Add a save parameter for chargemol calculation to select whether save the output files, use "link" rather than "copy" for the input file of chargemol calc, add mpi function to run chargemol.

[RedStar-Iron]

Revised Content

1. Add save parameter to control whether save the output files from chargemol calculation
2. Use link rather than copy for CHGCAR, POTCAR, ARCCAR0 and ARCCAR2 during the calculation
3. Support mpirun for chargemol calculation

[RedStar-Iron]

from pymatgen.command_line.chargemol_caller import *

chargemol = ChargemolAnalysis(mpi=True,ncores=32, save=True)

Job script to run chargemol program.

[RedStar-Iron]

Hi Dr. @Andrew-S-Rosen,

Are you available to have look the remaining problem in this commit?

I have tried several methods to handle this problem but it still remains. Do you have some experiences to solve this kind of problem?

Thanks a lot!
Gsliu

pymatgen/command_line/chargemol_caller.py:67: error: Incompatible types in assignment (expression has type "Optional[str]", variable has type "Union[str, list[str]]")  [assignment]
pymatgen/command_line/chargemol_caller.py:78: error: Incompatible types in assignment (expression has type "Optional[str]", variable has type "Union[str, list[str]]")  [assignment]
pymatgen/command_line/chargemol_caller.py:[20](https://github.com/materialsproject/pymatgen/actions/runs/6779786547/job/18427398503?pr=3456#step:6:21)6: error: Incompatible types in assignment (expression has type "Union[str, list[str]]", variable has type "list[Union[str, list[str]]]")  [assignment]
pymatgen/command_line/chargemol_caller.py:239: error: Argument 1 to "Popen" has incompatible type "list[Union[str, list[str]]]"; expected "Union[Union[str, bytes, PathLike[str], PathLike[bytes]], Sequence[Union[str, bytes, PathLike[str], PathLike[bytes]]]]"  [arg-type]
pymatgen/command_line/chargemol_caller.py:273: error: Argument 1 to "Popen" has incompatible type "list[Union[str, list[str]]]"; expected "Union[Union[str, bytes, PathLike[str], PathLike[bytes]], Sequence[Union[str, bytes, PathLike[str], PathLike[bytes]]]]"  [arg-type]
Found 5 errors in 1 file (checked 267 source files)
Error: Process completed with exit code 1.

[Andrew-S-Rosen]

@RedStar-Iron: Apologies, but I unfortunately don't have time to look at this PR. @chiang-yuan and/or @janosh might be interested, however.

[shyuep]

Thanks for your contribution. However, we have moved this to pymatgen-core. Please resubmit a PR there when ready.