Merge branch 'master' into lammps-icms
Resolved Conflicts: python/lammps.py src/MAKE/Makefile.mingw src/MAKE/Makefile.openmpi src/MAKE/Makefile.serial src/MAKE/Makefile.serial_debug src/USER-CUDA/verlet_cuda.cpp
This commit is contained in:
Axel Kohlmeyer
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@ -659,8 +659,8 @@ invoked with minimal overhead (no setup or clean-up) if you wish to do
|
||||
multiple short runs, driven by another program.
|
||||
</P>
|
||||
<P>Examples of driver codes that call LAMMPS as a library are included in
|
||||
the "couple" directory of the LAMMPS distribution; see couple/README
|
||||
for more details:
|
||||
the examples/COUPLE directory of the LAMMPS distribution; see
|
||||
examples/COUPLE/README for more details:
|
||||
</P>
|
||||
<UL><LI>simple: simple driver programs in C++ and C which invoke LAMMPS as a
|
||||
library
|
||||
@ -1820,11 +1820,12 @@ details.
|
||||
<P>The key idea of the library interface is that you can write any
|
||||
functions you wish to define how your code talks to LAMMPS and add
|
||||
them to src/library.cpp and src/library.h, as well as to the <A HREF = "Section_python.html">Python
|
||||
interface</A>. The routines you add can access
|
||||
or change any LAMMPS data you wish. The couple and python directories
|
||||
have example C++ and C and Python codes which show how a driver code
|
||||
can link to LAMMPS as a library, run LAMMPS on a subset of processors,
|
||||
grab data from LAMMPS, change it, and put it back into LAMMPS.
|
||||
interface</A>. The routines you add can access or
|
||||
change any LAMMPS data you wish. The examples/COUPLE and python
|
||||
directories have example C++ and C and Python codes which show how a
|
||||
driver code can link to LAMMPS as a library, run LAMMPS on a subset of
|
||||
processors, grab data from LAMMPS, change it, and put it back into
|
||||
LAMMPS.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
||||
@ -654,8 +654,8 @@ invoked with minimal overhead (no setup or clean-up) if you wish to do
|
||||
multiple short runs, driven by another program.
|
||||
|
||||
Examples of driver codes that call LAMMPS as a library are included in
|
||||
the "couple" directory of the LAMMPS distribution; see couple/README
|
||||
for more details:
|
||||
the examples/COUPLE directory of the LAMMPS distribution; see
|
||||
examples/COUPLE/README for more details:
|
||||
|
||||
simple: simple driver programs in C++ and C which invoke LAMMPS as a
|
||||
library :ulb,l
|
||||
@ -1807,11 +1807,12 @@ details.
|
||||
The key idea of the library interface is that you can write any
|
||||
functions you wish to define how your code talks to LAMMPS and add
|
||||
them to src/library.cpp and src/library.h, as well as to the "Python
|
||||
interface"_Section_python.html. The routines you add can access
|
||||
or change any LAMMPS data you wish. The couple and python directories
|
||||
have example C++ and C and Python codes which show how a driver code
|
||||
can link to LAMMPS as a library, run LAMMPS on a subset of processors,
|
||||
grab data from LAMMPS, change it, and put it back into LAMMPS.
|
||||
interface"_Section_python.html. The routines you add can access or
|
||||
change any LAMMPS data you wish. The examples/COUPLE and python
|
||||
directories have example C++ and C and Python codes which show how a
|
||||
driver code can link to LAMMPS as a library, run LAMMPS on a subset of
|
||||
processors, grab data from LAMMPS, change it, and put it back into
|
||||
LAMMPS.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -14,175 +14,153 @@
|
||||
<P>This section describes how to build and use LAMMPS via a Python
|
||||
interface.
|
||||
</P>
|
||||
<UL><LI>11.1 <A HREF = "#py_1">Extending Python with a serial version of LAMMPS</A>
|
||||
<LI>11.2 <A HREF = "#py_2">Creating a shared MPI library</A>
|
||||
<LI>11.3 <A HREF = "#py_3">Extending Python with a parallel version of LAMMPS</A>
|
||||
<LI>11.4 <A HREF = "#py_4">Extending Python with MPI</A>
|
||||
<LI>11.5 <A HREF = "#py_5">Testing the Python-LAMMPS interface</A>
|
||||
<LI>11.6 <A HREF = "#py_6">Using LAMMPS from Python</A>
|
||||
<LI>11.7 <A HREF = "#py_7">Example Python scripts that use LAMMPS</A>
|
||||
<UL><LI>11.1 <A HREF = "#py_1">Setting necessary environment variables</A>
|
||||
<LI>11.2 <A HREF = "#py_2">Building LAMMPS as a shared library</A>
|
||||
<LI>11.3 <A HREF = "#py_3">Extending Python with MPI to run in parallel</A>
|
||||
<LI>11.4 <A HREF = "#py_4">Testing the Python-LAMMPS interface</A>
|
||||
<LI>11.5 <A HREF = "#py_5">Using LAMMPS from Python</A>
|
||||
<LI>11.6 <A HREF = "#py_6">Example Python scripts that use LAMMPS</A>
|
||||
</UL>
|
||||
<P>The LAMMPS distribution includes some Python code in its python
|
||||
directory which wraps the library interface to LAMMPS. This makes it
|
||||
is possible to run LAMMPS, invoke LAMMPS commands or give it an input
|
||||
script, extract LAMMPS results, an modify internal LAMMPS variables,
|
||||
either from a Python script or interactively from a Python prompt.
|
||||
<P>The LAMMPS distribution includes the file python/lammps.py which wraps
|
||||
the library interface to LAMMPS. This file makes it is possible to
|
||||
run LAMMPS, invoke LAMMPS commands or give it an input script, extract
|
||||
LAMMPS results, an modify internal LAMMPS variables, either from a
|
||||
Python script or interactively from a Python prompt. You can do the
|
||||
former in serial or parallel. Running Python interactively in
|
||||
parallel does not generally work, unless you have a package installed
|
||||
that extends your Python to enable multiple instances of Python to
|
||||
read what you type.
|
||||
</P>
|
||||
<P><A HREF = "http://www.python.org">Python</A> is a powerful scripting and programming
|
||||
language which can be used to wrap software like LAMMPS and other
|
||||
packages. It can be used to glue multiple pieces of software
|
||||
together, e.g. to run a coupled or multiscale model. See <A HREF = "Section_howto.html#howto_10">this
|
||||
together, e.g. to run a coupled or multiscale model. See <A HREF = "Section_howto.html#howto_10">Section
|
||||
section</A> of the manual and the couple
|
||||
directory of the distribution for more ideas about coupling LAMMPS to
|
||||
other codes. See <A HREF = "Section_start.html#start_5">Section_start 4</A> about
|
||||
how to build LAMMPS as a library, and <A HREF = "Section_howto.html#howto_19">this
|
||||
section</A> for a description of the library
|
||||
how to build LAMMPS as a library, and <A HREF = "Section_howto.html#howto_19">Section_howto
|
||||
19</A> for a description of the library
|
||||
interface provided in src/library.cpp and src/library.h and how to
|
||||
extend it for your needs. As described below, that interface is what
|
||||
is exposed to Python. It is designed to be easy to add functions to.
|
||||
This has the effect of extending the Python inteface as well. See
|
||||
details below.
|
||||
This can easily extend the Python inteface as well. See details
|
||||
below.
|
||||
</P>
|
||||
<P>By using the Python interface LAMMPS can also be coupled with a GUI or
|
||||
visualization tools that display graphs or animations in real time as
|
||||
LAMMPS runs. Examples of such scripts are inlcluded in the python
|
||||
directory.
|
||||
<P>By using the Python interface, LAMMPS can also be coupled with a GUI
|
||||
or other visualization tools that display graphs or animations in real
|
||||
time as LAMMPS runs. Examples of such scripts are inlcluded in the
|
||||
python directory.
|
||||
</P>
|
||||
<P>Two advantages of using Python are how concise the language is and
|
||||
<P>Two advantages of using Python are how concise the language is, and
|
||||
that it can be run interactively, enabling rapid development and
|
||||
debugging of programs. If you use it to mostly invoke costly
|
||||
operations within LAMMPS, such as running a simulation for a
|
||||
reasonable number of timesteps, then the overhead cost of invoking
|
||||
LAMMPS thru Python will be negligible.
|
||||
</P>
|
||||
<P>Before using LAMMPS from a Python script, the Python on your machine
|
||||
must be "extended" to include an interface to the LAMMPS library. If
|
||||
your Python script will invoke MPI operations, you will also need to
|
||||
extend your Python with an interface to MPI itself.
|
||||
<P>Before using LAMMPS from a Python script, you have to do two things.
|
||||
You need to set two environment variables. And you need to build
|
||||
LAMMPS as a dynamic shared library, so it can be loaded by Python.
|
||||
Both these steps are discussed below. If you wish to run LAMMPS in
|
||||
parallel from Python, you also need to extend your Python with MPI.
|
||||
This is also discussed below.
|
||||
</P>
|
||||
<P>Thus you should first decide how you intend to use LAMMPS from Python.
|
||||
There are 3 options:
|
||||
</P>
|
||||
<P>(1) Use LAMMPS on a single processor running Python.
|
||||
</P>
|
||||
<P>(2) Use LAMMPS in parallel, where each processor runs Python, but your
|
||||
Python program does not use MPI.
|
||||
</P>
|
||||
<P>(3) Use LAMMPS in parallel, where each processor runs Python, and your
|
||||
Python script also makes MPI calls through a Python/MPI interface.
|
||||
</P>
|
||||
<P>Note that for (2) and (3) you will not be able to use Python
|
||||
interactively by typing commands and getting a response. This is
|
||||
because you will have multiple instances of Python running (e.g. on a
|
||||
parallel machine) and they cannot all read what you type.
|
||||
</P>
|
||||
<P>Working in mode (1) does not require your machine to have MPI
|
||||
installed. You should extend your Python with a serial version of
|
||||
LAMMPS and the dummy MPI library provided with LAMMPS. See
|
||||
instructions below on how to do this.
|
||||
</P>
|
||||
<P>Working in mode (2) requires your machine to have an MPI library
|
||||
installed, but your Python does not need to be extended with MPI
|
||||
itself. The MPI library must be a shared library (e.g. a *.so file on
|
||||
Linux) which is not typically created when MPI is built/installed.
|
||||
See instruction below on how to do this. You should extend your
|
||||
Python with the a parallel versionn of LAMMPS which will use the
|
||||
shared MPI system library. See instructions below on how to do this.
|
||||
</P>
|
||||
<P>Working in mode (3) requires your machine to have MPI installed (as a
|
||||
shared library as in (2)). You must also extend your Python with a
|
||||
parallel version of LAMMPS (same as in (2)) and with MPI itself, via
|
||||
one of several available Python/MPI packages. See instructions below
|
||||
on how to do the latter task.
|
||||
</P>
|
||||
<P>Several of the following sub-sections cover the rest of the Python
|
||||
setup discussion. The next to last sub-section describes the Python
|
||||
syntax used to invoke LAMMPS. The last sub-section describes example
|
||||
Python scripts included in the python directory.
|
||||
</P>
|
||||
<P>Before proceeding, there are 2 items to note.
|
||||
</P>
|
||||
<P>(1) The provided Python wrapper for LAMMPS uses the amazing and
|
||||
magical (to me) "ctypes" package in Python, which auto-generates the
|
||||
interface code needed between Python and a set of C interface routines
|
||||
for a library. Ctypes is part of standard Python for versions 2.5 and
|
||||
later. You can check which version of Python you have installed, by
|
||||
simply typing "python" at a shell prompt.
|
||||
</P>
|
||||
<P>(2) Any library wrapped by Python, including LAMMPS, must be built as
|
||||
a shared library (e.g. a *.so file on Linux and not a *.a file). The
|
||||
python/setup_serial.py and setup.py scripts do this build for LAMMPS
|
||||
itself (described below). But if you have LAMMPS configured to use
|
||||
additional packages that have their own libraries, then those
|
||||
libraries must also be shared libraries. E.g. MPI, FFTW, or any of
|
||||
the libraries in lammps/lib. When you build LAMMPS as a stand-alone
|
||||
code, you are not building shared versions of these libraries.
|
||||
</P>
|
||||
<P>The discussion below describes how to create a shared MPI library. I
|
||||
suggest you start by configuing LAMMPS without packages installed that
|
||||
require any libraries besides MPI. See <A HREF = "Section_start.html#start_3">this
|
||||
section</A> of the manual for a discussion of
|
||||
LAMMPS packages. E.g. do not use the KSPACE, GPU, MEAM, POEMS, or
|
||||
REAX packages.
|
||||
</P>
|
||||
<P>If you are successfully follow the steps belwo to build the Python
|
||||
wrappers and use this version of LAMMPS through Python, you can then
|
||||
take the next step of adding LAMMPS packages that use additional
|
||||
libraries. This will require you to build a shared library for that
|
||||
package's library, similar to what is described below for MPI. It
|
||||
will also require you to edit the python/setup_serial.py or setup.py
|
||||
scripts to enable Python to access those libraries when it builds the
|
||||
LAMMPS wrapper.
|
||||
<P>The Python wrapper for LAMMPS uses the amazing and magical (to me)
|
||||
"ctypes" package in Python, which auto-generates the interface code
|
||||
needed between Python and a set of C interface routines for a library.
|
||||
Ctypes is part of standard Python for versions 2.5 and later. You can
|
||||
check which version of Python you have installed, by simply typing
|
||||
"python" at a shell prompt.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<HR>
|
||||
|
||||
<A NAME = "py_1"></A><H4>11.1 Extending Python with a serial version of LAMMPS
|
||||
<A NAME = "py_1"></A><H4>11.1 Setting necessary environment variables
|
||||
</H4>
|
||||
<P>From the python directory in the LAMMPS distribution, type
|
||||
<P>For Python to use the LAMMPS interface, it needs to find two files.
|
||||
The paths to these files need to be added to two environment variables
|
||||
that Python checks.
|
||||
</P>
|
||||
<PRE>python setup_serial.py build
|
||||
<P>The first is the environment variable PYTHONPATH. It needs
|
||||
to include the directory where the python/lammps.py file is.
|
||||
</P>
|
||||
<P>For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
</P>
|
||||
<PRE>setenv PYTHONPATH $<I>PYTHONPATH</I>:/home/sjplimp/lammps/python
|
||||
</PRE>
|
||||
<P>and then one of these commands:
|
||||
<P>The second is the environment variable LD_LIBRARY_PATH, which is used
|
||||
by the operating system to find dynamic shared libraries when it loads
|
||||
them. It needs to include the directory where the shared LAMMPS
|
||||
library will be. Normally this is the LAMMPS src dir, as explained in
|
||||
the following section.
