mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10385 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
4bde9638de
commit
489dceb7e6
|
|
@ -91,81 +91,141 @@ namely http://openkim.org. The tarball you download is
|
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</P>
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<PRE>tar xvfz openkim*tgz
|
||||
</PRE>
|
||||
<P>The openkim/DOCs directory has further documentation. For more
|
||||
information on installing KIM and troubleshooting refer to
|
||||
<P>The openkim-api-vX.X.X/DOCS directory has further documentation. For
|
||||
more information on installing KIM and troubleshooting refer to
|
||||
openkim/INSTALL.
|
||||
</P>
|
||||
<P>Here is a brief summary of how to build KIM:
|
||||
</P>
|
||||
<OL><LI>Set the following environment variables. It is recommended to place
|
||||
the above environment variables definitions in your shell setup file
|
||||
which is located in your home directory (e.g. ~/.bashrc).
|
||||
<OL><LI>If you have previously used the openkim-api package (versions 1.1.1 or
|
||||
below), it is recommended that you remove all associated environment
|
||||
variables from your environment. (These include, KIM_DIR, KIM_INTEL,
|
||||
KIM_SYSTEM32, KIM_DYNAMIC, KIM_API_DIR, KIM_TESTS_DIR,
|
||||
KIM_MODEL_DRIVERS_DIR, and KIM_MODELS_DIR.) All setting are now
|
||||
specified in the Makefile.KIM_Config file.
|
||||
|
||||
<PRE> (a) Define the location of the openKIM API root directory. For example,
|
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if you untarred the `openkim-api-vX.X.X.tgz' tarball in your home
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||||
directory, you would do:
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</PRE>
|
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<PRE> bash:
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% export KIM_DIR=~/openkim-api-vX.X.X
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</PRE>
|
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<PRE> tcsh:
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% setenv KIM_DIR ~/openkim-api-vX.X.X
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</PRE>
|
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<PRE> The `%' symbol represents the bash sell prompt and should not be
|
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typed.
|
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</PRE>
|
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<PRE> (b) By default, all makefiles use the GNU compilers for 64 bit Linux.
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In order to use the Intel compiler, define the environment variable
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KIM_INTEL
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</PRE>
|
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<PRE> bash:
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% export KIM_INTEL="yes"
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</PRE>
|
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<PRE> tcsh:
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% setenv KIM_INTEL "yes"
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</PRE>
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<PRE> (c) For a 32 bit machine, define the environment variable KIM_SYSTEM32
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</PRE>
|
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<PRE> bash:
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% export KIM_SYSTEM32="yes"
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</PRE>
|
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<PRE> tchs:
|
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% setenv KIM_SYSTEM32 "yes"
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</PRE>
|
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<PRE> (d) Define variable for dynamic linking (recommended)
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</PRE>
|
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<PRE> bash:
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export KIM_DYNAMIC=yes
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</PRE>
|
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<PRE> tcsh:
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setenv KIM_DYNAMIC=yes
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</PRE>
|
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<PRE> If this environment variable is not set the default will be static
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||||
linking. In that case all KIM models will be linked, producing
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||||
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>
|
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<LI>To compile the package, go to the $KIM_DIR directory and execute
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make.
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<LI>Set up the Makefile.KIM_Config file
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|
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<PRE> % cd $KIM_DIR
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<PRE> (a) Copy the file Makefile.KIM_Config.example to Makefile.KIM_Config
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||||
For example, if you untarred the `openkim-api-vX.X.X.tgz' tarball in
|
||||
your home directory, you would do:
|
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</PRE>
|
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<PRE> % cd $HOME/openkim-api-vX.X.X
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||||
% cp Makefile.KIM_Config.example Makefile.KIM_Config
|
||||
</PRE>
|
||||
<PRE> The `%' symbol represents the bash sell prompt and should not be typed.
|
||||
|
||||
</PRE>
|
||||
<PRE> (Above `vX.X.X' represents the current release number.)
