Merge pull request #2434 from akohlmey/swig-wrappers
Provide an interface file for creating script wrappers for LAMMPS with SWIG
This commit is contained in:
Axel Kohlmeyer
@ -379,6 +379,13 @@ foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCD
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
# optionally enable building script wrappers using swig
|
||||
option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF)
|
||||
if(WITH_SWIG)
|
||||
get_filename_component(LAMMPS_SWIG_DIR ${LAMMPS_SOURCE_DIR}/../tools/swig ABSOLUTE)
|
||||
add_subdirectory(${LAMMPS_SWIG_DIR} swig)
|
||||
endif()
|
||||
|
||||
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
|
||||
separate_arguments(CMAKE_TUNE_FLAGS)
|
||||
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
|
||||
|
||||
@ -23,7 +23,7 @@ set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
|
||||
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
|
||||
set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
|
||||
set(CMAKE_TUNE_FLAGS "-Wno-missing-include-dirs" CACHE STRING "" FORCE)
|
||||
set(CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-stdcall-fixup" CACHE STRING "" FORCE)
|
||||
set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-stdcall-fixup" CACHE STRING "" FORCE)
|
||||
set(CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
|
||||
set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
|
||||
set(BUILD_TOOLS ON CACHE BOOL "" FORCE)
|
||||
set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")
|
||||
|
||||
@ -53,5 +53,5 @@ in two stages: the callback function is registered with the pair style
|
||||
and then called from the Pair::ev_tally() function, which is called for
|
||||
each pair after force and energy has been computed for this pair. Then
|
||||
the tallied values are retrieved with the standard compute_scalar or
|
||||
compute_vector or compute_peratom methods. The USER-TALLY package
|
||||
provides *examples*\ _compute_tally.html for utilizing this mechanism.
|
||||
compute_vector or compute_peratom methods. The :doc:`compute styles in the USER-TALLY package <compute_tally>`
|
||||
provide *examples* for utilizing this mechanism.
|
||||
|
||||
@ -21,7 +21,7 @@ distribution.
|
||||
+------------------------+--------------------------------------------------------------------+
|
||||
| ``gui.py`` | GUI go/stop/temperature-slider to control LAMMPS |
|
||||
+------------------------+--------------------------------------------------------------------+
|
||||
| ``plot.py`` | real-time temperature plot with GnuPlot via Pizza.py |
|
||||
| ``plot.py`` | real-time temperature plot with GnuPlot via Pizza.py |
|
||||
+------------------------+--------------------------------------------------------------------+
|
||||
| ``viz_TOOL.py`` | real-time viz via some viz package |
|
||||
+------------------------+--------------------------------------------------------------------+
|
||||
|
||||
@ -94,6 +94,7 @@ Miscellaneous tools
|
||||
* :ref:`kate <kate>`
|
||||
* :ref:`LAMMPS shell <lammps_shell>`
|
||||
* :ref:`singularity <singularity_tool>`
|
||||
* :ref:`SWIG interface <swig>`
|
||||
* :ref:`vim <vim>`
|
||||
|
||||
----------
|
||||
@ -559,6 +560,8 @@ More details about this are in the `readline documentation <https://tiswww.cwru.
|
||||
LAMMPS Shell tips and tricks
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
Below are some suggestions for how to use and customize the LAMMPS shell.
|
||||
|
||||
Enable tilde expansion
|
||||
""""""""""""""""""""""
|
||||
|
||||
@ -591,8 +594,8 @@ command line like this:
|
||||
xterm -title "LAMMPS Shell" -e /path/to/lammps-shell -i in.file.lmp
|
||||
|
||||
|
||||
Use history create input file
|
||||
"""""""""""""""""""""""""""""
|
||||
Use history to create an input file
|
||||
"""""""""""""""""""""""""""""""""""
|
||||
|
||||
When experimenting with commands to interactively to figure out a
|
||||
suitable choice of settings or simply the correct syntax, you may want
|
||||
@ -876,6 +879,123 @@ For more details please see the README.md file in that folder.
|
||||
|
||||
----------
|
||||
|
||||
.. _swig:
|
||||
|
||||
SWIG interface
|
||||
--------------
|
||||
|
||||
The `SWIG tool <http://swig.org>`_ offers a mostly automated way to
|
||||
incorporate compiled code modules into scripting languages. It
|
||||
processes the function prototypes in C and generates wrappers for a wide
|
||||
variety of scripting languages from it. Thus it can also be applied to
|
||||
the :doc:`C language library interface <Library>` of LAMMPS so that
|
||||
build a wrapper that allows to call LAMMPS from programming languages
|
||||
like: C#/Mono, Lua, Java, JavaScript, Perl, Python, R, Ruby, Tcl, and
|
||||
more.
|
||||
|
||||
What is included
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
We provide here an "interface file", ``lammps.i``, that has the content
|
||||
of the ``library.h`` file adapted so SWIG can process it. That will
|
||||
create wrappers for all the functions that are present in the LAMMPS C
|
||||
library interface. Please note that not all kinds of C functions can be
|
||||
automatically translated, so you would have to add custom functions to
|
||||
be able to utilize those where the automatic translation does not work.
|
||||
A few functions for converting pointers and accessing arrays are
|
||||
predefined. We provide the file here on an "as is" basis to help people
|
||||
getting started, but not as a fully tested and supported feature of the
|
||||
LAMMPS distribution. Any contributions to complete this are, of course,
|
||||
welcome. Please also note, that for the case of creating a Python wrapper,
|
||||
a fully supported :doc:`Ctypes based lammps module <Python_module>`
|
||||
already exists. That module is designed to be object oriented while
|
||||
SWIG will generate a 1:1 translation of the functions in the interface file.
|
||||
|
||||
Building the wrapper
|
||||
^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
When using CMake, the build steps for building a wrapper
|
||||
module are integrated for the languages: Java, Lua,
|
||||
Perl5, Python, Ruby, and Tcl. These require that the
|
||||
LAMMPS library is build as a shared library and all
|
||||
necessary development headers and libraries are present.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D WITH_SWIG=on # to enable building any SWIG wrapper
|
||||
-D BUILD_SWIG_JAVA=on # to enable building the Java wrapper
|
||||
-D BUILD_SWIG_LUA=on # to enable building the Lua wrapper
|
||||
-D BUILD_SWIG_PERL5=on # to enable building the Perl 5.x wrapper
|
||||
-D BUILD_SWIG_PYTHON=on # to enable building the Python wrapper
|
||||
-D BUILD_SWIG_RUBY=on # to enable building the Ruby wrapper
|
||||
-D BUILD_SWIG_TCL=on # to enable building the Tcl wrapper
|
||||
|
||||
|
||||
Manual building allows a little more flexibility. E.g. one can choose
|
||||
the name of the module and build and use a dynamically loaded object
|
||||
for Tcl with:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$ swig -tcl -module tcllammps lammps.i
|
||||
$ gcc -fPIC -shared $(pkgconf --cflags tcl) -o tcllammps.so \
|
||||
lammps_wrap.c -L ../src/ -llammps
|
||||
$ tclsh
|
||||
|
||||
Or one can build an extended Tcl shell command with the wrapped
|
||||
functions included with:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$ swig -tcl -module tcllmps lammps_shell.i
|
||||
$ gcc -o tcllmpsh lammps_wrap.c -Xlinker -export-dynamic \
|
||||
-DHAVE_CONFIG_H $(pkgconf --cflags tcl) \
|
||||
$(pkgconf --libs tcl) -L ../src -llammps
|
||||
|
||||
In both cases it is assumed that the LAMMPS library was compiled
|
||||
as a shared library in the ``src`` folder. Otherwise the last
|
||||
part of the commands needs to be adjusted.
|
||||
|
||||
Utility functions
|
||||
^^^^^^^^^^^^^^^^^
|
||||
|
||||
Definitions for several utility functions required to manage and access
|
||||
data passed or returned as pointers are included in the ``lammps.i``
|
||||
file. So most of the functionality of the library interface should be
|
||||
accessible. What works and what does not depends a bit on the
|
||||
individual language for which the wrappers are built and how well SWIG
|
||||
supports those. The `SWIG documentation <http://swig.org/doc.html>`_
|
||||
has very detailed instructions and recommendations.
|
||||
|
||||
Usage examples
|
||||
^^^^^^^^^^^^^^
|
||||
|
||||
The ``tools/swig`` folder has multiple shell scripts, ``run_<name>_example.sh``
|
||||
that will create a small example script and demonstrate how to load
|
||||
the wrapper and run LAMMPS through it in the corresponding programming
|
||||
language.
|
||||
|
||||
For illustration purposes below is a part of the Tcl example script.
|
||||
|
||||
.. code-block:: tcl
|
||||
|
||||
% load ./tcllammps.so
|
||||
% set lmp [lammps_open_no_mpi 0 NULL NULL]
|
||||
% lammps_command $lmp "units real"
|
||||
% lammps_command $lmp "lattice fcc 2.5"
|
||||
% lammps_command $lmp "region box block -5 5 -5 5 -5 5"
|
||||
% lammps_command $lmp "create_box 1 box"
|
||||
% lammps_command $lmp "create_atoms 1 box"
|
||||
%
|
||||
% set dt [doublep_value [voidp_to_doublep [lammps_extract_global $lmp dt]]]
|
||||
% puts "LAMMPS version $ver"
|
||||
% puts [format "Number of created atoms: %g" [lammps_get_natoms $lmp]]
|
||||
% puts "Current size of timestep: $dt"
|
||||
% puts "LAMMPS version: [lammps_version $lmp]"
|
||||
% lammps_close $lmp
|
||||
|
||||
----------
|
||||
|
||||
.. _vim:
|
||||
|
||||
vim tool
|
||||
|
||||
@ -24,8 +24,8 @@ Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that extracts the angle energy calculated by each
|
||||
of the angle sub-styles used in the "angle_style
|
||||
hybrid" angle_hybrid.html command. These values are made accessible
|
||||
of the angle sub-styles used in the doc:`angle_style hybrid <angle_hybrid>`
|
||||
command. These values are made accessible
|
||||
for output or further processing by other commands. The group
|
||||
specified for this command is ignored.
