Contribution to the project Transport property calculations

[Rohan Kumar Singh]

Hello, I am Rohan Kumar Singh. My interests lies in python, statistics and machine learning. Currently, I am involved with IIIT Kalyani in a project of transformer to translate Hinglish sentences(of roman script) into English which is supposed to be over by 5th of March. I am intermediate in python. Can you please guide me in what steps should I follow so that I am able to contribute to the project #4 Transport property calculations.

[Rocco Meli]

Hi Rohan,

welcome to MDAnalysis!

MDAnalysis is a Python package for the analysis of computer simulations of systems at the atomic scale. The best way to get started is to get your hands dirty following the MDAnalysis User Guide:

https://userguide.mdanalysis.org/stable/index.html

I would suggest starting with installing the MDAnalysis package (see https://userguide.mdanalysis.org/stable/installation.html) and going through the Quick Start Guide (https://userguide.mdanalysis.org/stable/examples/quickstart.html). Other sections of the User Guide go in much more details about the different capabilities of MDAnalysis.

Once you are a bit familiar with the MDAnalysis package, you can look at the sections of the User Guide explaining how to contribute:

https://userguide.mdanalysis.org/stable/contributing.html

There are detailed explanations on how to setup a developer environment (https://userguide.mdanalysis.org/stable/contributing_code.html) and how to contribute to the MDAnalysis codebase. This is a great starting point to start contributing to MDAnalysis and trying to solve some of the open issues (https://www.mdanalysis.org/2023/02/22/gsoc2023/).

The mentors of Project #4 (Hugo and Orion) will be able to give you more details on that specific project, but the above should get your started in the right direction.

All the best,

Rocco

[Rohan Kumar Singh]

I have successfully built MDAnalysis from source on my local machine and it's working fine. Can someone please suggest some beginner-friendly issues I can work upon. I am interested in project #4  Transport property calculations.

Regards,

[Rocco Meli]

Hi Rohan,

I'm glad to hear you have MDAnalysis working locally!

As explained on the blog post (https://www.mdanalysis.org/blog/#close-an-issue-of-mdanalysis), on the MDAnalysis repository you can find several issues tagged with "good first issue" or "difficulty easy". See for example the following:

https://github.com/MDAnalysis/mdanalysis/issues?q=is%3Aissue+is%3Aopen+label%3ADifficulty-easy

https://github.com/MDAnalysis/mdanalysis/issues?q=is%3Aissue+is%3Aopen+label%3Agood-first-issue

You can also find issues tagged as "GSoC Starter". Please bear in mind you can only attempt one issue tagged as such. 

Note also that we do not assign issues to people; we do review the first PR that solves an issue. Therefore, you can work or any issue you want that does not have an open/active PR against it. We also strongly suggest to work on a single issue/PR at a time. Once you have one PR merged, you are of course very welcome to tackle another issue, and so on.

With regard to project 4, we would recommend playing with the existing diffusion code, and learning about writing analysis tools (using AnalysisBase). As usual, you can use the User Guide as a good starting point:

https://userguide.mdanalysis.org/stable/examples/analysis/custom_trajectory_analysis.html

Best wishes,

Rocco