|
||||
</PRE>
|
||||
<PRE> (b) Edit the file Makefile.KIM_Config and set the appropriate value for the
|
||||
KIM_DIR variable. This must expand to an absolute path. Using the same
|
||||
assumptions as above, this would be
|
||||
</PRE>
|
||||
<PRE> KIM_DIR = $(HOME)/openkim-api-vX.X.X
|
||||
</PRE>
|
||||
<PRE> (c) If appropriate, set explicit values for the remaining three
|
||||
directories
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||||
</PRE>
|
||||
<PRE> KIM_MODEL_DRIVERS_DIR =
|
||||
KIM_MODELS_DIR =
|
||||
KIM_TESTS_DIR =
|
||||
</PRE>
|
||||
<PRE> If these lines are commented out, defaults will be provided by the
|
||||
openkim-api make system.
|
||||
</PRE>
|
||||
<PRE> (d) Set the value of KIM_COMPILERSUITE. Possible values are `GCC' and
|
||||
`INTEL'.
|
||||
</PRE>
|
||||
<PRE> KIM_COMPILERSUITE = GCC
|
||||
</PRE>
|
||||
<PRE> (e) Set the value of KIM_SYSTEMLINKER. Possible values are `linux',
|
||||
`freebsd', and `darwin'.
|
||||
</PRE>
|
||||
<PRE> KIM_SYSTEMLINKER = linux
|
||||
</PRE>
|
||||
<PRE> (f) Set the value of KIM_SYSTEMARCH. Possible values are `32bit' and
|
||||
`64bit'.
|
||||
</PRE>
|
||||
<PRE> KIM_SYSTEMARCH = 64bit
|
||||
</PRE>
|
||||
<PRE> (g) Set the value of KIM_LINK. Possible values are `dynamic-load',
|
||||
`dynamic-link', and `static-link'.
|
||||
</PRE>
|
||||
<PRE> KIM_LINK = dynamic-load
|
||||
</PRE>
|
||||
<PRE> `dynamic-load' is the preferred option. (Unless performance or
|
||||
other issues require it, you should use dynamic-load.)
|
||||
`dynamic-link' is like `dynamic-load' but does not use the dl.h
|
||||
library. This option requires a more complicated Makefile
|
||||
process, but may improve computation time in some instances.
|
||||
`static-link' only works with ONE Model and AT MOST ONE Model
|
||||
Driver (in order to avoid the possibility of symbol
|
||||
clashes).
|
||||
</PRE>
|
||||
<PRE> (h) Set override values for other variables, if necessary, by
|
||||
adding the desired variable name (after the "# overwrite
|
||||
default variable values here" line) and filling in appropriate
|
||||
values.
|
||||
</PRE>
|
||||
<PRE> # overwrite default variable values here
|
||||
</PRE>
|
||||
<PRE> # overwrite default compiler options
|
||||
</PRE>
|
||||
<PRE> CC =
|
||||
CXX =
|
||||
FC =
|
||||
</PRE>
|
||||
<PRE> # overwrite default compiler option flag lists
|
||||
FFLAGS =
|
||||
CCFLAGS =
|
||||
CXXFLAGS =
|
||||
LDFLAGS =
|
||||
</PRE>
|
||||
<PRE> # overwrite default linker options
|
||||
LDSHAREDFLAG =
|
||||
LINKSONAME =
|
||||
LDWHOLEARCHIVESTARTFLAG =
|
||||
LDWHOLEARCHIVEENDFLAG =
|
||||
</PRE>
|
||||
<PRE> # overwrite default install directories
|
||||
package_name =
|
||||
prefix =
|
||||
libdir =
|
||||
</PRE>
|
||||
<LI>In the remainder of the documentation we will use the string $KD to
|
||||
represent the location of the openkim-api source package (the value of
|
||||
the KIM_DIR variable discussed above). If you wish to, type the below
|
||||
commands exactly as written to set the shell variable KD to the
|
||||
appropriate value:
|
||||