|
||||
</P>
|
||||
<PRE>sudo python setup_serial.py install
|
||||
python setup_serial.py install --home=~/foo
|
||||
<P>For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
</P>
|
||||
<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src
|
||||
</PRE>
|
||||
<P>The "build" command should compile all the needed LAMMPS files,
|
||||
including its dummy MPI library. The first "install" command will put
|
||||
the needed files in your Python's site-packages sub-directory, so that
|
||||
Python can load them. For example, if you installed Python yourself
|
||||
on a Linux machine, it would typically be somewhere like
|
||||
/usr/local/lib/python2.5/site-packages. Installing Python packages
|
||||
this way often requires you to be able to write to the Python
|
||||
directories, which may require root priveleges, hence the "sudo"
|
||||
prefix. If this is not the case, you can drop the "sudo". If you use
|
||||
the "sudo" prefix and you have installed Python yourself, you should
|
||||
make sure that root uses the same Python as the one you did the
|
||||
"install" in. E.g. these 2 commands may do the install in different
|
||||
Python versions:
|
||||
<P>As discussed below, if your LAMMPS build includes auxiliary libraries,
|
||||
they must also be available as shared libraries for Python to
|
||||
successfully load LAMMPS. If they are not in default places where the
|
||||
operating system can find them, then you also have to add their paths
|
||||
to the LD_LIBRARY_PATH environment variable.
|
||||
</P>
|
||||
<PRE>python setup_serial.py install --home=~/foo
|
||||
python /usr/local/bin/python/setup_serial.py install --home=~/foo
|
||||
<P>For example, if you are using the dummy MPI library provided in
|
||||
src/STUBS, you need to add something like this to your ~/.cshrc file:
|
||||
</P>
|
||||
<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src/STUBS
|
||||
</PRE>
|
||||
<P>Alternatively, you can install the LAMMPS files (or any other Python
|
||||
packages) in your own user space. The second "install" command does
|
||||
this, where you should replace "foo" with your directory of choice.
|
||||
</P>
|
||||
<P>If these commands are successful, a <I>lammps.py</I> and
|
||||
<I>_lammps_serial.so</I> file will be put in the appropriate directory.
|
||||
<P>If you are using the LAMMPS USER-ATC package, you need to add
|
||||
something like this to your ~/.cshrc file:
|
||||
</P>
|
||||
<PRE>setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/lib/atc
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<A NAME = "py_2"></A><H4>11.2 Creating a shared MPI library
|
||||
<A NAME = "py_2"></A><H4>11.2 Building LAMMPS as a shared library
|
||||
</H4>
|
||||
<P>A shared library is one that is dynamically loadable, which is what
|
||||
Python requires. On Linux this is a library file that ends in ".so",
|
||||
not ".a". Such a shared library is normally not built if you
|
||||
installed MPI yourself, but it is easy to do. Here is how to do it
|
||||
for <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPICH</A>, a popular open-source version of MPI, distributed
|
||||
by Argonne National Labs. From within the mpich directory, type
|
||||
<P>Instructions on how to build LAMMPS as a shared library are given in
|
||||
<A HREF = "Section_start.html#start_5">Section_start 5</A>. A shared library is one
|
||||
that is dynamically loadable, which is what Python requires. On Linux
|
||||
this is a library file that ends in ".so", not ".a".
|
||||
</P>
|
||||
<P>>From the src directory, type
|
||||
</P>
|
||||
<P>make makeshlib
|
||||
make -f Makefile.shlib foo
|
||||
</P>
|
||||
<P>where foo is the machine target name, such as linux or g++ or serial.
|
||||
This should create the file liblmp_foo.so in the src directory, as
|
||||
well as a soft link liblmp.so which is what the Python wrapper will
|
||||
load by default. If you are building multiple machine versions of the
|
||||
shared library, the soft link is always set to the most recently built
|
||||
version.
|
||||
</P>
|
||||
<P>Note that as discussed in below, a LAMMPS build may depend on several
|
||||
auxiliary libraries, which are specified in your low-level
|
||||
src/Makefile.foo file. For example, an MPI library, the FFTW library,
|
||||
a JPEG library, etc. Depending on what LAMMPS packages you have
|
||||
installed, the build may also require additional libraries from the
|
||||
lib directories, such as lib/atc/libatc.so or lib/reax/libreax.so.
|
||||
</P>
|
||||
<P>You must insure that each of these libraries exist in shared library
|
||||
form (*.so file for Linux systems), or either the LAMMPS shared
|
||||
library build or the Python load of the library will fail. For the
|
||||
load to be successful all the shared libraries must also be in
|
||||
directories that the operating system checks. See the discussion in
|
||||
the preceding section about the LD_LIBRARY_PATH environment variable
|
||||
for how to insure this.
|
||||
</P>
|
||||
<P>Note that some system libraries, such as MPI, if you installed it
|
||||
yourself, may not be built by default as shared libraries. The build
|
||||
instructions for the library should tell you how to do this.
|
||||
</P>
|
||||
<P>For example, here is how to build and install the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPICH
|
||||
library</A>, a popular open-source version of MPI, distributed by
|
||||
Argonne National Labs, as a shared library in the default
|
||||
/usr/local/lib location:
|
||||
</P>
|
||||
|
||||
|
||||
@ -190,62 +168,26 @@ by Argonne National Labs. From within the mpich directory, type
|
||||
make
|
||||
make install
|
||||
</PRE>
|
||||
<P>You may need to use "sudo make install" in place of the last line.
|
||||
The end result should be the file libmpich.so in /usr/local/lib.
|
||||
<P>You may need to use "sudo make install" in place of the last line if
|
||||
you do not have write priveleges for /usr/local/lib. The end result
|
||||
should be the file /usr/local/lib/libmpich.so.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: If the file libmpich.a already exists in your
|
||||
installation directory (e.g. /usr/local/lib), you will now have both a
|
||||
static and shared MPI library. This will be fine for running LAMMPS
|
||||
from Python since it only uses the shared library. But if you now try
|
||||
to build LAMMPS by itself as a stand-alone program (cd lammps/src;
|
||||
make foo) or build other codes that expect to link against libmpich.a,
|
||||
then those builds may fail if the linker uses libmpich.so instead. If
|
||||
this happens, it means you will need to remove the file
|
||||
/usr/local/lib/libmich.so before building LAMMPS again as a
|
||||
stand-alone code.
|
||||
<P>Note that not all of the auxiliary libraries provided with LAMMPS have
|
||||
shared-library Makefiles in their lib directories. Typically this
|
||||
simply requires a Makefile.foo that adds a -fPIC switch when files are
|
||||
compiled and a "-fPIC -shared" switches when the library is linked
|
||||
with a C++ (or Fortran) compiler, as well as an output target that
|
||||
ends in ".so", like libatc.o. As we or others create and contribute
|
||||
these Makefiles, we will add them to the LAMMPS distribution.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "py_3"></A><H4>11.3 Extending Python with a parallel version of LAMMPS
|
||||
<A NAME = "py_3"></A><H4>11.3 Extending Python with MPI to run in parallel
|
||||
</H4>
|
||||
<P>From the python directory, type
|
||||
<P>If you wish to run LAMMPS in parallel from Python, you need to extend
|
||||
your Python with an interface to MPI. This also allows you to
|
||||
make MPI calls directly from Python in your script, if you desire.
|
||||
</P>
|
||||
<PRE>python setup.py build
|
||||
</PRE>
|
||||
<P>and then one of these commands:
|
||||
</P>
|
||||
<PRE>sudo python setup.py install
|
||||
python setup.py install --home=~/foo
|
||||
</PRE>
|
||||
<P>The "build" command should compile all the needed LAMMPS C++ files,
|
||||
which will require MPI to be installed on your system. This means it
|
||||
must find both the header file mpi.h and a shared library file,
|
||||
e.g. libmpich.so if the MPICH version of MPI is installed. See the
|
||||
preceding section for how to create a shared library version of MPI if
|
||||
it does not exist. You may need to adjust the "include_dirs" and
|
||||
"library_dirs" and "libraries" fields in python/setup.py to
|
||||
insure the Python build finds all the files it needs.
|
||||
</P>
|
||||
<P>The first "install" command will put the needed files in your Python's
|
||||
site-packages sub-directory, so that Python can load them. For
|
||||
example, if you installed Python yourself on a Linux machine, it would
|
||||
typically be somewhere like /usr/local/lib/python2.5/site-packages.
|
||||
Installing Python packages this way often requires you to be able to
|
||||
write to the Python directories, which may require root priveleges,
|
||||
hence the "sudo" prefix. If this is not the case, you can drop the
|
||||
"sudo".
|
||||
</P>
|
||||
<P>Alternatively, you can install the LAMMPS files (or any other Python
|
||||
packages) in your own user space. The second "install" command does
|
||||
this, where you should replace "foo" with your directory of choice.
|
||||
</P>
|
||||
<P>If these commands are successful, a <I>lammps.py</I> and <I>_lammps.so</I> file
|
||||
will be put in the appropriate directory.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "py_4"></A><H4>11.4 Extending Python with MPI
|
||||
</H4>
|
||||
<P>There are several Python packages available that purport to wrap MPI
|
||||
as a library and allow MPI functions to be called from Python.
|
||||
</P>
|
||||
@ -260,26 +202,26 @@ as a library and allow MPI functions to be called from Python.
|
||||
<P>All of these except pyMPI work by wrapping the MPI library (which must
|
||||
be available on your system as a shared library, as discussed above),
|
||||
and exposing (some portion of) its interface to your Python script.
|
||||
This means they cannot be used interactively in parallel, since they
|
||||
This means Python cannot be used interactively in parallel, since they
|
||||
do not address the issue of interactive input to multiple instances of
|
||||
Python running on different processors. The one exception is pyMPI,
|
||||
which alters the Python interpreter to address this issue, and (I
|
||||
believe) creates a new alternate executable (in place of python
|
||||
believe) creates a new alternate executable (in place of "python"
|
||||
itself) as a result.
|
||||
</P>
|
||||
<P>In principle any of these Python/MPI packages should work to invoke
|
||||
both calls to LAMMPS and MPI itself from a Python script running in
|
||||
parallel. However, when I downloaded and looked at a few of them,
|
||||
their docuemtation was incomplete and I had trouble with their
|
||||
installation. It's not clear if some of the packages are still being
|
||||
actively developed and supported.
|
||||
LAMMPS in parallel and MPI calls themselves from a Python script which
|
||||
is itself running in parallel. However, when I downloaded and looked
|
||||
at a few of them, their documentation was incomplete and I had trouble
|
||||
with their installation. It's not clear if some of the packages are
|
||||
still being actively developed and supported.
|
||||
</P>
|
||||
<P>The one I recommend, since I have successfully used it with LAMMPS, is
|
||||
Pypar. Pypar requires the ubiquitous <A HREF = "http://numpy.scipy.org">Numpy
|
||||
package</A> be installed in your Python. After
|
||||
launching python, type
|
||||
</P>
|
||||
<PRE>>>> import numpy
|
||||
<PRE>import numpy
|
||||
</PRE>
|
||||
<P>to see if it is installed. If not, here is how to install it (version
|
||||
1.3.0b1 as of April 2009). Unpack the numpy tarball and from its
|
||||
@ -303,106 +245,124 @@ your Python distribution's site-packages directory.
|
||||
<P>If you have successully installed Pypar, you should be able to run
|
||||
python serially and type
|
||||
</P>
|
||||
<PRE>>>> import pypar
|
||||
<PRE>import pypar
|
||||
</PRE>
|
||||
<P>without error. You should also be able to run python in parallel
|
||||
on a simple test script
|
||||
</P>
|
||||
<PRE>% mpirun -np 4 python test.script
|
||||
<PRE>% mpirun -np 4 python test.py
|
||||
</PRE>
|
||||
<P>where test.script contains the lines
|
||||
<P>where test.py contains the lines
|
||||
</P>
|
||||
<PRE>import pypar
|
||||
print "Proc %d out of %d procs" % (pypar.rank(),pypar.size())
|
||||
</PRE>
|
||||
<P>and see one line of output for each processor you ran on.
|
||||
<P>and see one line of output for each processor you run on.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "py_5"></A><H4>11.5 Testing the Python-LAMMPS interface
|
||||
<A NAME = "py_4"></A><H4>11.4 Testing the Python-LAMMPS interface
|
||||
</H4>
|
||||
<P>Before using LAMMPS in a Python program, one more step is needed. The
|
||||
interface to LAMMPS is via the Python ctypes package, which loads the
|
||||
shared LAMMPS library via a CDLL() call, which in turn is a wrapper on
|
||||
the C-library dlopen(). This command is different than a normal
|
||||
Python "import" and needs to be able to find the LAMMPS shared
|
||||
library, which is either in the Python site-packages directory or in a
|
||||
local directory you specified in the "python setup.py install"
|
||||
command, as described above.
|
||||
</P>
|
||||
<P>The simplest way to do this is add a line like this to your
|
||||
.cshrc or other shell start-up file.
|
||||
</P>
|
||||
<PRE>setenv LD_LIBRARY_PATH
|
||||
${LD_LIBRARY_PATH}:/usr/local/lib/python2.5/site-packages
|
||||
</PRE>
|
||||
<P>and then execute the shell file to insure the path has been updated.
|
||||
This will extend the path that dlopen() uses to look for shared
|
||||
libraries.
|
||||
</P>
|
||||
<P>To test if the serial LAMMPS library has been successfully installed
|
||||
(mode 1 above), launch Python and type
|
||||
<P>To test if LAMMPS is callable from Python, launch Python interactively
|
||||
and type:
|
||||
</P>
|
||||
<PRE>>>> from lammps import lammps
|
||||
>>> lmp = lammps()
|
||||
</PRE>
|
||||
<P>If you get no errors, you're ready to use serial LAMMPS from Python.
|
||||
<P>If you get no errors, you're ready to use LAMMPS from Python.
|
||||
If the load fails, the most common error to see is
|
||||
</P>
|
||||
<P>If you built LAMMPS for parallel use (mode 2 or 3 above), launch
|
||||
Python in parallel:
|
||||
<P>"CDLL: asdfasdfasdf"
|
||||
</P>
|
||||
<PRE>% mpirun -np 4 python test.script
|
||||
<P>which means Python was unable to load the LAMMPS shared library. This
|
||||
can occur if it can't find the LAMMMPS library; see the environment
|
||||
variable discussion <A HREF = "#python_1">above</A>. Or if it can't find one of the
|
||||
auxiliary libraries that was specified in the LAMMPS build, in a
|
||||
shared dynamic library format. This includes all libraries needed by
|
||||
main LAMMPS (e.g. MPI or FFTW or JPEG), system libraries needed by
|
||||
main LAMMPS (e.g. extra libs needed by MPI), or packages you have
|
||||
installed that require libraries provided with LAMMPS (e.g. the
|
||||
USER-ATC package require lib/atc/libatc.so) or system libraries
|
||||
(e.g. BLAS or Fortran-to-C libraries) listed in the
|
||||
lib/package/Makefile.lammps file. Again, all of these must be
|
||||
available as shared libraries, or the Python load will fail.
|
||||
</P>
|
||||
<P>Python (actually the operating system) isn't verbose about telling you
|
||||
why the load failed, so go through the steps above and in
|
||||
<A HREF = "Section_start.html#start_5">Section_start 5</A> carefully.
