[WIP] MPMorph Flows

[BryantLi-BLI]

Summary

This PR seeks to port the original MPMorph workflows from atomate to atomate2. These workflows are used to generate equilibrated amorphous/crystalline/glassy structures with MD runs via AIMD.

Tagging in @Tinaatucsd, @mcgalcode, @mattmcdermott, @esoteric-ephemera, @vir-k01, @sivonxay because they have used it recently or are apart of the original development team.

Completed

• Volume equilibration workflow meant to equilibrate structure without NPT via a series of NVT runs (Equilibration + production volume)
• Code independent equilibration and production workflow, with optional quench methods
• VASP workflows used in MP papers below recreated in this PR:
  • Hui Zheng et al.
  • Aykol and Persson 2018
  • Murat et al.
• There is an additional feature with this PR to incorporate MLFF MD runs with the same flow.
• Multi quench options available:
  • Fast quench (double relax and static)
  • Slow quench (series of MD runs to simulate cooling with different temperature profiles)
• Started to add tests for VASP
• MLFF tests are completed

TODO

• Packmol conversion to pymatgen interface (used to generated initial amorphous structure)
• Finish tests
• Finish slow quench temperature profiles

MISC

• Seeking feedback for code, missing features, usability

[codecov]

Codecov Report

Attention: Patch coverage is 41.02941% with 401 lines in your changes missing coverage. Please review.

Project coverage is 72.85%. Comparing base (29a5731) to head (5fd1b4e).
Report is 36 commits behind head on main.

❗ Current head 5fd1b4e differs from pull request most recent head 3032dd8

Please upload reports for the commit 3032dd8 to get more accurate results.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #818      +/-   ##
==========================================
- Coverage   74.94%   72.85%   -2.10%     
==========================================
  Files         136      142       +6     
  Lines       10513    11183     +670     
  Branches     1643     1802     +159     
==========================================
+ Hits         7879     8147     +268     
- Misses       2143     2511     +368     
- Partials      491      525      +34     

Files	Coverage Δ
src/atomate2/vasp/flows/md.py	89.36% <100.00%> (ø)
src/atomate2/vasp/sets/base.py	72.72% <0.00%> (-0.36%)	⬇️
src/atomate2/forcefields/md.py	84.48% <71.42%> (-0.33%)	⬇️
src/atomate2/common/jobs/eos.py	85.07% <83.33%> (-0.64%)	⬇️
src/atomate2/forcefields/jobs.py	90.79% <75.00%> (-2.78%)	⬇️
src/atomate2/vasp/sets/mpmorph.py	0.00% <0.00%> (ø)
src/atomate2/common/flows/mpmorph.py	79.25% <79.25%> (ø)
src/atomate2/vasp/jobs/mpmorph.py	0.00% <0.00%> (ø)
src/atomate2/forcefields/flows/mpmorph.py	74.83% <74.83%> (ø)
src/atomate2/vasp/flows/mpmorph.py	0.00% <0.00%> (ø)
... and 1 more

... and 4 files with indirect coverage changes