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@ -411,9 +411,16 @@ 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 class="reference external" href="http://numpy.scipy.org">Numpy package</a> be installed in your Python. After
launching python, type</p>
<p>The packages Pypar and mpi4py have both been successfully tested with
LAMMPS. Pypar is simpler and easy to set up and use, but supports
only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
bit more complex to use. As of version 2.0.0, mpi4py is the only
python MPI wrapper that allows passing a custom MPI communicator to
the LAMMPS constructor, which means one can easily run one or more
LAMMPS instances on subsets of the total MPI ranks.</p>
<hr class="docutils" />
<p>Pypar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a>
be installed in your Python. After launching Python, type</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">numpy</span>
</pre></div>
</div>
@ -466,6 +473,51 @@ address, e.g. by moving other MPI installations so that Pypar finds
the right one.</p>
</div>
<hr class="docutils" />
<p>To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it
and from its main directory, type</p>
<div class="highlight-python"><div class="highlight"><pre>python setup.py build
sudo python setup.py install
</pre></div>
</div>
<p>Again, the &#8220;sudo&#8221; is only needed if required to copy mpi4py files into
your Python distribution&#8217;s site-packages directory. To install with
user privilege into the user local directory type</p>
<div class="highlight-python"><div class="highlight"><pre>python setup.py install --user
</pre></div>
</div>
<p>If you have successully installed mpi4py, you should be able to run
Python and type</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="kn">import</span> <span class="n">MPI</span>
</pre></div>
</div>
<p>without error. You should also be able to run python in parallel
on a simple test script</p>
<div class="highlight-python"><div class="highlight"><pre>% mpirun -np 4 python test.py
</pre></div>
</div>
<p>where test.py contains the lines</p>
<div class="highlight-python"><div class="highlight"><pre>from mpi4py import MPI
comm = MPI.COMM_WORLD
print &quot;Proc %d out of %d procs&quot; % (comm.Get_rank(),comm.Get_size())
</pre></div>
</div>
<p>and see one line of output for each processor you run on.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">To use mpi4py and LAMMPS in parallel from Python, you
must insure both are using the same version of MPI. If you only have
one MPI installed on your system, this is not an issue, but it can be
if you have multiple MPIs. Your LAMMPS build is explicit about which
MPI it is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Mpi4py uses the &#8220;mpicc&#8221; command to find
information about the MPI it uses to build against. And it tries to
load &#8220;libmpi.so&#8221; from the LD_LIBRARY_PATH. This may or may not find
the MPI library that LAMMPS is using. If you have problems running
both mpi4py and LAMMPS together, this is an issue you may need to
address, e.g. by moving other MPI installations so that mpi4py finds
the right one.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="testing-the-python-lammps-interface">
<span id="py-6"></span><h2>11.6. Testing the Python-LAMMPS interface<a class="headerlink" href="#testing-the-python-lammps-interface" title="Permalink to this headline"></a></h2>
@ -517,8 +569,8 @@ typed something like:</p>
<div class="section" id="test-lammps-and-python-in-parallel">
<h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong><a class="headerlink" href="#test-lammps-and-python-in-parallel" title="Permalink to this headline"></a></h3>
<p>To run LAMMPS in parallel, assuming you have installed the
<a class="reference external" href="http://datamining.anu.edu.au/~ole/pypar">Pypar</a> package as discussed
above, create a test.py file containing these lines:</p>
<a class="reference external" href="Pypar">Pypar</a> package as discussed above, create a test.py file
containing these lines:</p>
<div class="highlight-python"><div class="highlight"><pre>import pypar
from lammps import lammps
lmp = lammps()
@ -527,7 +579,20 @@ print &quot;Proc %d out of %d procs has&quot; % (pypar.rank(),pypar.size()),lmp
pypar.finalize()
</pre></div>
</div>
<p>You can then run it in parallel as:</p>
<p>To run LAMMPS in parallel, assuming you have installed the
<a class="reference external" href="mpi4py">mpi4py</a> package as discussed above, create a test.py file
containing these lines:</p>