|
||||
|
||||
|
||||
@ -222,9 +222,9 @@ Default
|
||||
"""""""
|
||||
|
||||
The default keyword values specific to this fix are exy = xyz, strain
|
||||
= 0 0. The remaining defaults are the same as for *fix
|
||||
npt*\ _fix_nh.html except tchain = 1. The reason for this change is
|
||||
given in :doc:`fix nvt/sllod <fix_nvt_sllod>`.
|
||||
= 0 0. The remaining defaults are the same as for :doc:`fix npt <fix_nh>`
|
||||
except tchain = 1. The reason for this change is given in
|
||||
:doc:`fix nvt/sllod <fix_nvt_sllod>`.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -345,9 +345,9 @@ given by
|
||||
\rho_{\alpha\beta} (r_{ij})\right) +
|
||||
\frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
|
||||
|
||||
where :math:`\rho_{\alpha\beta}` refers to the density contributed
|
||||
where :math:`\rho_{\alpha\beta}` refers to the density contributed
|
||||
by a neighbor atom J of element :math:`\beta` at the site of atom I
|
||||
of element :math:`\alpha`.
|
||||
of element :math:`\alpha`.
|
||||
This has the same form as the EAM formula above, except that rho is
|
||||
now a functional specific to the elements of both atoms I and J,
|
||||
so that different elements can contribute differently to the total
|
||||
@ -408,7 +408,7 @@ each with the following format:
|
||||
|
||||
The units of these quantities in line 1 are the same as for *setfl*
|
||||
files. Note that the rho(r) arrays in Finnis/Sinclair can be
|
||||
asymmetric (:math:`\rho_{\alpha\beta} (r) \neq \rho_{\beta\alpha} (r)` )
|
||||
asymmetric (:math:`\rho_{\alpha\beta} (r) \neq \rho_{\beta\alpha} (r)` )
|
||||
so there are Nelements\^2 of them listed in the file.
|
||||
|
||||
Following the Nelements sections, Nr values for each pair potential
|
||||
|
||||
@ -1713,6 +1713,7 @@ lsfftw
|
||||
ltbbmalloc
|
||||
lubricateU
|
||||
lucy
|
||||
Lua
|
||||
Luding
|
||||
Lussetti
|
||||
Lustig
|
||||
@ -3035,6 +3036,7 @@ taubi
|
||||
tb
|
||||
tchain
|
||||
Tchain
|
||||
Tcl
|
||||
Tcom
|
||||
tcsh
|
||||
tdamp
|
||||
|
||||
@ -11,11 +11,11 @@ library.
|
||||
|
||||
See these sections of the LAMMPS manual for details:
|
||||
|
||||
Build LAMMPS as a library (doc/Build_basics.html)
|
||||
Link LAMMPS as a library to another code (doc/Build_link.html)
|
||||
Coupling LAMMPS to other codes (doc/Howto_couple.html)
|
||||
Using LAMMPS in client/server mode (doc/Howto_client_server.html)
|
||||
Library interface to LAMMPS (doc/Howto_library.html)
|
||||
Build LAMMPS as a library (doc/html/Build_basics.html)
|
||||
Link LAMMPS as a library to another code (doc/html/Build_link.html)
|
||||
Coupling LAMMPS to other codes (doc/html/Howto_couple.html)
|
||||
Using LAMMPS in client/server mode (doc/html/Howto_client_server.html)
|
||||
Library interface to LAMMPS (doc/html/Howto_library.html)
|
||||
|
||||
The library interface to LAMMPS is in src/library.cpp. Routines can
|
||||
be easily added to this file so an external program can perform the
|
||||
@ -25,23 +25,23 @@ LAMMPS tasks desired.
|
||||
|
||||
These are the sub-directories included in this directory:
|
||||
|
||||
simple simple example of driver code calling LAMMPS as a lib
|
||||
multiple example of driver code calling multiple instances of LAMMPS
|
||||
simple simple example of driver code calling LAMMPS as a lib
|
||||
multiple example of driver code calling multiple instances of LAMMPS
|
||||
plugin example for loading LAMMPS at runtime from a shared library
|
||||
lammps_mc client/server coupling of Monte Carlo client
|
||||
with LAMMPS server for energy evaluation
|
||||
lammps_nwchem client/server coupling of LAMMPS client with
|
||||
NWChem quantum DFT as server for quantum forces
|
||||
lammps_quest MD with quantum forces, coupling to Quest DFT code
|
||||
lammps_spparks grain-growth Monte Carlo with strain via MD,
|
||||
coupling to SPPARKS kinetic MC code
|
||||
lammps_quest MD with quantum forces, coupling to Quest DFT code
|
||||
lammps_spparks grain-growth Monte Carlo with strain via MD,
|
||||
coupling to SPPARKS kinetic MC code
|
||||
lammps_vasp client/server coupling of LAMMPS client with
|
||||
VASP quantum DFT as server for quantum forces
|
||||
library collection of useful inter-code communication routines
|
||||
library collection of useful inter-code communication routines
|
||||
fortran a simple wrapper on the LAMMPS library API that
|
||||
can be called from Fortran
|
||||
can be called from Fortran
|
||||
fortran2 a more sophisticated wrapper on the LAMMPS library API that
|
||||
can be called from Fortran
|
||||
can be called from Fortran
|
||||
fortran_dftb wrapper written by Nir Goldman (LLNL), as an
|
||||
extension to fortran2, used for calling LAMMPS
|
||||
from Fortran DFTB+ tight-binding code
|
||||
|
||||
@ -1,8 +1,8 @@
|
||||
Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
|
||||
|
||||
See the MESSAGE package (doc/Section_messages.html#MESSAGE)
|
||||
and Section_howto.html#howto10 for more details on how
|
||||
client/server coupling works in LAMMPS.
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the mc.cpp/h files are a standalone "client" MC code. It
|
||||
should be run on a single processor, though it could become a parallel
|
||||
@ -94,18 +94,18 @@ background.
|
||||
File mode of messaging:
|
||||
|
||||
% mpirun -np 1 mc in.mc file tmp.couple
|
||||
% mpirun -np 1 lmp_mpi -v mode file < in.mc.server
|
||||
% mpirun -np 1 lmp_mpi -v mode file -in in.mc.server
|
||||
|
||||
% mpirun -np 1 mc in.mc file tmp.couple
|
||||
% mpirun -np 4 lmp_mpi -v mode file < in.mc.server
|
||||
% mpirun -np 4 lmp_mpi -v mode file -in in.mc.server
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 mc in.mc zmq localhost:5555
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq < in.mc.server
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -in in.mc.server
|
||||
|
||||
% mpirun -np 1 mc in.mc zmq localhost:5555
|
||||
% mpirun -np 4 lmp_mpi -v mode zmq < in.mc.server
|
||||
% mpirun -np 4 lmp_mpi -v mode zmq -in in.mc.server
|
||||
|
||||
--------------
|
||||
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
Sample LAMMPS MD wrapper on NWChem via client/server coupling
|
||||
|
||||
See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
|
||||
Section_howto.html#howto10 for more details on how client/server
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the nwchem_wrap.py is a wrapper on the NWChem electronic
|
||||
@ -182,16 +182,16 @@ background.
|
||||
|
||||
File mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode file < in.client.W
|
||||
% mpirun -np 1 lmp_mpi -v mode file -in in.client.W
|
||||
% python nwchem_wrap.py file pw w.nw
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode file < in.client.h2o
|
||||
% mpirun -np 2 lmp_mpi -v mode file -in in.client.h2o
|
||||
% python nwchem_wrap.py file ao h2o.nw
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -in in.client.W
|
||||
% python nwchem_wrap.py zmq pw w.nw
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode zmq < in.client.h2o
|
||||
% mpirun -np 2 lmp_mpi -v mode zmq -in in.client.h2o
|
||||
% python nwchem_wrap.py zmq ao h2o.nw
|
||||
|
||||
@ -16,11 +16,11 @@ Lennard-Jones sigma between particles of different types that is
|
||||
larger than the sigma between particles of the same type (interior to
|
||||
grains).
|
||||
|
||||
lmpspk.cpp main program
|
||||
it links LAMMPS and SPPARKS as libraries
|
||||
in.spparks SPPARKS input script, without the run command
|
||||
lmppath.h contains path to LAMMPS home directory
|
||||
spkpath.h contains path to SPPARKS home directory
|
||||
lmpspk.cpp main program
|
||||
it links LAMMPS and SPPARKS as libraries
|
||||
in.spparks SPPARKS input script, without the run command
|
||||
lmppath.h contains path to LAMMPS home directory
|
||||
spkpath.h contains path to SPPARKS home directory
|
||||
|
||||
After editing the Makefile, lmppath.h, and spkpath.h to make them
|
||||
suitable for your box, type:
|
||||
|
||||
@ -1,8 +1,8 @@
|
||||
Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
|
||||
coupling
|
||||
|
||||
See the MESSAGE package (doc/Section_messages.html#MESSAGE) and
|
||||
Section_howto.html#howto10 for more details on how client/server
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
|
||||
@ -134,16 +134,16 @@ background.
