regenerate html pages with new txt2rst tool
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Axel Kohlmeyer
@ -343,10 +343,10 @@ described above.</p>
|
||||
<p>If you set the paths to these files as environment variables, you only
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have to do it once. For the csh or tcsh shells, add something like
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this to your ~/.cshrc file, one line for each of the two files:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span>setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
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<pre class="literal-block">
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setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
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setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
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</pre></div>
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</div>
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</pre>
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<p>If you use the python/install.py script, you need to invoke it every
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time you rebuild LAMMPS (as a shared library) or make changes to the
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python/lammps.py file.</p>
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@ -393,39 +393,21 @@ environment variable as described above.</p>
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your Python with an interface to MPI. This also allows you to
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make MPI calls directly from Python in your script, if you desire.</p>
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<p>There are several Python packages available that purport to wrap MPI
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as a library and allow MPI functions to be called from Python.</p>
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<p>These include</p>
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as a library and allow MPI functions to be called from Python. However,
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development on most of them seems to be halted except on:</p>
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<ul class="simple">
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<li><a class="reference external" href="http://pympi.sourceforge.net/">pyMPI</a></li>
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<li><a class="reference external" href="http://code.google.com/p/maroonmpi/">maroonmpi</a></li>
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<li><a class="reference external" href="http://code.google.com/p/mpi4py/">mpi4py</a></li>
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<li><a class="reference external" href="http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16">myMPI</a></li>
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<li><a class="reference external" href="http://code.google.com/p/pypar">Pypar</a></li>
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<li><a class="reference external" href="https://bitbucket.org/mpi4py/mpi4py">mpi4py</a></li>
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<li><a class="reference external" href="https://github.com/daleroberts/pypar">PyPar</a></li>
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</ul>
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<p>All of these except pyMPI work by wrapping the MPI library and
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exposing (some portion of) its interface to your Python script. This
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means Python cannot be used interactively in parallel, since they do
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not address the issue of interactive input to multiple instances of
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Python running on different processors. The one exception is pyMPI,
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which alters the Python interpreter to address this issue, and (I
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believe) creates a new alternate executable (in place of “python”
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itself) as a result.</p>
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<p>In principle any of these Python/MPI packages should work to invoke
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LAMMPS in parallel and to make MPI calls themselves from a Python
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script which is itself running in parallel. However, when I
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downloaded and looked at a few of them, their documentation was
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incomplete and I had trouble with their installation. It’s not clear
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if some of the packages are still being actively developed and
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supported.</p>
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<p>The packages Pypar and mpi4py have both been successfully tested with
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LAMMPS. Pypar is simpler and easy to set up and use, but supports
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<p>Both packages, PyPar and mpi4py have been successfully tested with
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LAMMPS. PyPar is simpler and easy to set up and use, but supports
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only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
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bit more complex to use. As of version 2.0.0, mpi4py is the only
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python MPI wrapper that allows passing a custom MPI communicator to
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the LAMMPS constructor, which means one can easily run one or more
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LAMMPS instances on subsets of the total MPI ranks.</p>
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<hr class="docutils" />
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<p>Pypar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a>
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<p>PyPar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a>
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be installed in your Python. After launching Python, type</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span>
