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88
doc/pair_kim.html
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@ -13,13 +13,14 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style kim model
<PRE>pair_style kim virialmode model
</PRE>
<P>model = name of KIM model (potential)
<P>virialmode = KIMvirial or LAMMPSvirial
model = name of KIM model (potential)
</P>
<P><B>Examples:</B>
</P>
<PRE>pair_style kim model_Ar_P_Morse
<PRE>pair_style kim KIMvirial model_Ar_P_Morse
pair_coeff * * Ar Ar
</PRE>
<P><B>Description:</B>
@ -33,10 +34,15 @@ analytic formulas that define the potential as well as the parameters
needed to run it for one or more materials, including coefficients and
cutoffs.
</P>
<P>The argument <I>model</I> 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
an incompatibility.
<P>The argument <I>virialmode</I> determines how the global virial is calculated. If
<I>KIMvirial</I> is specified, the KIM model performs the global virial calculation.
If <I>LAMMPSvirial</I> is specified, LAMMPS computes the global virial using its
fdotr mechanism.
</P>
<P>The argument <I>model</I> 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.
</P>
<P>Only a single pair_coeff command is used with the <I>kim</I> style which
specifies the mapping of LAMMPS atom types to KIM elements. This is
@ -46,7 +52,7 @@ pair_coeff command, where N is the number of LAMMPS atom types:
<UL><LI>N element names = mapping of KIM elements to atom types
</UL>
<P>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,
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:
</P>
<PRE>pair_coeff * * Si Si Si C
@ -55,7 +61,7 @@ and the 4th to be C, you would use the following pair_coeff command:
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. If a mapping value is specified as NULL, the
mapping is not performed. This can be used when a <I>kim</I> potential is
mapping is not performed. This can only be used when a <I>kim</I> potential is
used as part of the <I>hybrid</I> pair style. The NULL values are
placeholders for atom types that will be used with other potentials.
</P>
@ -70,11 +76,10 @@ directory where LAMMPS is running.
<HR>
<P>Here is information on how to build KIM for use with LAMMPS. There is
a directory lib/kim with an important file in it: Makefile.lammps.
When you build LAMMPS with its KIM package installed (which contains
the pair_style kim command), then it will use the settings in
lib/kim/Makefile.lammps to find KIM header files and the KIM library
itself for linking purposes. Thus you should insure Makefile.lammps
a directory src/KIM/ with an important file in it: Makefile.lammps.
When you do 'make yes-kim' LAMMPS will use the settings in
src/KIM/Makefile.lammps to find KIM header files and the KIM library
itself for linking purposes. Thus, you should ensure Makefile.lammps
has the correct settings for your system and your build of KIM.
</P>
<P>Consult the KIM documentation for further details on KIM specifics.
@ -100,13 +105,13 @@ which is located in your home directory (e.g. ~/.bashrc).
directory, you would do:
</PRE>
<PRE> bash:
% export KIM_DIR=~/openkim-api-vX.X.X/
% export KIM_DIR=~/openkim-api-vX.X.X
</PRE>
<PRE> tcsh:
% setenv KIM_DIR ~/openkim-api-vX.X.X/
% setenv KIM_DIR ~/openkim-api-vX.X.X
</PRE>
<PRE> Make sure to include the trailing slash. The `%' symbol represents the
bash sell prompt and should not be typed.
<PRE> The `%' symbol represents the bash sell prompt and should not be
typed.
</PRE>
<PRE> (b) By default, all makefiles use the GNU compilers for 64 bit Linux.
In order to use the Intel compiler, define the environment variable
@ -126,7 +131,7 @@ which is located in your home directory (e.g. ~/.bashrc).
<PRE> tchs:
% setenv KIM_SYSTEM32 "yes"
</PRE>
<PRE> (d) Define variable for dynamic linking (preferable option)
<PRE> (d) Define variable for dynamic linking (recommended)
</PRE>
<PRE> bash:
export KIM_DYNAMIC=yes
@ -134,12 +139,11 @@ which is located in your home directory (e.g. ~/.bashrc).
<PRE> tcsh:
setenv KIM_DYNAMIC=yes
</PRE>
<PRE> If this environment variable is not set the default will be
static linking. In that case all KIM models will be linked,
producing potentially a very large file. It is also possible
to build KIM with only a subset of models or a single
model you wish to use with LAMMPS. Consult the KIM
documentation for details.
