Metadata-Version: 2.1
Name: polypy
Version: 0.8
Summary: Molecular Dynamics analysis
Home-page: https://github.com/symmy596/Polypy
Author: Adam R. Symington
Author-email: ars44@bath.ac.uk
License: MIT license
Description: <p align="center"> 
        <img src="https://github.com/symmy596/Polypy/blob/master/docs/source/Figures/polypy_1.png?raw=true"/>
        </p>
        
        [![PyPI version](https://badge.fury.io/py/polypy.svg)](https://badge.fury.io/py/polypy)
        [![Build Status](https://travis-ci.com/symmy596/PolyPy.svg?branch=master)](https://travis-ci.com/symmy596/PolyPy)
        [![Build status](https://ci.appveyor.com/api/projects/status/eo426m99lmkbh5rx?svg=true)](https://ci.appveyor.com/project/symmy596/polypy)
        [![Documentation Status](https://readthedocs.org/projects/polypy/badge/?version=latest)](https://polypy.readthedocs.io/en/latest/?badge=latest)
        <a href='https://coveralls.io/github/symmy596/PolyPy?branch=master'><img src='https://coveralls.io/repos/github/symmy596/PolyPy/badge.svg?branch=master' alt='Coverage Status' /></a> 
        
        This is the documentation for the open-source Python project - `polypy`,
        A library designed to facilitate the analysis of [DL_POLY](https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx) and [DL_MONTE](https://www.ccp5.ac.uk/DL_MONTE) calculations.
        polypy is built on existing Python packages that those in the solid state physics/chemistry community should already be familiar with.
        It is hoped that this tool will bring some benfits to the solid state community and facilitate data analysis and the generation of publication ready plots (powered by Matplotlib.)
        
        The main features include:
        
        1. **Method to analyse the number denisty of a given species in one and two dimensions.**  
        
           - Generate a plot of the total number of species in bins perpendicular to a specified direction.  
           - Generate a plot of the total number of species in cuboids parallel to a specified direction.  
        
        2. **Method calculate the charge density from the number density.**  
        
           - Convert number densities of all species in bins perpendicular to a specified direction into the charge density.  
        
        3. **Calculate the electric field and electrostatic potential from the charge density.**  
        
           - Solves the Poisson Boltzmann equation to convert the charge density into the electric field and the electrostatic potential.
        
        4. **Calculate the diffusion coefficient for a given species from a mean squared displacement.**
        
           - Carries out a mean squared displacement on an MD trajectory.
           - Calculates the diffusion coefficient.
           - Uses the density analysis and the diffusion coefficient to calculate the ionic conductivity. 
           
        
        <p align="center"> 
        <img src="https://github.com/symmy596/PolyPy/blob/master/docs/source/Figures/Show_off.png?raw=true" width="100%"/>
        <figcaption>(a) Mean squared displacement for calcuim fluoride. (b) System volume of calcium fluoride during a molecular dynamics simulation. (c) Cerium and oxygen number density at a grain boundary. (d) Electrostatic potential across a grain boundary of cerium oxide. (e) Center of mass of cerium (blue) and oxygen (orange) in a cerium oxide grain boundary in two dimensions.</figcaption>
        </p>
        
        
        The code has been developed to analyse DL_POLY and DL_MONTE calculations however other codes can be incorporated if there is user demand. Other formats, such as pdb or xyz can be converted to `DL_POLY` format with codes such as [atomsk](https://atomsk.univ-lille.fr/) and then analysed with `polypy`. Users are welcome to increase the file coverage by adding a reading function for a different format. This can be accomplished by adding to the `read` module which has a class for each unique file type that converts it to a `polypy.read.trajectory` object. 
        
        `polypy` was developed during a PhD project and as such the functionality focuses on the research questions encountered during that project, which we should clarify are wide ranging. Code contributions aimed at expanding the code to new of problems are encouraged.
        
        `polypy` is free to use.
        
        ## Usage
        
        A full list of examples can be found in the examples folder of the git repository, these include both the Python scripts and jupyter notebook tutorials which combine the full theory with code examples. It should be noted however that DL_POLY HISTORY files and DL_MONTE ARCHIVE files are sizable (1-5GB) and as such only short example trajectories are included in this repository. Notebooks are provided here to illustrate the theory but are not practicle.
        