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</pre></div>
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@ -439,15 +421,15 @@ top-level directory, type</p>
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</div>
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<p>The “sudo” is only needed if required to copy Numpy files into your
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Python distribution’s site-packages directory.</p>
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<p>To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it
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<p>To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it
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and from its “source” directory, type</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span>
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||||
<span class="n">sudo</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
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||||
</pre></div>
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||||
</div>
|
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<p>Again, the “sudo” is only needed if required to copy Pypar files into
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||||
<p>Again, the “sudo” is only needed if required to copy PyPar files into
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your Python distribution’s site-packages directory.</p>
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||||
<p>If you have successully installed Pypar, you should be able to run
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<p>If you have successully installed PyPar, you should be able to run
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Python and type</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span>
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||||
</pre></div>
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@ -465,17 +447,17 @@ on a simple test script</p>
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<p>and see one line of output for each processor you run on.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">To use Pypar and LAMMPS in parallel from Python, you must insure
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<p class="last">To use PyPar and LAMMPS in parallel from Python, you must insure
|
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both are using the same version of MPI. If you only have one MPI
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||||
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
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src/MAKE/Makefile.foo file. Pypar uses the “mpicc” command to find
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||||
src/MAKE/Makefile.foo file. PyPar uses the “mpicc” command to find
|
||||
information about the MPI it uses to build against. And it tries to
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||||
load “libmpi.so” from the LD_LIBRARY_PATH. This may or may not find
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the MPI library that LAMMPS is using. If you have problems running
|
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both Pypar and LAMMPS together, this is an issue you may need to
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address, e.g. by moving other MPI installations so that Pypar finds
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||||
both PyPar and LAMMPS together, this is an issue you may need to
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||||
address, e.g. by moving other MPI installations so that PyPar finds
|
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the right one.</p>
|
||||
</div>
|
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<hr class="docutils" />
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@ -502,11 +484,11 @@ on a simple test script</p>
|
||||
</pre></div>
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</div>
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<p>where test.py contains the lines</p>
|
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="k">import</span> <span class="n">MPI</span>
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||||
<span class="n">comm</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span>
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||||
<span class="nb">print</span> <span class="s2">"Proc </span><span class="si">%d</span><span class="s2"> out of </span><span class="si">%d</span><span class="s2"> procs"</span> <span class="o">%</span> <span class="p">(</span><span class="n">comm</span><span class="o">.</span><span class="n">Get_rank</span><span class="p">(),</span><span class="n">comm</span><span class="o">.</span><span class="n">Get_size</span><span class="p">())</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
from mpi4py import MPI
|
||||
comm = MPI.COMM_WORLD
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||||
print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size())
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||||
</pre>
|
||||
<p>and see one line of output for each processor you run on.</p>
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||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
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||||
@ -568,15 +550,15 @@ interactively from the bench directory:</p>
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||||
<p>Either way, you should see the results of running the in.lj benchmark
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||||
on a single processor appear on the screen, the same as if you had
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||||
typed something like:</p>
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||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp_g++ -in in.lj
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||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="test-lammps-and-python-in-parallel">
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||||
<h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></h3>
|
||||
<p>To run LAMMPS in parallel, assuming you have installed the
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||||
<a class="reference external" href="Pypar">Pypar</a> package as discussed above, create a test.py file
|
||||
containing these lines:</p>
|
||||
<a class="reference external" href="https://github.com/daleroberts/pypar">PyPar</a> package as discussed
|
||||
above, create a test.py file containing these lines:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span>
