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@14590 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2016-02-15 15:28:30 +00:00
parent 70aa37e4c8
commit 729ba2cc21
13 changed files with 119 additions and 122 deletions
Download Patch File Download Diff File Expand all files Collapse all files

31
doc/Section_python.html
View File

@ -281,8 +281,10 @@ examples of Python code you can write for both pure Python operations
and callbacks to LAMMPS.</p>
<p>To run pure Python code from LAMMPS, you only need to build LAMMPS
with the PYTHON package installed:</p>
<p>make yes-python
make machine</p>
<div class="highlight-python"><div class="highlight"><pre>make yes-python
make machine
</pre></div>
</div>
<p>Note that this will link LAMMPS with the Python library on your
system, which typically requires several auxiliary system libraries to
also be linked. The list of these libraries and the paths to find
@ -303,7 +305,7 @@ file and the shared library.</p>
<a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a>. A shared library is one
that is dynamically loadable, which is what Python requires to wrap
LAMMPS. On Linux this is a library file that ends in &#8221;.so&#8221;, not &#8221;.a&#8221;.</p>
<p>&gt;From the src directory, type</p>
<p>From the src directory, type</p>
<div class="highlight-python"><div class="highlight"><pre>make foo mode=shlib
</pre></div>
</div>
@ -313,10 +315,14 @@ well as a soft link liblammps.so, which is what the Python wrapper will
load by default. Note that 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>If this fails, see <a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a> for
more details, especially if your LAMMPS build uses auxiliary libraries
like MPI or FFTW which may not be built as shared libraries on your
system.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you are building LAMMPS with an MPI or FFT library or other
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
<a class="reference internal" href="Section_start.html#start-5"><span>Section_start 5</span></a> for more details.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="installing-the-python-wrapper-into-python">
@ -715,17 +721,6 @@ lmp = lammps(name=&quot;g++&quot;,cmdargs=list) # add LAMMPS command-line arg
</pre></div>
</div>
<hr class="docutils" />
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Currently, the creation of a LAMMPS object from within lammps.py
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&#8217;t know how to do it from Pypar. So
for now, it runs with 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>
</div>
<p>The lines</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>