Add ddcMD file format supports

[XiaohuaZhangLLNL]

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Fixes #

Changes made in this Pull Request:

• add file format supports for ddcMD MD engine

PR Checklist

• [ ] Tests?
• [ ] Docs?
• [ ] CHANGELOG updated?
• [ ] Issue raised/referenced?

Developers certificate of origin

• [x] I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

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:books: Documentation preview :books:: https://mdanalysis--4252.org.readthedocs.build/en/4252/

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[codecov[bot]]

Codecov Report

Patch coverage: 13.81% and project coverage change: -1.33% :warning:

Comparison is base (9032eb0) 93.40% compared to head (8c1484e) 92.08%.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4252      +/-   ##
===========================================
- Coverage    93.40%   92.08%   -1.33%     
===========================================
  Files          169      186      +17     
  Lines        22204    23710    +1506     
  Branches      4064     4153      +89     
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+ Hits         20740    21833    +1093     
- Misses         948     1351     +403     
- Partials       516      526      +10     

Files Changed	Coverage Δ
package/MDAnalysis/coordinates/DDCMD.py	11.11% <11.11%> (ø)
package/MDAnalysis/coordinates/DDC.py	11.81% <11.81%> (ø)
package/MDAnalysis/coordinates/DDCMDTAR.py	15.47% <15.47%> (ø)
package/MDAnalysis/coordinates/__init__.py	100.00% <100.00%> (ø)

... and 14 files with indirect coverage changes

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[hmacdope]

@XiaohuaZhangLLNL I am excited for new formats to be added! Do you have a specification for the formats you could share on an issue so we can possibly discuss what is needed there? Just so we can fully understand the format (especially if it's binary).

[XiaohuaZhangLLNL]

@XiaohuaZhangLLNL I am excited for new formats to be added! Do you have a specification for the formats you could share on an issue so we can possibly discuss what is needed there? Just so we can fully understand the format (especially if it's binary).

We hope MDAnalysis could support file formats of our ddcMD MD engine (https://github.com/LLNL/ddcMD). ddcMD has both text and binary file formats.

The text file format can be find in: https://github.com/LLNL/ddcMD/blob/master/examples/waterbox/snapshot.mem/atoms%23000000

The binary file is similar to text file format but just in binary format. I can provide an example if it is needed.

[IAlibay]

@XiaohuaZhangLLNL is there any chance that the ddcMD folks might be willing to write a documented specification for this file format? Something like: https://ambermd.org/netcdf/nctraj.xhtml

This not only would be a great piece of documentation to your users & the wider community, but it would also make sure that we have a place to look to as the ground truth should you ever decide to change the file format specification.

[XiaohuaZhangLLNL]

@XiaohuaZhangLLNL is there any chance that the ddcMD folks might be willing to write a documented specification for this file format? Something like: https://ambermd.org/netcdf/nctraj.xhtml

This not only would be a great piece of documentation to your users & the wider community, but it would also make sure that we have a place to look to as the ground truth should you ever decide to change the file format specification.

I will try to provide a documentation on the code and file format as soon as possible.

[IAlibay]

I will try to provide a documentation on the code and file format as soon as possible.

That would be amazing, thank you so much! We would be happy help review the documentation / offer insights if needed.

[tylerjereddy]

Ah, this sounds like the thing that was developed during the DOE pilot 2 project with Helgi et al. IIRC they were vendoring their own in-house modified version of MDAnalysis at the time.

[orbeckst]

@tylerjereddy would you be able to act as the PR shepherd here? I am going to assign you but if this doesn't work for you, please unassign yourself and ping me so that I know. Thanks!

[tylerjereddy]

sounds good

[orbeckst]

@XiaohuaZhangLLNL are you able to continue on this PR? If so, it would be helpful if you could respond to @tylerjereddy 's initial review. Thank you!