GSoC Project 4

[Muhammad Ahsan]

Hello Dear,

I am writing to express my interest in the project "Transport Property Calculations" as part of the GSoC 2023. I believe this project is an exciting opportunity to contribute to the development of MDAnalysis and to advance the field of molecular simulations.

As a engineering student with a strong background in mathematics and physics, I have experience in working with transport properties such as diffusivity and conductivity. I am also proficient in Python, which is a key skill required for this project. I am eager to apply my knowledge and skills to this project and to work with experienced mentors to achieve the objectives of the project.

My proposal for the project is to implement self-diffusivity coefficient calculations and conductivity calculations using both the Nernst-Einstein and Green-Kubo methods. I believe that these implementations will greatly benefit the MDAnalysis community, as it will allow users to easily calculate these important transport properties and to gain insights into the behavior of molecular systems.

In addition to the main objectives, I am committed to writing clear documentation and tests to ensure the quality of the code. I am also open to implementing additional features or improvements that may arise during the development process.

Thank you for considering my proposal. I am excited about the opportunity to work on this project and to contribute to the open-source community.

Sincerely,
Muhammad Ahsan

[Project Manager MDAnalysis]

Hi Muhammad,

Welcome to MDAnalysis, and thank you for expressing your interest in the project! Since you are interested in Project 4, we recommend working with the existing diffusion code and learning about writing analysis tools (using AnalysisBase).

The best way to get started is to get your hands dirty following the MDAnalysis User Guide. We suggest starting with installing the MDAnalysis package and going through the Quick Start Guide. Other sections of the User Guide go into many 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. There are detailed explanations on how to set up a developer environment and how to contribute to the MDAnalysis codebase. This is a great starting point for contributing to MDAnalysis and trying to solve some of the open issues.

Our blog post is the starting point for all GSoC 2023 things, and we have a FAQ. As per the FAQ, candidates must have code merged to be eligible to apply to GSoC with MDAnalysis. On the MDAnalysis repository, you can find several issues tagged with "good first issue", "Difficulty easy", or "GSoC Starter". Please bear in mind, you can only attempt one issue tagged as a GSoC Starter. Note also that we do not assign issues to people; we review the first pull request (PR) that solves an issue. Therefore, you can work on any issue you would like that does not already have an open/active PR against it. We also strongly suggest working on a single issue/PR at a time. Once you have one PR merged, you are of course welcome to tackle another issue, and so on. 

Could you please provide your GitHub handle? This is helpful for GSoC mentors to track which applicants are working on which issues. Once you have had your first PR merged, the next step would be to draft your proposal. See here for our guidance on "How to write a great application." To seek feedback from the MDAnalysis mentors, register as a contributor and submit your project idea. Please upload a PDF (`DRAFT` in the file name) of your proposal - which includes a Google doc link to your proposal - to the GSoC program website. Mentors can then provide feedback directly on your Google doc. When you are ready to submit the final version of your proposal, you can export your Google doc proposal as a PDF and re-upload to the GSoC site.

We look forward to your contribution.

All the best,
Jenna

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GSoC 2023: Read https://www.mdanalysis.org/2023/02/22/gsoc2023/
Our FAQ: https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-FAQ
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[Muhammad Ahsan]

Hi,

Thanks for the quick response. All details mentioned are awesome and I'll definitely start setting up the development environment, and get my hands dirty. But I've one concern the time is really short so can I get your suggestions.

My GitHub: Muhammad-Ahsan-Rasheed  

Regards,

[Project Manager MDAnalysis]

Hi Muhammad,

Have you started to work on any issues in the MDAnalysis repository? If so, please let us know which one. One of our requirements for being eligible to apply for GSoC with MDAnalysis is that applicants must have code merged. I would strongly recommend focusing your initial efforts on submitting a PR. While your PR is being reviewed, you can then submit your drafted proposal for feedback from the mentors.

Thanks,

Jenna

[Project Manager MDAnalysis]

Hi Muhammad,

I believe you have replied to me personally rather than using "Reply All" to post to this mailing list. Do I have your permission to please copy-paste your reply here to ensure we have this thread in one place?

As a general note, please follow these instructions for submitting your draft proposal through the GSoC portal.  To protect your privacy (i.e., details and original academic work) as much as possible, we would like to avoid having applicants posting links to their proposals publicly via the mailing list.

Thank you,
Jenna

[Project Manager MDAnalysis]

Reply from Muhammad, which was sent to me privately (I am copy-pasting here after receiving permission to post this publicly):

Dear Mentors,

I hope this email finds you well. I am writing to inform you that I started working on Issue 2764, as per our discussions, but unfortunately, another member merged their pull request right before me, and I was not able to open a pull request.

Nonetheless, I have my development environment set up and have been exploring other issues and functionalities of MDAnalysis. As the deadline for submitting the GSoC proposal is approaching, I wanted to inquire if it would be appropriate for me to submit my proposal, even though I was unable to complete Issue 2764.

I have prepared my proposal and have attached the link to it in this email. I believe it outlines a feasible plan for contributing to the MDAnalysis project, and I am eager to work on any issue or feature you deem fit for the project.

Furthermore, I would like to mention that I am willing to write test cases for Issue 2764, given more time. However, as the deadline is fast approaching, I may not be able to complete them within the specified timeframe. Nevertheless, I would be happy to continue working on this issue and contributing to the project even after the GSoC program ends.

Thank you for your time and consideration. I look forward to hearing back from you soon.

Best regards,
Muhammad Ahsan

[Project Manager MDAnalysis]

Hi Muhammad,

As Issue 2764 is still open and not mentioned by any currently open PRs, please feel free to commit the work you have completed on the issue as a PR. Per my previous message, please also make sure to follow these instructions for submitting your drafted proposal through the GSoC portal. Just remember to resubmit the PDF of your final proposal before the deadline, Tuesday, April 4th at 18:00 UTC. 

We look forward to reviewing your proposal.

Best,
Jenna

[Project Manager MDAnalysis]

Hi Muhammad,

In order to protect your privacy and your work, we have developed these instructions for submitting your draft proposal through the GSoC portal (as opposed to sharing the Google doc link publicly). Specifically, please upload a PDF (`DRAFT` in the file name) of your proposal - which includes a Google doc link to your proposal - to the GSoC program website. Make sure you have enabled access to others; otherwise there might be a delay if mentors have to first request access to your document. When you are ready to submit the final version of your proposal, you can export your Google doc proposal as a PDF and re-upload to the GSoC site. We are doing our best to provide feedback on proposals we receive before the deadline, but due to the number of applications, we may not be able to comment on all proposals. 

Thanks,
Jenna

On Mon, Apr 3, 2023 at 4:28 PM Muhammad Ahsan <rasheed...@gmail.com> wrote:

Hi,

Thanks for letting me know. I opened the PR and am currently going through all the steps and procedures. My draft is ready and I need assistance in reviewing it. 
Draft link: https://docs.google.com/document/d/1Nb9Y4ijDS7kmBU2lys-BC5TWup4sMPk_wu2d0jxOXss/edit?usp=sharing

Regards,

Muhammad Ahsan