simphony-lammps

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

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.

EDM deployment

Enthought Deployment Manager packages can be created with:

python edmsetup.py egg

See documentation in simphony/buildrecipes-common for more information