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 = "https://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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2012-08-08 23:34:15 +08:00
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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 it knows how). If <I>LAMMPSvirial</I> is
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specified, LAMMPS 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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2012-01-31 06:53:42 +08:00
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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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2014-06-28 03:41:37 +08:00
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<P>Here is information on how to build KIM for use with LAMMPS.
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</P>
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<P>The KIM API is available for download from <A HREF = "https://openkim.org">this
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site</A>, namely https://openkim.org. The tarball
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you download is "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-api-vX.X.X/DOCS/ directory has further documentation. In
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order to compile and install the KIM API follow the instructions found
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in the file openkim-api-vX.X.X/INSTALL. (Don't forget to download and
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compile any Model Drivers and Models that you want to use.)
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</P>
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<P>Once you have successfully compiled and installed the KIM API, you
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need to set up LAMMPS to use your KIM API system. In the LAMMPS
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package there is a directory src/KIM/ with an important file in it:
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Makefile.lammps. When you do 'make yes-kim' LAMMPS will use the
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settings in src/KIM/Makefile.lammps to find the KIM API header files
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and the KIM API library itself for linking purposes. Thus, you should
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edit src/KIM/Makefile.lammps to ensure it has the correct settings for
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your system and your build of KIM.
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</P>
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<P>The following is an example of how to download, compile, and run
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LAMMPS with the KIM API:
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</P>
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<pre>
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mkdir lammps-kim
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cd lammps-kim
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#
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# download lammps and the KIM API
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#
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wget http://lammps.sandia.gov/tars/lammps-DDMMMYY.tar.gz # replace DDMMMYY as appropriate here and below
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wget http://s3.openkim.org/openkim-api/openkim-api-vX.X.X.tgz # replace X.X.X as appropriate here and below
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tar zxvf openkim-api-vX.X.X.tgz
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#
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# Get OpenKIM models, setup and compile
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#
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cd openkim-api-vX.X.X
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cp Makefile.KIM_Config.example Makefile.KIM_Config
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vi Makefile.KIM_Config # edit file as appropriate following the instructions given in the INSTALL file
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cd MODEL_DRIVERS
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wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo__MD_120291908751_000&compression=gz'
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tar zxvf EAM_Dynamo__MD_120291908751_000.tgz
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cd ../MODELS
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wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000&compression=gz'
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tar zxvf EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000.tgz
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cd ../
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make
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cd ../
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#
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# setup and compile lammps
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#
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tar zxvf lammps-DDMMMYY.tar.gz
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cd lammps-DDMMMYY/src/KIM
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vi Makefile.lammps # edit the three lines to look like below:
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# kim_SYSINC = -I../../../openkim-api-vX.X.X/KIM_API
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# kim_SYSLIB = -lkim
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# kim_SYSPATH = -L../../../openkim-api-vX.X.X/KIM_API
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cd ../
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make yes-kim
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cd STUBS
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make
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cd ../
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make serial
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#
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# run simple example with KIM model
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#
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cd ../../
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vi al-input # create file with the following content
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#----------------------------------------------------------------------------------------
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variable x index 1
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variable y index 1
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variable z index 1
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units metal
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atom_style atomic
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lattice fcc 4.0500
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region box block 0.0 ${xx} 0.0 ${yy} 0.0 ${zz}
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create_box 1 box
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create_atoms 1 box
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pair_style kim KIMvirial EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000
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pair_coeff * * Al
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mass 1 26.98
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velocity all create 200.0 232345 loop geom
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 all nve
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run 100
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#----------------------------------------------------------------------------------------
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./lammps-DDMMYY/src/lmp_serial < al-input
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</pre>
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2012-02-01 06:36:03 +08:00
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2012-01-31 06:53:42 +08:00
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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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<P>This current version of pair_style kim is compatible with the
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openkim-api package version 1.2.0 and higher.
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2012-01-31 06:53:42 +08:00
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</P>
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<P><B>Related commands:</B>
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</P>
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2012-08-08 23:34:15 +08:00
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<P><A HREF = "pair_coeff.html">pair_coeff</A>
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2012-01-31 06:53:42 +08:00
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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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