|
||||
|
||||
File mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode file < in.client.W
|
||||
% mpirun -np 1 lmp_mpi -v mode file -in in.client.W
|
||||
% python vasp_wrap.py file POSCAR_W
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode file < in.client.W
|
||||
% mpirun -np 2 lmp_mpi -v mode file -in in.client.W
|
||||
% python vasp_wrap.py file POSCAR_W
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq < in.client.W
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -in in.client.W
|
||||
% python vasp_wrap.py zmq POSCAR_W
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode zmq < in.client.W
|
||||
% mpirun -np 2 lmp_mpi -v mode zmq -in in.client.W
|
||||
% python vasp_wrap.py zmq POSCAR_W
|
||||
|
||||
@ -179,7 +179,7 @@ the same simulation in different unit systems.
|
||||
|
||||
The USER directory contains subdirectories of user-provided example
|
||||
scripts for ser packages. See the README files in those directories
|
||||
for more info. See the doc/Section_start.html file for more info
|
||||
for more info. See the doc/html/Build_package.html file for more info
|
||||
about installing and building user packages.
|
||||
|
||||
The VISCOSITY directory has example scripts for computing the
|
||||
|
||||
@ -36,7 +36,7 @@ In a separate terminal, then, you should run LAMMPS compiled to provide
|
||||
fix_ipi functionalities.
|
||||
|
||||
```bash
|
||||
$LAMMPS < in.graphene
|
||||
$LAMMPS -in in.graphene
|
||||
```
|
||||
|
||||
You can run multiple instances of LAMMPS if you want to exploit the
|
||||
|
||||
@ -11,9 +11,8 @@ LAMMPS as the server, e.g. a quantum code computing quantum forces, so
|
||||
that ab initio MD could be performed. See an example of the latter in
|
||||
examples/COUPLE/lammps_vasp.
|
||||
|
||||
See the doc pages for the "MESSAGE package"
|
||||
(Package_details.html#PKG-MESSAGE) and "Howto client/server"
|
||||
(Howto_client_server.html) for more details on how client/server
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
--------------
|
||||
@ -30,7 +29,7 @@ You can also run the in.message scripts with an NPT integrator
|
||||
instead of NVE, if you comment/uncomment the correct lines.
|
||||
|
||||
The client and server script define a "mode" variable
|
||||
which can be set to file, zmq, mpi/one, or mpi/two,
|
||||
which can be set to file, zmq, mpi/one, or mpi/two,
|
||||
as illustrated below.
|
||||
|
||||
--------------
|
||||
@ -38,8 +37,8 @@ as illustrated below.
|
||||
To run this problem in the traditional way (no client/server coupling)
|
||||
do one of these:
|
||||
|
||||
% lmp_serial < in.message
|
||||
% mpirun -np 4 lmp_mpi < in.message
|
||||
% lmp_serial -in in.message
|
||||
% mpirun -np 4 lmp_mpi -in in.message
|
||||
|
||||
Or run with in.message.tilt.
|
||||
|
||||
@ -87,14 +86,14 @@ runs listed below.
|
||||
|
||||
File or ZMQ or mpi/two modes of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode file -log log.client < in.message.client &
|
||||
% mpirun -np 2 lmp_mpi -v mode file -log log.server < in.message.server
|
||||
% mpirun -np 1 lmp_mpi -v mode file -log log.client -in in.message.client &
|
||||
% mpirun -np 2 lmp_mpi -v mode file -log log.server -in in.message.server
|
||||
|
||||
% mpirun -np 4 lmp_mpi -v mode zmq -log log.client < in.message.client &
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -log log.server < in.message.server
|
||||
% mpirun -np 4 lmp_mpi -v mode zmq -log log.client -in in.message.client &
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -log log.server -in in.message.server
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client < in.message.client &
|
||||
% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server < in.message.server
|
||||
% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client -in in.message.client &
|
||||
% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server -in in.message.server
|
||||
|
||||
Or run with in.message.tilt.client/server.
|
||||
Don't run the tilt files with the "file" mode; they run too slow.
|
||||
|
||||
@ -1,8 +0,0 @@
|
||||
If you get bogus, large energies on timestep 0 when you run this
|
||||
example in.peptide, you likely have a machine/compiler problem with
|
||||
the pair_style "long" potentials which use Coulombic tabling by
|
||||
default.
|
||||
|
||||
See the "Additional build tips" sub-section of the manual in
|
||||
Section_start.html in the "Making LAMMPS" section for details and
|
||||
suggestions on how to work around this issue.
|
||||
@ -6,7 +6,7 @@ More information about each feature can be found by reading its doc
|
||||
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
|
||||
input script commands is as follows:
|
||||
|
||||
doc/Section_commands.html, subsection 3.5
|
||||
doc/Commands_all.html
|
||||
|
||||
User-contributed features are listed at the bottom of the fix,
|
||||
compute, pair, etc sections.
|
||||
|
||||
@ -46,6 +46,7 @@ replica tool to reorder LAMMPS replica trajectories according to
|
||||
singularity Singularity container descriptions suitable for LAMMPS development
|
||||
smd convert Smooth Mach Dynamics triangles to VTK
|
||||
spin perform a cubic polynomial interpolation of a GNEB MEP
|
||||
swig SWIG generated script language wrappers for the LAMMPS C library interface
|
||||
valgrind suppression files for use with valgrind's memcheck tool
|
||||
vim add-ons to VIM editor for editing LAMMPS input scripts
|
||||
xmgrace a collection of scripts to generate xmgrace plots
|
||||
|
||||
100
tools/swig/CMakeLists.txt
Normal file
100
tools/swig/CMakeLists.txt
Normal file
@ -0,0 +1,100 @@
|
||||
# CMake configuration for generating script language interfaces with SWIG
|
||||
|
||||
# set minimum CMake version required and switch to new policies for SWIG
|
||||
cmake_minimum_required(VERSION 3.14)
|
||||
if(POLICY CMP0078)
|
||||
cmake_policy(SET CMP0078 NEW)
|
||||
endif()
|
||||
if(POLICY CMP0086)
|
||||
cmake_policy(SET CMP0086 NEW)
|
||||
endif()
|
||||
enable_language(C)
|
||||
|
||||
# some of the find_package() scripts trigger developer warnings
|
||||
# even though they are bundled with CMake; Suppress them
|
||||
set(CMAKE_SUPPRESS_DEVELOPER_WARNINGS TRUE)
|
||||
|
||||
if(NOT BUILD_SHARED_LIBS)
|
||||
message(FATAL_ERROR "Option BUILD_SHARED_LIBS must be enabled to use SWIG wrappers")
|
||||
endif()
|
||||
|
||||
find_package(SWIG REQUIRED)
|
||||
include(${SWIG_USE_FILE})
|
||||
|
||||
option(BUILD_SWIG_JAVA "Build Java JNI wrapper with SWIG" OFF)
|
||||
option(BUILD_SWIG_LUA "Build Lua wrapper with SWIG" OFF)
|
||||
option(BUILD_SWIG_PERL5 "Build Perl5 wrapper with SWIG" OFF)
|
||||
option(BUILD_SWIG_PYTHON "Build Python wrapper with SWIG" OFF)
|
||||
option(BUILD_SWIG_RUBY "Build Ruby wrapper with SWIG" OFF)
|
||||
option(BUILD_SWIG_TCL "Build Tcl wrapper with SWIG" OFF)
|
||||
|
||||
set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES
|
||||
pllammps.pm __pycache__ log.lammps
|
||||
example.class example.java example.lua example.pl example.py example.rb example.tcl example.tcllmp
|
||||
javalammps.class javalammpsJNI.class javalammps.java javalammpsJNI.java
|
||||
_LMP_DATATYPE_CONST.class _LMP_STYLE_CONST.class _LMP_TYPE_CONST.class
|
||||
_LMP_DATATYPE_CONST.java _LMP_STYLE_CONST.java _LMP_TYPE_CONST.java
|
||||
SWIGTYPE_p_double.class SWIGTYPE_p_int.class SWIGTYPE_p_p_char.class SWIGTYPE_p_p_double.class
|
||||
