2012-01-31 06:53:42 +08:00
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>pair_style kim command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style kim virialmode model
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</PRE>
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<UL><LI>virialmode = KIMvirial or LAMMPSvirial
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<LI>model = name of KIM model (potential)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style kim KIMvirial model_Ar_P_Morse
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pair_coeff * * Ar Ar
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This pair style is a wrapper on the <A HREF = "http://openkim.org">Knowledge Base for Interatomic
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Models (KIM)</A> repository of interatomic potentials,
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so that they can be used by LAMMPS scripts.
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</P>
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<P>In KIM lingo, a potential is a "model" and a model contains both the
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analytic formulas that define the potential as well as the parameters
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needed to run it for one or more materials, including coefficients and
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cutoffs.
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</P>
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<P>The argument <I>virialmode</I> determines how the global virial is
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calculated. If <I>KIMvirial</I> is specified, the KIM model performs the
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global virial calculation. If <I>LAMMPSvirial</I> is specified, LAMMPS
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computes the global virial using its fdotr mechanism.
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</P>
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<P>The argument <I>model</I> is the name of the KIM model for a specific
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potential as KIM defines it. In principle, LAMMPS can invoke any KIM
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model. You should get an error or warning message from either LAMMPS
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or KIM if there is an incompatibility.
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</P>
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<P>Only a single pair_coeff command is used with the <I>kim</I> style which
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specifies the mapping of LAMMPS atom types to KIM elements. This is
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done by specifying N additional arguments after the * * in the
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pair_coeff command, where N is the number of LAMMPS atom types:
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</P>
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<UL><LI>N element names = mapping of KIM elements to atom types
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</UL>
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<P>As an example, imagine the KIM model supports Si and C atoms. If your
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LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si,
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and the 4th to be C, you would use the following pair_coeff command:
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</P>
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<PRE>pair_coeff * * Si Si Si C
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</PRE>
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<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
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defined within KIM. The final C argument maps LAMMPS atom type 4 to C
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as defined within KIM. If a mapping value is specified as NULL, the
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mapping is not performed. This can only be used when a <I>kim</I>
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potential is used as part of the <I>hybrid</I> pair style. The NULL values
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are placeholders for atom types that will be used with other
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potentials.
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</P>
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<HR>
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2012-02-01 06:36:03 +08:00
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<P>In addition to the usual LAMMPS error messages, the KIM library itself
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may generate errors, which should be printed to the screen. In this
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case it is also useful to check the kim.log file for additional error
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information. This file kim.log should be generated in the same
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directory where LAMMPS is running.
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</P>
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<HR>
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2012-02-01 06:36:03 +08:00
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<P>Here is information on how to build KIM for use with LAMMPS. There is
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a directory src/KIM/ with an important file in it: Makefile.lammps.
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When you do 'make yes-kim' LAMMPS will use the settings in
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src/KIM/Makefile.lammps to find KIM header files and the KIM library
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itself for linking purposes. Thus, you should ensure Makefile.lammps
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has the correct settings for your system and your build of KIM.
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</P>
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<P>Consult the KIM documentation for further details on KIM specifics.
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</P>
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<P>OpenKIM is available for download from <A HREF = "http://openkim.org">this site</A>,
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namely http://openkim.org. The tarball you download is
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"openkim-api-vX.X.X.tgz", which can be unpacked via
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</P>
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<PRE>tar xvfz openkim*tgz
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</PRE>
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<P>The openkim/DOCs directory has further documentation. For more
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information on installing KIM and troubleshooting refer to
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openkim/INSTALL.
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</P>
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<P>Here is a brief summary of how to build KIM:
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</P>
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<OL><LI>Set the following environment variables. It is recommended to place
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the above environment variables definitions in your shell setup file
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which is located in your home directory (e.g. ~/.bashrc).
