Metadata-Version: 2.1
Name: pmda
Version: 0.3.0
Summary: Parallel Molecular Dynamics Analysis tools
Home-page: https://github.com/MDAnalysis/pmda/
Author: Max Linke
Author-email: max.linke88@gmail.com
License: GPLv2
Download-URL: https://github.com/MDAnalysis/pmda/releases
Project-URL: Issue Tracker, https://github.com/MDAnalysis/pmda/issues/
Project-URL: Source, https://github.com/MDAnalysis/pmda/
Project-URL: Documentation, https://www.mdanalysis.org/pmda/
Project-URL: Mailing list, https://groups.google.com/group/mdnalysis-discussion
Keywords: science parallel
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/x-rst
Requires-Dist: MDAnalysis (>=0.19.0)
Requires-Dist: dask (>=0.18)
Requires-Dist: distributed
Requires-Dist: six
Requires-Dist: joblib
Requires-Dist: networkx
Requires-Dist: scipy

==============================================
  PMDA - Parallel Molecular Dynamics Analysis
==============================================

|build| |cov| |PRwelcome| |zenodo| |conda|

Ready to use analysis and buildings blocks to write parallel analysis algorithms
using MDAnalysis_ with dask_.

.. warning::
   This project is **alpha software** and not API stable. It will and
   should rapidly evolve to test different approaches to implementing
   parallel analysis in a seamless and intuitive fashion.


For example, run a rmsd analysis on all available cores:

.. code:: python

   import MDAnalysis as mda
   from pmda import rms

   u = mda.Universe(top, traj)
   ref = mda.Universe(top, traj)

   rmsd_ana = rms.RMSD(u.atoms, ref.atoms).run(n_jobs=-1)

   print(rmsd_ana.rmsd)


By default PMDA use the multiprocessing scheduler of dask_. This is sufficient
if you want to run your simulation on a single machine. If your analysis takes
a very long time (>30 min) you can also spread it to several nodes using the
distributed_ scheduler. To do this you can pass a ``scheduler`` keyword
argument to the ``run`` method.

To write your own parallel algorithms you can subclass the
``pmda.parallel.ParallelAnalysisBase`` class.


License and source code
=======================

PMDA is released under the `GNU General Public License, version 2`_ (see the
files AUTHORS and LICENSE for details).

Source code is available in the public GitHub repository
https://github.com/MDAnalysis/pmda/.


Installation
============

Install a release with ``pip``
------------------------------

The latest release is available from https://pypi.org/project/pmda/
and can be installed with pip_

.. code-block:: sh

   pip install --upgrade pmda



Development version from source
-------------------------------

To install the latest development version from source, run

.. code-block:: sh

  git clone git@github.com:MDAnalysis/pmda.git
  cd pmda
  python setup.py install


Getting help
============

*Help* is also available through the *MDAnalysis mailing list*

     https://groups.google.com/group/mdnalysis-discussion

Please report *bugs and feature requests* for PMDA through the `Issue
Tracker`_.



Contributing
============

PMDA welcomes new contributions. Please drop by the `MDAnalysis developer
mailing list`_ to discuss and ask questions.

To contribute code, submit a *pull request* against the master branch in the
`PMDA repository`_.


Citation
========

If you use PMDA in published work please cite [Fan2019]_.

.. [Fan2019] Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard J. Gowers,
	     Michael Gecht, and Oliver Beckstein. PMDA --- Parallel Molecular Dynamics
	     Analysis. In Chris Calloway, David Lippa, Dillon Niederhut, and David Shupe,
	     editors, Proceedings of the 18th Python in Science Conference,
	     pages 134-142, Austin, TX, 2019.
	     doi: `10.25080/Majora-7ddc1dd1-013`_	     

.. _MDAnalysis: https://www.mdanalysis.org
.. _dask: https://dask.pydata.org/en/latest/
.. _distributed: https://distributed.readthedocs.io/
.. _`Issue tracker`: https://github.com/MDAnalysis/pmda/issues
.. _`PMDA repository`: https://github.com/MDAnalysis/pmda/
.. _pip: https://pip.pypa.io/en/stable/
.. _`GNU General Public License, version 2`:
   https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html
.. _`MDAnalysis developer mailing list`:
   https://groups.google.com/group/mdnalysis-devel
.. _`10.25080/Majora-7ddc1dd1-013`:
   https://doi.org/10.25080/Majora-7ddc1dd1-013

.. |build| image:: https://travis-ci.org/MDAnalysis/pmda.svg?branch=master
    :alt: Build Status
    :target: https://travis-ci.org/MDAnalysis/pmda

.. |cov| image:: https://codecov.io/gh/MDAnalysis/pmda/branch/master/graph/badge.svg
   :alt: Coverage
   :target: https://codecov.io/gh/MDAnalysis/pmda

.. |zenodo| image:: https://zenodo.org/badge/106346721.svg
   :alt: DOI
   :target: https://zenodo.org/badge/latestdoi/106346721

.. |conda| image:: https://anaconda.org/conda-forge/pmda/badges/version.svg
   :alt: conda release
   :target: https://anaconda.org/conda-forge/pmda

.. |PRwelcome| image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square
   :alt: PRs welcome
   :target: http://makeapullrequest.com