SWIGTYPE_p_p_int.class SWIGTYPE_p_p_void.class SWIGTYPE_p_void.class
|
||||
SWIGTYPE_p_double.java SWIGTYPE_p_int.java SWIGTYPE_p_p_char.java SWIGTYPE_p_p_double.java
|
||||
SWIGTYPE_p_p_int.java SWIGTYPE_p_p_void.java SWIGTYPE_p_void.java)
|
||||
|
||||
if(BUILD_SWIG_JAVA)
|
||||
set_property(SOURCE lammps.i PROPERTY SWIG_MODULE_NAME javalammps)
|
||||
swig_add_library(javalammps TYPE MODULE LANGUAGE java SOURCES lammps.i)
|
||||
find_package(JNI REQUIRED)
|
||||
target_include_directories(javalammps PRIVATE ${JNI_INCLUDE_DIRS})
|
||||
swig_link_libraries(javalammps PRIVATE lammps ${JNI_LIBRARIES})
|
||||
configure_file(run_java_example.sh run_java_example.sh COPYONLY)
|
||||
endif()
|
||||
|
||||
if(BUILD_SWIG_LUA)
|
||||
set_property(SOURCE lammps.i PROPERTY SWIG_MODULE_NAME lualammps)
|
||||
swig_add_library(lualammps TYPE MODULE LANGUAGE lua SOURCES lammps.i)
|
||||
find_package(Lua REQUIRED)
|
||||
target_include_directories(lualammps PRIVATE ${LUA_INCLUDE_PATH})
|
||||
swig_link_libraries(lualammps PRIVATE lammps ${LUA_LIBRARY})
|
||||
configure_file(run_lua_example.sh run_lua_example.sh COPYONLY)
|
||||
endif()
|
||||
|
||||
if(BUILD_SWIG_PERL5)
|
||||
set_property(SOURCE lammps.i PROPERTY SWIG_MODULE_NAME pllammps)
|
||||
swig_add_library(pllammps TYPE MODULE LANGUAGE perl5 SOURCES lammps.i)
|
||||
find_package(PerlLibs REQUIRED 5.0)
|
||||
target_compile_definitions(pllammps PRIVATE _LARGEFILE64_SOURCE)
|
||||
target_include_directories(pllammps PRIVATE ${PERL_INCLUDE_PATH})
|
||||
swig_link_libraries(pllammps PRIVATE lammps ${PERL_LIBRARY})
|
||||
configure_file(run_perl_example.sh run_perl_example.sh COPYONLY)
|
||||
endif()
|
||||
|
||||
if(BUILD_SWIG_PYTHON)
|
||||
set_property(SOURCE lammps.i PROPERTY SWIG_MODULE_NAME pylammps)
|
||||
swig_add_library(pylammps TYPE MODULE LANGUAGE python SOURCES lammps.i)
|
||||
find_package(Python REQUIRED COMPONENTS Development)
|
||||
swig_link_libraries(pylammps PRIVATE lammps Python::Python)
|
||||
configure_file(run_python_example.sh run_python_example.sh COPYONLY)
|
||||
endif()
|
||||
|
||||
if(BUILD_SWIG_RUBY)
|
||||
set_property(SOURCE lammps.i PROPERTY SWIG_MODULE_NAME rubylammps)
|
||||
swig_add_library(rubylammps TYPE MODULE LANGUAGE ruby SOURCES lammps.i)
|
||||
find_package(Ruby REQUIRED)
|
||||
target_include_directories(rubylammps PRIVATE ${RUBY_INCLUDE_DIRS})
|
||||
swig_link_libraries(rubylammps PRIVATE lammps ${RUBY_LIBRARY})
|
||||
configure_file(run_ruby_example.sh run_ruby_example.sh COPYONLY)
|
||||
endif()
|
||||
|
||||
if(BUILD_SWIG_TCL)
|
||||
set_property(SOURCE lammps.i PROPERTY SWIG_MODULE_NAME tcllammps)
|
||||
swig_add_library(tcllammps TYPE MODULE LANGUAGE tcl SOURCES lammps.i)
|
||||
find_package(TCL REQUIRED)
|
||||
target_include_directories(tcllammps PRIVATE ${TCL_INCLUDE_PATH})
|
||||
swig_link_libraries(tcllammps PRIVATE lammps ${TCL_LIBRARY})
|
||||
configure_file(run_tcl_example.sh run_tcl_example.sh COPYONLY)
|
||||
set_property(SOURCE lammps_shell.i PROPERTY SWIG_MODULE_NAME tcllmpsh)
|
||||
swig_add_library(libtcllmpsh TYPE STATIC LANGUAGE tcl SOURCES lammps_shell.i)
|
||||
add_executable(tcllmpsh tcldummy.c)
|
||||
target_include_directories(tcllmpsh PRIVATE ${TCL_INCLUDE_PATH})
|
||||
target_link_libraries(tcllmpsh PRIVATE libtcllmpsh lammps ${TCL_LIBRARY})
|
||||
endif()
|
||||
|
||||
36
tools/swig/README
Normal file
36
tools/swig/README
Normal file
@ -0,0 +1,36 @@
|
||||
SWIG generated script library wrappers
|
||||
|
||||
The SWIG tool ( http://swig.org ) offers a mostly automated way to
|
||||
incorporate compiled code modules into scripting languages. It
|
||||
processes the function prototypes in C and generates wrappers for a wide
|
||||
variety of scripting languages from it.
|
||||
|
||||
We provide here an "interface file", "lammps.i", that has the content of
|
||||
the "library.h" file adapted so SWIG can process it. Please note that
|
||||
not all kinds of C functions can be automatically translated, so you
|
||||
would have to add custom functions to be able to utilize them. A few
|
||||
functions for converting pointers and accessing arrays are predefined.
|
||||
We provide the files here on an "as is" basis to help people getting
|
||||
started, but not as a fully tested and supported feature of the
|
||||
distribution. Any contributions to complete this are, of course,
|
||||
welcome.
|
||||
|
||||
In the case of Python, a fully supported and complete wrapper already
|
||||
exists in the "lammps" module in the "python" folder. This wrapper is
|
||||
based on Ctypes and is object oriented while SWIG will generate a 1:1
|
||||
translation of the functions in the interface file.
|
||||
|
||||
When using the CMake build system, steps for building wrapper modules
|
||||
are integrated for the languages: Java, Lua, Perl5, Python, Ruby, and
|
||||
Tcl and can be selected during the configuration step. These require
|
||||
that the LAMMPS library is build as a shared library and all necessary
|
||||
development headers and libraries of the selected script languages are
|
||||
present. To demonstrate the resulting wrappers, several example shell
|
||||
scripts (run_*_example.sh) are provided that contain commands to create
|
||||
an example script file and to demonstrate the use of the wrapped library
|
||||
functions in the respective programming language.
|
||||
|
||||
For details on how to build and adjust wrappers for individual
|
||||
languages please refer to the SWIG documentation at http://swig.org/doc.html
|
||||
|
||||
This functionality has been tested on Fedora 32 with SWIG 4.0.1.
|
||||
255
tools/swig/lammps.i
Normal file
255
tools/swig/lammps.i
Normal file
@ -0,0 +1,255 @@
|
||||
%include "cpointer.i"
|
||||
%include "carrays.i"
|
||||
%include "cdata.i"
|
||||
%include "cstring.i"
|
||||
|
||||
%pointer_functions(int, int_p);
|
||||
%pointer_functions(int, int64_p);
|
||||
%pointer_functions(double, double_p);
|
||||
|
||||
%array_functions(char, char_1d);
|
||||
%array_functions(int, int_1d);
|
||||
%array_functions(double, double_1d);
|
||||
|
||||
%pointer_cast(void *, int *, void_p_to_int_p);
|
||||
%pointer_cast(void *, int **, void_p_to_int2d_p);
|
||||
%pointer_cast(void *, int *, void_p_to_int64_p);
|
||||
%pointer_cast(void *, int **, void_p_to_int64_2d_p);
|
||||
%pointer_cast(void *, double *, void_p_to_double_p);
|
||||
%pointer_cast(void *, double **, void_p_to_double_2d_p);
|
||||
|
||||
%cstring_output_maxsize(char *buffer, int buf_size);
|
||||
|
||||
%{
|
||||
|
||||
enum _LMP_DATATYPE_CONST {
|
||||
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
|
||||
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
|
||||
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
|
||||
LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
|
||||
LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
|
||||
LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
|
||||
LAMMPS_STRING = 6 /*!< C-String */
|
||||
};
|
||||
|
||||
/** Style constants for extracting data from computes and fixes.
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in lammps.py */
|
||||
|
||||
enum _LMP_STYLE_CONST {
|
||||
LMP_STYLE_GLOBAL=0, /*!< return global data */
|
||||
LMP_STYLE_ATOM =1, /*!< return per-atom data */
|
||||
LMP_STYLE_LOCAL =2 /*!< return local data */
|
||||
};
|
||||
|
||||
/** Type and size constants for extracting data from computes and fixes.