        ## Installation
        
        `polypy` is a Python 3 package and requires a typical scientific Python stack. Use of the tutorials requires Anaconda/Jupyter to be installed.
        
        To build from source:
        
            pip install -r requirements.txt
        
            python setup.py build
        
            python setup.py install
        
        Or alternatively install with pip
        
            pip install polypy
        
        Using conda, 
        
            conda skeleton pypi polypy
        
            conda build polypy
            
            conda install --use-local polypy
        
        
        ### Tests
        
        Tests can be run by typing:
        
            python setup.py test
        
        
        in the root directory. 
        
        
        ### Documentation
        
        To build the documentation from scratch
          
            cd docs
            make html
        
        An online version of the documentation can be found [here](https://polypy.readthedocs.io/en/latest/index.html). The documentation contains an extensive explanation of the underlying theory, function documentation and tutorials. 
        
        
        ### License
        
        `polypy` is made available under the MIT License.
        
        ### Detailed requirements
        
        `polypy` is compatible with Python 3.5+ and relies on a number of open source Python packages, specifically:
        
        - matplotlib
        - numpy
        - scipy
        - coveralls
        - coverage
        - seaborn
        - pandas
        - jupyter
        - nbsphinx
        - jupyter-sphinx==0.2.4
        - sphinx_rtd_theme
        
        ## Contributing
        
        ### Contact
        
        If you have questions regarding any aspect of the software then please get in touch with the developer Adam Symington via email - ars44@bath.ac.uk.
        Alternatively you can create an issue on the [Issue Tracker](https://github.com/symmy596/PolyPy/issues).
        
        ### Bugs
        
        There may be bugs. If you think you've caught one, please report it on the [Issue Tracker](https://github.com/symmy596/PolyPy/issues).
        This is also the place to propose new ideas for features or ask questions about the design of `polypy`. Poor documentation is considered a bug
        so feel free to request improvements.
        
        ### Code contributions
        
        We welcome help in improving and extending the package. This is managed through Github pull requests; for external contributions we prefer the
        ["fork and pull"](https://guides.github.com/activities/forking/)
        workflow while core developers use branches in the main repository:
        
           1. First open an Issue to discuss the proposed contribution. This
              discussion might include how the changes fit polypy's scope and a
              general technical approach.
           2. Make your own project fork and implement the changes
              there. Please keep your code style compliant with PEP8.
           3. Open a pull request to merge the changes into the main
              project. A more detailed discussion can take place there before
              the changes are accepted.
        
        For further information please contact Adam Symington, ars44@bath.ac.uk
        
        ## Future
        
        Listed below are a series of useful additions that we would like to make to the codebase. Users are encouraged to fork the repository and work on any of these problems. Indeed, if functionality is not listed below you are more than welcome to add it. 
        
        - RDF
        - Diagonal slices
        - Regional MSDs in a cube
        
        
        ## Author
        
        * Adam R.Symington
          
        ## Research 
        
        - [Defect segregation facilitates oxygen transport at fluorite UO2 grain boundaries](https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0026)
        - [The role of dopant segregation on the oxygen vacancy distribution and oxygen diffusion in CeO2 grain boundaries](https://iopscience.iop.org/article/10.1088/2515-7655/ab28b5/meta)
        - [Quantifying the impact of disorder on Li-ion and Na-ion transport in perovskite titanate solid electrolytes for solid-state batteries](https://pubs.rsc.org/en/content/articlehtml/2020/ta/d0ta05343k)
        
        
        ## Acknowledgements
          
        This package was written during a PhD project that was funded by AWE and EPSRC (EP/R010366/1). The `polypy` software package was developed to analyse data generated using the Balena HPC facility at the University of Bath and the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk) via our membership of the UK's HEC Ma-terials Chemistry Consortium funded by EPSRC (EP/L000202).The author would like to thank Andrew R. McCluskey, Benjamin Morgan, Marco Molinari, James Grant and Stephen C. Parker for their help and guidance during this PhD project.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