<div class="highlight-python"><div class="highlight"><pre>from mpi4py import MPI
from lammps import lammps
lmp = lammps()
lmp.file(&quot;in.lj&quot;)
me = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
print &quot;Proc %d out of %d procs has&quot; % (me,nprocs),lmp
MPI.Finalize()
</pre></div>
</div>
<p>You can either script in parallel as:</p>
<div class="highlight-python"><div class="highlight"><pre>% mpirun -np 4 python test.py
</pre></div>
</div>
@ -590,11 +655,12 @@ Python script, as follows:</p>
the files src/library.cpp and src/library.h 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>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span> <span class="c"># create a LAMMPS object using the default liblammps.so library</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">ptr</span><span class="o">=</span><span class="n">lmpptr</span><span class="p">)</span> <span class="c"># ditto, but use lmpptr as previously created LAMMPS object</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="s">&quot;g++&quot;</span><span class="p">)</span> <span class="c"># create a LAMMPS object using the liblammps_g++.so library</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="s">&quot;&quot;</span><span class="p">,</span><span class="nb">list</span><span class="p">)</span> <span class="c"># ditto, with command-line args, e.g. list = [&quot;-echo&quot;,&quot;screen&quot;]</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="s">&quot;g++&quot;</span><span class="p">,</span><span class="nb">list</span><span class="p">)</span>
<div class="highlight-python"><div class="highlight"><pre>lmp = lammps() # create a LAMMPS object using the default liblammps.so library
4 optional args are allowed: name, cmdargs, ptr, comm
lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
lmp = lammps(name=&quot;g++&quot;) # create a LAMMPS object using the liblammps_g++.so library
lmp = lammps(name=&quot;g++&quot;,cmdargs=list) # add LAMMPS command-line args, e.g. list = [&quot;-echo&quot;,&quot;screen&quot;]
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre><span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> <span class="c"># destroy a LAMMPS object</span>
@ -706,8 +772,8 @@ argument.</p>
returned, which you can use via normal Python subscripting. See the
extract() method in the src/atom.cpp file for a list of valid names.
Again, new names could easily be added. A pointer to a vector of
doubles or integers, or a pointer to an array of doubles (double <a href="#id2"><span class="problematic" id="id3">**</span></a>)
or integers (int <a href="#id4"><span class="problematic" id="id5">**</span></a>) is returned. You need to specify the appropriate
doubles or integers, or a pointer to an array of doubles (double <a href="#id3"><span class="problematic" id="id4">**</span></a>)
or integers (int <a href="#id5"><span class="problematic" id="id6">**</span></a>) is returned. You need to specify the appropriate
data type via the type argument.</p>
<p>For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is
@ -802,8 +868,8 @@ own scripts, send them to us and we can include them in the LAMMPS
distribution.</p>
<table border="1" class="docutils">
<colgroup>
<col width="27%" />
<col width="73%" />
<col width="56%" />
<col width="44%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>trivial.py</td>
@ -813,19 +879,25 @@ distribution.</p>
<td>invoke various LAMMPS library interface routines</td>
</tr>
<tr class="row-odd"><td>simple.py</td>
<td>mimic operation of couple/simple/simple.cpp in Python</td>
<td>run in parallel</td>
</tr>
<tr class="row-even"><td>gui.py</td>
<td>GUI go/stop/temperature-slider to control LAMMPS</td>
<tr class="row-even"><td>similar to examples/COUPLE/simple/simple.cpp</td>
<td>split.py</td>
</tr>
<tr class="row-odd"><td>plot.py</td>
<td>real-time temeperature plot with GnuPlot via Pizza.py</td>
<tr class="row-odd"><td>same as simple.py but running in parallel on a subset of procs</td>
<td>gui.py</td>
</tr>
<tr class="row-even"><td>viz_tool.py</td>
<td>real-time viz via some viz package</td>
<tr class="row-even"><td>GUI go/stop/temperature-slider to control LAMMPS</td>
<td>plot.py</td>
</tr>
<tr class="row-odd"><td>vizplotgui_tool.py</td>
<td>combination of viz_tool.py and plot.py and gui.py</td>
<tr class="row-odd"><td>real-time temeperature plot with GnuPlot via Pizza.py</td>
<td>viz_tool.py</td>
</tr>
<tr class="row-even"><td>real-time viz via some viz package</td>
<td>vizplotgui_tool.py</td>
</tr>
<tr class="row-odd"><td>combination of viz_tool.py and plot.py and gui.py</td>
<td>&nbsp;</td>
</tr>
</tbody>
</table>