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in lammps.py */
|
||||
|
||||
enum _LMP_TYPE_CONST {
|
||||
LMP_TYPE_SCALAR=0, /*!< return scalar */
|
||||
LMP_TYPE_VECTOR=1, /*!< return vector */
|
||||
LMP_TYPE_ARRAY =2, /*!< return array */
|
||||
LMP_SIZE_VECTOR=3, /*!< return length of vector */
|
||||
LMP_SIZE_ROWS =4, /*!< return number of rows */
|
||||
LMP_SIZE_COLS =5 /*!< return number of columns */
|
||||
};
|
||||
|
||||
/*
|
||||
extern void *lammps_open(int argc, char **argv, MPI_Comm comm, void **ptr);
|
||||
*/
|
||||
extern void *lammps_open_no_mpi(int argc, char **argv, void **ptr);
|
||||
extern void *lammps_open_fortran(int argc, char **argv, int f_comm);
|
||||
extern void lammps_close(void *handle);
|
||||
extern void lammps_mpi_init();
|
||||
extern void lammps_mpi_finalize();
|
||||
extern void lammps_free(void *ptr);
|
||||
extern void lammps_file(void *handle, const char *file);
|
||||
extern char *lammps_command(void *handle, const char *cmd);
|
||||
extern void lammps_commands_list(void *handle, int ncmd, const char **cmds);
|
||||
extern void lammps_commands_string(void *handle, const char *str);
|
||||
extern int lammps_version(void *handle);
|
||||
extern void lammps_get_os_info(char *buffer, int buf_size);
|
||||
extern void lammps_memory_usage(void *handle, double *meminfo);
|
||||
extern int lammps_get_mpi_comm(void *handle);
|
||||
extern double lammps_get_natoms(void *handle);
|
||||
extern double lammps_get_thermo(void *handle, const char *keyword);
|
||||
extern void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
|
||||
double *xy, double *yz, double *xz,
|
||||
int *pflags, int *boxflag);
|
||||
extern void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
|
||||
double xy, double yz, double xz);
|
||||
extern int lammps_extract_setting(void *handle, const char *keyword);
|
||||
extern void *lammps_extract_global(void *handle, const char *name);
|
||||
extern void *lammps_extract_atom(void *handle, const char *name);
|
||||
extern int lammps_extract_global_datatype(void *handle, const char *name);
|
||||
extern int lammps_extract_atom_datatype(void *handle, const char *name);
|
||||
extern int lammps_create_atoms(void *handle, int n, int *id, int *type,
|
||||
double *x, double *v, int *image, int bexpand);
|
||||
/*
|
||||
extern int lammps_create_atoms(void *handle, int n, int64_t *id, int *type, */
|
||||
extern void *lammps_extract_compute(void *handle, char *id, int, int);
|
||||
extern void *lammps_extract_fix(void *handle, char *, int, int, int, int);
|
||||
extern void *lammps_extract_variable(void *handle, char *, char *);
|
||||
extern int lammps_set_variable(void *, char *, char *);
|
||||
extern void lammps_gather(void *, char *, int, int, void *);
|
||||
extern void lammps_gather_concat(void *, char *, int, int, void *);
|
||||
extern void lammps_gather_subset(void *, char *, int, int, int, int *, void *);
|
||||
extern void lammps_scatter(void *, char *, int, int, void *);
|
||||
extern void lammps_scatter_subset(void *, char *, int, int, int, int *, void *);
|
||||
extern void lammps_gather_atoms(void *, char *, int, int, void *);
|
||||
extern void lammps_gather_atoms_concat(void *, char *, int, int, void *);
|
||||
extern void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
|
||||
extern void lammps_scatter_atoms(void *, char *, int, int, void *);
|
||||
extern void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
|
||||
extern int lammps_config_has_mpi_support();
|
||||
extern int lammps_config_has_package(const char *);
|
||||
extern int lammps_config_package_count();
|
||||
extern int lammps_config_package_name(int, char *, int);
|
||||
extern int lammps_config_has_gzip_support();
|
||||
extern int lammps_config_has_png_support();
|
||||
extern int lammps_config_has_jpeg_support();
|
||||
extern int lammps_config_has_ffmpeg_support();
|
||||
extern int lammps_config_has_exceptions();
|
||||
extern int lammps_has_style(void *, const char *, const char *);
|
||||
extern int lammps_style_count(void *, const char *);
|
||||
extern int lammps_style_name(void *, const char *, int, char *buffer, int buf_size);
|
||||
extern int lammps_has_id(void *, const char *, const char *);
|
||||
extern int lammps_id_count(void *, const char *);
|
||||
extern int lammps_id_name(void *, const char *, int, char *buffer, int buf_size);
|
||||
extern int lammps_find_pair_neighlist(void*, char *, int, int, int);
|
||||
extern int lammps_find_fix_neighlist(void*, char *, int);
|
||||
extern int lammps_find_compute_neighlist(void*, char *, int);
|
||||
extern int lammps_neighlist_num_elements(void*, int);
|
||||
extern void lammps_neighlist_element_neighbors(void *, int, int, int *, int *, int ** );
|
||||
/*
|
||||
extern int lammps_encode_image_flags(int ix, int iy, int iz);
|
||||
extern void lammps_decode_image_flags(int image, int *flags);
|
||||
extern int64_t lammps_encode_image_flags(int ix, int iy, int iz);
|
||||
extern void lammps_decode_image_flags(int64_t image, int *flags);
|
||||
extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
|
||||
extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
|
||||
extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
|
||||
extern void lammps_fix_external_set_energy_global(void *, char *, double);
|
||||
extern void lammps_fix_external_set_virial_global(void *, char *, double *);
|
||||
*/
|
||||
extern int lammps_is_running(void *handle);
|
||||
extern void lammps_force_timeout(void *handle);
|
||||
extern int lammps_has_error(void *handle);
|
||||
extern int lammps_get_last_error_message(void *handle, char *buffer, int buf_size);
|
||||
%}
|
||||
|
||||
enum _LMP_DATATYPE_CONST {
|
||||
LAMMPS_INT = 0, /*!< 32-bit integer (array) */
|
||||
LAMMPS_INT_2D = 1, /*!< two-dimensional 32-bit integer array */
|
||||
LAMMPS_DOUBLE = 2, /*!< 64-bit double (array) */
|
||||
LAMMPS_DOUBLE_2D = 3, /*!< two-dimensional 64-bit double array */
|
||||
LAMMPS_INT64 = 4, /*!< 64-bit integer (array) */
|
||||
LAMMPS_INT64_2D = 5, /*!< two-dimensional 64-bit integer array */
|
||||
LAMMPS_STRING = 6 /*!< C-String */
|
||||
};
|
||||
|
||||
/** Style constants for extracting data from computes and fixes.
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in lammps.py */
|
||||
|
||||
enum _LMP_STYLE_CONST {
|
||||
LMP_STYLE_GLOBAL=0, /*!< return global data */
|
||||
LMP_STYLE_ATOM =1, /*!< return per-atom data */
|
||||
LMP_STYLE_LOCAL =2 /*!< return local data */
|
||||
};
|
||||
|
||||
/** Type and size constants for extracting data from computes and fixes.
|
||||
*
|
||||
* Must be kept in sync with the equivalent constants in lammps.py */
|
||||
|
||||
enum _LMP_TYPE_CONST {
|
||||
LMP_TYPE_SCALAR=0, /*!< return scalar */
|
||||
LMP_TYPE_VECTOR=1, /*!< return vector */
|
||||
LMP_TYPE_ARRAY =2, /*!< return array */
|
||||
LMP_SIZE_VECTOR=3, /*!< return length of vector */
|
||||
LMP_SIZE_ROWS =4, /*!< return number of rows */
|
||||
LMP_SIZE_COLS =5 /*!< return number of columns */
|
||||
};
|
||||
|
||||
/* extern void *lammps_open(int argc, char **argv, MPI_Comm comm, void **ptr); */
|
||||
extern void *lammps_open_no_mpi(int argc, char **argv, void **ptr);
|
||||
extern void *lammps_open_fortran(int argc, char **argv, int f_comm);
|
||||
extern void lammps_close(void *handle);
|
||||
extern void lammps_mpi_init();
|
||||
extern void lammps_mpi_finalize();
|
||||
extern void lammps_free(void *ptr);
|
||||
extern void lammps_file(void *handle, const char *file);
|
||||
extern char *lammps_command(void *handle, const char *cmd);
|
||||
extern void lammps_commands_list(void *handle, int ncmd, const char **cmds);
|
||||
extern void lammps_commands_string(void *handle, const char *str);
|
||||
extern int lammps_version(void *handle);
|
||||
extern void lammps_get_os_info(char *buffer, int buf_size);
|
||||
extern void lammps_memory_usage(void *handle, double *meminfo);
|
||||
extern int lammps_get_mpi_comm(void *handle);
|
||||
extern double lammps_get_natoms(void *handle);
|
||||
extern double lammps_get_thermo(void *handle, const char *keyword);
|
||||