|
||||
<PRE> bash:
|
||||
% export KD=$HOME/openkim-api-vX.X.X
|
||||
</PRE>
|
||||
<LI>To compile the package, including the provided examples, change to the
|
||||
$KD directory and execute `make examples' and then `make':
|
||||
|
||||
<PRE> % cd $KD
|
||||
% make examples
|
||||
% make
|
||||
</PRE>
|
||||
<PRE> This builds all Models, Tests, and the openKIM API service routine
|
||||
library. The targets defined by the Makefile in this directory include:
|
||||
<PRE> This builds all Model Drivers, 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
|
||||
(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> `make' -- compiles the API and all Models and Tests
|
||||
`make all' -- same as `make'
|
||||
`make clean' -- will remove appropriate .o, .mod, .a, .so and
|
||||
executable files
|
||||
`make install' -- install files to `/usr/local/lib' by default
|
||||
`make uninstall' -- delete files installed by `make install'
|
||||
`make openkim-api' -- compiles only the API
|
||||
`make examples' -- copies examples into the appropriate
|
||||
directories (no overwrite)
|
||||
`make examples-force' -- copies examples into the appropriate
|
||||
directories (overwrite)
|
||||
`make examples-clean' -- remove all examples from the MODEL_DRIVERS,
|
||||
MODELS, and TESTS directories.
|
||||
</PRE>
|
||||
<LI>Verify that the compilation was successful by running a Test.
|
||||
|
||||
|
|
@ -174,24 +234,16 @@ make.
|
|||
name of the Model can be piped in using an `echo' command. For
|
||||
example, the following Fortran 90 Test reads in one Model:
|
||||
</PRE>
|
||||
<PRE> % cd $KIM_DIR/TESTs/test_Ar_free_cluster_CLUSTER_F90
|
||||
<PRE> % cd $KD/TESTs/test_Ar_free_cluster_CLUSTER_F90
|
||||
% echo "model_Ar_P_MLJ_CLUSTER_C" | ./test_Ar_free_cluster_CLUSTER_F90
|
||||
</PRE>
|
||||
<PRE> (See the README files in the Test directories for an explanation of what
|
||||
<PRE> (See the README files in the Test directories for an explanation of what
|
||||
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, re-compile (from the $KIM_DIR directory).
|
||||
|
||||
<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:
|
||||
If changes are made to the code, re-compile (from the $KD
|
||||
directory).
|
||||
</OL>
|
||||
<PRE> KIM_API_DIR
|
||||
KIM_TESTS_DIR
|
||||
KIM_MODEL_DRIVERS_DIR
|
||||
KIM_MODELS_DIR
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
|
|
@ -217,7 +269,7 @@ 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 1.1.0 and higher.
|
||||
openkim-api package version 1.2.0 and higher.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
183
doc/pair_kim.txt
183
doc/pair_kim.txt
|
|
@ -88,82 +88,141 @@ namely http://openkim.org. The tarball you download is
|
|||
|
||||
tar xvfz openkim*tgz :pre
|
||||
|
||||
The openkim/DOCs directory has further documentation. For more
|
||||
information on installing KIM and troubleshooting refer to
|
||||
The openkim-api-vX.X.X/DOCS directory has further documentation. For
|
||||
more information on installing KIM and troubleshooting refer to
|
||||
openkim/INSTALL.
