jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12264 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-08-06 23:29:18 +00:00
parent edb0fc0def
commit c7454ea146
2 changed files with 35 additions and 64 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

49
doc/pair_kim.html
View File

@ -80,23 +80,18 @@ directory where LAMMPS is running.
</P>
<P>The KIM API is available for download from <A HREF = "https://openkim.org">this
site</A>, namely https://openkim.org. The tarball
you download is "openkim-api-vX.X.X.tgz", which can be unpacked via
you download is "kim-api-vX.X.X.tgz", which can be unpacked via
</P>
<PRE>tar xvfz openkim*tgz
<PRE>tar xvfz kim*tgz
</PRE>
<P>The openkim-api-vX.X.X/DOCS/ directory has further documentation. In
<P>The kim-api-vX.X.X/docs/ directory has further documentation. In
order to compile and install the KIM API follow the instructions found
in the file openkim-api-vX.X.X/INSTALL. (Don't forget to download and
in the file kim-api-vX.X.X/INSTALL. (Don't forget to download and
compile any Model Drivers and Models that you want to use.)
</P>
<P>Once you have successfully compiled and installed the KIM API, you
need to set up LAMMPS to use your KIM API system. In the LAMMPS
package there is 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 the KIM API header files
and the KIM API library itself for linking purposes. Thus, you should
edit src/KIM/Makefile.lammps to ensure it has the correct settings for
your system and your build of KIM.
need to make sure the utility kim-api-build-config is on your PATH
so that the LAMMPS build system can properly work with the KIM API.
</P>
<P>The following is an example of how to download, compile, and run
LAMMPS with the KIM API:
@ -109,38 +104,28 @@ cd lammps-kim
# download lammps and the KIM API
#
wget http://lammps.sandia.gov/tars/lammps-DDMMMYY.tar.gz # replace DDMMMYY as appropriate here and below
wget http://s3.openkim.org/openkim-api/openkim-api-vX.X.X.tgz # replace X.X.X as appropriate here and below
tar zxvf openkim-api-vX.X.X.tgz
wget http://lammps.sandia.gov/tars/lammps-DDMMMYY.tar.gz # replace DDMMMYY as appropriate here and below
wget http://s3.openkim.org/kim-api/kim-api-vX.X.X.tgz # replace X.X.X as appropriate here and below
tar zxvf kim-api-vX.X.X.tgz
#
# Get OpenKIM models, setup and compile
#
cd openkim-api-vX.X.X
cd kim-api-vX.X.X
cp Makefile.KIM_Config.example Makefile.KIM_Config
vi Makefile.KIM_Config # edit file as appropriate following the instructions given in the INSTALL file
cd MODEL_DRIVERS
wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo__MD_120291908751_000&compression=gz'
tar zxvf EAM_Dynamo__MD_120291908751_000.tgz
cd ../MODELS
wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000&compression=gz'
tar zxvf EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000.tgz
cd ../
make add-EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_001
make
cd ../
make install
make install-set-default-to-vX # replace X with the KIM API major version number
#
# setup and compile lammps
#
tar zxvf lammps-DDMMMYY.tar.gz
cd lammps-DDMMMYY/src/KIM
vi Makefile.lammps # edit the three lines to look like below:
# kim_SYSINC = -I../../../openkim-api-vX.X.X/KIM_API
# kim_SYSLIB = -lkim
# kim_SYSPATH = -L../../../openkim-api-vX.X.X/KIM_API
cd ../
cd lammps-DDMMMYY/src
make yes-kim
cd STUBS
make
@ -170,7 +155,7 @@ region box block 0.0 ${xx} 0.0 ${yy} 0.0 ${zz}
create_box 1 box
create_atoms 1 box
pair_style kim KIMvirial EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000
pair_style kim KIMvirial EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_001
pair_coeff * * Al
mass 1 26.98
@ -184,7 +169,7 @@ fix 1 all nve
run 100
#----------------------------------------------------------------------------------------
./lammps-DDMMYY/src/lmp_serial < al-input
./lammps-DDMMYY/src/lmp_serial -in al-input
</pre>
@ -213,7 +198,7 @@ LAMMPS was built with that package. See the <A HREF = "Section_start.html#start
LAMMPS</A> section for more info.
</P>
<P>This current version of pair_style kim is compatible with the
openkim-api package version 1.2.0 and higher.
kim-api package version 1.6.0 and higher.
</P>
<P><B>Related commands:</B>
</P>