extern void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
|
||||
double *xy, double *yz, double *xz,
|
||||
int *pflags, int *boxflag);
|
||||
extern void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
|
||||
double xy, double yz, double xz);
|
||||
extern int lammps_extract_setting(void *handle, const char *keyword);
|
||||
extern void *lammps_extract_global(void *handle, const char *name);
|
||||
extern void *lammps_extract_atom(void *handle, const char *name);
|
||||
extern int lammps_extract_global_datatype(void *handle, const char *name);
|
||||
extern int lammps_extract_atom_datatype(void *handle, const char *name);
|
||||
extern int lammps_create_atoms(void *handle, int n, int *id, int *type,
|
||||
double *x, double *v, int *image, int bexpand);
|
||||
/*
|
||||
extern int lammps_create_atoms(void *handle, int n, int64_t *id, int *type, */
|
||||
extern void *lammps_extract_compute(void *handle, char *id, int, int);
|
||||
extern void *lammps_extract_fix(void *handle, char *, int, int, int, int);
|
||||
extern void *lammps_extract_variable(void *handle, char *, char *);
|
||||
extern int lammps_set_variable(void *, char *, char *);
|
||||
extern void lammps_gather(void *, char *, int, int, void *);
|
||||
extern void lammps_gather_concat(void *, char *, int, int, void *);
|
||||
extern void lammps_gather_subset(void *, char *, int, int, int, int *, void *);
|
||||
extern void lammps_scatter(void *, char *, int, int, void *);
|
||||
extern void lammps_scatter_subset(void *, char *, int, int, int, int *, void *);
|
||||
extern void lammps_gather_atoms(void *, char *, int, int, void *);
|
||||
extern void lammps_gather_atoms_concat(void *, char *, int, int, void *);
|
||||
extern void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *);
|
||||
extern void lammps_scatter_atoms(void *, char *, int, int, void *);
|
||||
extern void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *);
|
||||
extern int lammps_config_has_mpi_support();
|
||||
extern int lammps_config_has_package(const char *);
|
||||
extern int lammps_config_package_count();
|
||||
extern int lammps_config_package_name(int, char *, int);
|
||||
extern int lammps_config_has_gzip_support();
|
||||
extern int lammps_config_has_png_support();
|
||||
extern int lammps_config_has_jpeg_support();
|
||||
extern int lammps_config_has_ffmpeg_support();
|
||||
extern int lammps_config_has_exceptions();
|
||||
extern int lammps_has_style(void *, const char *, const char *);
|
||||
extern int lammps_style_count(void *, const char *);
|
||||
extern int lammps_style_name(void *, const char *, int, char *buffer, int buf_size);
|
||||
extern int lammps_has_id(void *, const char *, const char *);
|
||||
extern int lammps_id_count(void *, const char *);
|
||||
extern int lammps_id_name(void *, const char *, int, char *buffer, int buf_size);
|
||||
extern int lammps_find_pair_neighlist(void*, char *, int, int, int);
|
||||
extern int lammps_find_fix_neighlist(void*, char *, int);
|
||||
extern int lammps_find_compute_neighlist(void*, char *, int);
|
||||
extern int lammps_neighlist_num_elements(void*, int);
|
||||
extern void lammps_neighlist_element_neighbors(void *, int, int, int *, int *, int ** );
|
||||
/*
|
||||
extern int lammps_encode_image_flags(int ix, int iy, int iz);
|
||||
extern void lammps_decode_image_flags(int image, int *flags);
|
||||
extern int64_t lammps_encode_image_flags(int ix, int iy, int iz);
|
||||
extern void lammps_decode_image_flags(int64_t image, int *flags);
|
||||
extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
|
||||
extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
|
||||
extern void lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*);
|
||||
extern void lammps_fix_external_set_energy_global(void *, char *, double);
|
||||
extern void lammps_fix_external_set_virial_global(void *, char *, double *);
|
||||
*/
|
||||
extern int lammps_is_running(void *handle);
|
||||
extern void lammps_force_timeout(void *handle);
|
||||
extern int lammps_has_error(void *handle);
|
||||
extern int lammps_get_last_error_message(void *handle, char *buffer, int buf_size);
|
||||
|
||||
2
tools/swig/lammps_shell.i
Normal file
2
tools/swig/lammps_shell.i
Normal file
@ -0,0 +1,2 @@
|
||||
%include "tclsh.i"
|
||||
%include "lammps.i"
|
||||
63
tools/swig/run_java_example.sh
Executable file
63
tools/swig/run_java_example.sh
Executable file
@ -0,0 +1,63 @@
|
||||
#!/bin/sh
|
||||
|
||||
if [ ! -f libjavalammps.so ]
|
||||
then \
|
||||
echo "Need to compile 'libjavalammps.so' first for this script to work"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
cat > example.java <<EOF
|
||||
public class example {
|
||||
static {
|
||||
System.loadLibrary("javalammps");
|
||||
}
|
||||
|
||||
public static void main(String argv[]) {
|
||||
SWIGTYPE_p_void lmp = javalammps.lammps_open_no_mpi(0, null, null);
|
||||
int ver = javalammps.lammps_version(lmp);
|
||||
|
||||
int npair_styles = javalammps.lammps_style_count(lmp, "pair");
|
||||
System.out.println("LAMMPS includes " + npair_styles + " pair styles");
|
||||
|
||||
javalammps.lammps_command(lmp, "units real");
|
||||
javalammps.lammps_command(lmp, "lattice fcc 2.5");
|
||||
javalammps.lammps_command(lmp, "region box block -5 5 -5 5 -5 5");
|
||||
javalammps.lammps_command(lmp, "create_box 1 box");
|
||||
javalammps.lammps_command(lmp, "create_atoms 1 box");
|
||||
|
||||
SWIGTYPE_p_double boxlo_p = javalammps.new_double_1d(3);
|
||||
SWIGTYPE_p_double boxhi_p = javalammps.new_double_1d(3);
|
||||
SWIGTYPE_p_double xy_p = javalammps.new_double_p();
|
||||
SWIGTYPE_p_double yz_p = javalammps.new_double_p();
|
||||
SWIGTYPE_p_double xz_p = javalammps.new_double_p();
|
||||
SWIGTYPE_p_int pflags_p = javalammps.new_int_1d(3);
|
||||
SWIGTYPE_p_int boxflag_p = javalammps.new_int_p();
|
||||
|
||||
javalammps.lammps_extract_box(lmp, boxlo_p, boxhi_p, xy_p, yz_p, xz_p, pflags_p, boxflag_p);
|
||||
System.out.println("boxlo: " + javalammps.double_1d_getitem(boxlo_p, 0) + " " + javalammps.double_1d_getitem(boxlo_p, 1) + " " + javalammps.double_1d_getitem(boxlo_p, 2));
|
||||
System.out.println("boxhi: " + javalammps.double_1d_getitem(boxhi_p, 0) + " " + javalammps.double_1d_getitem(boxhi_p, 1) + " " + javalammps.double_1d_getitem(boxhi_p, 2));
|
||||
System.out.println("xy/yz/xz: " + javalammps.double_p_value(xy_p) + " " + javalammps.double_p_value(yz_p) + " " + javalammps.double_p_value(xz_p));
|
||||
System.out.println("periodicity: " + javalammps.int_1d_getitem(pflags_p, 0) + " " + javalammps.int_1d_getitem(pflags_p, 1) + " " + javalammps.int_1d_getitem(pflags_p, 2));
|
||||
System.out.println("boxflag: " + javalammps.int_p_value(boxflag_p));
|
||||
javalammps.delete_double_1d(boxlo_p);
|
||||
javalammps.delete_double_1d(boxhi_p);
|
||||
javalammps.delete_int_1d(pflags_p);
|
||||
javalammps.delete_double_p(xy_p);
|
||||
javalammps.delete_double_p(yz_p);
|
||||
javalammps.delete_double_p(xz_p);
|
||||
javalammps.delete_int_p(boxflag_p);
|
||||
|
||||
System.out.println("LAMMPS version " + ver);
|
||||
System.out.println("Number of created atoms: " + javalammps.lammps_get_natoms(lmp));
|
||||
javalammps.lammps_close(lmp);
|
||||
}
|
||||
}
|
||||
EOF
|
||||
|
||||
CLASSPATH=${PWD}:${CLASSPATH-${PWD}}
|
||||
LD_LIBRARY_PATH=${PWD}:${LD_LIBARARY_PATH-${PWD}}
|
||||
|
||||
export CLASSPATH LD_LIBRARY_PATH
|
||||
|
||||
javac *.java
|
||||
java example
|
||||
65
tools/swig/run_lua_example.sh
Executable file
65
tools/swig/run_lua_example.sh
Executable file
@ -0,0 +1,65 @@
|
||||
#!/bin/sh
|
||||
|
||||
if [ ! -f lualammps.so ]
|
||||
then \
|
||||
echo "Need to compile 'lualammps.so' first for this script to work"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
cat > example.lua <<EOF
|
||||
require("lualammps")
|
||||
|
||||
-- Lua does not seem to support %cstring_output_maxsize so this
|
||||
-- currently does not work and complains about a missing argument.
|
||||
--
|
||||
-- osinfo = lualammps.lammps_get_os_info(512)
|
||||
-- print(osinfo)
|
||||
|
||||
lmp = lualammps.lammps_open_no_mpi(0,nil,nil)
|
||||
ver = lualammps.lammps_version(lmp)
|
||||
|
||||
