Add pymatgen.io.pwmat module (#3512)

* Add pymatgen.io.pwmat module

* rm unitest inside pymatgen.io.pwmat dir

* remove try,except expression: remove format expression: remove format expression: codespell

* Add pwmat fmt within Structure.from_file() and Structure.from_str()

* Remove abtractclass LineLocaterBase

* Add output file of PWmat: Report, OUT.FERMI

* Add output file of PWmat: DOS.totalspin, DOS.spinup, DOS.spindown

* Rename part to part_upper to impove code quality to pass automatically test

* add OutFermi, Report, Dosspin object to __init__.py in pwmat

* Add input file named gen.kpt

* Add high_symmetry_point

* Add test for all new features

* snake case variables, fix doc strings and return types

* Revise comments and compress the test file. to pass test

* Revise annotation again

* Further modify the annotations

* Further modify the annotations

* Fix mispelling according to codespell

* Modify annotation according to mypy

* Modify annotation of filename: str -> PathLike

* Add pwmat in FileFormats

* Change the type annotation of filename to PathLike

* Change type annotation: np.array -> np.ndarray

* Utilize mypy check locally to pass 21 tests for pymatgen.io.pwmat

* fix typos

* del tests/io/pwmat/__init__.py

* more informative unrecognized file extension error in Structure.from_file()

* fnmatch compressed *.config* or *.pwmat* files

* compress test files

* snake_case dict keys and method names

* don't write tmp test files to git repo

* re.escape err msg

* drop filename from expected err msg

* Add test for Structure pwmat IO format

* Add test for Structure pwmat IO format

* Try to pass test in win

* Decompress the test file and reduce the number of lines.

* Add test for Structure.from_file() and Structure.to() in pwmat format

* improve test_inputs.py assertions

---------

Signed-off-by: LiuHanyu <[email protected]>
Co-authored-by: Janosh Riebesell <[email protected]>

Author: lhycms

pymatgen/core/structure.py

@@ -60,7 +60,7 @@
 
     from pymatgen.util.typing import CompositionLike, SpeciesLike
 
-FileFormats = Literal["cif", "poscar", "cssr", "json", "yaml", "yml", "xsf", "mcsqs", "res", ""]
+FileFormats = Literal["cif", "poscar", "cssr", "json", "yaml", "yml", "xsf", "mcsqs", "res", "pwmat", ""]
 
 
 class Neighbor(Site):
@@ -2671,7 +2671,7 @@ def to(self, filename: str | Path = "", fmt: FileFormats = "", **kwargs) -> str:
             fmt (str): Format to output to. Defaults to JSON unless filename
                 is provided. If fmt is specifies, it overrides whatever the
                 filename is. Options include "cif", "poscar", "cssr", "json",
-                "xsf", "mcsqs", "prismatic", "yaml", "yml", "fleur-inpgen".
+                "xsf", "mcsqs", "prismatic", "yaml", "yml", "fleur-inpgen", "pwmat".
                 Non-case sensitive.
             **kwargs: Kwargs passthru to relevant methods. E.g., This allows
                 the passing of parameters like symprec to the
@@ -2752,6 +2752,10 @@ def to(self, filename: str | Path = "", fmt: FileFormats = "", **kwargs) -> str:
                 with zopen(filename, mode="wt", encoding="utf8") as file:
                     file.write(res_str)
             return res_str
+        elif fmt == "pwmat" or fnmatch(filename.lower(), "*.pwmat") or fnmatch(filename.lower(), "*.config"):
+            from pymatgen.io.pwmat import AtomConfig
+
+            writer = AtomConfig(self, **kwargs)
         else:
             if fmt == "":
                 raise ValueError(f"Format not specified and could not infer from {filename=}")
@@ -2832,6 +2836,10 @@ def from_str(  # type: ignore[override]
             from pymatgen.io.res import ResIO
 
             struct = ResIO.structure_from_str(input_string, **kwargs)
+        elif fmt == "pwmat":
+            from pymatgen.io.pwmat import AtomConfig
+
+            struct = AtomConfig.from_str(input_string, **kwargs).structure
         else:
             raise ValueError(f"Invalid {fmt=}, valid options are {get_args(FileFormats)}")
 
@@ -2910,8 +2918,12 @@ def from_file(  # type: ignore[override]
             from pymatgen.io.res import ResIO
 
             struct = ResIO.structure_from_file(filename, **kwargs)
+        elif fnmatch(fname.lower(), "*.config*") or fnmatch(fname.lower(), "*.pwmat*"):
+            from pymatgen.io.pwmat import AtomConfig
+
+            struct = AtomConfig.from_file(filename, **kwargs).structure
         else:
-            raise ValueError("Unrecognized file extension!")
+            raise ValueError(f"Unrecognized extension in {filename=}")
         if sort:
             struct = struct.get_sorted_structure()
         if merge_tol:

pymatgen/io/pwmat/__init__.py

@@ -0,0 +1,5 @@
+"""This package implements modules for input and output to and from PWmat."""
+from __future__ import annotations
+
+from .inputs import AtomConfig
+from .outputs import DosSpin, Movement, OutFermi, Report