forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7609 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
04407d4f15
commit
a1d98696c4
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@ -422,16 +422,16 @@ potentials. Click on the style itself for a full description:
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||||||
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD></TR>
|
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
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<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
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</TD></TR></TABLE></DIV>
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</TD></TR></TABLE></DIV>
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<P>These are pair styles contributed by users, which can be used if
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<P>These are pair styles contributed by users, which can be used if
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@ -649,6 +649,7 @@ potentials. Click on the style itself for a full description:
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"gran/hooke/history"_pair_gran.html,
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"gran/hooke/history"_pair_gran.html,
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"hbond/dreiding/lj"_pair_hbond_dreiding.html,
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"hbond/dreiding/lj"_pair_hbond_dreiding.html,
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"hbond/dreiding/morse"_pair_hbond_dreiding.html,
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"hbond/dreiding/morse"_pair_hbond_dreiding.html,
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"kim"_pair_kim.html,
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"line/lj"_pair_line_lj.html,
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"line/lj"_pair_line_lj.html,
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"lj/charmm/coul/charmm"_pair_charmm.html,
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"lj/charmm/coul/charmm"_pair_charmm.html,
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"lj/charmm/coul/charmm/implicit"_pair_charmm.html,
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"lj/charmm/coul/charmm/implicit"_pair_charmm.html,
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@ -0,0 +1,128 @@
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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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</CENTER>
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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 model
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</PRE>
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<P>model = name of KIM model (potential)
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</P>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style kim 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 Knowledge Base for Interatomic
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Models (KIM) repository of interatomic potentials, so that they can be
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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>model</I> is the name of the model for a specific potential
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as KIM defines it. In principle, LAMMPS can invoke any KIM model.
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You should get an error message from either LAMMPS or KIM if there is
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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 atoms 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 be used when a <I>kim</I> potential is
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used as part of the <I>hybrid</I> pair style. The NULL values are
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placeholders for atom types that will be used with other potentials.
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</P>
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<HR>
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<P>Where to look for error messages
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</P>
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<P>Some of the KIM models might fail to work with lammps. Check generated
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kim.log file for error messages.
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</P>
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<HR>
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<P>How to build KIM
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</P>
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<P>ENV variables
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</P>
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<P>setenv KIM_MODELS_DIR `pwd`/MODELs/
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setenv KIM_DIR `pwd`/
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setenv KIM_DYNAMIC yes
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</P>
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<P>It is required that OPENKIM directory with
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needed file structure is installed (can be downloaded from openkim.org)
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and needed environment variables are set:
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KIM_DIR = path openkim-api directory
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KIM_DYNAMIC -- if dynamic linking is used during building (default --static)
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KIM_MODELS_DIR = path to kim models directory (default -- $KIM_DIR/MODELs)
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See openkim-api/INSTALL for detailed instruction.
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</P>
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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 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 pair style requires the <A HREF = "newton.html">newton</A> setting to be "off"
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for pair interactions.
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</P>
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<P>Currently this pair style only works with LAMMPS metal
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<A HREF = "units.html">units</A>, since KIM models are written using
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those units.
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</P>
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<P>Only KIM models that are using NEIGH-PURE-H, NEIGH-PURE-F and
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NEIGH-RVEC-F can be used with lammps. (see KIM documentation on NBC
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methods)
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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>, <A HREF = "pair_eam.html">pair_style eam</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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@ -0,0 +1,123 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style kim command :h3
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[Syntax:]
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pair_style kim model :pre
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model = name of KIM model (potential)
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[Examples:]
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pair_style kim model_Ar_P_Morse
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pair_coeff * * Ar Ar :pre
|
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|
||||||
|
[Description:]
|
||||||
|
|
||||||
|
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 {model} is the name of the model for a specific potential
|
||||||
|
as KIM defines it. In principle, LAMMPS can invoke any KIM model.
|
||||||
|
You should get an error message from either LAMMPS or KIM if there is
|
||||||
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an incompatibility.
|
||||||
|
|
||||||
|
Only a single pair_coeff command is used with the {kim} style which
|
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|
specifies the mapping of LAMMPS atom types to KIM elements. This is
|
||||||
|
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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N element names = mapping of KIM elements to atom types :ul
|
||||||
|
|
||||||
|
As an example, imagine the KIM model supports Si and C atoms. If your
|
||||||
|
LAMMPS simulation has 4 atoms 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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|
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pair_coeff * * Si Si Si C :pre
|
||||||
|
|
||||||
|
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
|
||||||
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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
|
||||||
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mapping is not performed. This can be used when a {kim} potential is
|
||||||
|
used as part of the {hybrid} pair style. The NULL values are
|
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placeholders for atom types that will be used with other potentials.
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
Where to look for error messages
|
||||||
|
|
||||||
|
Some of the KIM models might fail to work with lammps. Check generated
|
||||||
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kim.log file for error messages.
|
||||||
|
|
||||||
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:line
|
||||||
|
|
||||||
|
How to build KIM
|
||||||
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|
||||||
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ENV variables
|
||||||
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|
||||||
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setenv KIM_MODELS_DIR `pwd`/MODELs/
|
||||||
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setenv KIM_DIR `pwd`/
|
||||||
|
setenv KIM_DYNAMIC yes
|
||||||
|
|
||||||
|
It is required that OPENKIM directory with
|
||||||
|
needed file structure is installed (can be downloaded from openkim.org)
|
||||||
|
and needed environment variables are set:
|
||||||
|
KIM_DIR = path openkim-api directory
|
||||||
|
KIM_DYNAMIC -- if dynamic linking is used during building (default --static)
|
||||||
|
KIM_MODELS_DIR = path to kim models directory (default -- $KIM_DIR/MODELs)
|
||||||
|
See openkim-api/INSTALL for detailed instruction.
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||||
|
|
||||||
|
This pair style does not support the "pair_modify"_pair_modify.html
|
||||||
|
mix, shift, table, and tail options.
|
||||||
|
|
||||||
|
This pair style does not write its information to "binary restart
|
||||||
|
files"_restart.html, since KIM stores the 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"_run_style.html command. It does not support the
|
||||||
|
{inner}, {middle}, {outer} keywords.
|
||||||
|
|
||||||
|
:line
|
||||||
|
|
||||||
|
[Restrictions:]
|
||||||
|
|
||||||
|
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_start.html#start_3 section for more info.
|
||||||
|
|
||||||
|
This pair style requires the "newton"_newton.html setting to be "off"
|
||||||
|
for pair interactions.
|
||||||
|
|
||||||
|
Currently this pair style only works with LAMMPS metal
|
||||||
|
"units"_units.html, since KIM models are written using
|
||||||
|
those units.
|
||||||
|
|
||||||
|
Only KIM models that are using NEIGH-PURE-H, NEIGH-PURE-F and
|
||||||
|
NEIGH-RVEC-F can be used with lammps. (see KIM documentation on NBC
|
||||||
|
methods)
|
||||||
|
|
||||||
|
[Related commands:]
|
||||||
|
|
||||||
|
"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html
|
||||||
|
|
||||||
|
[Default:] none
|
||||||
Loading…
Reference in New Issue