|
||||
</P>
|
||||
<H5><B>Test LAMMPS and Python in serial:</B>
|
||||
</H5>
|
||||
<P>To run a LAMMPS test in serial, type these lines into Python
|
||||
interactively from the bench directory:
|
||||
</P>
|
||||
<PRE>>>> from lammps import lammps
|
||||
>>> lmp = lammps()
|
||||
>>> lmp.file("in.lj")
|
||||
</PRE>
|
||||
<P>where test.script contains the lines
|
||||
<P>Or put the same lines in the file test.py and run it as
|
||||
</P>
|
||||
<PRE>% python test.py
|
||||
</PRE>
|
||||
<P>Either way, you should see the results of running the in.lj benchmark
|
||||
on a single processor appear on the screen, the same as if you had
|
||||
typed something like:
|
||||
</P>
|
||||
<PRE>lmp_g++ < in.lj
|
||||
</PRE>
|
||||
<H5><B>Test LAMMPS and Python in parallel:</B>
|
||||
</H5>
|
||||
<P>To run LAMMPS in parallel, assuming you have installed the
|
||||
<A HREF = "http://datamining.anu.edu.au/~ole/pypar">Pypar</A> package as discussed
|
||||
above, create a test.py file containing these lines:
|
||||
</P>
|
||||
<PRE>import pypar
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()), lmp
|
||||
lmp.file("in.lj")
|
||||
print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
|
||||
pypar.finalize()
|
||||
</PRE>
|
||||
<P>Again, if you get no errors, you're good to go.
|
||||
<P>You can then run it in parallel as:
|
||||
</P>
|
||||
<P>Note that if you left out the "import pypar" line from this script,
|
||||
you would instantiate and run LAMMPS independently on each of the P
|
||||
processors specified in the mpirun command. You can test if Pypar is
|
||||
enabling true parallel Python and LAMMPS by adding a line to the above
|
||||
sequence of commands like lmp.file("in.lj") to run an input script and
|
||||
see if the LAMMPS run says it ran on P processors or if you get output
|
||||
from P duplicated 1-processor runs written to the screen. In the
|
||||
latter case, Pypar is not working correctly.
|
||||
</P>
|
||||
<P>Note that this line:
|
||||
</P>
|
||||
<PRE>from lammps import lammps
|
||||
<PRE>% mpirun -np 4 python test.py
|
||||
</PRE>
|
||||
<P>will import either the serial or parallel version of the LAMMPS
|
||||
library, as wrapped by lammps.py. But if you installed both via
|
||||
setup_serial.py and setup.py, it will always import the parallel
|
||||
version, since it attempts that first.
|
||||
<P>and you should see the same output as if you had typed
|
||||
</P>
|
||||
<P>Note that if your Python script imports the Pypar package (as above),
|
||||
so that it can use MPI calls directly, then Pypar initializes MPI for
|
||||
you. Thus the last line of your Python script should be
|
||||
pypar.finalize(), to insure MPI is shut down correctly.
|
||||
<PRE>% mpirun -np 4 lmp_g++ < in.lj
|
||||
</PRE>
|
||||
<P>Note that if you leave out the 3 lines from test.py that specify Pypar
|
||||
commands you will instantiate and run LAMMPS independently on each of
|
||||
the P processors specified in the mpirun command. In this case you
|
||||
should get 4 sets of output, each showing that a run was made on a
|
||||
single processor, instead of one set of output showing that it ran on
|
||||
4 processors. If the 1-processor outputs occur, it means that Pypar
|
||||
is not working correctly.
|
||||
</P>
|
||||
<P>Also note that a Python script can be invoked in one of several ways:
|
||||
<P>Also note that once you import the PyPar module, Pypar initializes MPI
|
||||
for you, and you can use MPI calls directly in your Python script, as
|
||||
described in the Pypar documentation. The last line of your Python
|
||||
script should be pypar.finalize(), to insure MPI is shut down
|
||||
correctly.
|
||||
</P>
|
||||
<P>% python foo.script
|
||||
<P>Note that any Python script (not just for LAMMPS) can be invoked in
|
||||
one of several ways:
|
||||
</P>
|
||||
<PRE>% python foo.script
|
||||
% python -i foo.script
|
||||
% foo.script
|
||||
</P>
|
||||
% foo.script
|
||||
</PRE>
|
||||
<P>The last command requires that the first line of the script be
|
||||
something like this:
|
||||
</P>
|
||||
<P>#!/usr/local/bin/python
|
||||
#!/usr/local/bin/python -i
|
||||
</P>
|
||||
<PRE>#!/usr/local/bin/python
|
||||
#!/usr/local/bin/python -i
|
||||
</PRE>
|
||||
<P>where the path points to where you have Python installed, and that you
|
||||
have made the script file executable:
|
||||
</P>
|
||||
<P>% chmod +x foo.script
|
||||
</P>
|
||||
<PRE>% chmod +x foo.script
|
||||
</PRE>
|
||||
<P>Without the "-i" flag, Python will exit when the script finishes.
|
||||
With the "-i" flag, you will be left in the Python interpreter when
|
||||
the script finishes, so you can type subsequent commands. As
|
||||
@ -413,14 +373,15 @@ Python on a single processor, not in parallel.
|
||||
|
||||
<HR>
|
||||
|
||||
<A NAME = "py_6"></A><H4>11.6 Using LAMMPS from Python
|
||||
<A NAME = "py_5"></A><H4>11.5 Using LAMMPS from Python
|
||||
</H4>
|
||||
<P>The Python interface to LAMMPS consists of a Python "lammps" module,
|
||||
the source code for which is in python/lammps.py, which creates a
|
||||
"lammps" object, with a set of methods that can be invoked on that
|
||||
object. The sample Python code below assumes you have first imported
|
||||
the "lammps" module in your Python script and its settings as
|
||||
follows:
|
||||
the "lammps" module in your Python script. You can also include its
|
||||
settings as follows, which are useful in test return values from some
|
||||
of the methods described below:
|
||||
</P>
|
||||
<PRE>from lammps import lammps
|
||||
from lammps import LMPINT as INT
|
||||
@ -434,8 +395,10 @@ at the file src/library.cpp you will see that they correspond
|
||||
one-to-one with calls you can make to the LAMMPS library from a C++ or
|
||||
C or Fortran program.
|
||||
</P>
|
||||
<PRE>lmp = lammps() # create a LAMMPS object
|
||||
lmp = lammps(list) # ditto, with command-line args, list = ["-echo","screen"]
|
||||
<PRE>lmp = lammps() # create a LAMMPS object using the default liblmp.so library
|
||||
lmp = lammps("g++") # create a LAMMPS object using the liblmp_g++.so library
|
||||
lmp = lammps("",list) # ditto, with command-line args, list = ["-echo","screen"]
|
||||
lmp = lammps("g++",list)
|
||||
</PRE>
|
||||
<PRE>lmp.close() # destroy a LAMMPS object
|
||||
</PRE>
|
||||
@ -443,16 +406,16 @@ lmp = lammps(list) # ditto, with command-line args, list = ["-echo","scree
|
||||
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100"
|
||||
</PRE>
|
||||
<PRE>xlo = lmp.extract_global(name,type) # extract a global quantity
|
||||
# name = "boxxlo", "nlocal", etc
|
||||
# name = "boxxlo", "nlocal", etc
|
||||
# type = INT or DOUBLE
|
||||
</PRE>
|
||||
<PRE>coords = lmp.extract_atom(name,type) # extract a per-atom quantity
|
||||
# name = "x", "type", etc
|
||||
# name = "x", "type", etc
|
||||
# type = IPTR or DPTR or DPTRPTR
|
||||
</PRE>
|
||||
<PRE>eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
|
||||
v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
|
||||
# id = ID of compute or fix
|
||||
# id = ID of compute or fix
|
||||
# style = 0 = global data
|
||||
# 1 = per-atom data
|
||||
# 2 = local data
|
||||
@ -473,12 +436,23 @@ lmp.put_coords(x) # set all atom coords via x
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<P>The creation of a LAMMPS object does not take an MPI communicator as
|
||||
an argument. There should be a way to do this, so that the LAMMPS
|
||||
instance runs on a subset of processors, if desired, but I don't yet
|
||||
know how from Pypar. So for now, it runs on MPI_COMM_WORLD, which is
|
||||
all the processors.
|
||||
<P>IMPORTANT NOTE: Currently, the creation of a LAMMPS object does not
|
||||
take an MPI communicator as an argument. There should be a way to do
|
||||
this, so that the LAMMPS instance runs on a subset of processors if
|
||||
desired, but I don't know how to do it from Pypar. So for now, it
|
||||
runs on MPI_COMM_WORLD, which is all the processors. If someone
|
||||
figures out how to do this with one or more of the Python wrappers for
|
||||
MPI, like Pypar, please let us know and we will amend these doc pages.
|
||||
</P>
|
||||
<P>Note that you can create multiple LAMMPS objects in your Python
|
||||
script, and coordinate and run multiple simulations, e.g.
|
||||
</P>
|
||||
<PRE>from lammps import lammps
|
||||
lmp1 = lammps()
|
||||
lmp2 = lammps()
|
||||
lmp1.file("in.file1")
|
||||
lmp2.file("in.file2")
|
||||
</PRE>
|
||||
<P>The file() and command() methods allow an input script or single
|
||||
commands to be invoked.
|
||||
</P>
|
||||
@ -588,15 +562,10 @@ following steps:
|
||||
<UL><LI>Add a new interface function to src/library.cpp and
|
||||
src/library.h.
|
||||
|
||||
<LI>Verify the new function is syntactically correct by building LAMMPS as
|
||||
a library - see <A HREF = "Section_start.html#start_5">Section_start 4</A> of the
|
||||
manual.
|
||||
<LI>Rebuild LAMMPS as a shared library.
|
||||
|
||||
<LI>Add a wrapper method in the Python LAMMPS module to python/lammps.py
|
||||
for this interface function.
|
||||
|
||||
<LI>Rebuild the Python wrapper via python/setup_serial.py or
|
||||
python/setup.py.
|
||||
<LI>Add a wrapper method to python/lammps.py for this interface
|
||||
function.
|
||||
|
||||
<LI>You should now be able to invoke the new interface function from a
|
||||
Python script. Isn't ctypes amazing?
|
||||
@ -605,7 +574,7 @@ Python script. Isn't ctypes amazing?
|
||||
|
||||
<HR>
|
||||
|
||||
<A NAME = "py_7"></A><H4>11.7 Example Python scripts that use LAMMPS
|
||||
<A NAME = "py_6"></A><H4>11.6 Example Python scripts that use LAMMPS
|
||||
</H4>
|
||||
<P>These are the Python scripts included as demos in the python/examples
|
||||
directory of the LAMMPS distribution, to illustrate the kinds of
|
||||
|
||||
@ -11,174 +11,152 @@
|
||||
This section describes how to build and use LAMMPS via a Python
|
||||
interface.
|
||||
|
||||
11.1 "Extending Python with a serial version of LAMMPS"_#py_1
|
||||
11.2 "Creating a shared MPI library"_#py_2
|
||||
11.3 "Extending Python with a parallel version of LAMMPS"_#py_3
|
||||
11.4 "Extending Python with MPI"_#py_4
|
||||
11.5 "Testing the Python-LAMMPS interface"_#py_5
|
||||
11.6 "Using LAMMPS from Python"_#py_6
|
||||
11.7 "Example Python scripts that use LAMMPS"_#py_7 :ul
|
||||
11.1 "Setting necessary environment variables"_#py_1
|
||||
11.2 "Building LAMMPS as a shared library"_#py_2
|
||||
11.3 "Extending Python with MPI to run in parallel"_#py_3
|
||||
11.4 "Testing the Python-LAMMPS interface"_#py_4
|
||||
11.5 "Using LAMMPS from Python"_#py_5
|
||||
11.6 "Example Python scripts that use LAMMPS"_#py_6 :ul
|
||||
|
||||
The LAMMPS distribution includes some Python code in its python
|
||||
directory which wraps the library interface to LAMMPS. This makes it
|
||||
is possible to run LAMMPS, invoke LAMMPS commands or give it an input
|
||||
script, extract LAMMPS results, an modify internal LAMMPS variables,
|
||||
either from a Python script or interactively from a Python prompt.
|
||||
The LAMMPS distribution includes the file python/lammps.py which wraps
|
||||
the library interface to LAMMPS. This file makes it is possible to
|
||||
run LAMMPS, invoke LAMMPS commands or give it an input script, extract
|
||||
LAMMPS results, an modify internal LAMMPS variables, either from a
|
||||
Python script or interactively from a Python prompt. You can do the
|
||||
former in serial or parallel. Running Python interactively in
|
||||
parallel does not generally work, unless you have a package installed
|
||||
that extends your Python to enable multiple instances of Python to
|
||||
read what you type.
|
||||
|
||||
"Python"_http://www.python.org is a powerful scripting and programming
|
||||
language which can be used to wrap software like LAMMPS and other
|
||||
packages. It can be used to glue multiple pieces of software
|
||||
together, e.g. to run a coupled or multiscale model. See "this
|
||||
together, e.g. to run a coupled or multiscale model. See "Section
|
||||
section"_Section_howto.html#howto_10 of the manual and the couple
|
||||
directory of the distribution for more ideas about coupling LAMMPS to
|
||||
other codes. See "Section_start 4"_Section_start.html#start_5 about
|
||||
how to build LAMMPS as a library, and "this
|
||||
section"_Section_howto.html#howto_19 for a description of the library
|
||||
how to build LAMMPS as a library, and "Section_howto
|
||||
19"_Section_howto.html#howto_19 for a description of the library
|
||||
interface provided in src/library.cpp and src/library.h and how to
|
||||
extend it for your needs. As described below, that interface is what
|
||||
is exposed to Python. It is designed to be easy to add functions to.
|
||||
This has the effect of extending the Python inteface as well. See
|
||||
details below.
|
||||
This can easily extend the Python inteface as well. See details
|
||||
below.
|
||||
|
||||
By using the Python interface LAMMPS can also be coupled with a GUI or
|
||||
visualization tools that display graphs or animations in real time as
|
||||
LAMMPS runs. Examples of such scripts are inlcluded in the python
|
||||
directory.
|
||||
By using the Python interface, LAMMPS can also be coupled with a GUI
|
||||
or other visualization tools that display graphs or animations in real
|
||||
time as LAMMPS runs. Examples of such scripts are inlcluded in the
|
||||
python directory.
|
||||
|
||||
Two advantages of using Python are how concise the language is and
|
||||
Two advantages of using Python are how concise the language is, and
|
||||
that it can be run interactively, enabling rapid development and
|
||||
debugging of programs. If you use it to mostly invoke costly
|
||||
operations within LAMMPS, such as running a simulation for a
|
||||
reasonable number of timesteps, then the overhead cost of invoking
|
||||
LAMMPS thru Python will be negligible.
|
||||
|
||||
Before using LAMMPS from a Python script, the Python on your machine
|
||||
must be "extended" to include an interface to the LAMMPS library. If
|
||||
your Python script will invoke MPI operations, you will also need to
|
||||
extend your Python with an interface to MPI itself.
|
||||
Before using LAMMPS from a Python script, you have to do two things.
|
||||
You need to set two environment variables. And you need to build
|
||||
LAMMPS as a dynamic shared library, so it can be loaded by Python.
|
||||
Both these steps are discussed below. If you wish to run LAMMPS in
|
||||
parallel from Python, you also need to extend your Python with MPI.
|
||||
This is also discussed below.
|
||||
|
||||
Thus you should first decide how you intend to use LAMMPS from Python.
|
||||
There are 3 options:
|
||||
|
||||
(1) Use LAMMPS on a single processor running Python.
|
||||
|
||||
(2) Use LAMMPS in parallel, where each processor runs Python, but your
|
||||
Python program does not use MPI.
|
||||
|
||||
(3) Use LAMMPS in parallel, where each processor runs Python, and your
|
||||
Python script also makes MPI calls through a Python/MPI interface.
|
||||
|
||||
Note that for (2) and (3) you will not be able to use Python
|
||||
interactively by typing commands and getting a response. This is
|
||||
because you will have multiple instances of Python running (e.g. on a
|
||||
parallel machine) and they cannot all read what you type.
|
||||
|
||||
Working in mode (1) does not require your machine to have MPI
|
||||
installed. You should extend your Python with a serial version of
|
||||
LAMMPS and the dummy MPI library provided with LAMMPS. See
|
||||
instructions below on how to do this.
|
||||
|
||||
Working in mode (2) requires your machine to have an MPI library
|
||||
installed, but your Python does not need to be extended with MPI
|
||||
itself. The MPI library must be a shared library (e.g. a *.so file on
|
||||
Linux) which is not typically created when MPI is built/installed.
|
||||
See instruction below on how to do this. You should extend your
|
||||
Python with the a parallel versionn of LAMMPS which will use the
|
||||
shared MPI system library. See instructions below on how to do this.
|
||||
|
||||
Working in mode (3) requires your machine to have MPI installed (as a
|
||||
shared library as in (2)). You must also extend your Python with a
|
||||
parallel version of LAMMPS (same as in (2)) and with MPI itself, via
|
||||
one of several available Python/MPI packages. See instructions below
|
||||
on how to do the latter task.
|
||||
|
||||
Several of the following sub-sections cover the rest of the Python
|
||||
setup discussion. The next to last sub-section describes the Python
|
||||
syntax used to invoke LAMMPS. The last sub-section describes example
|
||||
Python scripts included in the python directory.
|
||||
|
||||
Before proceeding, there are 2 items to note.
|
||||
|
||||
(1) The provided Python wrapper for LAMMPS uses the amazing and
|
||||
magical (to me) "ctypes" package in Python, which auto-generates the
|
||||
interface code needed between Python and a set of C interface routines
|
||||
for a library. Ctypes is part of standard Python for versions 2.5 and
|
||||
later. You can check which version of Python you have installed, by
|
||||
simply typing "python" at a shell prompt.
|
||||
|
||||
(2) Any library wrapped by Python, including LAMMPS, must be built as
|
||||
a shared library (e.g. a *.so file on Linux and not a *.a file). The
|
||||
python/setup_serial.py and setup.py scripts do this build for LAMMPS
|
||||
itself (described below). But if you have LAMMPS configured to use
|
||||
additional packages that have their own libraries, then those
|
||||
libraries must also be shared libraries. E.g. MPI, FFTW, or any of
|
||||
the libraries in lammps/lib. When you build LAMMPS as a stand-alone
|
||||
code, you are not building shared versions of these libraries.
|
||||
|
||||
The discussion below describes how to create a shared MPI library. I
|
||||
suggest you start by configuing LAMMPS without packages installed that
|
||||
require any libraries besides MPI. See "this
|
||||
section"_Section_start.html#start_3 of the manual for a discussion of
|
||||
LAMMPS packages. E.g. do not use the KSPACE, GPU, MEAM, POEMS, or
|
||||
REAX packages.
|
||||
|
||||
If you are successfully follow the steps belwo to build the Python
|
||||
wrappers and use this version of LAMMPS through Python, you can then
|
||||
take the next step of adding LAMMPS packages that use additional
|
||||
libraries. This will require you to build a shared library for that
|
||||
package's library, similar to what is described below for MPI. It
|
||||
will also require you to edit the python/setup_serial.py or setup.py
|
||||
scripts to enable Python to access those libraries when it builds the
|
||||
LAMMPS wrapper.
|
||||
The Python wrapper for LAMMPS uses the amazing and magical (to me)
|
||||
"ctypes" package in Python, which auto-generates the interface code
|
||||
needed between Python and a set of C interface routines for a library.
|
||||
Ctypes is part of standard Python for versions 2.5 and later. You can
|
||||
check which version of Python you have installed, by simply typing
|
||||
"python" at a shell prompt.
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
11.1 Extending Python with a serial version of LAMMPS :link(py_1),h4
|
||||
11.1 Setting necessary environment variables :link(py_1),h4
|
||||
|
||||
From the python directory in the LAMMPS distribution, type
|
||||
For Python to use the LAMMPS interface, it needs to find two files.
|
||||
The paths to these files need to be added to two environment variables
|
||||
that Python checks.
|
||||
|
||||
python setup_serial.py build :pre
|
||||
The first is the environment variable PYTHONPATH. It needs
|
||||
to include the directory where the python/lammps.py file is.
|
||||
|
||||
and then one of these commands:
|
||||
For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
|
||||
sudo python setup_serial.py install
|
||||
python setup_serial.py install --home=~/foo :pre
|
||||
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python :pre
|
||||
|
||||
The "build" command should compile all the needed LAMMPS files,
|
||||
including its dummy MPI library. The first "install" command will put
|
||||
the needed files in your Python's site-packages sub-directory, so that
|
||||
Python can load them. For example, if you installed Python yourself
|
||||
on a Linux machine, it would typically be somewhere like
|
||||
/usr/local/lib/python2.5/site-packages. Installing Python packages
|
||||
this way often requires you to be able to write to the Python
|
||||
directories, which may require root priveleges, hence the "sudo"
|
||||
prefix. If this is not the case, you can drop the "sudo". If you use
|
||||
the "sudo" prefix and you have installed Python yourself, you should
|
||||
make sure that root uses the same Python as the one you did the
|
||||
"install" in. E.g. these 2 commands may do the install in different
|
||||
Python versions:
|
||||
The second is the environment variable LD_LIBRARY_PATH, which is used
|
||||
by the operating system to find dynamic shared libraries when it loads
|
||||
them. It needs to include the directory where the shared LAMMPS
|
||||
library will be. Normally this is the LAMMPS src dir, as explained in
|
||||
the following section.
|
||||
|
||||
python setup_serial.py install --home=~/foo
|
||||
python /usr/local/bin/python/setup_serial.py install --home=~/foo :pre
|
||||
For the csh or tcsh shells, you could add something like this to your
|
||||
~/.cshrc file:
|
||||
|
||||
Alternatively, you can install the LAMMPS files (or any other Python
|
||||
packages) in your own user space. The second "install" command does
|
||||
this, where you should replace "foo" with your directory of choice.
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src :pre
|
||||
|
||||
If these commands are successful, a {lammps.py} and
|
||||
{_lammps_serial.so} file will be put in the appropriate directory.
|
||||
As discussed below, if your LAMMPS build includes auxiliary libraries,
|
||||
they must also be available as shared libraries for Python to
|
||||
successfully load LAMMPS. If they are not in default places where the
|
||||
operating system can find them, then you also have to add their paths
|
||||
to the LD_LIBRARY_PATH environment variable.
|
||||
|
||||
For example, if you are using the dummy MPI library provided in
|
||||
src/STUBS, you need to add something like this to your ~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src/STUBS :pre
|
||||
|
||||
If you are using the LAMMPS USER-ATC package, you need to add
|
||||
something like this to your ~/.cshrc file:
|
||||
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/atc :pre
|
||||
|
||||
:line
|
||||
|
||||
11.2 Creating a shared MPI library :link(py_2),h4
|
||||
11.2 Building LAMMPS as a shared library :link(py_2),h4
|
||||
|
||||
A shared library is one that is dynamically loadable, which is what
|
||||
Python requires. On Linux this is a library file that ends in ".so",
|
||||
not ".a". Such a shared library is normally not built if you
|
||||
installed MPI yourself, but it is easy to do. Here is how to do it
|
||||
for "MPICH"_mpich, a popular open-source version of MPI, distributed
|
||||
by Argonne National Labs. From within the mpich directory, type
|
||||
Instructions on how to build LAMMPS as a shared library are given in
|
||||
"Section_start 5"_Section_start.html#start_5. A shared library is one
|
||||
that is dynamically loadable, which is what Python requires. On Linux
|
||||
this is a library file that ends in ".so", not ".a".
|
||||
|
||||
>From the src directory, type
|
||||
|
||||
make makeshlib
|
||||
make -f Makefile.shlib foo
|
||||
|
||||
where foo is the machine target name, such as linux or g++ or serial.
|
||||
This should create the file liblmp_foo.so in the src directory, as
|
||||
well as a soft link liblmp.so which is what the Python wrapper will
|
||||
load by default. If you are building multiple machine versions of the
|
||||
shared library, the soft link is always set to the most recently built
|
||||
version.
|
||||
|
||||
Note that as discussed in below, a LAMMPS build may depend on several
|
||||
auxiliary libraries, which are specified in your low-level
|
||||
src/Makefile.foo file. For example, an MPI library, the FFTW library,
|
||||
a JPEG library, etc. Depending on what LAMMPS packages you have
|
||||
installed, the build may also require additional libraries from the
|
||||
lib directories, such as lib/atc/libatc.so or lib/reax/libreax.so.
|
||||
|
||||
You must insure that each of these libraries exist in shared library
|
||||
form (*.so file for Linux systems), or either the LAMMPS shared
|
||||
library build or the Python load of the library will fail. For the
|
||||
load to be successful all the shared libraries must also be in
|
||||
directories that the operating system checks. See the discussion in
|
||||
the preceding section about the LD_LIBRARY_PATH environment variable
|
||||
for how to insure this.
|
||||
|
||||
Note that some system libraries, such as MPI, if you installed it
|
||||
yourself, may not be built by default as shared libraries. The build
|
||||
instructions for the library should tell you how to do this.
|
||||
|
||||
For example, here is how to build and install the "MPICH
|
||||
library"_mpich, a popular open-source version of MPI, distributed by
|
||||
Argonne National Labs, as a shared library in the default
|
||||
/usr/local/lib location:
|
||||
|
||||
:link(mpich,http://www-unix.mcs.anl.gov/mpi)
|
||||
|
||||
@ -186,61 +164,25 @@ by Argonne National Labs. From within the mpich directory, type
|
||||
make
|
||||
make install :pre
|
||||
|
||||
You may need to use "sudo make install" in place of the last line.
|
||||
The end result should be the file libmpich.so in /usr/local/lib.
|
||||
You may need to use "sudo make install" in place of the last line if
|
||||
you do not have write priveleges for /usr/local/lib. The end result
|
||||
should be the file /usr/local/lib/libmpich.so.
|
||||
|
||||
IMPORTANT NOTE: If the file libmpich.a already exists in your
|
||||
installation directory (e.g. /usr/local/lib), you will now have both a
|
||||
static and shared MPI library. This will be fine for running LAMMPS
|
||||
from Python since it only uses the shared library. But if you now try
|
||||
to build LAMMPS by itself as a stand-alone program (cd lammps/src;
|
||||
make foo) or build other codes that expect to link against libmpich.a,
|
||||
then those builds may fail if the linker uses libmpich.so instead. If
|
||||
this happens, it means you will need to remove the file
|
||||
/usr/local/lib/libmich.so before building LAMMPS again as a
|
||||
stand-alone code.
|
||||
Note that not all of the auxiliary libraries provided with LAMMPS have
|
||||
shared-library Makefiles in their lib directories. Typically this
|
||||
simply requires a Makefile.foo that adds a -fPIC switch when files are
|
||||
compiled and a "-fPIC -shared" switches when the library is linked
|
||||
with a C++ (or Fortran) compiler, as well as an output target that
|
||||
ends in ".so", like libatc.o. As we or others create and contribute
|
||||
these Makefiles, we will add them to the LAMMPS distribution.
|
||||
|
||||
:line
|
||||
|
||||
11.3 Extending Python with a parallel version of LAMMPS :link(py_3),h4
|
||||
11.3 Extending Python with MPI to run in parallel :link(py_3),h4
|
||||
|
||||
From the python directory, type
|
||||
|
||||
python setup.py build :pre
|
||||
|
||||
and then one of these commands:
|
||||
|
||||
sudo python setup.py install
|
||||
python setup.py install --home=~/foo :pre
|
||||
|
||||
The "build" command should compile all the needed LAMMPS C++ files,
|
||||
which will require MPI to be installed on your system. This means it
|
||||
must find both the header file mpi.h and a shared library file,
|
||||
e.g. libmpich.so if the MPICH version of MPI is installed. See the
|
||||
preceding section for how to create a shared library version of MPI if
|
||||
it does not exist. You may need to adjust the "include_dirs" and
|
||||
"library_dirs" and "libraries" fields in python/setup.py to
|
||||
insure the Python build finds all the files it needs.
|
||||
|
||||
The first "install" command will put the needed files in your Python's
|
||||
site-packages sub-directory, so that Python can load them. For
|
||||
example, if you installed Python yourself on a Linux machine, it would
|
||||
typically be somewhere like /usr/local/lib/python2.5/site-packages.
|
||||
Installing Python packages this way often requires you to be able to
|
||||
write to the Python directories, which may require root priveleges,
|
||||
hence the "sudo" prefix. If this is not the case, you can drop the
|
||||
"sudo".
|
||||
|
||||
Alternatively, you can install the LAMMPS files (or any other Python
|
||||
packages) in your own user space. The second "install" command does
|
||||
this, where you should replace "foo" with your directory of choice.
|
||||
|
||||
If these commands are successful, a {lammps.py} and {_lammps.so} file
|
||||
will be put in the appropriate directory.
|
||||
|
||||
:line
|
||||
|
||||
11.4 Extending Python with MPI :link(py_4),h4
|
||||
If you wish to run LAMMPS in parallel from Python, you need to extend
|
||||
your Python with an interface to MPI. This also allows you to
|
||||
make MPI calls directly from Python in your script, if you desire.
|
||||
|
||||
There are several Python packages available that purport to wrap MPI
|
||||
as a library and allow MPI functions to be called from Python.
|
||||
@ -256,26 +198,26 @@ These include
|
||||
All of these except pyMPI work by wrapping the MPI library (which must
|
||||
be available on your system as a shared library, as discussed above),
|
||||
and exposing (some portion of) its interface to your Python script.
