forked from lijiext/lammps
205 lines
6.2 KiB
Plaintext
205 lines
6.2 KiB
Plaintext
"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 virialmode model :pre
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virialmode = KIMvirial or LAMMPSvirial
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model = name of KIM model (potential) :ul
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[Examples:]
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pair_style kim KIMvirial model_Ar_P_Morse
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pair_coeff * * Ar Ar :pre
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[Description:]
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This pair style is a wrapper on the "Knowledge Base for Interatomic
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Models (KIM)"_https://openkim.org repository of interatomic potentials,
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so that they can be used by LAMMPS scripts.
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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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The argument {virialmode} determines how the global virial is
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calculated. If {KIMvirial} is specified, the KIM model performs the
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global virial calculation (if it knows how). If {LAMMPSvirial} is
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specified, LAMMPS computes the global virial using its fdotr mechanism.
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The argument {model} 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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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
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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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N element names = mapping of KIM elements to atom types :ul
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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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pair_coeff * * Si Si Si C :pre
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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 {kim}
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potential is used as part of the {hybrid} 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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:line
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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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:line
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Here is information on how to build KIM for use with LAMMPS.
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The KIM API is available for download from "this
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site"_https://openkim.org, namely https://openkim.org. The tarball
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you download is "kim-api-vX.X.X.tgz", which can be unpacked via
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tar xvfz kim*tgz :pre
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The kim-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 kim-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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Once you have successfully compiled and installed the KIM API, you
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need to make sure the utility kim-api-build-config is on your PATH
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so that the LAMMPS build system can properly work with the KIM API.
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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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<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/kim-api/kim-api-vX.X.X.tgz # replace X.X.X as appropriate here and below
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tar zxvf kim-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 kim-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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make add-EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_001
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make
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make install
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make install-set-default-to-vX # replace X with the KIM API major version number :
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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
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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_001
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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 -in al-input :
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</pre>
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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This pair style does not support the "pair_modify"_pair_modify.html
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mix, shift, table, and tail options.
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This pair style does not write its information to "binary restart
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files"_restart.html, 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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This pair style can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. It does not support the
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{inner}, {middle}, {outer} keywords.
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:line
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[Restrictions:]
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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 "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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This current version of pair_style kim is compatible with the
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kim-api package version 1.6.0 and higher.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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