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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8673 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -58,12 +58,13 @@ operations within LAMMPS, such as running a simulation for a
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reasonable number of timesteps, then the overhead cost of invoking
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LAMMPS thru Python will be negligible.
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</P>
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<P>Before using LAMMPS from a Python script, you have to do two things.
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You need to set two environment variables. And you need to build
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LAMMPS as a dynamic shared library, so it can be loaded by Python.
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Both these steps are discussed below. If you wish to run LAMMPS in
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parallel from Python, you also need to extend your Python with MPI.
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This is also discussed below.
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<P>Before using LAMMPS from a Python script, you need to do two things.
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You need to build LAMMPS as a dynamic shared library, so it can be
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loaded by Python. And you need to tell Python how to find the library
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and the Python wrapper file python/lammps.py. Both these steps are
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discussed below. If you wish to run LAMMPS in parallel from Python,
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you also need to extend your Python with MPI. This is also discussed
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below.
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</P>
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<P>The Python wrapper for LAMMPS uses the amazing and magical (to me)
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"ctypes" package in Python, which auto-generates the interface code
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@ -131,7 +132,7 @@ python/lammps.py file.
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</P>
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<P>You can invoke install.py from the python directory as
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</P>
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<PRE>% python install.py <B>libdir</B> <B>pydir</B>
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<PRE>% python install.py [libdir] [pydir]
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</PRE>
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<P>The optional libdir is where to copy the LAMMPS shared library to; the
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default is /usr/local/lib. The optional pydir is where to copy the
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@ -146,12 +147,12 @@ non-standard locations, such as within your own user space, you will
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need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
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accordingly, as above.
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</P>
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<P>If the instally.py script does not allow you to copy files into system
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<P>If the install.py script does not allow you to copy files into system
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directories, prefix the python command with "sudo". If you do this,
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make sure that the Python that root runs is the same as the Python you
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run. E.g. you may need to do something like
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</P>
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<PRE>% sudo /usr/local/bin/python install.py <B>libdir</B> <B>pydir</B>
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<PRE>% sudo /usr/local/bin/python install.py [libdir] [pydir]
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</PRE>
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<P>You can also invoke install.py from the make command in the src
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directory as
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@ -275,8 +276,8 @@ If the load fails, the most common error to see is
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<PRE>OSError: Could not load LAMMPS dynamic library
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</PRE>
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<P>which means Python was unable to load the LAMMPS shared library. This
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typically occurs if the system can't find the LAMMMPS shared library
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or one of the auxiliary shared libraries it depends on.
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typically occurs if the system can't find the LAMMPS shared library or
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one of the auxiliary shared libraries it depends on.
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</P>
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<P>Python (actually the operating system) isn't verbose about telling you
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why the load failed, so carefully go through the steps above regarding
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@ -55,12 +55,13 @@ operations within LAMMPS, such as running a simulation for a
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reasonable number of timesteps, then the overhead cost of invoking
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LAMMPS thru Python will be negligible.
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Before using LAMMPS from a Python script, you have to do two things.
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You need to set two environment variables. And you need to build
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LAMMPS as a dynamic shared library, so it can be loaded by Python.
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Both these steps are discussed below. If you wish to run LAMMPS in
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parallel from Python, you also need to extend your Python with MPI.
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This is also discussed below.
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Before using LAMMPS from a Python script, you need to do two things.
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You need to build LAMMPS as a dynamic shared library, so it can be
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loaded by Python. And you need to tell Python how to find the library
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and the Python wrapper file python/lammps.py. Both these steps are
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discussed below. If you wish to run LAMMPS in parallel from Python,
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you also need to extend your Python with MPI. This is also discussed
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below.
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The Python wrapper for LAMMPS uses the amazing and magical (to me)
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"ctypes" package in Python, which auto-generates the interface code
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@ -127,7 +128,7 @@ python/lammps.py file.
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You can invoke install.py from the python directory as
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% python install.py [libdir] [pydir] :pre
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% python install.py \[libdir\] \[pydir\] :pre
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The optional libdir is where to copy the LAMMPS shared library to; the
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default is /usr/local/lib. The optional pydir is where to copy the
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@ -142,12 +143,12 @@ non-standard locations, such as within your own user space, you will
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need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
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accordingly, as above.
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If the instally.py script does not allow you to copy files into system
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If the install.py script does not allow you to copy files into system
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directories, prefix the python command with "sudo". If you do this,
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make sure that the Python that root runs is the same as the Python you
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run. E.g. you may need to do something like
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% sudo /usr/local/bin/python install.py [libdir] [pydir] :pre
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% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
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You can also invoke install.py from the make command in the src
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directory as
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@ -271,8 +272,8 @@ If the load fails, the most common error to see is
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OSError: Could not load LAMMPS dynamic library :pre
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which means Python was unable to load the LAMMPS shared library. This
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typically occurs if the system can't find the LAMMMPS shared library
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or one of the auxiliary shared libraries it depends on.
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typically occurs if the system can't find the LAMMPS shared library or
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one of the auxiliary shared libraries it depends on.
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Python (actually the operating system) isn't verbose about telling you
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why the load failed, so carefully go through the steps above regarding
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|
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@ -850,7 +850,7 @@ should be the file /usr/local/lib/libmpich.so.
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the environment variable LD_LIBRARY_PATH. So you may wish to copy the
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file src/liblammps.so or src/liblammps_g++.so (for example) to a place
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the system can find it by default, such as /usr/local/lib, or you may
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wish to add the lammps src directory to LD_LIBRARY_PATH, so that the
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wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
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current version of the shared library is always available to programs
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that use it.
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</P>
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@ -844,7 +844,7 @@ The operating system finds shared libraries to load at run-time using
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the environment variable LD_LIBRARY_PATH. So you may wish to copy the
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file src/liblammps.so or src/liblammps_g++.so (for example) to a place
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the system can find it by default, such as /usr/local/lib, or you may
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wish to add the lammps src directory to LD_LIBRARY_PATH, so that the
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wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
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current version of the shared library is always available to programs
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that use it.
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