Lammps Support

[jaclark5]

Resolves: Issue #349

This module will allow for alchemlyb to be used with LAMMPS outputs. An independent package for easily generating the LAMMPS input files will shortly follow, although the functions have been designed to be flexible.

In addition to the extract_dHdl and extract_u_nk functions, additional functions, extract_dHdl_from_u_n and extract_u_nk_from_u_n have been added to allow these data frames to be generated from potential energy information that is separable from the target variable (e.g., epsilon in the LJ).

[xiki-tempula]

This is really good!
For going forward, might be good to add some dataset to the https://github.com/alchemistry/alchemtest and we can use those file for testing.

[xiki-tempula]

Also would be good to add the docs with regard to this as well.

[jaclark5]

@xiki-tempula

• I did update the rst files where appropriate in the docs, did you have something more in mind?
• I am also working on an addition to alchemtests, but since this PR is actively used in my research I'm also doing some stress testing on the side before I'll open this up for review. I think I'm just about happy with it.
• There are some changes to the convergence modules that I added to this branch for convenience with my workflow, but I'll be moving those changes to another branch for a separate PR.

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 392 lines in your changes missing coverage. Please review.

Project coverage is 82.66%. Comparing base (968d4f2) to head (0fb967b).

Files with missing lines	Patch %	Lines
src/alchemlyb/parsing/lammps.py	0.00%	392 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #348       +/-   ##
===========================================
- Coverage   98.80%   82.66%   -16.14%     
===========================================
  Files          28       29        +1     
  Lines        2008     2400      +392     
  Branches      356      465      +109     
===========================================
  Hits         1984     1984               
- Misses          2      394      +392     
  Partials       22       22               

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[xiki-tempula]

There is really a lot of stuff in this PR and makes it kind of hard to review. I have given some suggestion and will do another review when the tests are there.

[orbeckst]

There are plenty of conflicts that need to be resolved. I'd say, ideally rebase this branch against the current main branch.

I also opened alchemistry/alchemtest#95 to add data files to alchemlyb. I would actually prioritize tests over pretty much anything else as (1) the tests show how your code will be used (and that's important for review) and (2) without tests we cannot merge code.

[jaclark5]

I also opened alchemistry/alchemtest#95 to add data files to alchemlyb.

Thanks!

I would actually prioritize tests over pretty much anything else as (1) the tests show how your code will be used (and that's important for review) and (2) without tests we cannot merge code.

Yes, I've been putting together an example to add to alchemtest, but in the process I found a couple issues with the way I ran TI and BAR. At this point I'm 100% confident in the results and since alchemtest has a license associated with each simulation example I'm submitting my simulation data to our internal review process to associate the NIST license.