|
||||
|
||||
Here is a brief summary of how to build KIM:
|
||||
|
||||
Set the following environment variables. It is recommended to place
|
||||
the above environment variables definitions in your shell setup file
|
||||
which is located in your home directory (e.g. ~/.bashrc). :olb,l
|
||||
If you have previously used the openkim-api package (versions 1.1.1 or
|
||||
below), it is recommended that you remove all associated environment
|
||||
variables from your environment. (These include, KIM_DIR, KIM_INTEL,
|
||||
KIM_SYSTEM32, KIM_DYNAMIC, KIM_API_DIR, KIM_TESTS_DIR,
|
||||
KIM_MODEL_DRIVERS_DIR, and KIM_MODELS_DIR.) All setting are now
|
||||
specified in the Makefile.KIM_Config file. :olb,l
|
||||
|
||||
(a) Define the location of the openKIM API root directory. For example,
|
||||
if you untarred the `openkim-api-vX.X.X.tgz' tarball in your home
|
||||
directory, you would do: :pre
|
||||
Set up the Makefile.KIM_Config file :l
|
||||
|
||||
bash:
|
||||
% export KIM_DIR=~/openkim-api-vX.X.X :pre
|
||||
(a) Copy the file Makefile.KIM_Config.example to Makefile.KIM_Config
|
||||
For example, if you untarred the `openkim-api-vX.X.X.tgz' tarball in
|
||||
your home directory, you would do: :pre
|
||||
|
||||
tcsh:
|
||||
% setenv KIM_DIR ~/openkim-api-vX.X.X :pre
|
||||
% cd $HOME/openkim-api-vX.X.X
|
||||
% cp Makefile.KIM_Config.example Makefile.KIM_Config :pre
|
||||
|
||||
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
|
||||
KIM_INTEL :pre
|
||||
(Above `vX.X.X' represents the current release number.) :pre
|
||||
|
||||
bash:
|
||||
% export KIM_INTEL="yes" :pre
|
||||
(b) Edit the file Makefile.KIM_Config and set the appropriate value for the
|
||||
KIM_DIR variable. This must expand to an absolute path. Using the same
|
||||
assumptions as above, this would be :pre
|
||||
|
||||
tcsh:
|
||||
% setenv KIM_INTEL "yes" :pre
|
||||
KIM_DIR = $(HOME)/openkim-api-vX.X.X :pre
|
||||
|
||||
(c) For a 32 bit machine, define the environment variable KIM_SYSTEM32 :pre
|
||||
(c) If appropriate, set explicit values for the remaining three
|
||||
directories :pre
|
||||
|
||||
bash:
|
||||
% export KIM_SYSTEM32="yes" :pre
|
||||
KIM_MODEL_DRIVERS_DIR =
|
||||
KIM_MODELS_DIR =
|
||||
KIM_TESTS_DIR = :pre
|
||||
|
||||
tchs:
|
||||
% setenv KIM_SYSTEM32 "yes" :pre
|
||||
If these lines are commented out, defaults will be provided by the
|
||||
openkim-api make system. :pre
|
||||
|
||||
(d) Define variable for dynamic linking (recommended) :pre
|
||||
|
||||
bash:
|
||||
export KIM_DYNAMIC=yes :pre
|
||||
(d) Set the value of KIM_COMPILERSUITE. Possible values are `GCC' and
|
||||
`INTEL'. :pre
|
||||
|
||||
tcsh:
|
||||
setenv KIM_DYNAMIC=yes :pre
|
||||
KIM_COMPILERSUITE = GCC :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
|
||||
(e) Set the value of KIM_SYSTEMLINKER. Possible values are `linux',
|
||||
`freebsd', and `darwin'. :pre
|
||||
|
||||
To compile the package, go to the $KIM_DIR directory and execute
|
||||
make. :l
|
||||
KIM_SYSTEMLINKER = linux :pre
|
||||
|
||||
% cd $KIM_DIR
|
||||
(f) Set the value of KIM_SYSTEMARCH. Possible values are `32bit' and
|
||||
`64bit'. :pre
|
||||
|
||||
KIM_SYSTEMARCH = 64bit :pre
|
||||
|
||||
(g) Set the value of KIM_LINK. Possible values are `dynamic-load',
|
||||
`dynamic-link', and `static-link'. :pre
|
||||
|
||||
KIM_LINK = dynamic-load :pre
|
||||
|
||||
`dynamic-load' is the preferred option. (Unless performance or
|
||||
other issues require it, you should use dynamic-load.)
|
||||
`dynamic-link' is like `dynamic-load' but does not use the dl.h
|
||||
library. This option requires a more complicated Makefile
|
||||
process, but may improve computation time in some instances.