|
||||
This means they cannot be used interactively in parallel, since they
|
||||
This means Python cannot be used interactively in parallel, since they
|
||||
do not address the issue of interactive input to multiple instances of
|
||||
Python running on different processors. The one exception is pyMPI,
|
||||
which alters the Python interpreter to address this issue, and (I
|
||||
believe) creates a new alternate executable (in place of python
|
||||
believe) creates a new alternate executable (in place of "python"
|
||||
itself) as a result.
|
||||
|
||||
In principle any of these Python/MPI packages should work to invoke
|
||||
both calls to LAMMPS and MPI itself from a Python script running in
|
||||
parallel. However, when I downloaded and looked at a few of them,
|
||||
their docuemtation was incomplete and I had trouble with their
|
||||
installation. It's not clear if some of the packages are still being
|
||||
actively developed and supported.
|
||||
LAMMPS in parallel and MPI calls themselves from a Python script which
|
||||
is itself running in parallel. However, when I downloaded and looked
|
||||
at a few of them, their documentation was incomplete and I had trouble
|
||||
with their installation. It's not clear if some of the packages are
|
||||
still being actively developed and supported.
|
||||
|
||||
The one I recommend, since I have successfully used it with LAMMPS, is
|
||||
Pypar. Pypar requires the ubiquitous "Numpy
|
||||
package"_http://numpy.scipy.org be installed in your Python. After
|
||||
launching python, type
|
||||
|
||||
>>> import numpy :pre
|
||||
import numpy :pre
|
||||
|
||||
to see if it is installed. If not, here is how to install it (version
|
||||
1.3.0b1 as of April 2009). Unpack the numpy tarball and from its
|
||||
@ -299,105 +241,123 @@ your Python distribution's site-packages directory.
|
||||
If you have successully installed Pypar, you should be able to run
|
||||
python serially and type
|
||||
|
||||
>>> import pypar :pre
|
||||
import pypar :pre
|
||||
|
||||
without error. You should also be able to run python in parallel
|
||||
on a simple test script
|
||||
|
||||
% mpirun -np 4 python test.script :pre
|
||||
% mpirun -np 4 python test.py :pre
|
||||
|
||||
where test.script contains the lines
|
||||
where test.py contains the lines
|
||||
|
||||
import pypar
|
||||
print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre
|
||||
|
||||
and see one line of output for each processor you ran on.
|
||||
and see one line of output for each processor you run on.
|
||||
|
||||
:line
|
||||
|
||||
11.5 Testing the Python-LAMMPS interface :link(py_5),h4
|
||||
11.4 Testing the Python-LAMMPS interface :link(py_4),h4
|
||||
|
||||
Before using LAMMPS in a Python program, one more step is needed. The
|
||||
interface to LAMMPS is via the Python ctypes package, which loads the
|
||||
shared LAMMPS library via a CDLL() call, which in turn is a wrapper on
|
||||
the C-library dlopen(). This command is different than a normal
|
||||
Python "import" and needs to be able to find the LAMMPS shared
|
||||
library, which is either in the Python site-packages directory or in a
|
||||
local directory you specified in the "python setup.py install"
|
||||
command, as described above.
|
||||
|
||||
The simplest way to do this is add a line like this to your
|
||||
.cshrc or other shell start-up file.
|
||||
|
||||
setenv LD_LIBRARY_PATH
|
||||
$\{LD_LIBRARY_PATH\}:/usr/local/lib/python2.5/site-packages :pre
|
||||
|
||||
and then execute the shell file to insure the path has been updated.
|
||||
This will extend the path that dlopen() uses to look for shared
|
||||
libraries.
|
||||
|
||||
To test if the serial LAMMPS library has been successfully installed
|
||||
(mode 1 above), launch Python and type
|
||||
To test if LAMMPS is callable from Python, launch Python interactively
|
||||
and type:
|
||||
|
||||
>>> from lammps import lammps
|
||||
>>> lmp = lammps() :pre
|
||||
|
||||
If you get no errors, you're ready to use serial LAMMPS from Python.
|
||||
If you get no errors, you're ready to use LAMMPS from Python.
|
||||
If the load fails, the most common error to see is
|
||||
|
||||
If you built LAMMPS for parallel use (mode 2 or 3 above), launch
|
||||
Python in parallel:
|
||||
"CDLL: asdfasdfasdf"
|
||||
|
||||
% mpirun -np 4 python test.script :pre
|
||||
which means Python was unable to load the LAMMPS shared library. This
|
||||
can occur if it can't find the LAMMMPS library; see the environment
|
||||
variable discussion "above"_#python_1. Or if it can't find one of the
|
||||
auxiliary libraries that was specified in the LAMMPS build, in a
|
||||
shared dynamic library format. This includes all libraries needed by
|
||||
main LAMMPS (e.g. MPI or FFTW or JPEG), system libraries needed by
|
||||
main LAMMPS (e.g. extra libs needed by MPI), or packages you have
|
||||
installed that require libraries provided with LAMMPS (e.g. the
|
||||
USER-ATC package require lib/atc/libatc.so) or system libraries
|
||||
(e.g. BLAS or Fortran-to-C libraries) listed in the
|
||||
lib/package/Makefile.lammps file. Again, all of these must be
|
||||
available as shared libraries, or the Python load will fail.
|
||||
|
||||
where test.script contains the lines
|
||||
Python (actually the operating system) isn't verbose about telling you
|
||||
why the load failed, so go through the steps above and in
|
||||
"Section_start 5"_Section_start.html#start_5 carefully.
|
||||
|
||||
[Test LAMMPS and Python in serial:] :h5
|
||||
|
||||
To run a LAMMPS test in serial, type these lines into Python
|
||||
interactively from the bench directory:
|
||||
|
||||
>>> from lammps import lammps
|
||||
>>> lmp = lammps()
|
||||
>>> lmp.file("in.lj") :pre
|
||||
|
||||
Or put the same lines in the file test.py and run it as
|
||||
|
||||
% python test.py :pre
|
||||
|
||||
Either way, you should see the results of running the in.lj benchmark
|
||||
on a single processor appear on the screen, the same as if you had
|
||||
typed something like:
|
||||
|
||||
lmp_g++ < in.lj :pre
|
||||
|
||||
[Test LAMMPS and Python in parallel:] :h5
|
||||
|
||||
To run LAMMPS in parallel, assuming you have installed the
|
||||
"Pypar"_http://datamining.anu.edu.au/~ole/pypar package as discussed
|
||||
above, create a test.py file containing these lines:
|
||||
|
||||
import pypar
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()), lmp
|
||||
lmp.file("in.lj")
|
||||
print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
|
||||
pypar.finalize() :pre
|
||||
|
||||
Again, if you get no errors, you're good to go.
|
||||
You can then run it in parallel as:
|
||||
|
||||
Note that if you left out the "import pypar" line from this script,
|
||||
you would instantiate and run LAMMPS independently on each of the P
|
||||
processors specified in the mpirun command. You can test if Pypar is
|
||||
enabling true parallel Python and LAMMPS by adding a line to the above
|
||||
sequence of commands like lmp.file("in.lj") to run an input script and
|
||||
see if the LAMMPS run says it ran on P processors or if you get output
|
||||
from P duplicated 1-processor runs written to the screen. In the
|
||||
latter case, Pypar is not working correctly.
|
||||
% mpirun -np 4 python test.py :pre
|
||||
|
||||
Note that this line:
|
||||
and you should see the same output as if you had typed
|
||||
|
||||
from lammps import lammps :pre
|
||||
% mpirun -np 4 lmp_g++ < in.lj :pre
|
||||
|
||||
will import either the serial or parallel version of the LAMMPS
|
||||
library, as wrapped by lammps.py. But if you installed both via
|
||||
setup_serial.py and setup.py, it will always import the parallel
|
||||
version, since it attempts that first.
|
||||
Note that if you leave out the 3 lines from test.py that specify Pypar
|
||||
commands you will instantiate and run LAMMPS independently on each of
|
||||
the P processors specified in the mpirun command. In this case you
|
||||
should get 4 sets of output, each showing that a run was made on a
|
||||
single processor, instead of one set of output showing that it ran on
|
||||
4 processors. If the 1-processor outputs occur, it means that Pypar
|
||||
is not working correctly.
|
||||
|
||||
Note that if your Python script imports the Pypar package (as above),
|
||||
so that it can use MPI calls directly, then Pypar initializes MPI for
|
||||
you. Thus the last line of your Python script should be
|
||||
pypar.finalize(), to insure MPI is shut down correctly.
|
||||
Also note that once you import the PyPar module, Pypar initializes MPI
|
||||
for you, and you can use MPI calls directly in your Python script, as
|
||||
described in the Pypar documentation. The last line of your Python
|
||||
script should be pypar.finalize(), to insure MPI is shut down
|
||||
correctly.
|
||||
|
||||
Also note that a Python script can be invoked in one of several ways:
|
||||
Note that any Python script (not just for LAMMPS) can be invoked in
|
||||
one of several ways:
|
||||
|
||||
% python foo.script
|
||||
% python -i foo.script
|
||||
% foo.script
|
||||
% foo.script :pre
|
||||
|
||||
The last command requires that the first line of the script be
|
||||
something like this:
|
||||
|
||||
#!/usr/local/bin/python
|
||||
#!/usr/local/bin/python -i
|
||||
#!/usr/local/bin/python -i :pre
|
||||
|
||||
where the path points to where you have Python installed, and that you
|
||||
have made the script file executable:
|
||||
|
||||
% chmod +x foo.script
|
||||
% chmod +x foo.script :pre
|
||||
|
||||
Without the "-i" flag, Python will exit when the script finishes.
|
||||
With the "-i" flag, you will be left in the Python interpreter when
|
||||
@ -408,14 +368,15 @@ Python on a single processor, not in parallel.
|
||||
:line
|
||||
:line
|
||||
|
||||
11.6 Using LAMMPS from Python :link(py_6),h4
|
||||
11.5 Using LAMMPS from Python :link(py_5),h4
|
||||
|
||||
The Python interface to LAMMPS consists of a Python "lammps" module,
|
||||
the source code for which is in python/lammps.py, which creates a
|
||||
"lammps" object, with a set of methods that can be invoked on that
|
||||
object. The sample Python code below assumes you have first imported
|
||||
the "lammps" module in your Python script and its settings as
|
||||
follows:
|
||||
the "lammps" module in your Python script. You can also include its
|
||||
settings as follows, which are useful in test return values from some
|
||||
of the methods described below:
|
||||
|
||||
from lammps import lammps
|
||||
from lammps import LMPINT as INT
|
||||
@ -429,8 +390,10 @@ at the file src/library.cpp you will see that they correspond
|
||||
one-to-one with calls you can make to the LAMMPS library from a C++ or
|
||||
C or Fortran program.
|
||||
|
||||
lmp = lammps() # create a LAMMPS object
|
||||
lmp = lammps(list) # ditto, with command-line args, list = \["-echo","screen"\] :pre
|
||||
lmp = lammps() # create a LAMMPS object using the default liblmp.so library
|
||||
lmp = lammps("g++") # create a LAMMPS object using the liblmp_g++.so library
|
||||
lmp = lammps("",list) # ditto, with command-line args, list = \["-echo","screen"\]
|
||||
lmp = lammps("g++",list) :pre
|
||||
|
||||
lmp.close() # destroy a LAMMPS object :pre
|
||||
|
||||
@ -438,16 +401,16 @@ lmp.file(file) # run an entire input script, file = "in.lj"
|
||||
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre
|
||||
|
||||
xlo = lmp.extract_global(name,type) # extract a global quantity
|
||||
# name = "boxxlo", "nlocal", etc
|
||||
# name = "boxxlo", "nlocal", etc
|
||||
# type = INT or DOUBLE :pre
|
||||
|
||||
coords = lmp.extract_atom(name,type) # extract a per-atom quantity
|
||||
# name = "x", "type", etc
|
||||
# name = "x", "type", etc
|
||||
# type = IPTR or DPTR or DPTRPTR :pre
|
||||
|
||||
eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
|
||||
v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
|
||||
# id = ID of compute or fix
|
||||
# id = ID of compute or fix
|
||||
# style = 0 = global data
|
||||
# 1 = per-atom data
|
||||
# 2 = local data
|
||||
@ -468,11 +431,22 @@ lmp.put_coords(x) # set all atom coords via x :pre
|
||||
|
||||
:line
|
||||
|
||||
The creation of a LAMMPS object does not take an MPI communicator as
|
||||
an argument. There should be a way to do this, so that the LAMMPS
|
||||
instance runs on a subset of processors, if desired, but I don't yet
|
||||
know how from Pypar. So for now, it runs on MPI_COMM_WORLD, which is
|
||||
all the processors.
|
||||
IMPORTANT NOTE: Currently, the creation of a LAMMPS object does not
|
||||
take an MPI communicator as an argument. There should be a way to do
|
||||
this, so that the LAMMPS instance runs on a subset of processors if
|
||||
desired, but I don't know how to do it from Pypar. So for now, it
|
||||
runs on MPI_COMM_WORLD, which is all the processors. If someone
|
||||
figures out how to do this with one or more of the Python wrappers for
|
||||
MPI, like Pypar, please let us know and we will amend these doc pages.
|
||||
|
||||
Note that you can create multiple LAMMPS objects in your Python
|
||||
script, and coordinate and run multiple simulations, e.g.
|
||||
|
||||
from lammps import lammps
|
||||
lmp1 = lammps()
|
||||
lmp2 = lammps()
|
||||
lmp1.file("in.file1")
|
||||
lmp2.file("in.file2") :pre
|
||||
|
||||
The file() and command() methods allow an input script or single
|
||||
commands to be invoked.
|
||||
@ -583,15 +557,10 @@ following steps:
|
||||
Add a new interface function to src/library.cpp and
|
||||
src/library.h. :ulb,l
|
||||
|
||||
Verify the new function is syntactically correct by building LAMMPS as
|
||||
a library - see "Section_start 4"_Section_start.html#start_5 of the
|
||||
manual. :l
|
||||
Rebuild LAMMPS as a shared library. :l
|
||||
|
||||
Add a wrapper method in the Python LAMMPS module to python/lammps.py
|
||||
for this interface function. :l
|
||||
|
||||
Rebuild the Python wrapper via python/setup_serial.py or
|
||||
python/setup.py. :l
|
||||
Add a wrapper method to python/lammps.py for this interface
|
||||
function. :l
|
||||
|
||||
You should now be able to invoke the new interface function from a
|
||||
Python script. Isn't ctypes amazing? :l,ule
|
||||
@ -599,7 +568,7 @@ Python script. Isn't ctypes amazing? :l,ule
|
||||
:line
|
||||
:line
|
||||
|
||||
11.7 Example Python scripts that use LAMMPS :link(py_7),h4
|
||||
11.6 Example Python scripts that use LAMMPS :link(py_6),h4
|
||||
|
||||
These are the Python scripts included as demos in the python/examples
|
||||
directory of the LAMMPS distribution, to illustrate the kinds of
|
||||
|
||||
@ -44,7 +44,6 @@ sub-directories:
|
||||
<TR><TD >README</TD><TD > text file</TD></TR>
|
||||
<TR><TD >LICENSE</TD><TD > the GNU General Public License (GPL)</TD></TR>
|
||||
<TR><TD >bench</TD><TD > benchmark problems</TD></TR>
|
||||
<TR><TD >couple</TD><TD > code coupling examples, using LAMMPS as a library</TD></TR>
|
||||
<TR><TD >doc</TD><TD > documentation</TD></TR>
|
||||
<TR><TD >examples</TD><TD > simple test problems</TD></TR>
|
||||
<TR><TD >potentials</TD><TD > embedded atom method (EAM) potential files</TD></TR>
|
||||
@ -774,39 +773,80 @@ input scripts.
