Metadata-Version: 2.1
Name: lammps-cython
Version: 0.4.3
Summary: Pythonic Wrapper to LAMMPS using cython
Home-page: https://gitlab.com/costrouc/lammps-cython
Author: Christopher Ostrouchov
Author-email: chris.ostrouchov+lammps@gmail.com
License: MIT
Download-URL: https://gitlab.com/costrouc/lammps-cython/-/archive/master/lammps-cython-master.zip
Description: **All issues and contributions should be done on
        [Gitlab](https://gitlab.com/costrouc/lammps-cython). Github is used only as a
        mirror for visibility**
        
        # lammps-cython
        
        A high-performance cython wrapper around LAMMPS. Lammps is a great
        molecular dynamics package that has an unmatched set of potentials and
        fixes. This package offers unique features such as minimizing I/O by
        allowing direct access to thermostats and atom properties and allowing
        interactive lammps within python interpreters such a `ipython`.  The
        goal of this project is to put an opinionated wrapper around LAMMPS
        (the good parts) and allow the user to easily extend it's
        functionality in python. The api should feel very similar to
        [HOOMD](https://codeblue.umich.edu/hoomd-blue/) and is being actively
        developed.
        
        <table>
        <tr>
          <td>Latest Release</td>
          <td><img src="https://img.shields.io/pypi/v/lammps-cython.svg" alt="latest release"/></td>
        </tr>
        <tr>
          <td></td>
          <td><img src="https://anaconda.org/costrouc/lammps-cython/badges/version.svg" alt="latest release" /></td>
        </tr>
        <tr>
          <td>Package Status</td>
          <td><img src="https://img.shields.io/pypi/status/lammps-cython.svg" alt="status" /></td>
        </tr>
        <tr>
          <td>License</td>
          <td><img src="https://img.shields.io/pypi/l/lammps-cython.svg" alt="license" /></td>
        </tr>
        <tr>
          <td>Build Status</td>
          <td> <a href="https://gitlab.com/costrouc/lammps-cython/pipelines"> <img
        src="https://gitlab.com/costrouc/lammps-cython/badges/master/pipeline.svg"
        alt="gitlab pipeline status" /> </a> </td>
        </tr>
        <tr>
          <td>Binder Notebooks</td>
          <td><a href="http://mybinder.org/v2/gh/costrouc/lammps-cython-notebooks/master?filepath=notebooks/basic.ipynb"><img src="https://mybinder.org/badge.svg" alt="binder notebooks"/></a></td>
        </tr>
        </table>
        
        
        # Documentation
        
        Full documentation can be found at
        [lammps-cython](https://costrouc.gitlab.io/lammps-cython/).
        
        # Features
        
         - Full MPI support
         - Pythonic API inspired by
         [HOOMD](https://codeblue.umich.edu/hoomd-blue/)
         - Supports Python 2 and 3
         - Heavily documented and tested
         - Elimination of unnecessary file I/O for thermostats and atoms properties
        
        A neat feature of the wrapper is that lammps can be run regularly
        using the following script (use "-i" instead of stdin). This is the
        command `pylammps` when the package is installed.
        
        ```python
        from lammps import Lammps
        import sys
        Lammps(args=sys.args)
        ```
        
        # Installation
        
        `lammps-cython` has several options for installation. The easiest way
        is using the provided docker containter image
        [costrouc/lammps-cython](https://hub.docker.com/r/costrouc/lammps-cython/)
        or `conda install`.There is no plan to support pip wheels. Other
        methods require manual installation of lammps. Detailed installation
        are provieded in the
        [documentation](https://costrouc.gitlab.io/lammps-cython/installation.html). If
        you have any issues with installation be submit an issue at the
        [gitlab repository](https://gitlab.com/costrouc/lammps-cython/).
        
         - conda: `conda install -c costrouc -c conda-forge lammps-cython`
         - docker: `docker pull costrouc/lammps-cython:latest`
        
        Otherwise the general path to installation is install [LAMMPS as a
        shared
        library](http://lammps.sandia.gov/doc/Section_start.html#start-4) then
        edit `~/.config/lammps-site.cfg` to include the paths of necissary
        libraries. See example below.
        
        ``` ini
        [lammps]
        lammps_include_dir = /usr/local/include/lammps/
        lammps_library_dir = /usr/local/lib/
        # true library filename is liblammps.so notice lib and .so are removed
        lammps_library = lammps
        
        # use mpic++ -showme to list libraries and includes
        [mpi]
        mpi_include_dir = /usr/lib/x86_64-linux-gnu/openmpi/include
        mpi_library_dir = /usr/lib/x86_64-linux-gnu/openmpi/lib
        # no necissarily needed (default are mpi, mpi_cxx)
        mpi_library     = mpi
        ```
        
        Then `pip install lammps-cython` should just work.
        
        ## Conda Image
        
        The conda image is built only for linux and python versions (3.5,
        3.6). There is no plan to support Windows due to `MPI` being a
        dependency. However, if OSX is needed please raise an issue. 
        
        `conda install -c costrouc -c conda-forge lammps-cython`
        
        ## Docker Image
        
        The docker image
        [costrouc/lammps-cython](https://hub.docker.com/r/costrouc/lammps-cython/)
        uses `python3.5` and has the library preinstalled with the executables
        `pylammps` and `lammps` available.
        
        
        # Tutorials
        
        Work is being done to show how to use the features of `lammps-cython`
        for now just visit the [tutorial page](https://costrouc.gitlab.io/lammps-cython/tutorial.html).
        
        These will turn to links when the tutorial exists.
        
          - basic usage
          - modify atom positions
          - get forces and velocity for each atom and compute potential energy
        
        # Contributing
        
        All contributions, bug reports, bug fixes, documentation improvements,
        enhancements and ideas are welcome! These should be submitted at the
        [Gitlab repository](https://gitlab.com/costrouc/lammps-cython). Github is
        only used for visibility.
        
        Contributors:
        
          - [Chris Ostrouchov](https://gitlab.com/costrouc) (maintainer)
        
        # License
        
        MIT
        
Keywords: lammps,molecular dynamics,cython,wrapper,mpi
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