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||||
<span class="kn">from</span> <span class="nn">lammps</span> <span class="k">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>
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||||
@ -586,36 +568,36 @@ containing these lines:</p>
|
||||
</pre></div>
|
||||
</div>
|
||||
<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-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="k">import</span> <span class="n">MPI</span>
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||||
<span class="kn">from</span> <span class="nn">lammps</span> <span class="k">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>
|
||||
<span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="s2">"in.lj"</span><span class="p">)</span>
|
||||
<span class="n">me</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_rank</span><span class="p">()</span>
|
||||
<span class="n">nprocs</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_size</span><span class="p">()</span>
|
||||
<span class="nb">print</span> <span class="s2">"Proc </span><span class="si">%d</span><span class="s2"> out of </span><span class="si">%d</span><span class="s2"> procs has"</span> <span class="o">%</span> <span class="p">(</span><span class="n">me</span><span class="p">,</span><span class="n">nprocs</span><span class="p">),</span><span class="n">lmp</span>
|
||||
<span class="n">MPI</span><span class="o">.</span><span class="n">Finalize</span><span class="p">()</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<a class="reference external" href="https://bitbucket.org/mpi4py/mpi4py">mpi4py</a> package as discussed
|
||||
above, create a test.py file containing these lines:</p>
|
||||
<pre class="literal-block">
|
||||
from mpi4py import MPI
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
lmp.file("in.lj")
|
||||
me = MPI.COMM_WORLD.Get_rank()
|
||||
nprocs = MPI.COMM_WORLD.Get_size()
|
||||
print "Proc %d out of %d procs has" % (me,nprocs),lmp
|
||||
MPI.Finalize()
|
||||
</pre>
|
||||
<p>You can either script in parallel as:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">python</span> <span class="n">test</span><span class="o">.</span><span class="n">py</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>and you should see the same output as if you had typed</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Note that if you leave out the 3 lines from test.py that specify Pypar
|
||||
<pre class="literal-block">
|
||||
% mpirun -np 4 lmp_g++ -in 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 LAMMPS run was made
|
||||
on a single processor, instead of one set of output showing that
|
||||
LAMMPS ran on 4 processors. If the 1-processor outputs occur, it
|
||||
means that Pypar is not working correctly.</p>
|
||||
<p>Also note that once you import the PyPar module, Pypar initializes MPI
|
||||
means that PyPar is not working correctly.</p>
|
||||
<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
|
||||
described in the PyPar documentation. The last line of your Python
|
||||
script should be pypar.finalize(), to insure MPI is shut down
|
||||
correctly.</p>
|
||||
</div>
|
||||
@ -661,14 +643,14 @@ 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-default"><div class="highlight"><pre><span></span><span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span> <span class="c1"># create a LAMMPS object using the default liblammps.so library</span>
|
||||
<span class="mi">4</span> <span class="n">optional</span> <span class="n">args</span> <span class="n">are</span> <span class="n">allowed</span><span class="p">:</span> <span class="n">name</span><span class="p">,</span> <span class="n">cmdargs</span><span class="p">,</span> <span class="n">ptr</span><span class="p">,</span> <span class="n">comm</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="c1"># 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="n">comm</span><span class="o">=</span><span class="n">split</span><span class="p">)</span> <span class="c1"># create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later</span>
|
||||
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"g++"</span><span class="p">)</span> <span class="c1"># 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="n">name</span><span class="o">=</span><span class="s2">"g++"</span><span class="p">,</span><span class="n">cmdargs</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span> <span class="c1"># add LAMMPS command-line args, e.g. list = ["-echo","screen"]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
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="g++") # create a LAMMPS object using the liblammps_g++.so library
|
||||
lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = ["-echo","screen"]
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> <span class="c1"># destroy a LAMMPS object</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
@ -677,49 +659,49 @@ from a C++ or C or Fortran program.</p>
|
||||
<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span> <span class="c1"># invoke a single LAMMPS command, cmd = "run 100"</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">xlo</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_global</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span> <span class="c1"># extract a global quantity</span>
|
||||
<span class="c1"># name = "boxxlo", "nlocal", etc</span>
|
||||
<span class="c1"># type = 0 = int</span>
|
||||
<span class="c1"># 1 = double</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">coords</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_atom</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span> <span class="c1"># extract a per-atom quantity</span>
|
||||
<span class="c1"># name = "x", "type", etc</span>
|
||||
<span class="c1"># type = 0 = vector of ints</span>
|
||||
<span class="c1"># 1 = array of ints</span>
|
||||
<span class="c1"># 2 = vector of doubles</span>
|
||||
<span class="c1"># 3 = array of doubles</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">eng</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_compute</span><span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">style</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span> <span class="c1"># extract value(s) from a compute</span>
|
||||
<span class="n">v3</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_fix</span><span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">style</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">)</span> <span class="c1"># extract value(s) from a fix</span>
|
||||
<span class="c1"># id = ID of compute or fix</span>
|
||||
<span class="c1"># style = 0 = global data</span>
|
||||