|
||||
|
||||
<H4><A NAME = "start_5"></A>2.5 Building LAMMPS as a library
|
||||
</H4>
|
||||
<P>LAMMPS itself can be built as a library, which can then be called from
|
||||
another application or a scripting language. See <A HREF = "Section_howto.html#howto_10">this
|
||||
section</A> for more info on coupling LAMMPS
|
||||
to other codes. Building LAMMPS as a library is done by typing
|
||||
<P>LAMMPS can be built as either a static or shared library, which can
|
||||
then be called from another application or a scripting language. See
|
||||
<A HREF = "Section_howto.html#howto_10">this section</A> for more info on coupling
|
||||
LAMMPS to other codes. See <A HREF = "Section_python.html">this section</A> for
|
||||
more info on wrapping and running LAMMPS from Python.
|
||||
</P>
|
||||
<P>To build LAMMPS as a static library (*.a file on Linux), type
|
||||
</P>
|
||||
<PRE>make makelib
|
||||
make -f Makefile.lib foo
|
||||
</PRE>
|
||||
<P>where foo is the machine name. Note that inclusion or exclusion of
|
||||
any desired optional packages should be done before typing "make
|
||||
makelib". The first "make" command will create a current Makefile.lib
|
||||
with all the file names in your src dir. The 2nd "make" command will
|
||||
use it to build LAMMPS as a library. This requires that Makefile.foo
|
||||
have a library target (lib) and system-specific settings for ARCHIVE
|
||||
and ARFLAGS. See Makefile.linux for an example. The build will
|
||||
create the file liblmp_foo.a which another application can link to.
|
||||
<P>where foo is the machine name. This kind of library is typically used
|
||||
to statically link a driver application to all of LAMMPS, so that you
|
||||
can insure all dependencies are satisfied at compile time. Note that
|
||||
inclusion or exclusion of any desired optional packages should be done
|
||||
before typing "make makelib". The first "make" command will create a
|
||||
current Makefile.lib with all the file names in your src dir. The 2nd
|
||||
"make" command will use it to build LAMMPS as a static library, using
|
||||
the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
|
||||
will create the file liblmp_foo.a which another application can link
|
||||
to.
|
||||
</P>
|
||||
<P>When used from a C++ program, the library allows one or more LAMMPS
|
||||
objects to be instantiated. All of LAMMPS is wrapped in a LAMMPS_NS
|
||||
<P>To build LAMMPS as a shared library (*.so file on Linux), which can be
|
||||
dynamically loaded, type
|
||||
</P>
|
||||
<PRE>make makeshlib
|
||||
make -f Makefile.shlib foo
|
||||
</PRE>
|
||||
<P>where foo is the machine name. This kind of library is required when
|
||||
wrapping LAMMPS with Python; see <A HREF = "Section_python.html">Section_python</A>
|
||||
for details. Again, note that inclusion or exclusion of any desired
|
||||
optional packages should be done before typing "make makelib". The
|
||||
first "make" command will create a current Makefile.shlib with all the
|
||||
file names in your src dir. The 2nd "make" command will use it to
|
||||
build LAMMPS as a shared library, using the SHFLAGS and SHLIBFLAGS
|
||||
settings in src/MAKE/Makefile.foo. The build will create the file
|
||||
liblmp_foo.so which another application can link to dyamically, as
|
||||
well as a soft link liblmp.so, which the Python wrapper uses by
|
||||
default.
|
||||
</P>
|
||||
<P>Note that for a shared library to be usable by a calling program, all
|
||||
the auxiliary libraries it depends on must also exist as shared
|
||||
libraries, and be find-able by the operating system. Else you will
|
||||
get a run-time error when the shared library is loaded. For LAMMPS,
|
||||
this includes all libraries needed by main LAMMPS (e.g. MPI or FFTW or
|
||||
JPEG), system libraries needed by main LAMMPS (e.g. extra libs needed
|
||||
by MPI), or packages you have installed that require libraries
|
||||
provided with LAMMPS (e.g. the USER-ATC package require
|
||||
lib/atc/libatc.so) or system libraries (e.g. BLAS or Fortran-to-C
|
||||
libraries) listed in the lib/package/Makefile.lammps file. See the
|
||||
discussion about the LAMMPS shared library in
|
||||
<A HREF = "Section_python.html">Section_python</A> for details about how to build
|
||||
shared versions of these libraries, and how to insure the operating
|
||||
system can find them, by setting the LD_LIBRARY_PATH environment
|
||||
variable correctly.
|
||||
</P>
|
||||
<P>Either flavor of library allows one or more LAMMPS objects to be
|
||||
instantiated from the calling program.
|
||||
</P>
|
||||
<P>When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
|
||||
namespace; you can safely use any of its classes and methods from
|
||||
within your application code, as needed.
|
||||
within the calling code, as needed.
|
||||
</P>
|
||||
<P>When used from a C or Fortran program or a scripting language, the
|
||||
library has a simple function-style interface, provided in
|
||||
<P>When used from a C or Fortran program or a scripting language like
|
||||
Python, the library has a simple function-style interface, provided in
|
||||
src/library.cpp and src/library.h.
|
||||
</P>
|
||||
<P>See the sample codes couple/simple/simple.cpp and simple.c as examples
|
||||
of C++ and C codes that invoke LAMMPS thru its library interface.
|
||||
There are other examples as well in the couple directory which are
|
||||
discussed in <A HREF = "Section_howto.html#howto_10">Section_howto 10</A> of the
|
||||
manual. See <A HREF = "Section_python.html">Section_python</A> of the manual for a
|
||||
description of the Python wrapper provided with LAMMPS that operates
|
||||
through the LAMMPS library interface.
|
||||
<P>See the sample codes in examples/COUPLE/simple for examples of C++ and
|
||||
C codes that invoke LAMMPS thru its library interface. There are
|
||||
other examples as well in the COUPLE directory which are discussed in
|
||||
<A HREF = "Section_howto.html#howto_10">Section_howto 10</A> of the manual. See
|
||||
<A HREF = "Section_python.html">Section_python</A> of the manual for a description
|
||||
of the Python wrapper provided with LAMMPS that operates through the
|
||||
LAMMPS library interface.
|
||||
</P>
|
||||
<P>The files src/library.cpp and library.h contain the C-style interface
|
||||
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">Section_howto 19</A> of the
|
||||
|
||||
@ -39,7 +39,6 @@ sub-directories:
|
||||
README: text file
|
||||
LICENSE: the GNU General Public License (GPL)
|
||||
bench: benchmark problems
|
||||
couple: code coupling examples, using LAMMPS as a library
|
||||
doc: documentation
|
||||
examples: simple test problems
|
||||
potentials: embedded atom method (EAM) potential files
|
||||
@ -768,39 +767,80 @@ input scripts.
|
||||
|
||||
2.5 Building LAMMPS as a library :h4,link(start_5)
|
||||
|
||||
LAMMPS itself can be built as a library, which can then be called from
|
||||
another application or a scripting language. See "this
|
||||
section"_Section_howto.html#howto_10 for more info on coupling LAMMPS
|
||||
to other codes. Building LAMMPS as a library is done by typing
|
||||
LAMMPS can be built as either a static or shared library, which can
|
||||
then be called from another application or a scripting language. See
|
||||
"this section"_Section_howto.html#howto_10 for more info on coupling
|
||||
LAMMPS to other codes. See "this section"_Section_python.html for
|
||||
more info on wrapping and running LAMMPS from Python.
|
||||
|
||||
To build LAMMPS as a static library (*.a file on Linux), type
|
||||
|
||||
make makelib
|
||||
make -f Makefile.lib foo :pre
|
||||
|
||||
where foo is the machine name. Note that inclusion or exclusion of
|
||||
any desired optional packages should be done before typing "make
|
||||
makelib". The first "make" command will create a current Makefile.lib
|
||||
with all the file names in your src dir. The 2nd "make" command will
|
||||
use it to build LAMMPS as a library. This requires that Makefile.foo
|
||||
have a library target (lib) and system-specific settings for ARCHIVE
|
||||
and ARFLAGS. See Makefile.linux for an example. The build will
|
||||
create the file liblmp_foo.a which another application can link to.
|
||||
where foo is the machine name. This kind of library is typically used
|
||||
to statically link a driver application to all of LAMMPS, so that you
|
||||
can insure all dependencies are satisfied at compile time. Note that
|
||||
inclusion or exclusion of any desired optional packages should be done
|
||||
before typing "make makelib". The first "make" command will create a
|
||||
current Makefile.lib with all the file names in your src dir. The 2nd
|
||||
"make" command will use it to build LAMMPS as a static library, using
|
||||
the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build
|
||||
will create the file liblmp_foo.a which another application can link
|
||||
to.
|
||||
|
||||
When used from a C++ program, the library allows one or more LAMMPS
|
||||
objects to be instantiated. All of LAMMPS is wrapped in a LAMMPS_NS
|
||||
To build LAMMPS as a shared library (*.so file on Linux), which can be
|
||||
dynamically loaded, type
|
||||
|
||||
make makeshlib
|
||||
make -f Makefile.shlib foo :pre
|
||||
|
||||
where foo is the machine name. This kind of library is required when
|
||||
wrapping LAMMPS with Python; see "Section_python"_Section_python.html
|
||||
for details. Again, note that inclusion or exclusion of any desired
|
||||
optional packages should be done before typing "make makelib". The
|
||||
first "make" command will create a current Makefile.shlib with all the
|
||||
file names in your src dir. The 2nd "make" command will use it to
|
||||
build LAMMPS as a shared library, using the SHFLAGS and SHLIBFLAGS
|
||||
settings in src/MAKE/Makefile.foo. The build will create the file
|
||||
liblmp_foo.so which another application can link to dyamically, as
|
||||
well as a soft link liblmp.so, which the Python wrapper uses by
|
||||
default.
|
||||
|
||||
Note that for a shared library to be usable by a calling program, all
|
||||
the auxiliary libraries it depends on must also exist as shared
|
||||
libraries, and be find-able by the operating system. Else you will
|
||||
get a run-time error when the shared library is loaded. For LAMMPS,
|
||||
this includes all libraries needed by main LAMMPS (e.g. MPI or FFTW or
|
||||
JPEG), system libraries needed by main LAMMPS (e.g. extra libs needed
|
||||
by MPI), or packages you have installed that require libraries
|
||||
provided with LAMMPS (e.g. the USER-ATC package require
|
||||
lib/atc/libatc.so) or system libraries (e.g. BLAS or Fortran-to-C
|
||||
libraries) listed in the lib/package/Makefile.lammps file. See the
|
||||
discussion about the LAMMPS shared library in
|
||||
"Section_python"_Section_python.html for details about how to build
|
||||
shared versions of these libraries, and how to insure the operating
|
||||
system can find them, by setting the LD_LIBRARY_PATH environment
|
||||
variable correctly.
|
||||
|
||||
Either flavor of library allows one or more LAMMPS objects to be
|
||||
instantiated from the calling program.
|
||||
|
||||
When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
|
||||
namespace; you can safely use any of its classes and methods from
|
||||
within your application code, as needed.
|
||||
within the calling code, as needed.
|
||||
|
||||
When used from a C or Fortran program or a scripting language, the
|
||||
library has a simple function-style interface, provided in
|
||||
When used from a C or Fortran program or a scripting language like
|
||||
Python, the library has a simple function-style interface, provided in
|
||||
src/library.cpp and src/library.h.
|
||||
|
||||
See the sample codes couple/simple/simple.cpp and simple.c as examples
|
||||
of C++ and C codes that invoke LAMMPS thru its library interface.
|
||||
There are other examples as well in the couple directory which are
|
||||
discussed in "Section_howto 10"_Section_howto.html#howto_10 of the
|
||||
manual. See "Section_python"_Section_python.html of the manual for a
|
||||
description of the Python wrapper provided with LAMMPS that operates
|
||||
through the LAMMPS library interface.
|
||||
See the sample codes in examples/COUPLE/simple for examples of C++ and
|
||||
C codes that invoke LAMMPS thru its library interface. There are
|
||||
other examples as well in the COUPLE directory which are discussed in
|
||||
"Section_howto 10"_Section_howto.html#howto_10 of the manual. See
|
||||
"Section_python"_Section_python.html of the manual for a description
|
||||
of the Python wrapper provided with LAMMPS that operates through the
|
||||
LAMMPS library interface.
|
||||
|
||||
The files src/library.cpp and library.h contain the C-style interface
|
||||
to LAMMPS. See "Section_howto 19"_Section_howto.html#howto_19 of the
|
||||
|
||||
@ -21,15 +21,17 @@
|
||||
|
||||
<LI>input = one or more attributes
|
||||
|
||||
<PRE> possible attributes = natom1 natom2
|
||||
patom1 patom2
|
||||
<PRE> possible attributes = natom1 natom2 ntype1 ntype2
|
||||
patom1 patom2 ptype1 ptype2
|
||||
batom1 batom2 btype
|
||||
aatom1 aatom2 aatom3 atype
|
||||
datom1 datom2 datom3 dtype
|
||||
iatom1 iatom2 iatom3 itype
|
||||
</PRE>
|
||||
<PRE> natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
|
||||
ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
|
||||
patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
|
||||
ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
|
||||
batom1, batom2 = IDs of 2 atoms in each bond
|
||||
btype = bond type of each bond
|
||||
aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
|
||||
@ -91,7 +93,9 @@ local</A> command in a consistent way.
|
||||
</P>
|
||||
<P>The <I>natom1</I> and <I>natom2</I>, or <I>patom1</I> and <I>patom2</I> attributes refer
|
||||
to the atom IDs of the 2 atoms in each pairwise interaction computed
|
||||
by the <A HREF = "pair_style.html">pair_style</A> command.
|
||||
by the <A HREF = "pair_style.html">pair_style</A> command. The <I>ntype1</I> and
|
||||
<I>ntype2</I>, or <I>ptype1</I> and <I>ptype2</I> attributes refer to the atom types
|
||||
of the 2 atoms in each pairwise interaction.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3,
|
||||
1-4 interactions within the molecular topology, their pairwise
|
||||
@ -107,9 +111,11 @@ command.