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<PRE> (a) Define the location of the openKIM API root directory. For example,
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if you untarred the `openkim-api-vX.X.X.tgz' tarball in your home
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directory, you would do:
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</PRE>
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<PRE> bash:
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% export KIM_DIR=~/openkim-api-vX.X.X
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</PRE>
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<PRE> tcsh:
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% setenv KIM_DIR ~/openkim-api-vX.X.X
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</PRE>
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<PRE> The `%' symbol represents the bash sell prompt and should not be
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typed.
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</PRE>
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<PRE> (b) By default, all makefiles use the GNU compilers for 64 bit Linux.
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In order to use the Intel compiler, define the environment variable
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KIM_INTEL
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</PRE>
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<PRE> bash:
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% export KIM_INTEL="yes"
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</PRE>
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<PRE> tcsh:
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% setenv KIM_INTEL "yes"
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</PRE>
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<PRE> (c) For a 32 bit machine, define the environment variable KIM_SYSTEM32
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</PRE>
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<PRE> bash:
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% export KIM_SYSTEM32="yes"
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</PRE>
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<PRE> tchs:
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% setenv KIM_SYSTEM32 "yes"
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</PRE>
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<PRE> (d) Define variable for dynamic linking (recommended)
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</PRE>
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<PRE> bash:
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export KIM_DYNAMIC=yes
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</PRE>
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<PRE> tcsh:
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setenv KIM_DYNAMIC=yes
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</PRE>
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<PRE> If this environment variable is not set the default will be static
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linking. In that case all KIM models will be linked, producing
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potentially a very large executable file. It is also possible to build
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KIM with only a subset of models or a single model you wish to use with
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LAMMPS. Consult the KIM documentation for details.
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</PRE>
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<LI>To compile the package, go to the $KIM_DIR directory and execute
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make.
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<PRE> % cd $KIM_DIR
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% make examples
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% make
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</PRE>
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<PRE> This builds all Models, Tests, and the openKIM API service routine
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library. The targets defined by the Makefile in this directory include:
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</PRE>
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<PRE> make -- compiles the API and all Models and Tests
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make all -- same as `make'
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make examples -- copy examples into the appropriate directories
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(no overwrite)
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make examples-force -- copy examples into the appropriate directories
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(overwrite)
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make openkim-api -- compiles only the API
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make clean -- will remove .o, .mod, .a, .so and executable files
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make examples-clean -- remove all examples from the MODEL_DRIVERs,
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MODELs, and TESTs directories.
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</PRE>
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<LI>Verify that the compilation was successful by running a Test.
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<PRE> The provided example Tests read in the name of a Model (or Models)
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which they use to perform their calculations. For most Tests the
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name of the Model can be piped in using an `echo' command. For
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example, the following Fortran 90 Test reads in one Model:
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</PRE>
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<PRE> % cd $KIM_DIR/TESTs/test_Ar_free_cluster_CLUSTER_F90
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% echo "model_Ar_P_MLJ_CLUSTER_C" | ./test_Ar_free_cluster_CLUSTER_F90
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</PRE>
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<PRE> (See the README files in the Test directories for an explanation of what
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the Tests do.)
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</PRE>
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<LI>Each Test (and Model) has its own make file for compiling and linking.
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If changes are made to the code, re-compile (from the $KIM_DIR directory).
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2012-08-08 23:32:02 +08:00
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<LI>In case of using a non-standard location for any of the directories KIM_API,
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TESTs, MODEL_DRIVERS, or MODELs one or more of the following environment
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variables must be set:
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</OL>
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<PRE> KIM_API_DIR
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KIM_TESTS_DIR
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KIM_MODEL_DRIVERS_DIR
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KIM_MODELS_DIR
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</PRE>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
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mix, shift, table, and tail options.
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</P>
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<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
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files</A>, since KIM stores the potential parameters.
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Thus, you need to re-specify the pair_style and pair_coeff commands in
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an input script that reads a restart file.
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</P>
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<P>This pair style can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. It does not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>This pair style is part of the KIM package. It is only enabled if
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LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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2012-08-08 23:34:15 +08:00
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<P>This current version of pair_style kim is compatible with the
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openkim-api package version 1.1.0 and higher.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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