npair_styles = lualammps.lammps_style_count(lmp, "pair")
|
||||
print("LAMMPS includes ", npair_styles, " pair styles")
|
||||
|
||||
-- this also does not work (see above)
|
||||
-- for i = 0, 10, 1 do
|
||||
-- res = lualammps.lammps_style_name(lmp, 'pair', i, 128)
|
||||
-- print("Pair style ",i, ': ', res[1])
|
||||
-- end
|
||||
|
||||
lualammps.lammps_command(lmp, "units real")
|
||||
lualammps.lammps_command(lmp, "lattice fcc 2.5")
|
||||
lualammps.lammps_command(lmp, "region box block -5 5 -5 5 -5 5")
|
||||
lualammps.lammps_command(lmp, "create_box 1 box")
|
||||
lualammps.lammps_command(lmp, "create_atoms 1 box")
|
||||
|
||||
boxlo_p = lualammps.new_double_1d(3)
|
||||
boxhi_p = lualammps.new_double_1d(3)
|
||||
xy_p = lualammps.new_double_p()
|
||||
yz_p = lualammps.new_double_p()
|
||||
xz_p = lualammps.new_double_p()
|
||||
pflags_p = lualammps.new_int_1d(3)
|
||||
boxflag_p = lualammps.new_int_p()
|
||||
|
||||
lualammps.lammps_extract_box(lmp, boxlo_p, boxhi_p, xy_p, yz_p, xz_p, pflags_p, boxflag_p)
|
||||
|
||||
print('boxlo: ', lualammps.double_1d_getitem(boxlo_p, 0), ' ', lualammps.double_1d_getitem(boxlo_p, 1), ' ', lualammps.double_1d_getitem(boxlo_p, 2))
|
||||
print('boxhi: ', lualammps.double_1d_getitem(boxhi_p, 0), ' ', lualammps.double_1d_getitem(boxhi_p, 1), ' ', lualammps.double_1d_getitem(boxhi_p, 2))
|
||||
print('xy/yz/xz: ', lualammps.double_p_value(xy_p), ' ', lualammps.double_p_value(yz_p), ' ', lualammps.double_p_value(xz_p))
|
||||
print('periodicity: ', lualammps.int_1d_getitem(pflags_p, 0), ' ', lualammps.int_1d_getitem(pflags_p, 1), ' ', lualammps.int_1d_getitem(pflags_p, 2))
|
||||
print('boxflag: ', lualammps.int_p_value(boxflag_p))
|
||||
lualammps.delete_double_1d(boxlo_p)
|
||||
lualammps.delete_double_1d(boxhi_p)
|
||||
lualammps.delete_int_1d(pflags_p)
|
||||
lualammps.delete_double_p(xy_p)
|
||||
lualammps.delete_double_p(yz_p)
|
||||
lualammps.delete_double_p(xz_p)
|
||||
lualammps.delete_int_p(boxflag_p)
|
||||
|
||||
print("LAMMPS version ", ver)
|
||||
print("Number of created atoms: ", lualammps.lammps_get_natoms(lmp))
|
||||
print("Current size of timestep: ", lualammps.double_p_value(lualammps.void_p_to_double_p(lualammps.lammps_extract_global(lmp,"dt"))))
|
||||
lualammps.lammps_close(lmp)
|
||||
EOF
|
||||
|
||||
lua example.lua
|
||||
66
tools/swig/run_perl_example.sh
Executable file
66
tools/swig/run_perl_example.sh
Executable file
@ -0,0 +1,66 @@
|
||||
#!/bin/sh
|
||||
|
||||
if [ ! -f pllammps.so ]
|
||||
then \
|
||||
echo "Need to compile 'pllammps.so' first for this script to work"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
cat > example.pl <<EOF
|
||||
use pllammps;
|
||||
|
||||
\$osinfo = pllammps::lammps_get_os_info(512);
|
||||
print("\$osinfo\n");
|
||||
|
||||
\$lmp = pllammps::lammps_open_no_mpi(0,undef,undef);
|
||||
\$ver = pllammps::lammps_version(\$lmp);
|
||||
|
||||
\$npair_styles = pllammps::lammps_style_count(\$lmp, "pair");
|
||||
print("LAMMPS includes \$npair_styles pair styles\n");
|
||||
for (my \$i=0; \$i < 10; ++\$i) {
|
||||
@res = pllammps::lammps_style_name(\$lmp, "pair", \$i, 128);
|
||||
if (\$res[0] == 1) {
|
||||
print("Style \$i: \$res[1]\n");
|
||||
}
|
||||
}
|
||||
|
||||
pllammps::lammps_command(\$lmp, "units real");
|
||||
pllammps::lammps_command(\$lmp, "lattice fcc 2.5");
|
||||
pllammps::lammps_command(\$lmp, "region box block -5 5 -5 5 -5 5");
|
||||
pllammps::lammps_command(\$lmp, "create_box 1 box");
|
||||
pllammps::lammps_command(\$lmp, "create_atoms 1 box");
|
||||
|
||||
\$boxlo_p = pllammps::new_double_1d(3);
|
||||
\$boxhi_p = pllammps::new_double_1d(3);
|
||||
\$xy_p = pllammps::new_double_p();
|
||||
\$yz_p = pllammps::new_double_p();
|
||||
\$xz_p = pllammps::new_double_p();
|
||||
\$pflags_p = pllammps::new_int_1d(3);
|
||||
\$boxflag_p = pllammps::new_int_p();
|
||||
|
||||
pllammps::lammps_extract_box(\$lmp, \$boxlo_p, \$boxhi_p, \$xy_p, \$yz_p, \$xz_p, \$pflags_p, \$boxflag_p);
|
||||
|
||||
printf "boxlo: %g %g %g\n", pllammps::double_1d_getitem(\$boxlo_p, 0), pllammps::double_1d_getitem(\$boxlo_p, 1), pllammps::double_1d_getitem(\$boxlo_p, 2);
|
||||
printf "boxhi: %g %g %g\n", pllammps::double_1d_getitem(\$boxhi_p, 0), pllammps::double_1d_getitem(\$boxhi_p, 1), pllammps::double_1d_getitem(\$boxhi_p, 2);
|
||||
printf "xy/yz/xz: %g %g %g\n", pllammps::double_p_value(\$xy_p), pllammps::double_p_value(\$yz_p), pllammps::double_p_value(\$xz_p);
|
||||
printf "periodicity: %d %d %d\n", pllammps::int_1d_getitem(\$pflags_p, 0), pllammps::int_1d_getitem(\$pflags_p, 1), pllammps::int_1d_getitem(\$pflags_p, 2);
|
||||
printf "boxflag: %d\n", pllammps::int_p_value(\$boxflag_p);
|
||||
pllammps::delete_double_1d(\$boxlo_p);
|
||||
pllammps::delete_double_1d(\$boxhi_p);
|
||||
pllammps::delete_int_1d(\$pflags_p);
|
||||
pllammps::delete_double_p(\$xy_p);
|
||||
pllammps::delete_double_p(\$yz_p);
|
||||
pllammps::delete_double_p(\$xz_p);
|
||||
pllammps::delete_int_p(\$boxflag_p);
|
||||
|
||||
print "LAMMPS version ", \$ver, "\n";
|
||||
print "Number of created atoms: ", pllammps::lammps_get_natoms(\$lmp), "\n";
|
||||
print "Current size of timestep: ", pllammps::double_p_value(pllammps::void_p_to_double_p(pllammps::lammps_extract_global(\$lmp,"dt"))), "\n";
|
||||
pllammps::lammps_close(\$lmp)
|
||||
EOF
|
||||
|
||||
PERL5LIB=${PWD}:${PERL5LIB-${PWD}}
|
||||
|
||||
export PERL5LIB
|
||||
|
||||
perl example.pl
|
||||
63
tools/swig/run_python_example.sh
Executable file
63
tools/swig/run_python_example.sh
Executable file
@ -0,0 +1,63 @@
|
||||
#!/bin/sh
|
||||
|
||||
if [ ! -f _pylammps.so ]
|
||||
then \
|
||||
echo "Need to compile '_pylammps.so' first for this script to work"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
cat > example.py <<EOF
|
||||
from pylammps import *
|
||||
|
||||
osinfo = lammps_get_os_info(512)
|
||||
print(osinfo)
|
||||
|
||||
lmp = lammps_open_no_mpi(0,None,None)
|
||||
ver = lammps_version(lmp)
|
||||
|
||||
npair_styles = lammps_style_count(lmp, 'pair')
|
||||
print("LAMMPS includes %d pair styles" % npair_styles)
|
||||
for i in range(10):
|
||||
found, style = lammps_style_name(lmp, 'pair', i, 128)
|
||||
if found == 1: print("Style %d: " % i, style)
|
||||
|
||||
lammps_command(lmp, "units real")
|
||||
lammps_command(lmp, "lattice fcc 2.5")
|
||||
lammps_command(lmp, "region box block -5 5 -5 5 -5 5")
|
||||
lammps_command(lmp, "create_box 1 box")
|
||||
lammps_command(lmp, "create_atoms 1 box")
|
||||
|
||||
boxlo_p = new_double_1d(3)
|
||||
boxhi_p = new_double_1d(3)
|
||||
xy_p = new_double_p()
|
||||
yz_p = new_double_p()
|
||||
xz_p = new_double_p()
|
||||
pflags_p = new_int_1d(3)
|
||||
boxflag_p = new_int_p()
|
||||
|
||||
lammps_extract_box(lmp, boxlo_p, boxhi_p, xy_p, yz_p, xz_p, pflags_p, boxflag_p)
|
||||
|
||||
print("boxlo: %g %g %g" % (double_1d_getitem(boxlo_p, 0), double_1d_getitem(boxlo_p, 1), double_1d_getitem(boxlo_p, 2)))
|
||||
print("boxhi: %g %g %g" % (double_1d_getitem(boxhi_p, 0), double_1d_getitem(boxhi_p, 1), double_1d_getitem(boxhi_p, 2)))
|
||||
print("xy/yz/xz: %g %g %g" % (double_p_value(xy_p), double_p_value(yz_p), double_p_value(xz_p)))
|
||||
print("periodicity: %d %d %d" % (int_1d_getitem(pflags_p, 0), int_1d_getitem(pflags_p, 1), int_1d_getitem(pflags_p, 2)))
|
||||
print("boxflag: %d" % int_p_value(boxflag_p))
|
||||
delete_double_1d(boxlo_p)
|
||||
delete_double_1d(boxhi_p)
|
||||
delete_int_1d(pflags_p)
|
||||
delete_double_p(xy_p)
|
||||
delete_double_p(yz_p)
|
||||
delete_double_p(xz_p)
|
||||
delete_int_p(boxflag_p)
|
||||
|
||||
print("LAMMPS version ",ver)
|
||||
print("Number of created atoms: %g" % lammps_get_natoms(lmp))
|
||||
print("Current size of timestep: %g" % double_p_value(void_p_to_double_p(lammps_extract_global(lmp,'dt'))))
|
||||
lammps_close(lmp)
|
||||
EOF
|
||||
|
||||
PYTHONPATH=${PWD}:${PYTHONPATH-${PWD}}
|
||||
|
||||
export PYTHONPATH
|
||||
|
||||
python example.py
|
||||
63
tools/swig/run_ruby_example.sh
Executable file
63
tools/swig/run_ruby_example.sh
Executable file
@ -0,0 +1,63 @@
|
||||
#!/bin/sh
|
||||
|
||||
if [ ! -f rubylammps.so ]
|
||||
then \
|
||||
