Lammps Support

[jaclark5]

This is a Draft I am actively using this and expect it's ready to go, but still needs tests.

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[bot]]

Codecov Report

Attention: Patch coverage is 1.37300% with 431 lines in your changes missing coverage. Please review.

Project coverage is 80.54%. Comparing base (f40b89b) to head (368f314).

Files	Patch %	Lines
src/alchemlyb/parsing/lammps.py	0.00%	305 Missing and 2 partials :warning:
src/alchemlyb/postprocessors/dF_state.py	0.00%	48 Missing :warning:
src/alchemlyb/convergence/convergence.py	4.34%	43 Missing and 1 partial :warning:
src/alchemlyb/visualisation/convergence.py	3.22%	30 Missing :warning:
src/alchemlyb/estimators/bar_.py	33.33%	1 Missing and 1 partial :warning:

:exclamation: There is a different number of reports uploaded between BASE (f40b89b) and HEAD (368f314). Click for more details.

HEAD has 8 uploads less than BASE

| Flag | BASE (f40b89b) | HEAD (368f314) | |------|------|------| ||16|8|

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #348 +/- ## =========================================== - Coverage 98.83% 80.54% -18.29% =========================================== Files 28 30 +2 Lines 1895 2329 +434 Branches 407 546 +139 =========================================== + Hits 1873 1876 +3 - Misses 2 429 +427 - Partials 20 24 +4 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.