Ryan Kingsbury

QChem: add CMIRS solvent model support

3

## Summary Additions to `QCInput` and `QChemDictSet` needed to support the new CMIRS implicit solvent model and the isodensity implementation of SS(V)PE. See relevant Q-Chem manual pages: - https://manual.q-chem.com/latest/subsec_PCM_job_control.html -...

## Summary This PR includes minimal changes to FEFF I/O to support the use of non-periodic input structures (e.g., `Molecule` rather than `Structure` objects. Tested with `MPXANESSet` * Modify `Header`...

**Is your feature request related to a problem? Please describe.** The format of data output by LAMMPS is completely dependent on what a user specifies in the input file, making...

LAMMPS IO: update to accomodate pandas deprecation

3

**Describe the bug** Several lines in `pymatgen.io.lammps.data.py` make use of the pandas `DataFrame.append` method, which is being deprecated, causing many warnings along the lines of: ``` /Users/ryan/miniconda3/envs/md/code/pymatgen/pymatgen/io/lammps/data.py:1283: FutureWarning: The frame.append...

[WIP] Pourbaix: new methods and enhancements for customizability

5

## Summary The eventual goal of this PR is to provide some additional methods that make `PourbaixDiagram` more easily customizable within pymatgen. This is a WIP motivated by requests and...

CombinedData serialization with monty is broken

11

**Describe the bug** I am unable to serialize and deserialize a `CombinedData` object using `loadfn` / `dumpfn`. I believe this occurs because `CombinedData` inherits `from_dict` from `LammpsData`, but `CombinedData.init()` takes...

Inconsistency between `formula` and `reduced_formula` for diatomic molecules and Ions

1

**Describe the bug** The output of `Composition.formula` and `Composition.reduced_formula` is counterintuitive for formulas listed in [`special_formulas`](https://github.com/materialsproject/pymatgen/blob/937eff5cc83febdea57258c0488a5b81cb550506/pymatgen/core/composition.py#L78), especially diatomic gases. In addition, the output of `reduced_formula` is not correct for `Ion`...

**Describe the bug** V+2 and V+3 species do not appear on our `PourbaixDiagram` for vanadium, even though several credible sources indicate that they should. This shortcoming was reported by an...

Function or conditional branch/case not yet implemented.

1

I recently compiled [nwchem](https://nwchemgit.github.io/) using libflame in place of LAPACK. When trying to run a simple calculation, execution fails with ``` libflame: /home/amd/harish/rome2.2/aocl-rel/aocl22-rc4/final-packages/libflame/src/lapack/red/tridiagut/front/flamec/FLA_Tridiag_UT_internal.c (line 26): libflame: Function or conditional branch/case...

Feature Request: It is currently not possible to use the CLI `set_priority()` command to query workflows, only fireworks. But sometimes the workflow contains metadata that is useful for assigning priorities...