echo "Need to compile 'rubylammps.so' first for this script to work"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
cat > example.rb <<EOF
|
||||
require 'rubylammps'
|
||||
|
||||
osinfo = Rubylammps.lammps_get_os_info(512)
|
||||
puts osinfo
|
||||
|
||||
lmp = Rubylammps.lammps_open_no_mpi(0,nil,nil)
|
||||
ver = Rubylammps.lammps_version(lmp)
|
||||
|
||||
npair_styles = Rubylammps.lammps_style_count(lmp, 'pair')
|
||||
puts "LAMMPS includes #{npair_styles} pair styles"
|
||||
(0..9).each { |i|
|
||||
res = Rubylammps.lammps_style_name(lmp, 'pair', i, 128)
|
||||
if res[0] == 1
|
||||
puts "Pair style #{i}: #{res[1]}\n"
|
||||
end
|
||||
}
|
||||
|
||||
Rubylammps.lammps_command(lmp, 'units real')
|
||||
Rubylammps.lammps_command(lmp, 'lattice fcc 2.5')
|
||||
Rubylammps.lammps_command(lmp, 'region box block -5 5 -5 5 -5 5')
|
||||
Rubylammps.lammps_command(lmp, 'create_box 1 box')
|
||||
Rubylammps.lammps_command(lmp, 'create_atoms 1 box')
|
||||
|
||||
boxlo_p = Rubylammps.new_double_1d(3)
|
||||
boxhi_p = Rubylammps.new_double_1d(3)
|
||||
xy_p = Rubylammps.new_double_p()
|
||||
yz_p = Rubylammps.new_double_p()
|
||||
xz_p = Rubylammps.new_double_p()
|
||||
pflags_p = Rubylammps.new_int_1d(3)
|
||||
boxflag_p = Rubylammps.new_int_p()
|
||||
|
||||
Rubylammps.lammps_extract_box(lmp, boxlo_p, boxhi_p, xy_p, yz_p, xz_p, pflags_p, boxflag_p)
|
||||
|
||||
print('boxlo: ', Rubylammps.double_1d_getitem(boxlo_p, 0), ' ', Rubylammps.double_1d_getitem(boxlo_p, 1), ' ', Rubylammps.double_1d_getitem(boxlo_p, 2), "\n")
|
||||
print('boxhi: ', Rubylammps.double_1d_getitem(boxhi_p, 0), ' ', Rubylammps.double_1d_getitem(boxhi_p, 1), ' ', Rubylammps.double_1d_getitem(boxhi_p, 2), "\n")
|
||||
print('xy/yz/xz: ', Rubylammps.double_p_value(xy_p), ' ', Rubylammps.double_p_value(yz_p), ' ', Rubylammps.double_p_value(xz_p), "\n")
|
||||
print('periodicity: ', Rubylammps.int_1d_getitem(pflags_p, 0), ' ', Rubylammps.int_1d_getitem(pflags_p, 1), ' ', Rubylammps.int_1d_getitem(pflags_p, 2), "\n")
|
||||
print('boxflag: ', Rubylammps.int_p_value(boxflag_p), "\n")
|
||||
Rubylammps.delete_double_1d(boxlo_p)
|
||||
Rubylammps.delete_double_1d(boxhi_p)
|
||||
Rubylammps.delete_int_1d(pflags_p)
|
||||
Rubylammps.delete_double_p(xy_p)
|
||||
Rubylammps.delete_double_p(yz_p)
|
||||
Rubylammps.delete_double_p(xz_p)
|
||||
Rubylammps.delete_int_p(boxflag_p)
|
||||
|
||||
puts "LAMMPS version #{ver}"
|
||||
print('Number of created atoms: ', Rubylammps.lammps_get_natoms(lmp), "\n")
|
||||
print('Current size of timestep: ', Rubylammps.double_p_value(Rubylammps.void_p_to_double_p(Rubylammps.lammps_extract_global(lmp,'dt'))), "\n")
|
||||
Rubylammps.lammps_close(lmp)
|
||||
EOF
|
||||
|
||||
export RUBYLIB=${PWD}:${RUBYLIB-${PWD}}
|
||||
ruby example.rb
|
||||
123
tools/swig/run_tcl_example.sh
Executable file
123
tools/swig/run_tcl_example.sh
Executable file
@ -0,0 +1,123 @@
|
||||
#!/bin/sh
|
||||
|
||||
if [ ! -f tcllammps.so ]
|
||||
then \
|
||||
echo "Need to compile 'tcllammps.so' first for this script to work"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
cat > example.tcl <<EOF
|
||||
load ./tcllammps.so
|
||||
|
||||
set osinfo [lammps_get_os_info 512]
|
||||
puts "[lindex \$osinfo 0] [lindex \$osinfo 1]"
|
||||
|
||||
set lmp [lammps_open_no_mpi 0 NULL NULL ]
|
||||
set ver [lammps_version \$lmp]
|
||||
|
||||
set npair_styles [lammps_style_count \$lmp "pair"]
|
||||
puts "LAMMPS includes \$npair_styles pair styles"
|
||||
for {set i 0} {\$i < 10} {incr i} {
|
||||
set style [lammps_style_name \$lmp "pair" \$i 128]
|
||||
if {[lindex \$style 0]} {puts "Style \$i: [lindex \$style 1]"}
|
||||
}
|
||||
|
||||
lammps_command \$lmp "units real"
|
||||
lammps_command \$lmp "lattice fcc 2.5"
|
||||
lammps_command \$lmp "region box block -5 5 -5 5 -5 5"
|
||||
lammps_command \$lmp "create_box 1 box"
|
||||
lammps_command \$lmp "create_atoms 1 box"
|
||||
|
||||
set boxlo_p [new_double_1d 3]
|
||||
set boxhi_p [new_double_1d 3]
|
||||
set xy_p [new_double_p]
|
||||
set yz_p [new_double_p]
|
||||
set xz_p [new_double_p]
|
||||
set pflags_p [new_int_1d 3]
|
||||
set boxflag_p [new_int_p]
|
||||
|
||||
lammps_extract_box \$lmp \$boxlo_p \$boxhi_p \$xy_p \$yz_p \$xz_p \$pflags_p \$boxflag_p
|
||||
|
||||
puts [format "boxlo: %g %g %g" [double_1d_getitem \$boxlo_p 0] [double_1d_getitem \$boxlo_p 1] [double_1d_getitem \$boxlo_p 2]]
|
||||
puts [format "boxhi: %g %g %g" [double_1d_getitem \$boxhi_p 0] [double_1d_getitem \$boxhi_p 1] [double_1d_getitem \$boxhi_p 2]]
|
||||
puts [format "xy/yz/xz: %g %g %g" [double_p_value \$xy_p] [double_p_value \$yz_p] [double_p_value \$xz_p]]
|
||||
puts [format "periodicity: %d %d %d" [int_1d_getitem \$pflags_p 0] [int_1d_getitem \$pflags_p 1] [int_1d_getitem \$pflags_p 2]]
|
||||
puts [format "boxflag: %d" [int_p_value \$boxflag_p]]
|
||||
delete_double_1d \$boxlo_p
|
||||
delete_double_1d \$boxhi_p
|
||||
delete_int_1d \$pflags_p
|
||||
delete_double_p \$xy_p
|
||||
delete_double_p \$yz_p
|
||||
delete_double_p \$xz_p
|
||||
delete_int_p \$boxflag_p
|
||||
|
||||
set dt [double_p_value [void_p_to_double_p [lammps_extract_global \$lmp dt]]]
|
||||
puts "LAMMPS version \$ver"
|
||||
puts [format "Number of created atoms: %g" [lammps_get_natoms \$lmp]]
|
||||
puts "Current size of timestep: \$dt"
|
||||
lammps_close \$lmp
|
||||
EOF
|
||||
|
||||
tclsh example.tcl
|
||||
|
||||
# now try again with static extended shell
|
||||
echo '====================================================================='
|
||||
|
||||
if [ ! -f tcllmpsh ]
|
||||
then \
|
||||
echo "Need to compile 'tcllmpsh' first for this script to work"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
cat > example.tcllmp <<EOF
|
||||
|
||||
set osinfo [lammps_get_os_info 512]
|
||||
puts "[lindex \$osinfo 0] [lindex \$osinfo 1]"
|
||||
|
||||
set lmp [lammps_open_no_mpi 0 NULL NULL ]
|
||||
set ver [lammps_version \$lmp]
|
||||
|
||||
set npair_styles [lammps_style_count \$lmp "pair"]
|
||||
puts "LAMMPS includes \$npair_styles pair styles"
|
||||
for {set i 0} {\$i < 10} {incr i} {
|
||||
set style [lammps_style_name \$lmp "pair" \$i 128]
|
||||
if {[lindex \$style 0]} {puts "Style \$i: [lindex \$style 1]"}
|
||||
}
|
||||
|
||||
lammps_command \$lmp "units real"
|
||||
lammps_command \$lmp "lattice fcc 2.5"
|
||||
lammps_command \$lmp "region box block -5 5 -5 5 -5 5"
|
||||
lammps_command \$lmp "create_box 1 box"
|
||||
lammps_command \$lmp "create_atoms 1 box"
|
||||
|
||||
set boxlo_p [new_double_1d 3]
|
||||
set boxhi_p [new_double_1d 3]
|
||||
set xy_p [new_double_p]
|
||||
set yz_p [new_double_p]
|
||||
set xz_p [new_double_p]
|
||||
set pflags_p [new_int_1d 3]
|
||||
set boxflag_p [new_int_p]
|
||||
|
||||
lammps_extract_box \$lmp \$boxlo_p \$boxhi_p \$xy_p \$yz_p \$xz_p \$pflags_p \$boxflag_p
|
||||
|
||||
puts [format "boxlo: %g %g %g" [double_1d_getitem \$boxlo_p 0] [double_1d_getitem \$boxlo_p 1] [double_1d_getitem \$boxlo_p 2]]
|
||||
puts [format "boxhi: %g %g %g" [double_1d_getitem \$boxhi_p 0] [double_1d_getitem \$boxhi_p 1] [double_1d_getitem \$boxhi_p 2]]
|
||||
puts [format "xy/yz/xz: %g %g %g" [double_p_value \$xy_p] [double_p_value \$yz_p] [double_p_value \$xz_p]]
|
||||
puts [format "periodicity: %d %d %d" [int_1d_getitem \$pflags_p 0] [int_1d_getitem \$pflags_p 1] [int_1d_getitem \$pflags_p 2]]
|
||||
puts [format "boxflag: %d" [int_p_value \$boxflag_p]]
|
||||
delete_double_1d \$boxlo_p
|
||||
delete_double_1d \$boxhi_p
|
||||
delete_int_1d \$pflags_p
|
||||
delete_double_p \$xy_p
|
||||
delete_double_p \$yz_p
|
||||
delete_double_p \$xz_p
|
||||
delete_int_p \$boxflag_p
|
||||
|
||||
set dt [double_p_value [void_p_to_double_p [lammps_extract_global \$lmp dt]]]
|
||||
puts "LAMMPS version \$ver"
|
||||
puts [format "Number of created atoms: %g" [lammps_get_natoms \$lmp]]
|
||||
puts "Current size of timestep: \$dt"
|
||||
lammps_close \$lmp
|
||||
EOF
|
||||
|
||||
${PWD}/tcllmpsh example.tcllmp
|
||||
5
tools/swig/tcldummy.c
Normal file
5
tools/swig/tcldummy.c
Normal file
@ -0,0 +1,5 @@
|
||||
int i_am_a_dummy_function()
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user