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Updated the pair_kim docs

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Ellad Tadmor
2019-06-23 17:36:10 -05:00
parent b5d4cf4bfd
commit 881f9ff043
1 changed files with 38 additions and 45 deletions
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doc/src/pair_kim.txt
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@ -12,76 +12,71 @@ pair_style kim command :h3
pair_style kim model :pre
model = name of KIM model (potential)
model = name of a KIM model (the KIM ID for models archived in OpenKIM)
[Examples:]
pair_style kim ex_model_Ar_P_LJ
pair_coeff * * Ar Ar :pre
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si :pre
[Description:]
This pair style is a wrapper on the "Knowledge Base for Interatomic
This pair style is a wrapper on the "Open Knowledgebase of Interatomic
Models (OpenKIM)"_https://openkim.org repository of interatomic
potentials, so that they can be used by LAMMPS scripts.
potentials to enable their use in LAMMPS scripts.
Note that in LAMMPS lingo, a KIM model driver is a pair style
(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
element or alloy and set of parameters, e.g. EAM for Cu with a
specific EAM potential file.
The preferred interface for using interatomic models archived in
OpenKIM is the "kim_commands interface"_kim_commands.html. That
interface supports both "KIM Models" that conform to the KIM API
and can be used by any KIM-compliant simulation code, and
"KIM Simulator Models" that are natively implemented within a single
simulation code (like LAMMPS) and can only be used with it.
The {pair_style kim} command is limited to KIM Models. It is
used by the "kim_commands interface"_kim_commands.html as needed.
See the current list of "KIM model
drivers"_https://openkim.org/browse/model-drivers/alphabetical.
NOTE: Since {pair_style kim} is called by {kim_interactions} as needed,
is not recommended to be directly used in input scripts.
See the current list of all "KIM
models"_https://openkim.org/browse/models/by-model-drivers
To use this pair style, you must first download and install the KIM
API library from the "OpenKIM website"_https://openkim.org. The KIM
section of the "Packages details"_Packages_details.html doc page has
instructions on how to do this with a simple make command, when
building LAMMPS.
See the examples/kim dir for an input script that uses a KIM model
(potential) for Lennard-Jones.
:line
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.
potential as KIM defines it. For potentials archived in OpenKIM
this is the extended KIM ID (see "kim_commands"_kim_commands.html
for details). LAMMPS can invoke any KIM Model, however there can
be incompatibilities (for example unit matching issues).
In the event of an incompatibility, the code will terminate with
an error message. Check both the LAMMPS and KIM log files for details.
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:
Only a single {pair_coeff} command is used with the {kim} style, which
specifies the mapping of LAMMPS atom types to the species supported by
the KIM Model. This is done by specifying {N} additional arguments
after the * * in the {pair_coeff} command, where {N} is the number of
LAMMPS atom types:
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 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:
For example, consider a KIM Model that supports Si and C species.
If the LAMMPS simulation has four atom types, where the first three are Si,
and the fourth is C, the following {pair_coeff} command would be used:
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
defined within KIM. The final C argument maps LAMMPS atom type 4 to C
as defined within KIM.
The first two arguments must be * * so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as
defined within KIM Model. The final C argument maps LAMMPS atom type 4 to C.
:line
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
case it is also useful to check the {kim.log} file for additional error
information. The file kim.log should be generated in the same
directory where LAMMPS is running.
To download, build, and install the KIM library on your system, see
the lib/kim/README file. Once you have done this and built LAMMPS
the {lib/kim/README} file. Once you have done this and built LAMMPS
with the KIM package installed you can run the example input scripts
in examples/kim.
in {examples/kim}.
:line
@ -103,16 +98,14 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the KIM package. It is only enabled if
LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info.
This pair style is part of the KIM package. See details on
restrictions in "kim_commands"_kim_commands.html.
This current version of pair_style kim is compatible with the
kim-api package version 2.0.0 and higher.
[Related commands:]
"pair_coeff"_pair_coeff.html, "kim_init"_kim_commands.html,
"kim_interactions"_kim_commands, "kim_query"_kim_commands.html
"pair_coeff"_pair_coeff.html, "kim_commands"_kim_commands.html
[Default:] none