Merging/overlap of electronic structure + job handling classes

[phockett]

Currently in progress, sort-of working for some dev/test cases, but still painful (as of 10/06/21, https://github.com/phockett/epsman/commit/04469f56c052794ca2f9a932e0013074d02b05a6).

Outstanding items to fix:

• [ ] Very ugly... need to finish merging EShandler and ESjob class, currently have to keep passing former to latter methods, even though it's already set to self.esData (may want to rename!).
• [x] Symmetry code still needs manual fixing for generating full sym list with ePS syms (and also for general use).
• [ ] Still have some bug with writeGen() code, which throws file IO errors on first run... missing paths until self.createJobDirTree() is run?
• [ ] Manually setting up job each time, still, did this not already get fixed? It's a pain. symTest() method is working, so should just wrap single job in the same manner?

Improvements to implement:

• [ ] Wrapping for multiple ionization channels and/or electronic structure files cases. Currently sets one file and one channel per class object. May want to wrap in another class, or set items to dictionaries to allow multiple cases in the current class.
• [ ] More tests & debug for job creation ordering
  • as of 14/02/22 working for ESjob with files, e.g. job = ESjob(fileName = 'xe_SPKrATZP_rel.log', fileBase = testFilePath), OR job tree, but not mixed case (e.g. job = ESjob(mol = 'Xe', fileName = 'xe_SPKrATZP_rel.log', fileBase = testFilePath) fails)? Due to setJob and/or setPaths routines, but ends up a bit circular, cf. default paths and debugging.
  • After file import, job.buildePSjob(channel = 18) is OK, and sets paths.
• [ ] Master dictionary to collect all job settings. Currently set partly as class attributes (main epsJob settings) and/or sub-classes and/or dictionaries/lists. For easy back-compatibility should just push to dicts at creation, then point attribs to these, although this may get messy. Alternatively stick with attribs and just parse relevant properties to dict with a separate function?

Bugs:

• [x] Orbital indexing currently inconsistent, with 0-indexing for labels. FIXED in 27f16bf7656bcfa9b8bef3b0c2069544c59ecfcd

[phockett]

Testing for OCS multi-orb jobs... almost working nicely, but still a lot of manual set-up/workarounds required. See http://jake/jupyter/user/paul/lab/tree/ePS/OCS/epsman2021/OCS_ePS_ePSman_multijob-dev_100621.ipynb

[phockett]

Symmetry handling

• 8f9f38c9f2ec99cdfb99e8fb33e184f92872e0e4 sym handling updated in setOrbInfoPD().
• 8f9f38c9f2ec99cdfb99e8fb33e184f92872e0e4 adds symmetry parsing and remapping (Gamess to ePS labels only).
• 56383f264abcfd3a8d0e6554fb745612ff3c7e50 adds Point Group handling (Gamess input files only).

[phockett]

2023 reboot

Revisiting geometry scan case for OCS, and running on remote cluster - more paths issues!

Now working for remote job writing after 57eb513d5c6522425af520ae35abae1ea5da1d63

May still want to address some other issues, see dev notebook for details.

[phockett]

Multi job case - e.g. bond scans

Also needs a lot of work. See epsman/elecStructure/ESmulti.py for an initial attempt.

Currently manual cases loop over electronic structure files and overwrite class objects each time. Should be able to pass a connection object and use multiple class instances instead? Otherwise it gets very ugly.