<PRE> If this environment variable is not set the default will be static
linking. In that case all KIM models will be linked, producing
potentially a very large executable file. It is also possible to build
KIM with only a subset of models or a single model you wish to use with
LAMMPS. Consult the KIM documentation for details.
</PRE>
<LI>To compile the package, go to the $KIM_DIR directory and execute
make.
@ -151,11 +155,14 @@ make.
<PRE> This builds all Models, Tests, and the openKIM API service routine
library. The targets defined by the Makefile in this directory include:
</PRE>
<PRE> make -- compiles the API and all Models and Tests
make all -- same as `make'
make examples -- copy examples into the appropriate directories
then do a `make all'
make openkim-api -- compiles only the API
<PRE> make -- compiles the API and all Models and Tests
make all -- same as `make'
make examples -- copy examples into the appropriate directories
(no overwrite)
make examples-force -- copy examples into the appropriate directories
(overwrite)
make openkim-api -- compiles only the API
make clean -- will remove .o, .mod, .a, .so and executable files
make examples-clean -- remove all examples from the MODEL_DRIVERs,
MODELs, and TESTs directories.
</PRE>
@ -173,17 +180,16 @@ make.
the Tests do.)
</PRE>
<LI>Each Test (and Model) has its own make file for compiling and linking.
If changes are made to the code, perform step (2) again (from the
$KIM_DIR directory).
If changes are made to the code, re-compile (from the $KIM_DIR directory).
<LI>In case of using a non-standard location for any of the directories
KIM_API, TESTs, or MODELs one or more of the following environment
<LI>In case of using a non-standard location for any of the directories KIM_API,
TESTs, MODEL_DRIVERS, or MODELs one or more of the following environment
variables must be set:
</OL>
<PRE> KIM_API_DIR
KIM_TESTS_DIR
KIM_MODELS_DIR
KIM_MODEL_DRIVERS_DIR
KIM_MODEL_DRIVERS_DIR
KIM_MODELS_DIR
</PRE>
<HR>
@ -193,7 +199,7 @@ variables must be set:
mix, shift, table, and tail options.
</P>
<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
files</A>, since KIM stores the the potential parameters.
files</A>, since KIM stores 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.
</P>
@ -209,12 +215,8 @@ an input script that reads a restart file.
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>This pair style requires the <A HREF = "newton.html">newton</A> setting to be "off"
for pair interactions.
</P>
<P>Currently this pair style only works with LAMMPS metal
<A HREF = "units.html">units</A>. In the future changes will be made so it can work
with LAMMPS unit choices as well.
<P>This version of pair_style kim is compatible with the openkim-api package
version 1.1.0 and higher.
</P>
<P><B>Related commands:</B>
</P>

86
doc/pair_kim.txt
View File

@ -10,13 +10,14 @@ pair_style kim command :h3
[Syntax:]
pair_style kim model :pre
pair_style kim virialmode model :pre
virialmode = KIMvirial or LAMMPSvirial
model = name of KIM model (potential)
[Examples:]
pair_style kim model_Ar_P_Morse
pair_style kim KIMvirial model_Ar_P_Morse
pair_coeff * * Ar Ar :pre
[Description:]
@ -30,10 +31,15 @@ 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
an incompatibility.
The argument {virialmode} determines how the global virial is calculated. If
{KIMvirial} is specified, the KIM model performs the global virial calculation.
If {LAMMPSvirial} is specified, LAMMPS computes the global virial using its
fdotr mechanism.
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.
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
@ -43,7 +49,7 @@ 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 atoms types and you want the 1st 3 to be Si,
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:
pair_coeff * * Si Si Si C :pre
@ -52,7 +58,7 @@ 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. If a mapping value is specified as NULL, the
mapping is not performed. This can be used when a {kim} potential is
mapping is not performed. This can only be used when a {kim} potential is
used as part of the {hybrid} pair style. The NULL values are
placeholders for atom types that will be used with other potentials.
@ -67,11 +73,10 @@ directory where LAMMPS is running.
:line
Here is information on how to build KIM for use with LAMMPS. There is
a directory lib/kim with an important file in it: Makefile.lammps.