<span class="c1"># 1 = per-atom data</span>
|
||||
<span class="c1"># 2 = local data</span>
|
||||
<span class="c1"># type = 0 = scalar</span>
|
||||
<span class="c1"># 1 = vector</span>
|
||||
<span class="c1"># 2 = array</span>
|
||||
<span class="c1"># i,j = indices of value in global vector or array</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">var</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_variable</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">group</span><span class="p">,</span><span class="n">flag</span><span class="p">)</span> <span class="c1"># extract value(s) from a variable</span>
|
||||
<span class="c1"># name = name of variable</span>
|
||||
<span class="c1"># group = group ID (ignored for equal-style variables)</span>
|
||||
<span class="c1"># flag = 0 = equal-style variable</span>
|
||||
<span class="c1"># 1 = atom-style variable</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">flag</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">value</span><span class="p">)</span> <span class="c1"># set existing named string-style variable to value, flag = 0 if successful</span>
|
||||
<span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span> <span class="c1"># total # of atoms as int</span>
|
||||
<span class="n">data</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">gather_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">)</span> <span class="c1"># return atom attribute of all atoms gathered into data, ordered by atom ID</span>
|
||||
<span class="c1"># name = "x", "charge", "type", etc</span>
|
||||
<span class="c1"># count = # of per-atom values, 1 or 3, etc</span>
|
||||
<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> <span class="c1"># scatter atom attribute of all atoms from data, ordered by atom ID</span>
|
||||
<span class="c1"># name = "x", "charge", "type", etc</span>
|
||||
<span class="c1"># count = # of per-atom values, 1 or 3, etc</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
xlo = lmp.extract_global(name,type) # extract a global quantity
|
||||
# name = "boxxlo", "nlocal", etc
|
||||
# type = 0 = int
|
||||
# 1 = double
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
coords = lmp.extract_atom(name,type) # extract a per-atom quantity
|
||||
# name = "x", "type", etc
|
||||
# type = 0 = vector of ints
|
||||
# 1 = array of ints
|
||||
# 2 = vector of doubles
|
||||
# 3 = array of doubles
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
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
|
||||
# style = 0 = global data
|
||||
# 1 = per-atom data
|
||||
# 2 = local data
|
||||
# type = 0 = scalar
|
||||
# 1 = vector
|
||||
# 2 = array
|
||||
# i,j = indices of value in global vector or array
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
|
||||
# name = name of variable
|
||||
# group = group ID (ignored for equal-style variables)
|
||||
# flag = 0 = equal-style variable
|
||||
# 1 = atom-style variable
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
|
||||
natoms = lmp.get_natoms() # total # of atoms as int
|
||||
data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
|
||||
# name = "x", "charge", "type", etc
|
||||
# count = # of per-atom values, 1 or 3, etc
|
||||
lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms from data, ordered by atom ID
|
||||
# name = "x", "charge", "type", etc
|
||||
# count = # of per-atom values, 1 or 3, etc
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>The lines</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
|
||||
@ -767,8 +749,8 @@ 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="#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
|
||||
doubles or integers, or a pointer to an array of doubles (double **)
|
||||
or integers (int **) 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
|
||||
@ -824,19 +806,19 @@ consecutively ordered, no coordinates are reset.</p>
|
||||
<p>The array of coordinates passed to scatter_atoms() must be a ctypes
|
||||
vector of ints or doubles, allocated and initialized something like
|
||||
this:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ctypes</span> <span class="k">import</span> <span class="o">*</span>
|
||||
<span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span>
|
||||
<span class="n">n3</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="n">natoms</span>
|
||||
<span class="n">x</span> <span class="o">=</span> <span class="p">(</span><span class="n">n3</span><span class="o">*</span><span class="n">c_double</span><span class="p">)()</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">y</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">2</span>
|
||||
<span class="o">...</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="n">n3</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="n">natoms</span>
|
||||
<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_coords</span><span class="p">(</span><span class="s2">"x"</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="n">x</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
from ctypes import *
|
||||
natoms = lmp.get_natoms()
|
||||
n3 = 3*natoms
|
||||
x = (n3*c_double)()
|
||||
x[0] = x coord of atom with ID 1
|
||||
x[1] = y coord of atom with ID 1
|
||||
x[2] = z coord of atom with ID 1
|
||||
x[3] = x coord of atom with ID 2
|
||||
...
|
||||
x[n3-1] = z coord of atom with ID natoms
|
||||
lmp.scatter_coords("x",1,3,x)
|
||||
</pre>
|
||||
<p>Alternatively, you can just change values in the vector returned by
|
||||
gather_atoms(“x”,1,3), since it is a ctypes vector of doubles.</p>
|
||||
<hr class="docutils" />
|
||||
@ -915,10 +897,10 @@ capability needed by these Python scripts.</p>
|
||||
open-source version of PyMol in your Python, so that you can import it
|
||||
from a Python script. See the PyMol WWW pages <a class="reference external" href="http://www.pymol.org">here</a> or
|
||||
<a class="reference external" href="http://sourceforge.net/scm/?type=svn&group_id=4546">here</a> for more details:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>http://www.pymol.org
|
||||
http://sourceforge.net/scm/?type=svn&group_id=4546
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
<a class="reference external" href="http://www.pymol.org">http://www.pymol.org</a>
|
||||
<a class="reference external" href="http://sourceforge.net/scm/?type=svn&group_id=4546">http://sourceforge.net/scm/?type=svn&group_id=4546</a>
|
||||
</pre>
|
||||
<p>The latter link is to the open-source version.</p>
|
||||
<p>Note that for VMD, you need a fairly current version (1.8.7 works for
|
||||
me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
|
||||
|
||||
Reference in New Issue
Block a user