|
||||
atoms in each <A HREF = "bond_style.html">bond</A>. The <I>btype</I> attribute refers to
|
||||
the type of the bond, from 1 to Nbtypes = # of bond types. The number
|
||||
of bond types is defined in the data file read by the
|
||||
<A HREF = "read_data.html">read_data</A> command. The attributes that start with
|
||||
"a", "d", "i", refer to similar values for <A HREF = "angle_style.html">angles</A>,
|
||||
<A HREF = "dihedral_style.html">dihedrals</A>, and <A HREF = "improper_style.html">impropers</A>.
|
||||
<A HREF = "read_data.html">read_data</A> command.
|
||||
</P>
|
||||
<P>The attributes that start with "a", "d", "i", refer to similar values
|
||||
for <A HREF = "angle_style.html">angles</A>, <A HREF = "dihedral_style.html">dihedrals</A>, and
|
||||
<A HREF = "improper_style.html">impropers</A>.
|
||||
</P>
|
||||
<P><B>Output info:</B>
|
||||
</P>
|
||||
|
||||
@ -15,15 +15,17 @@ compute ID group-ID property/local input1 input2 ... :pre
|
||||
ID, group-ID are documented in "compute"_compute.html command :ulb,l
|
||||
property/local = style name of this compute command :l
|
||||
input = one or more attributes :l
|
||||
possible attributes = natom1 natom2
|
||||
patom1 patom2
|
||||
possible attributes = natom1 natom2 ntype1 ntype2
|
||||
patom1 patom2 ptype1 ptype2
|
||||
batom1 batom2 btype
|
||||
aatom1 aatom2 aatom3 atype
|
||||
datom1 datom2 datom3 dtype
|
||||
iatom1 iatom2 iatom3 itype :pre
|
||||
|
||||
natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
|
||||
ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
|
||||
patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
|
||||
ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
|
||||
batom1, batom2 = IDs of 2 atoms in each bond
|
||||
btype = bond type of each bond
|
||||
aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
|
||||
@ -84,7 +86,9 @@ local"_dump.html command in a consistent way.
|
||||
|
||||
The {natom1} and {natom2}, or {patom1} and {patom2} attributes refer
|
||||
to the atom IDs of the 2 atoms in each pairwise interaction computed
|
||||
by the "pair_style"_pair_style.html command.
|
||||
by the "pair_style"_pair_style.html command. The {ntype1} and
|
||||
{ntype2}, or {ptype1} and {ptype2} attributes refer to the atom types
|
||||
of the 2 atoms in each pairwise interaction.
|
||||
|
||||
IMPORTANT NOTE: For pairs, if two atoms I,J are involved in 1-2, 1-3,
|
||||
1-4 interactions within the molecular topology, their pairwise
|
||||
@ -100,9 +104,11 @@ The {batom1} and {batom2} attributes refer to the atom IDs of the 2
|
||||
atoms in each "bond"_bond_style.html. The {btype} attribute refers to
|
||||
the type of the bond, from 1 to Nbtypes = # of bond types. The number
|
||||
of bond types is defined in the data file read by the
|
||||
"read_data"_read_data.html command. The attributes that start with
|
||||
"a", "d", "i", refer to similar values for "angles"_angle_style.html,
|
||||
"dihedrals"_dihedral_style.html, and "impropers"_improper_style.html.
|
||||
"read_data"_read_data.html command.
|
||||
|
||||
The attributes that start with "a", "d", "i", refer to similar values
|
||||
for "angles"_angle_style.html, "dihedrals"_dihedral_style.html, and
|
||||
"impropers"_improper_style.html.
|
||||
|
||||
[Output info:]
|
||||
|
||||
|
||||
@ -8,8 +8,8 @@ model a realistic problem.
|
||||
|
||||
See these sections of the LAMMPS manaul for details:
|
||||
|
||||
2.4 Building LAMMPS as a library (doc/Section_start.html#2_4)
|
||||
4.10 Coupling LAMMPS to other codes (doc/Section_howto.html#4_10)
|
||||
2.5 Building LAMMPS as a library (doc/Section_start.html#start_5)
|
||||
6.10 Coupling LAMMPS to other codes (doc/Section_howto.html#howto_10)
|
||||
|
||||
In all of the examples included here, LAMMPS must first be built as a
|
||||
library. Basically, you type something like
|
||||
114
examples/COUPLE/lammps_spparks/in.lammps
Normal file
114
examples/COUPLE/lammps_spparks/in.lammps
Normal file
@ -0,0 +1,114 @@
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
read_data data.lammps
|
||||
mass * 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.2
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 1.0
|
||||
pair_coeff 3 3 1.0 1.0
|
||||
pair_coeff 4 4 1.0 1.0
|
||||
pair_coeff 5 5 1.0 1.0
|
||||
pair_coeff 6 6 1.0 1.0
|
||||
pair_coeff 7 7 1.0 1.0
|
||||
pair_coeff 8 8 1.0 1.0
|
||||
pair_coeff 9 9 1.0 1.0
|
||||
pair_coeff 10 10 1.0 1.0
|
||||
pair_coeff 11 11 1.0 1.0
|
||||
pair_coeff 12 12 1.0 1.0
|
||||
pair_coeff 13 13 1.0 1.0
|
||||
pair_coeff 14 14 1.0 1.0
|
||||
pair_coeff 15 15 1.0 1.0
|
||||
pair_coeff 16 16 1.0 1.0
|
||||
pair_coeff 17 17 1.0 1.0
|
||||
pair_coeff 18 18 1.0 1.0
|
||||
pair_coeff 19 19 1.0 1.0
|
||||
pair_coeff 20 20 1.0 1.0
|
||||
pair_coeff 21 21 1.0 1.0
|
||||
pair_coeff 22 22 1.0 1.0
|
||||
pair_coeff 23 23 1.0 1.0
|
||||
pair_coeff 24 24 1.0 1.0
|
||||
pair_coeff 25 25 1.0 1.0
|
||||
pair_coeff 26 26 1.0 1.0
|
||||
pair_coeff 27 27 1.0 1.0
|
||||
pair_coeff 28 28 1.0 1.0
|
||||
pair_coeff 29 29 1.0 1.0
|
||||
pair_coeff 30 30 1.0 1.0
|
||||
pair_coeff 31 31 1.0 1.0
|
||||
pair_coeff 32 32 1.0 1.0
|
||||
pair_coeff 33 33 1.0 1.0
|
||||
pair_coeff 34 34 1.0 1.0
|
||||
pair_coeff 35 35 1.0 1.0
|
||||
pair_coeff 36 36 1.0 1.0
|
||||
pair_coeff 37 37 1.0 1.0
|
||||
pair_coeff 38 38 1.0 1.0
|
||||
pair_coeff 39 39 1.0 1.0
|
||||
pair_coeff 40 40 1.0 1.0
|
||||
pair_coeff 41 41 1.0 1.0
|
||||
pair_coeff 42 42 1.0 1.0
|
||||
pair_coeff 43 43 1.0 1.0
|
||||
pair_coeff 44 44 1.0 1.0
|
||||
pair_coeff 45 45 1.0 1.0
|
||||
pair_coeff 46 46 1.0 1.0
|
||||
pair_coeff 47 47 1.0 1.0
|
||||
pair_coeff 48 48 1.0 1.0
|
||||
pair_coeff 49 49 1.0 1.0
|
||||
pair_coeff 50 50 1.0 1.0
|
||||
pair_coeff 51 51 1.0 1.0
|
||||
pair_coeff 52 52 1.0 1.0
|
||||
pair_coeff 53 53 1.0 1.0
|
||||
pair_coeff 54 54 1.0 1.0
|
||||
pair_coeff 55 55 1.0 1.0
|
||||
pair_coeff 56 56 1.0 1.0
|
||||
pair_coeff 57 57 1.0 1.0
|
||||
pair_coeff 58 58 1.0 1.0
|
||||
pair_coeff 59 59 1.0 1.0
|
||||
pair_coeff 60 60 1.0 1.0
|
||||
pair_coeff 61 61 1.0 1.0
|
||||
pair_coeff 62 62 1.0 1.0
|
||||
pair_coeff 63 63 1.0 1.0
|
||||
pair_coeff 64 64 1.0 1.0
|
||||
pair_coeff 65 65 1.0 1.0
|
||||
pair_coeff 66 66 1.0 1.0
|
||||
pair_coeff 67 67 1.0 1.0
|
||||
pair_coeff 68 68 1.0 1.0
|
||||
pair_coeff 69 69 1.0 1.0
|
||||
pair_coeff 70 70 1.0 1.0
|
||||
pair_coeff 71 71 1.0 1.0
|
||||
pair_coeff 72 72 1.0 1.0
|
||||
pair_coeff 73 73 1.0 1.0
|
||||
pair_coeff 74 74 1.0 1.0
|
||||
pair_coeff 75 75 1.0 1.0
|
||||
pair_coeff 76 76 1.0 1.0
|
||||
pair_coeff 77 77 1.0 1.0
|
||||
pair_coeff 78 78 1.0 1.0
|
||||
pair_coeff 79 79 1.0 1.0
|
||||
pair_coeff 80 80 1.0 1.0
|
||||
pair_coeff 81 81 1.0 1.0
|
||||
pair_coeff 82 82 1.0 1.0
|
||||
pair_coeff 83 83 1.0 1.0
|
||||
pair_coeff 84 84 1.0 1.0
|
||||
pair_coeff 85 85 1.0 1.0
|
||||
pair_coeff 86 86 1.0 1.0
|
||||
pair_coeff 87 87 1.0 1.0
|
||||
pair_coeff 88 88 1.0 1.0
|
||||
pair_coeff 89 89 1.0 1.0
|
||||
pair_coeff 90 90 1.0 1.0
|
||||
pair_coeff 91 91 1.0 1.0
|
||||
pair_coeff 92 92 1.0 1.0
|
||||
pair_coeff 93 93 1.0 1.0
|
||||
pair_coeff 94 94 1.0 1.0
|
||||
pair_coeff 95 95 1.0 1.0
|
||||
pair_coeff 96 96 1.0 1.0
|
||||
pair_coeff 97 97 1.0 1.0
|
||||
pair_coeff 98 98 1.0 1.0
|
||||
pair_coeff 99 99 1.0 1.0
|
||||
pair_coeff 100 100 1.0 1.0
|
||||
|
||||
compute da all displace/atom
|
||||
|
||||
dump 1 all atom 10 dump.md
|
||||
thermo 1
|
||||
@ -26,13 +26,13 @@ This builds the C++ driver with the LAMMPS library using a C++ compiler:
|
||||
|
||||
g++ -I/home/sjplimp/lammps/src -c simple.cpp
|
||||
g++ -L/home/sjplimp/lammps/src simple.o \
|
||||
-llmp_g++ -lfftw -lmpich -lpthread -o simpleCC
|
||||
-llmp_g++ -lfftw -lmpich -lmpl -lpthread -o simpleCC
|
||||
|
||||
This builds the C driver with the LAMMPS library using a C compiler:
|
||||
|
||||
gcc -I/home/sjplimp/lammps/src -c simple.c
|
||||
gcc -L/home/sjplimp/lammps/src simple.o \
|
||||
-llmp_g++ -lfftw -lmpich -lpthread -lstdc++ -o simpleC
|
||||
-llmp_g++ -lfftw -lmpich -lmpl -lpthread -lstdc++ -o simpleC
|
||||
|
||||
This builds the Fortran wrapper and driver with the LAMMPS library
|
||||
using a Fortran and C compiler:
|
||||
@ -1,12 +1,26 @@
|
||||
LAMMPS example problems
|
||||
|
||||
There are 3 flavors of sub-directories in this file, each with sample
|
||||
problems you can run with LAMMPS.
|
||||
|
||||
lower-case directories = simple test problems for LAMMPS and its packages
|
||||
upper-case directories = more complex problems
|
||||
USER directory with its own sub-directories = tests for USER packages
|
||||
|
||||
Each is discussed below.
|
||||
|
||||
------------------------------------------
|
||||
|
||||
Lower-case directories
|
||||
|
||||
Each of these sub-directories contains a sample problem you can run
|
||||
with LAMMPS. Most are 2d models so that they run quickly, requiring a
|
||||
few seconds to a few minutes to run on a desktop machine. Each
|
||||
problem has an input script (in.*) and produces a log file (log.*) and
|
||||
(optionally) a dump file (dump.*) or image files (image.*) when it
|
||||
runs. Some use a data file (data.*) of initial coordinates as
|
||||
additional input.
|
||||
additional input. Some require that you install one or more optional
|
||||
LAMMPS packages.
|
||||
|
||||
A few sample log file outputs on different machines and different
|
||||
numbers of processors are included in the directories to compare your
|
||||
@ -77,12 +91,22 @@ create a GIF file suitable for viewing in a browser.
|
||||
|
||||
------------------------------------------
|
||||
|
||||
There is also an ELASTIC directory with an example script for
|
||||
computing elastic constants, using a zero temperature Si example. See
|
||||
the in.elastic file for more info.
|
||||
Upper-case directories
|
||||
|
||||
There is also a USER directory which contains subdirectories of
|
||||
user-provided examples for user packages. See the README files in
|
||||
those directories for more info. See the doc/Section_start.html file
|
||||
for more info about user packages.
|
||||
The COUPLE directory has examples of how to use LAMMPS as a library,
|
||||
either by itself or in tandem with another code or library. See the
|
||||
COUPLE/README file to get started.
|
||||
|
||||
The ELASTIC directory has an example script for computing elastic
|
||||
constants, using a zero temperature Si example. See the
|
||||
ELASTIC/in.elastic file for more info.
|
||||
|
||||
------------------------------------------
|
||||
|
||||
USER directory
|
||||
|
||||
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
|
||||
about installing and building user packages.
|
||||
|
||||
|
||||
@ -1,26 +1,48 @@
|
||||
This directory contains Python code which wraps LAMMPS as a library
|
||||
and allows the library interface to be invoked from a Python, either
|
||||
from a script or interactively.
|
||||
and allows the LAMMPS library interface to be invoked from Python,
|
||||
either from a script or interactively.
|
||||
|
||||
Details on how to build and use this Python interface are given in
|
||||
Details on the Python interface to LAMMPS and how to build LAMMPS as a
|
||||
shared library for use with Python are given in
|
||||
doc/Section_python.html.
|
||||
|
||||
Basically you have to extend the Python on your box to include the
|
||||
LAMMPS wrappers:
|
||||
Basically you need to follow these 3 steps:
|
||||
|
||||
python setup_serial.py build # for serial LAMMPS and Python
|
||||
sudo python setup_serial.py install
|
||||
a) Add paths to environment variables in your shell script
|
||||
|
||||
python setup.py build # for parallel LAMMPS and Python
|
||||
sudo python setup.py install
|
||||
For example, for csh or tcsh, add something like this to ~/.cshrc:
|
||||
|
||||
but there are several issues to be aware of, as discussed in the doc
|
||||
pages.
|
||||
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src/STUBS
|
||||
|
||||
The latter is only necessary if you will use the MPI stubs library
|
||||
instead of an MPI installed on your machine.
