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-api-vX.X.X/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) Copy the file Makefile.KIM_Config.example to Makefile.KIM_Config For example, if you untarred the `openkim-api-vX.X.X.tgz' tarball in your home directory, you would do:
% cd $HOME/openkim-api-vX.X.X % cp Makefile.KIM_Config.example Makefile.KIM_Config
The `%' symbol represents the bash sell prompt and should not be typed.
(Above `vX.X.X' represents the current release number.)
(b) Edit the file Makefile.KIM_Config and set the appropriate value for the KIM_DIR variable. This must expand to an absolute path. Using the same assumptions as above, this would be
KIM_DIR = $(HOME)/openkim-api-vX.X.X
(c) If appropriate, set explicit values for the remaining three directories
KIM_MODEL_DRIVERS_DIR = KIM_MODELS_DIR = KIM_TESTS_DIR =
If these lines are commented out, defaults will be provided by the openkim-api make system.
(d) Set the value of KIM_COMPILERSUITE. Possible values are `GCC' and `INTEL'.
KIM_COMPILERSUITE = GCC
(e) Set the value of KIM_SYSTEMLINKER. Possible values are `linux', `freebsd', and `darwin'.
KIM_SYSTEMLINKER = linux
(f) Set the value of KIM_SYSTEMARCH. Possible values are `32bit' and `64bit'.
KIM_SYSTEMARCH = 64bit
(g) Set the value of KIM_LINK. Possible values are `dynamic-load', `dynamic-link', and `static-link'.
KIM_LINK = dynamic-load
`dynamic-load' is the preferred option. (Unless performance or other issues require it, you should use dynamic-load.) `dynamic-link' is like `dynamic-load' but does not use the dl.h library. This option requires a more complicated Makefile process, but may improve computation time in some instances. `static-link' only works with ONE Model and AT MOST ONE Model Driver (in order to avoid the possibility of symbol clashes).
(h) Set override values for other variables, if necessary, by adding the desired variable name (after the "# overwrite default variable values here" line) and filling in appropriate values.
# overwrite default variable values here
# overwrite default compiler options
CC = CXX = FC =
# overwrite default compiler option flag lists FFLAGS = CCFLAGS = CXXFLAGS = LDFLAGS =
# overwrite default linker options LDSHAREDFLAG = LINKSONAME = LDWHOLEARCHIVESTARTFLAG = LDWHOLEARCHIVEENDFLAG =
# overwrite default install directories package_name = prefix = libdir =
bash: % export KD=$HOME/openkim-api-vX.X.X
% cd $KD % make examples % make
This builds all Model Drivers, 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 clean' -- will remove appropriate .o, .mod, .a, .so and executable files `make install' -- install files to `/usr/local/lib' by default `make uninstall' -- delete files installed by `make install' `make openkim-api' -- compiles only the API `make examples' -- copies examples into the appropriate directories (no overwrite) `make examples-force' -- copies examples into the appropriate directories (overwrite) `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 $KD/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.)
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 1.2.0 and higher.