Fix reading of lammpsdump ATOM card.

[hmacdope]

Fixes #3358
Supersedes #2333
Changes made in this Pull Request:

• Allow coordinates in different conventions to be read by LAMMPSDumpReader
• Unhardcode LAMMPSDumpReader to expect a set number of columns
• S->R transform with distances.transform_StoR is no longer applied by default, only if the coordinates are in the scaled (xs,ys,zs) or scaled_unwrapped (xsu, ysu, zsu) convention
• On the way to allowing reading of other ts data from the LAMMPS dump file.

PR Checklist

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

[pep8speaks]

Hello @hmacdope! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/coordinates/LAMMPS.py:

Line 459:80: E501 line too long (109 > 79 characters)
Line 591:80: E501 line too long (89 > 79 characters)
Line 601:80: E501 line too long (81 > 79 characters)
Line 604:14: E713 test for membership should be 'not in'
Line 605:80: E501 line too long (122 > 79 characters)

• In the file testsuite/MDAnalysisTests/datafiles.py:

Line 140:80: E501 line too long (100 > 79 characters)
Line 141:80: E501 line too long (125 > 79 characters)
Line 490:80: E501 line too long (83 > 79 characters)
Line 491:80: E501 line too long (95 > 79 characters)
Line 492:80: E501 line too long (93 > 79 characters)

• In the file testsuite/MDAnalysisTests/topology/test_lammpsdata.py:

Line 275:1: E302 expected 2 blank lines, found 1

Comment last updated at 2021-08-21 05:17:47 UTC

[codecov]

Codecov Report

Merging #3360 (11d8518) into develop (bd0ed5d) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop    #3360   +/-   ##
========================================
  Coverage    93.70%   93.70%           
========================================
  Files          177      177           
  Lines        22990    23017   +27     
  Branches      3247     3257   +10     
========================================
+ Hits         21542    21569   +27     
  Misses        1397     1397           
  Partials        51       51           

Impacted Files	Coverage Δ
package/MDAnalysis/coordinates/LAMMPS.py	93.23% <100.00%> (+0.66%)	⬆️
package/MDAnalysis/topology/LAMMPSParser.py	96.23% <100.00%> (+0.03%)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update bd0ed5d...11d8518. Read the comment docs.

[richardjgowers]

What happens when multiple coordinate columns are present?

[IAlibay]

Couple of quick comments, probably needs more tests?

[hmacdope]

I think I have addressed everyone's comments :)

[hmacdope]

Do people have any further comments? :)

[IAlibay]

I think we're nearly there, but I'm a little bit hesitant since I'm not sure how modular the standard is, can coordinates be in the wrong order? Or does it not matter - does the way we loop through coord_cols on setting positions enforce ordering?

@MDAnalysis/coredevs if you have a chance to look here, maybe we can sneak this into 2.0.

[IAlibay]

lgtm

[IAlibay]

@richardjgowers do you want to review / approve since you still have a blocking review?