ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8657 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2012-08-14 20:18:19 +00:00
parent 7f5e8cb896
commit 617a28d8f4
2 changed files with 44 additions and 32 deletions
Download Patch File Download Diff File Expand all files Collapse all files

38
doc/Section_python.html
View File

@ -107,11 +107,11 @@ system.
<P>For Python to invoke LAMMPS, there are 2 files it needs to have: <P>For Python to invoke LAMMPS, there are 2 files it needs to have:
</P> </P>
<UL><LI>python/lammps.py <UL><LI>python/lammps.py
<LI>src/liblmp.so <LI>src/liblammps.so
</UL> </UL>
<P>Lammps.py is the Python wrapper on the LAMMPS library interface. <P>Lammps.py is the Python wrapper on the LAMMPS library interface.
Liblmp.so is the shared LAMMPS library that Python loads, as described Liblammps.so is the shared LAMMPS library that Python loads, as
above. described above.
</P> </P>
<P>You can insure Python can find these files in one of two ways: <P>You can insure Python can find these files in one of two ways:
</P> </P>
@ -125,32 +125,38 @@ this to your ~/.cshrc file, one line for each of the two files:
<PRE>setenv PYTHONPATH $<I>PYTHONPATH</I>:/home/sjplimp/lammps/python <PRE>setenv PYTHONPATH $<I>PYTHONPATH</I>:/home/sjplimp/lammps/python
setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src setenv LD_LIBRARY_PATH $<I>LD_LIBRARY_PATH</I>:/home/sjplimp/lammps/src
</PRE> </PRE>
<P>If you run the python/install.py script, you need to rerun it every <P>If you use the python/install.py script, you need to invoke it every
time you rebuild LAMMPS (as a shared library) or make changes to the time you rebuild LAMMPS (as a shared library) or make changes to the
python/lammps.py file. python/lammps.py file.
</P> </P>
<P>You can invoke install.py from the python directory as <P>You can invoke install.py from the python directory as
</P> </P>
<PRE>% python install.py <PRE>% python install.py <B>libdir</B> <B>pydir</B>
</PRE> </PRE>
<P>Prefix this command with "sudo" if it does not allow you to copy files <P>The optional libdir is where to copy the LAMMPS shared library to;
into the Python site-packages directory. If you do this, make sure the default is /usr/local/lib. The optional pydir is where to copy
that the Python run by root is the same as the Python you run. the lammps.py file to; the default is the site-packages directory
E.g. you may need to do something like of the Python running the install script.
</P> </P>
<PRE>% sudo /usr/local/bin/python install.py <P>Prefix the python command with "sudo" if it does not allow you to copy
files into system directories. If you do this, make sure that the
Python that root runs is the same as the Python you run. E.g. you may
need to do something like
</P>
<PRE>% sudo /usr/local/bin/python install.py <B>libdir</B> <B>pydir</B>
</PRE> </PRE>
<P>You can also invoke install.py from the src directory as <P>You can also invoke install.py from the src directory as
</P> </P>
<PRE>% make install-python <PRE>% make install-python
</PRE> </PRE>
<P>Again, you may need to prefix this with "sudo". In this mode you <P>In this mode you cannot append optional arguments. Again, you may
cannot control which Python root invokes. need to prefix this with "sudo". In this mode you cannot control
which Python is invoked by root.
</P> </P>
<P>Note that if you want Python to be able to load different versions of <P>Note that if you want Python to be able to load different versions of
the LAMMPS shared library (see <A HREF = "#py_5">this section</A> below), you will the LAMMPS shared library (see <A HREF = "#py_5">this section</A> below), you will
need to manually copy files like lmplmp_g++.so into the site-packages need to manually copy files like lmplammps_g++.so into the appropriate
directory as well. This is not needed if you set the LD_LIBRARY_PATH system directory. This is not needed if you set the LD_LIBRARY_PATH
environment variable as described above. environment variable as described above.
</P> </P>
<HR> <HR>
@ -368,8 +374,8 @@ 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 one-to-one with calls you can make to the LAMMPS library from a C++ or
C or Fortran program. C or Fortran program.
</P> </P>
<PRE>lmp = lammps() # create a LAMMPS object using the default liblmp.so library <PRE>lmp = lammps() # create a LAMMPS object using the default liblammps.so library
lmp = lammps("g++") # create a LAMMPS object using the liblmp_g++.so library lmp = lammps("g++") # create a LAMMPS object using the liblammps_g++.so library
lmp = lammps("",list) # ditto, with command-line args, e.g. list = ["-echo","screen"] lmp = lammps("",list) # ditto, with command-line args, e.g. list = ["-echo","screen"]
lmp = lammps("g++",list) lmp = lammps("g++",list)
</PRE> </PRE>

