Objective

The aim of this project is to develop a python module for processing molecular dynamics data. We currently use

CP2K: https://www.cp2k.org/

DL_POLY: https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx

LAMMPS: http:https://lammps.sandia.gov/

to probe the mineral/water and mineral/organics interfaces.

This project is divided into following parts:

1. io
2. structure
3. dynamics
4. energy and forces

The development language is Python. We will follow PEP8 guide.

All comments and documentation should be written in English.

I started this project in 2016 for my undergraduate thesis.

I open-sourced it in 2017 and in an organized form.

Just add the geolab directory to your PYTHONPATH like:

export PYTHONPATH=/path/to/geolab:$PYTHONPATH

Once installed, you have to run these commands to use the project:

import geolab

or

from geolab import io

Enjoy!

We’re really happy to accept contributions from the community, that’s the main reason why we open-sourced it! There are many ways to contribute, even if you’re not a technical person.

We’re using the Github workflow to accept modifications (even internally), basically you’ll have to:

• fork the repository

• create a branch (optionally with the reference to the issue in the name)

• hack hack hack

• commit incrementally with readable and detailed commit messages

  • API: an (incompatible) API change
  • BLD: change related to building geolab
  • BUG: bug fix
  • DEP: deprecate something, or remove a deprecated object
  • DEV: development tool or utility
  • DOC: documentation
  • ENH: enhancement
  • MAINT: maintenance commit (refactoring, typos, etc.)
  • REV: revert an earlier commit
  • STY: style fix
  • TST: addition or modification of tests
  • REL: related to releasing geolab

  • make it compatible with all supported Pythons (see Installation).
  • write more comments
  • fix docstrings -------- using Numpy docstring style
  • write a test
  • add some documentation

• submit a pull-request against the master branch of this repository

We’ll take care of tagging your issue with the appropriated labels and answer within a week (hopefully less!) to the problem you encounter.

If you’re not familiar with open-source workflows or our set of technologies, do not hesitate to ask for help! We can mentor you or propose good first bugs (as labeled in our issues). Also welcome to add your name to Credits section of this document.

You can report issues directly on Github, that would be a really useful contribution given that we lack some user testing on the project. Please document as much as possible the steps to reproduce your problem (even better with screenshots).

We’re trying to develop this project in the open as much as possible. We have a dedicated mailing-list where we discuss each new strategic change and invite the community to give a valuable feedback. You’re encouraged to subscribe to it and participate.

We’re doing our best to document each usage of the project but you can improve it or add you own sections. The documentation is available within the /doc/ folder. You don’t have to build anything, we’ll take care of it once your changes are merged.

We’re using the GPL-3.0 license.

The GNU General Public License is a free, copyleft license for software and other kinds of works.

The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.

• Author: Yingchun Zhang

• E-mail: [email protected]

• Collaborator 1: Mengzi Zhou

• E-mail: [email protected]