When you build LAMMPS with its KIM package installed (which contains
the pair_style kim command), then it will use the settings in
lib/kim/Makefile.lammps to find KIM header files and the KIM library
itself for linking purposes. Thus you should insure Makefile.lammps
a directory src/KIM/ with an important file in it: Makefile.lammps.
When you do 'make yes-kim' LAMMPS will use the settings in
src/KIM/Makefile.lammps to find KIM header files and the KIM library
itself for linking purposes. Thus, you should ensure Makefile.lammps
has the correct settings for your system and your build of KIM.
Consult the KIM documentation for further details on KIM specifics.
@ -97,13 +102,13 @@ which is located in your home directory (e.g. ~/.bashrc). :olb,l
directory, you would do: :pre
bash:
% export KIM_DIR=~/openkim-api-vX.X.X/ :pre
% export KIM_DIR=~/openkim-api-vX.X.X :pre
tcsh:
% setenv KIM_DIR ~/openkim-api-vX.X.X/ :pre
% setenv KIM_DIR ~/openkim-api-vX.X.X :pre
Make sure to include the trailing slash. The `%' symbol represents the
bash sell prompt and should not be typed. :pre
The `%' symbol represents the bash sell prompt and should not be
typed. :pre
(b) By default, all makefiles use the GNU compilers for 64 bit Linux.
In order to use the Intel compiler, define the environment variable
@ -123,7 +128,7 @@ which is located in your home directory (e.g. ~/.bashrc). :olb,l
tchs:
% setenv KIM_SYSTEM32 "yes" :pre
(d) Define variable for dynamic linking (preferable option) :pre
(d) Define variable for dynamic linking (recommended) :pre
bash:
export KIM_DYNAMIC=yes :pre
@ -131,12 +136,11 @@ which is located in your home directory (e.g. ~/.bashrc). :olb,l
tcsh:
setenv KIM_DYNAMIC=yes :pre
If this environment variable is not set the default will be
static linking. In that case all KIM models will be linked,
producing potentially a very large file. It is also possible
to build KIM with only a subset of models or a single
model you wish to use with LAMMPS. Consult the KIM
documentation for details. :pre
If this environment variable is not set the default will be static
linking. In that case all KIM models will be linked, producing
potentially a very large executable file. It is also possible to build
KIM with only a subset of models or a single model you wish to use with
LAMMPS. Consult the KIM documentation for details. :pre
To compile the package, go to the $KIM_DIR directory and execute
make. :l
@ -148,11 +152,14 @@ make. :l
This builds all Models, Tests, and the openKIM API service routine
library. The targets defined by the Makefile in this directory include: :pre
make -- compiles the API and all Models and Tests
make all -- same as `make'
make examples -- copy examples into the appropriate directories
then do a `make all'
make openkim-api -- compiles only the API
make -- compiles the API and all Models and Tests
make all -- same as `make'
make examples -- copy examples into the appropriate directories
(no overwrite)
make examples-force -- copy examples into the appropriate directories
(overwrite)
make openkim-api -- compiles only the API
make clean -- will remove .o, .mod, .a, .so and executable files
make examples-clean -- remove all examples from the MODEL_DRIVERs,
MODELs, and TESTs directories. :pre
@ -170,17 +177,16 @@ Verify that the compilation was successful by running a Test. :l
the Tests do.) :pre
Each Test (and Model) has its own make file for compiling and linking.
If changes are made to the code, perform step (2) again (from the
$KIM_DIR directory). :l
If changes are made to the code, re-compile (from the $KIM_DIR directory). :l
In case of using a non-standard location for any of the directories
KIM_API, TESTs, or MODELs one or more of the following environment
In case of using a non-standard location for any of the directories KIM_API,
TESTs, MODEL_DRIVERS, or MODELs one or more of the following environment
variables must be set: :l,ole
KIM_API_DIR
KIM_TESTS_DIR
KIM_MODELS_DIR
KIM_MODEL_DRIVERS_DIR :pre
KIM_MODEL_DRIVERS_DIR
KIM_MODELS_DIR :pre
:line
@ -190,7 +196,7 @@ 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.
files"_restart.html, since KIM stores 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.
@ -206,12 +212,8 @@ 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. In the future changes will be made so it can work
with LAMMPS unit choices as well.
This version of pair_style kim is compatible with the openkim-api package
version 1.1.0 and higher.
[Related commands:]