Metadata-Version: 2.1
Name: pmda
Version: 0.2.1
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: Documentation, https://www.mdanalysis.org/pmda/
Project-URL: Source, https://github.com/MDAnalysis/pmda/
Project-URL: Issue Tracker, https://github.com/MDAnalysis/pmda/issues/
Project-URL: Mailing list, https://groups.google.com/group/mdnalysis-discussion
Description: ==============================================
          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 [Linke2018]_.
        
        .. [Linke2018] Max Linke, & Oliver Beckstein. (2018, May 11). MDAnalysis/pmda:
                       0.1.0 (Version 0.1.0). Zenodo. http://doi.org/10.5281/zenodo.1245759
        
        	       
        .. _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
        
        .. |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
        
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