50
doc/pair_kim.txt
View File

@ -77,23 +77,19 @@ Here is information on how to build KIM for use with LAMMPS.
The KIM API is available for download from "this
site"_https://openkim.org, namely https://openkim.org. The tarball
you download is "openkim-api-vX.X.X.tgz", which can be unpacked via
you download is "kim-api-vX.X.X.tgz", which can be unpacked via
tar xvfz openkim*tgz :pre
tar xvfz kim*tgz :pre
The openkim-api-vX.X.X/DOCS/ directory has further documentation. In
The kim-api-vX.X.X/docs/ directory has further documentation. In
order to compile and install the KIM API follow the instructions found
in the file openkim-api-vX.X.X/INSTALL. (Don't forget to download and
in the file kim-api-vX.X.X/INSTALL. (Don't forget to download and
compile any Model Drivers and Models that you want to use.)
Once you have successfully compiled and installed the KIM API, you
need to set up LAMMPS to use your KIM API system. In the LAMMPS
package there is 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 the KIM API header files
and the KIM API library itself for linking purposes. Thus, you should
edit src/KIM/Makefile.lammps to ensure it has the correct settings for
your system and your build of KIM.
need to make sure the utility kim-api-build-config is on your PATH
so that the LAMMPS build system can properly work with the KIM API.
The following is an example of how to download, compile, and run
LAMMPS with the KIM API:
@ -106,38 +102,28 @@ cd lammps-kim :
# download lammps and the KIM API
# :
wget http://lammps.sandia.gov/tars/lammps-DDMMMYY.tar.gz # replace DDMMMYY as appropriate here and below
wget http://s3.openkim.org/openkim-api/openkim-api-vX.X.X.tgz # replace X.X.X as appropriate here and below
tar zxvf openkim-api-vX.X.X.tgz :
wget http://lammps.sandia.gov/tars/lammps-DDMMMYY.tar.gz # replace DDMMMYY as appropriate here and below
wget http://s3.openkim.org/kim-api/kim-api-vX.X.X.tgz # replace X.X.X as appropriate here and below
tar zxvf kim-api-vX.X.X.tgz :
#
# Get OpenKIM models, setup and compile
# :
cd openkim-api-vX.X.X
cd kim-api-vX.X.X
cp Makefile.KIM_Config.example Makefile.KIM_Config
vi Makefile.KIM_Config # edit file as appropriate following the instructions given in the INSTALL file
cd MODEL_DRIVERS
wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo__MD_120291908751_000&compression=gz'
tar zxvf EAM_Dynamo__MD_120291908751_000.tgz
cd ../MODELS
wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000&compression=gz'
tar zxvf EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000.tgz
cd ../
make add-EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_001
make
cd ../ :
make install
make install-set-default-to-vX # replace X with the KIM API major version number :
#
# setup and compile lammps
# :
tar zxvf lammps-DDMMMYY.tar.gz
cd lammps-DDMMMYY/src/KIM
vi Makefile.lammps # edit the three lines to look like below:
# kim_SYSINC = -I../../../openkim-api-vX.X.X/KIM_API
# kim_SYSLIB = -lkim
# kim_SYSPATH = -L../../../openkim-api-vX.X.X/KIM_API
cd ../
cd lammps-DDMMMYY/src
make yes-kim
cd STUBS
make
@ -167,7 +153,7 @@ region box block 0.0 $\{xx\} 0.0 $\{yy\} 0.0 $\{zz\}
create_box 1 box
create_atoms 1 box :
pair_style kim KIMvirial EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000
pair_style kim KIMvirial EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_001
pair_coeff * * Al :
mass 1 26.98
@ -181,7 +167,7 @@ fix 1 all nve :
run 100
#---------------------------------------------------------------------------------------- :
./lammps-DDMMYY/src/lmp_serial < al-input :
./lammps-DDMMYY/src/lmp_serial -in al-input :
</pre>
:line
@ -209,7 +195,7 @@ LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This current version of pair_style kim is compatible with the
openkim-api package version 1.2.0 and higher.
kim-api package version 1.6.0 and higher.
[Related commands:]