Allow LammpsDumpParser Topology reader more flexibility in coordinate column data.

[hmacdope]

Is your feature request related to a problem?

The LAMMPS DumpParser topology creator is somewhat inflexible in the column format it expects.
Now that we support other coordinate conventions #3360 and velocities #3448 (WIP), we should relax the requirement for an

id, type, x, y, z 

format and make it somewhat more flexible.

Describe the solution you'd like

Allow the parser more flexibility in available column data.

Describe alternatives you've considered

Additional context

[orbeckst]

@hmacdope I un-assigned you from this issue, otherwise GSoC Contributors will wonder if they can pick the issue to work on.

[hmacdope]

Okay all good 👍

[Riyabelle25]

Hello, I'm RIya Elizabeth John, an Outreachy applicant. Could you provide some more context about the LAMMPS DumpParser topology creator (perhaps it's location in the codebase), and the feature request?

[hmacdope]

The LAMMPs parser is in this file. Currently it expects dump files produced by LAMMPs to have a very specific format, when the file format is actually very flexible and can have many different columns in different orders. The job would be to add a flexible parser to fix this issue.

[Riyabelle25]

Apologies for the late response, I had been travelling on our class trip.
Adding a parser would mean adding a separate class for the same in a separate file right?
Or should I look into adding a specific method to handle this usecase?

[hmacdope]

@Riyabelle25 sorry should have been clearer, you just need to change the logic in the existing class :)

[sayantan-bhattacharyya]

I want to contribute.

[Davichet-e]

Hey! I'm interested in contributing to this issue, I would have one question, when talking about: "we should relax the requirement for an id, type, x, y, z format and make it somewhat more flexible." You mean deleting totally/some fields of these lines?:

mdanalysis/package/MDAnalysis/topology/LAMMPSParser.py

Line 249 in 02a6443

reqd_attrs = ['id', 'type', 'x', 'y', 'z']

mdanalysis/package/MDAnalysis/topology/LAMMPSParser.py

Line 250 in 02a6443

missing_attrs = [attr for attr in reqd_attrs if attr not in style_dict]

or what exactly is meant by: "more flexible". Thank you so much in advance!

[aliehlen]

Hi! I am an MDAnalysis user and have just started using lammps. I would absolutely use this functionality, especially if it were general (for example, I have been needing to hack around to read forces using MDAnalysis). I don't think I could contribute to changing the parser, but let me know if I can help out in any other way (providing example dump files with different properties, testing things out).

[orbeckst]

@aliehlen any kind of help is appreciated. If you are a user of LAMMPS then please say how MDAnalysis could work better for you. Issues should focus on one specific thing. You can open new issues or starting a discussion on the developer mailing list. Examples of input files (maybe a snippet in a comment for discussion) and links to format specifications that you know to be relevant are useful. For example, I know very little about LAMMPS (so I also can't say much about #3449 (comment) ) but I can judge an approach if someone clearly explains

1. what the current situation is (what doesn't work — example)
2. what they want to achieve (eg an example of what it should look like)
3. how they want to solve the problem

The last point is not necessary to get a discussion started. Initially, it's more important to understand what the problem is and what a solution should provide.