38
doc/Section_python.txt
View File

@ -103,11 +103,11 @@ system.
For Python to invoke LAMMPS, there are 2 files it needs to have: For Python to invoke LAMMPS, there are 2 files it needs to have:
python/lammps.py python/lammps.py
src/liblmp.so :ul src/liblammps.so :ul
Lammps.py is the Python wrapper on the LAMMPS library interface. Lammps.py is the Python wrapper on the LAMMPS library interface.
Liblmp.so is the shared LAMMPS library that Python loads, as described Liblammps.so is the shared LAMMPS library that Python loads, as
above. described above.
You can insure Python can find these files in one of two ways: You can insure Python can find these files in one of two ways:
@ -121,32 +121,38 @@ this to your ~/.cshrc file, one line for each of the two files:
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src :pre setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src :pre
If you run the python/install.py script, you need to rerun it every If you use the python/install.py script, you need to invoke it every
time you rebuild LAMMPS (as a shared library) or make changes to the time you rebuild LAMMPS (as a shared library) or make changes to the
python/lammps.py file. python/lammps.py file.
You can invoke install.py from the python directory as You can invoke install.py from the python directory as
% python install.py :pre % python install.py [libdir] [pydir] :pre
Prefix this command with "sudo" if it does not allow you to copy files The optional libdir is where to copy the LAMMPS shared library to;
into the Python site-packages directory. If you do this, make sure the default is /usr/local/lib. The optional pydir is where to copy
that the Python run by root is the same as the Python you run. the lammps.py file to; the default is the site-packages directory
E.g. you may need to do something like of the Python running the install script.
% sudo /usr/local/bin/python install.py :pre Prefix the python command with "sudo" if it does not allow you to copy
files into system directories. If you do this, make sure that the
Python that root runs is the same as the Python you run. E.g. you may
need to do something like
% sudo /usr/local/bin/python install.py [libdir] [pydir] :pre
You can also invoke install.py from the src directory as You can also invoke install.py from the src directory as
% make install-python :pre % make install-python :pre
Again, you may need to prefix this with "sudo". In this mode you In this mode you cannot append optional arguments. Again, you may
cannot control which Python root invokes. need to prefix this with "sudo". In this mode you cannot control
which Python is invoked by root.
Note that if you want Python to be able to load different versions of Note that if you want Python to be able to load different versions of
the LAMMPS shared library (see "this section"_#py_5 below), you will the LAMMPS shared library (see "this section"_#py_5 below), you will
need to manually copy files like lmplmp_g++.so into the site-packages need to manually copy files like lmplammps_g++.so into the appropriate
directory as well. This is not needed if you set the LD_LIBRARY_PATH system directory. This is not needed if you set the LD_LIBRARY_PATH
environment variable as described above. environment variable as described above.
:line :line
@ -363,8 +369,8 @@ 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 one-to-one with calls you can make to the LAMMPS library from a C++ or
C or Fortran program. C or Fortran program.
lmp = lammps() # create a LAMMPS object using the default liblmp.so library lmp = lammps() # create a LAMMPS object using the default liblammps.so library
lmp = lammps("g++") # create a LAMMPS object using the liblmp_g++.so library lmp = lammps("g++") # create a LAMMPS object using the liblammps_g++.so library
lmp = lammps("",list) # ditto, with command-line args, e.g. list = \["-echo","screen"\] lmp = lammps("",list) # ditto, with command-line args, e.g. list = \["-echo","screen"\]
lmp = lammps("g++",list) :pre lmp = lammps("g++",list) :pre