LAMMPS error messages, the KIM library itself may generate errors, which should be printed to the screen. In this case it is also useful to check the kim.log file for additional error information. This file kim.log should be generated in the same directory where LAMMPS is running.
Here is information on how to build KIM for use with LAMMPS. There is a directory src/KIM/ with an important file in it: Makefile.lammps. When you do 'make yes-kim' LAMMPS will use the settings in src/KIM/Makefile.lammps to find KIM header files and the KIM library itself for linking purposes. Thus, you should ensure Makefile.lammps has the correct settings for your system and your build of KIM.
Consult the KIM documentation for further details on KIM specifics.
OpenKIM is available for download from this site, namely http://openkim.org. The tarball you download is "openkim-api-vX.X.X.tgz", which can be unpacked via
tar xvfz openkim*tgz
The openkim/DOCs directory has further documentation. For more information on installing KIM and troubleshooting refer to openkim/INSTALL.
Here is a brief summary of how to build KIM:
(a) Define the location of the openKIM API root directory. For example, if you untarred the `openkim-api-vX.X.X.tgz' tarball in your home directory, you would do:
bash: % export KIM_DIR=~/openkim-api-vX.X.X
tcsh: % setenv KIM_DIR ~/openkim-api-vX.X.X
The `%' symbol represents the bash sell prompt and should not be typed.
(b) By default, all makefiles use the GNU compilers for 64 bit Linux. In order to use the Intel compiler, define the environment variable KIM_INTEL
bash: % export KIM_INTEL="yes"
tcsh: % setenv KIM_INTEL "yes"
(c) For a 32 bit machine, define the environment variable KIM_SYSTEM32
bash: % export KIM_SYSTEM32="yes"
tchs: % setenv KIM_SYSTEM32 "yes"
(d) Define variable for dynamic linking (recommended)
bash: export KIM_DYNAMIC=yes
tcsh: setenv KIM_DYNAMIC=yes
If this environment variable is not set the default will be static linking. In that case all KIM models will be linked, producing potentially a very large executable file. It is also possible to build KIM with only a subset of models or a single model you wish to use with LAMMPS. Consult the KIM documentation for details.
% cd $KIM_DIR % make examples % make
This builds all Models, Tests, and the openKIM API service routine library. The targets defined by the Makefile in this directory include:
make -- compiles the API and all Models and Tests make all -- same as `make' make examples -- copy examples into the appropriate directories (no overwrite) make examples-force -- copy examples into the appropriate directories (overwrite) make openkim-api -- compiles only the API make clean -- will remove .o, .mod, .a, .so and executable files make examples-clean -- remove all examples from the MODEL_DRIVERs, MODELs, and TESTs directories.
The provided example Tests read in the name of a Model (or Models) which they use to perform their calculations. For most Tests the name of the Model can be piped in using an `echo' command. For example, the following Fortran 90 Test reads in one Model:
% cd $KIM_DIR/TESTs/test_Ar_free_cluster_CLUSTER_F90 % echo "model_Ar_P_MLJ_CLUSTER_C" | ./test_Ar_free_cluster_CLUSTER_F90
(See the README files in the Test directories for an explanation of what the Tests do.)
KIM_API_DIR KIM_TESTS_DIR KIM_MODEL_DRIVERS_DIR KIM_MODELS_DIR
Mixing, shift, table, tail correction, restart, rRESPA info:
This pair style does not support the pair_modify mix, shift, table, and tail options.
This pair style does not write its information to binary restart files, since KIM stores the potential parameters. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file.
This pair style can only be used via the pair keyword of the run_style respa command. It does not support the inner, middle, outer keywords.
This pair style is part of the KIM package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.
This current version of pair_style kim is compatible with the openkim-api package version 1.1.0 and higher.