|
||||
`static-link' only works with ONE Model and AT MOST ONE Model
|
||||
Driver (in order to avoid the possibility of symbol
|
||||
clashes). :pre
|
||||
|
||||
(h) Set override values for other variables, if necessary, by
|
||||
adding the desired variable name (after the "# overwrite
|
||||
default variable values here" line) and filling in appropriate
|
||||
values. :pre
|
||||
|
||||
# overwrite default variable values here :pre
|
||||
|
||||
# overwrite default compiler options :pre
|
||||
CC =
|
||||
CXX =
|
||||
FC = :pre
|
||||
|
||||
# overwrite default compiler option flag lists
|
||||
FFLAGS =
|
||||
CCFLAGS =
|
||||
CXXFLAGS =
|
||||
LDFLAGS = :pre
|
||||
|
||||
# overwrite default linker options
|
||||
LDSHAREDFLAG =
|
||||
LINKSONAME =
|
||||
LDWHOLEARCHIVESTARTFLAG =
|
||||
LDWHOLEARCHIVEENDFLAG = :pre
|
||||
|
||||
# overwrite default install directories
|
||||
package_name =
|
||||
prefix =
|
||||
libdir = :pre
|
||||
|
||||
In the remainder of the documentation we will use the string $KD to
|
||||
represent the location of the openkim-api source package (the value of
|
||||
the KIM_DIR variable discussed above). If you wish to, type the below
|
||||
commands exactly as written to set the shell variable KD to the
|
||||
appropriate value: :l
|
||||
|
||||
bash:
|
||||
% export KD=$HOME/openkim-api-vX.X.X :pre
|
||||
|
||||
To compile the package, including the provided examples, change to the
|
||||
$KD directory and execute `make examples' and then `make': :l
|
||||
|
||||
% cd $KD
|
||||
% make examples
|
||||
% 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
|
||||
This builds all Model Drivers, 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 clean' -- will remove appropriate .o, .mod, .a, .so and
|
||||
executable files
|
||||
`make install' -- install files to `/usr/local/lib' by default
|
||||
`make uninstall' -- delete files installed by `make install'
|
||||
`make openkim-api' -- compiles only the API
|
||||
`make examples' -- copies examples into the appropriate
|
||||
directories (no overwrite)
|
||||
`make examples-force' -- copies examples into the appropriate
|
||||
directories (overwrite)
|
||||
`make examples-clean' -- remove all examples from the MODEL_DRIVERS,
|
||||
MODELS, and TESTS directories. :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
|
||||
|
||||
Verify that the compilation was successful by running a Test. :l
|
||||
|
||||
The provided example Tests read in the name of a Model (or Models)
|
||||
|
|
@ -171,23 +230,15 @@ Verify that the compilation was successful by running a Test. :l
|
|||
name of the Model can be piped in using an `echo' command. For
|
||||
example, the following Fortran 90 Test reads in one Model: :pre
|
||||
|
||||
% cd $KIM_DIR/TESTs/test_Ar_free_cluster_CLUSTER_F90
|
||||
% cd $KD/TESTs/test_Ar_free_cluster_CLUSTER_F90
|
||||
% echo "model_Ar_P_MLJ_CLUSTER_C" | ./test_Ar_free_cluster_CLUSTER_F90 :pre
|
||||
|
||||
(See the README files in the Test directories for an explanation of what
|
||||
(See the README files in the Test directories for an explanation of what
|
||||
the Tests do.) :pre
|
||||
|
||||
Each Test (and Model) has its own make file for compiling and linking.
|
||||
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, MODEL_DRIVERS, or MODELs one or more of the following environment
|
||||
variables must be set: :l,ole
|
||||
|
||||
KIM_API_DIR
|
||||
KIM_TESTS_DIR
|
||||
KIM_MODEL_DRIVERS_DIR
|
||||
KIM_MODELS_DIR :pre
|
||||
If changes are made to the code, re-compile (from the $KD
|
||||
directory). :l,ole
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -214,7 +265,7 @@ 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 1.1.0 and higher.
|
||||
openkim-api package version 1.2.0 and higher.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue