simphony-lammps

The LAMMPS engine-wrapper for the SimPhoNy framework (www.simphony-project.eu).

.. image:: https://travis-ci.org/simphony/simphony-lammps.svg?branch=master :target: https://travis-ci.org/simphony/simphony-lammps :alt: Build status

.. image:: http://codecov.io/github/simphony/simphony-lammps/coverage.svg?branch=master :target: http://codecov.io/github/simphony/simphony-lammps?branch=master :alt: Test coverage

.. image:: https://readthedocs.org/projects/simphony-lammps/badge/?version=master :target: https://readthedocs.org/projects/simphony-lammps/?badge=master :alt: Documentation Status

.. image:: https://img.shields.io/docker/automated/jrottenberg/ffmpeg.svg :target: https://hub.docker.com/r/simphony/simphony-lammps/ :alt: Docker Image

Repository

simphony-lammps is hosted on github: https://github.com/simphony/simphony-lammps

Requirements

simphony-common_ >= 0.2.0

Optional requirements


To support the documentation built you need the following packages:

- sphinx >= 1.2.3
- sphinxcontrib-napoleon >= 0.2.10

Installation
------------

The package requires python 2.7.x. Installation is based on setuptools::

    # build and install
    python setup.py install

or::

    # build for in-place development
    python setup.py develop

LAMMPS installation

This engine-wrapper uses LAMMPS Molecular Dynamics Simulator. A recent stable version (11 Aug 2017) of LAMMPS is supported and has been tested. See install_lammps.sh for an example installation instructions. For general LAMMPS install information, see http://lammps.sandia.gov/index.html

LAMMPS installation varies depending on which interface is being used. See the manual for more details. SimPhoNy-lammps in file-mode will look for LAMMPS binary named lammps. You can change this by setting the SIM_LAMMPS_BIN environment variable.

Usage

After installation, the user should be able to import the lammps engine plugin module by::

from simphony.engine import lammps engine = lammps.LammpsWrapper()

Testing

To run the full test-suite run::

python -m unittest discover

Documentation

To build the documentation in the doc/build directory run::

python setup.py build_sphinx

.. note::

- One can use the --help option with a setup.py command
  to see all available options.
- The documentation will be saved in the ``./build`` directory.

Directory structure

simlammps -- hold the lammps wrapper implementation
- bench - benchmarking
- common - contains general global files
- config - holds configuration related files
- internal - internal library communication with LAMMPS
- io -- file-io related communication with LAMMPS
- testing -- testing related utilities
examples -- holds different examples
doc -- Documentation related files
- source -- Sphinx rst source files
- build -- Documentation build directory, if documentation has been generated using the make script in the doc directory.

.. _simphony-common: https://github.com/simphony/simphony-common

EDM deployment

Enthought Deployment Manager packages can be created with::

python edmsetup.py egg

See documentation in simphony/buildrecipes-common for more information

simphony / simphony-lammps

readme