|
||||
|
||||
b) Build LAMMPS as a dynamic library, including dynamic versions of
|
||||
any libraries it includes for the packages you have installed,
|
||||
e.g. STUBS, MPI, FFTW, JPEG, package libs.
|
||||
|
||||
From the src directory:
|
||||
|
||||
% make makeshlib
|
||||
% make -f Makefile.shlib g++
|
||||
|
||||
If successful, this results in the file src/liblmp_g++.so
|
||||
|
||||
c) Launch Python and import the LAMMPS wrapper
|
||||
|
||||
% python
|
||||
>>> from lammps import lammps
|
||||
>>> lmp = lammps()
|
||||
|
||||
If that gives no errors, you have succesfully wrapped LAMMPS with
|
||||
Python.
|
||||
|
||||
-------------------------------------------------------------------
|
||||
|
||||
Once you have successfully built and tested the wrappers, you can run
|
||||
the Python scripts in the examples sub-directory:
|
||||
Once you have successfully wrapped LAMMPS, you can run the Python
|
||||
scripts in the examples sub-directory:
|
||||
|
||||
trivial.py read/run a LAMMPS input script thru Python
|
||||
demo.py invoke various LAMMPS library interface routines
|
||||
|
||||
@ -26,28 +26,26 @@ LMPDPTRPTR = 4
|
||||
LOCATION = os.path.dirname(__file__)
|
||||
|
||||
class lammps:
|
||||
def __init__(self,args=None):
|
||||
def __init__(self,name="",cmdlineargs=None):
|
||||
|
||||
# attempt to load parallel library first, serial library next
|
||||
# could provide caller a flag to choose which library to load
|
||||
# load liblmp.so by default
|
||||
# if name = "g++", load liblmp_g++.so
|
||||
|
||||
try:
|
||||
self.lib = CDLL(os.path.join(LOCATION, "_lammps.so"))
|
||||
if not name: self.lib = CDLL("liblmp.so")
|
||||
else: self.lib = CDLL("liblmp_%s.so" % name)
|
||||
except:
|
||||
try:
|
||||
self.lib = CDLL(os.path.join(LOCATION, "_lammps_serial.so"))
|
||||
except:
|
||||
raise OSError,"Could not load LAMMPS dynamic library"
|
||||
raise OSError,"Could not load LAMMPS dynamic library"
|
||||
|
||||
# create an instance of LAMMPS
|
||||
# don't know how to pass an MPI communicator from PyPar
|
||||
# no_mpi call lets LAMMPS use MPI_COMM_WORLD
|
||||
# cargs = array of C strings from args
|
||||
|
||||
if args:
|
||||
args.insert(0,"lammps.py")
|
||||
narg = len(args)
|
||||
cargs = (c_char_p*narg)(*args)
|
||||
if cmdlineargs:
|
||||
cmdlineargs.insert(0,"lammps.py")
|
||||
narg = len(cmdlineargs)
|
||||
cargs = (c_char_p*narg)(*cmdlineargs)
|
||||
self.lmp = c_void_p()
|
||||
self.lib.lammps_open_no_mpi(narg,cargs,byref(self.lmp))
|
||||
else:
|
||||
|
||||
@ -1,39 +0,0 @@
|
||||
#!/usr/local/bin/python
|
||||
|
||||
"""
|
||||
setup.py file for LAMMPS with system MPICH library
|
||||
"""
|
||||
|
||||
from distutils.core import setup, Extension
|
||||
|
||||
import os, glob
|
||||
path = os.path.dirname(os.getcwd())
|
||||
|
||||
# list of src files for LAMMPS
|
||||
|
||||
libfiles = glob.glob("%s/src/*.cpp" % path)
|
||||
|
||||
lammps_library = Extension("_lammps",
|
||||
sources = libfiles,
|
||||
define_macros = [("MPICH_IGNORE_CXX_SEEK",1),
|
||||
("LAMMPS_GZIP",1),
|
||||
("FFT_NONE",1),],
|
||||
# src files for LAMMPS
|
||||
include_dirs = ["../src"],
|
||||
# additional libs for MPICH on Linux
|
||||
libraries = ["mpich","mpl","pthread"],
|
||||
# where to find the MPICH lib on Linux
|
||||
library_dirs = ["/usr/local/lib"],
|
||||
# additional libs for MPI on Mac
|
||||
# libraries = ["mpi"],
|
||||
)
|
||||
|
||||
setup(name = "lammps",
|
||||
version = "28Nov11",
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "http://lammps.sandia.gov",
|
||||
description = """LAMMPS molecular dynamics library - parallel""",
|
||||
py_modules = ["lammps"],
|
||||
ext_modules = [lammps_library]
|
||||
)
|
||||
@ -1,34 +0,0 @@
|
||||
#!/usr/local/bin/python
|
||||
|
||||
"""
|
||||
setup_serial.py file for LAMMPS with dummy serial MPI library
|
||||
"""
|
||||
|
||||
from distutils.core import setup, Extension
|
||||
|
||||
import os, glob
|
||||
path = os.path.dirname(os.getcwd())
|
||||
|
||||
# list of src files for LAMMPS and MPI STUBS
|
||||
|
||||
libfiles = glob.glob("%s/src/*.cpp" % path) + \
|
||||
glob.glob("%s/src/STUBS/*.c" % path)
|
||||
|
||||
lammps_library = Extension("_lammps_serial",
|
||||
sources = libfiles,
|
||||
define_macros = [("MPICH_IGNORE_CXX_SEEK",1),
|
||||
("LAMMPS_GZIP",1),
|
||||
("FFT_NONE",1),],
|
||||
# src files for LAMMPS and MPI STUBS
|
||||
include_dirs = ["../src", "../src/STUBS"]
|
||||
)
|
||||
|
||||
setup(name = "lammps_serial",
|
||||
version = "28Nov11",
|
||||
author = "Steve Plimpton",
|
||||
author_email = "sjplimp@sandia.gov",
|
||||
url = "http://lammps.sandia.gov",
|
||||
description = """LAMMPS molecular dynamics library - serial""",
|
||||
py_modules = ["lammps"],
|
||||
ext_modules = [lammps_library]
|
||||
)
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -O2
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = icc
|
||||
LINKFLAGS = -O2
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -9,7 +9,9 @@ SHELL = /bin/sh
|
||||
|
||||
CC = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC
|
||||
CCFLAGS = -O3
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC
|
||||
LINKFLAGS = -O \
|
||||
-L/opt/ibmcmp/xlf/9.1/blrts_lib \
|
||||
@ -18,9 +20,11 @@ LINKFLAGS = -O \
|
||||
-L/bgl/local/bglfftwgel-2.1.5.pre5/lib
|
||||
LIB = -lxlopt -lxlomp_ser -lxl -lxlfmath -lm \
|
||||
-lmsglayer.rts -lrts.rts -ldevices.rts -lmassv
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -82,15 +86,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpicxx
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -O
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpicxx
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = c++
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = c++
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -34,8 +38,8 @@ LMP_INC = -DLAMMPS_GZIP
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I../STUBS
|
||||
MPI_PATH =
|
||||
MPI_LIB = ../STUBS/libmpi.a
|
||||
MPI_PATH = -L../STUBS
|
||||
MPI_LIB = -lmpi_stubs
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -g -O # -Wunused
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = g++
|
||||
LINKFLAGS = -g -O
|
||||
LIB =
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -g -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = g++
|
||||
LINKFLAGS = -g -O
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -25,13 +25,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpicxx
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++ -lm
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -93,15 +97,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CXX = CC
|
||||
CCFLAGS = -g -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = $(CXX)
|
||||
LINKFLAGS = -g -O
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,18 +80,22 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CXX) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CXX) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
# Individual dependencies
|
||||
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpic++
|
||||
CCFLAGS = -O3
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpic++
|
||||
LINKFLAGS = -O3
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = icc
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = c++
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = c++
|
||||
LINKFLAGS = -O
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -34,8 +38,8 @@ LMP_INC = -DLAMMPS_GZIP
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I../STUBS
|
||||
MPI_PATH =
|
||||
MPI_LIB = ../STUBS/libmpi.a
|
||||
MPI_PATH = -L../STUBS
|
||||
MPI_LIB = -lmpi_stubs
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -9,13 +9,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = ${MPI_GCC46_PATH}/mpic++
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = ${MPI_GCC46_PATH}/mpic++
|
||||
LINKFLAGS = -O
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -79,15 +83,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -9,13 +9,17 @@ SHELL = /bin/sh
|
||||
CC = i686-pc-mingw32-g++
|
||||
CCFLAGS = -O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
|
||||
-ffast-math -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = i686-pc-mingw32-g++
|
||||
LINKFLAGS = -O
|
||||
LIB = -lwsock32 # -lwsock32 is needed for USER-IMD which uses tcp/ip sockets.
|
||||
SIZE = i686-pc-mingw32-size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rcsv
|
||||
SIZE = i686-pc-mingw32-size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -34,9 +38,9 @@ LMP_INC = -DLAMMPS_XDR # -DLAMMPS_GZIP -DMALLOC_MEMALIGN=64
|
||||
# PATH = path for MPI library
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I../STUBS
|
||||
MPI_INC = -I../STUBS
|
||||
MPI_PATH =
|
||||
MPI_LIB = mpi.o
|
||||
MPI_LIB = mpi.o
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
|
||||
@ -14,13 +14,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpiicc
|
||||
CCFLAGS = -O3 -fno-alias -ip -unroll0
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpiicc
|
||||
LINKFLAGS = -O -L/opt/intel/mkl/10.0.011/lib/em64t
|
||||
LIB = -lstdc++ -lpthread -lmkl_em64t -lguide
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -82,15 +86,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = G++
|
||||
LINKFLAGS = -O
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -10,13 +10,17 @@ CC = mpic++
|
||||
CCFLAGS = -O2 -fomit-frame-pointer -fno-rtti -fno-exceptions -g \
|
||||
-march=native -ffast-math -mpc64 -finline-functions \
|
||||
-funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpic++
|
||||
LINKFLAGS = -O -g -fno-rtti -fno-exceptions -mpc64
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rcsv
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -78,15 +82,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = pgCC
|
||||
CCFLAGS = -fast
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = pgCC
|
||||
LINKFLAGS =
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -9,13 +9,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpCC_r
|
||||
CCFLAGS = -O3 -qnoipa -qlanglvl=oldmath
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpCC_r
|
||||
LINKFLAGS = -O -qnoipa -qlanglvl=oldmath -bmaxdata:0x70000000
|
||||
LIB = -lm
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -77,15 +81,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpiCC
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpiCC
|
||||
LINKFLAGS = -O
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -36,13 +36,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpic++
|
||||
CCFLAGS = -O2 -xsse4.2 -funroll-loops -fstrict-aliasing
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpic++
|
||||
LINKFLAGS = -O -xsse4.2
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rcsv
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -104,15 +108,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -10,16 +10,20 @@ SHELL = /bin/sh
|
||||
CC = blrts_xlC
|
||||
CCFLAGS = -I/bgl/BlueLight/ppcfloor/bglsys/include \
|
||||
-O2 -qarch=440 -qtune=440
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M -qmakedep=gcc
|
||||
|
||||
LINK = blrts_xlC
|
||||
LINKFLAGS = -O \
|
||||
-L/bgl/BlueLight/ppcfloor/bglsys/lib \
|
||||
-L/opt/ibmcmp/xlf/bg/10.1/blrts_lib \
|
||||
-L/opt/ibmcmp/vacpp/bg/8.0/blrts_lib
|
||||
LIB = -lm
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -81,15 +85,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -9,13 +9,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpCC_r
|
||||
CCFLAGS = -O2 -qnoipa
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpCC_r
|
||||
LINKFLAGS = -O -L/usr/lib
|
||||
LIB = -lm
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -77,15 +81,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -O -g
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = g++
|
||||
LINKFLAGS = -O -g
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -34,8 +38,8 @@ LMP_INC = #-DLAMMPS_GZIP -DMALLOC_MEMALIGN=64
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I../STUBS
|
||||
MPI_PATH =
|
||||
MPI_LIB = ../STUBS/libmpi.a
|
||||
MPI_PATH = -L../STUBS
|
||||
MPI_LIB = -lmpi_stubs
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
@ -44,7 +48,7 @@ MPI_LIB = ../STUBS/libmpi.a
|
||||
# PATH = path for FFT library
|
||||
# LIB = name of FFT library
|
||||
|
||||
FFT_INC =
|
||||
FFT_INC =
|
||||
FFT_PATH =
|
||||
FFT_LIB = -lfftw3f
|
||||
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -O0 -g -Wall -W -fstrict-aliasing
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = g++
|
||||
LINKFLAGS = -O0 -g
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rcsv
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -34,8 +38,8 @@ LMP_INC = -DLAMMPS_GZIP
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I../STUBS
|
||||
MPI_PATH =
|
||||
MPI_LIB = ../STUBS/libmpi.a
|
||||
MPI_PATH = -L../STUBS
|
||||
MPI_LIB = -lmpi_stubs
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = CC
|
||||
CCFLAGS = -64 -O -mp
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = CC
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = c++
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = c++
|
||||
LINKFLAGS = -O
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -34,8 +38,8 @@ LMP_INC = -DLAMMPS_GZIP
|
||||
# LIB = name of MPI library
|
||||
|
||||
MPI_INC = -I../STUBS
|
||||
MPI_PATH =
|
||||
MPI_LIB = ../STUBS/libmpi.a
|
||||
MPI_PATH = -L../STUBS
|
||||
MPI_LIB = -lmpi_stubs
|
||||
|
||||
# FFT library, OPTIONAL
|
||||
# see discussion in doc/Section_start.html#2_2 (step 6)
|
||||
@ -76,15 +80,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -14,13 +14,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpicxx
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -O
|
||||
LIB = -lm
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -84,15 +88,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -9,13 +9,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = CC
|
||||
CCFLAGS = -fastsse
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = CC
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -77,11 +81,15 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
.cpp.o:
|
||||
|
||||
@ -8,13 +8,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpiCC
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpiCC
|
||||
LINKFLAGS = -O
|
||||
LIB =
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -79,15 +83,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
@ -27,13 +27,17 @@ SHELL = /bin/sh
|
||||
|
||||
CC = mpicxx
|
||||
CCFLAGS = -O
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -O
|
||||
LIB = -lstdc++ -lm
|
||||
SIZE = size
|
||||
|
||||
ARCHIVE = ar
|
||||
ARFLAGS = -rc
|
||||
SIZE = size
|
||||
SHLIBFLAGS = -shared
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# LAMMPS-specific settings
|
||||
@ -95,15 +99,19 @@ $(EXE): $(OBJ)
|
||||
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
|
||||
$(SIZE) $(EXE)
|
||||
|
||||
# Library target
|
||||
# Library targets
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
|
||||
|
||||
shlib: $(OBJ)
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
|
||||
$(OBJ) $(EXTRA_LIB) $(LIB)
|
||||
|
||||
# Compilation rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) -c $<
|
||||
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
|
||||
|
||||
%.d:%.cpp
|
||||
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
|
||||
|
||||
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Reference in New Issue
Block a user