Update VASP sets to transition atomate2 to use pymatgen input sets ex…

…clusively (#3835)

* updates for consistency with atomate2 updates

* lint

* further patch for atomate2 support, make sure tests are respected or updated

* linting

* merge DictSet into VaspInputSet, deprecate DictSet as an alias of VaspInputSet to avoid breakage

* test_dict_set_alias subclass and deprecation message

* Change deprecation warning to be on init of DictSet

* remove deprecated decorator, only works for functions, error msg less clear when wrapped on init

* move remaining VaspInputGenerator features to PMG

* pre-commit auto-fixes

* added tests

* add incar, kpoints, poscar, potcar attr to io.vasp.inputs.VaspInput + tests

* linted

* Bump rexml from 3.2.5 to 3.2.8 in /docs (#3836)

Bumps [rexml](https://github.com/ruby/rexml) from 3.2.5 to 3.2.8.
- [Release notes](https://github.com/ruby/rexml/releases)
- [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md)
- [Commits](ruby/rexml@v3.2.5...v3.2.8)

---
updated-dependencies:
- dependency-name: rexml
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

* Bump nokogiri from 1.16.2 to 1.16.5 in /docs (#3828)

Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.16.2 to 1.16.5.
- [Release notes](https://github.com/sparklemotion/nokogiri/releases)
- [Changelog](https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md)
- [Commits](sparklemotion/nokogiri@v1.16.2...v1.16.5)

---
updated-dependencies:
- dependency-name: nokogiri
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

* shift features of VaspInputSet.write_input to VaspInput.write_input

* pre-commit /linting

* move file transfer from write_input method of VaspInputSet to VaspInput

* add missing `output_dir` kwarg to vaspinputset.write_input

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

pymatgen/io/vasp/inputs.py

@@ -19,7 +19,10 @@
 from enum import Enum, unique
 from glob import glob
 from hashlib import sha256
+from pathlib import Path
+from shutil import copyfileobj
 from typing import TYPE_CHECKING, NamedTuple, cast
+from zipfile import ZipFile
 
 import numpy as np
 import scipy.constants as const
@@ -38,7 +41,6 @@
 
 if TYPE_CHECKING:
     from collections.abc import Iterator
-    from pathlib import Path
     from typing import Any, ClassVar, Literal
 
     from numpy.typing import ArrayLike
@@ -2412,7 +2414,7 @@ def identify_potcar_hash_based(
             potcar_functionals (list): List of potcar functionals associated with
                 the PotcarSingle
         """
-        # Dict to translate the sets in the .json file to the keys used in DictSet
+        # Dict to translate the sets in the .json file to the keys used in VaspInputSet
         mapping_dict = {
             "potUSPP_GGA": {
                 "pymatgen_key": "PW91_US",
@@ -2737,7 +2739,8 @@ def __init__(
         incar: dict | Incar,
         kpoints: Kpoints | None,
         poscar: Poscar,
-        potcar: Potcar | None,
+        potcar: Potcar | str | None,
+        potcar_spec: bool = False,
         optional_files: dict[PathLike, object] | None = None,
         **kwargs,
     ) -> None:
@@ -2748,14 +2751,18 @@ def __init__(
             incar (Incar): The Incar object.
             kpoints (Kpoints): The Kpoints object.
             poscar (Poscar): The Poscar object.
-            potcar (Potcar): The Potcar object.
+            potcar (Potcar or str): The Potcar object.
+            potcar_spec (bool = False) : used to share POTCAR info without license issues.
+                True --> POTCAR is a list of symbols, write POTCAR.spec
+                False --> POTCAR is a VASP POTCAR, write POTCAR
             optional_files (dict): Other input files supplied as a dict of {filename: object}.
                 The object should follow standard pymatgen conventions in implementing a
                 as_dict() and from_dict method.
             **kwargs: Additional keyword arguments to be stored in the VaspInput object.
         """
         super().__init__(**kwargs)
-        self.update({"INCAR": incar, "KPOINTS": kpoints, "POSCAR": poscar, "POTCAR": potcar})
+        self._potcar_filename = "POTCAR" + (".spec" if potcar_spec else "")
+        self.update({"INCAR": incar, "KPOINTS": kpoints, "POSCAR": poscar, self._potcar_filename: potcar})
         if optional_files is not None:
             self.update(optional_files)
 
@@ -2793,6 +2800,9 @@ def write_input(
         self,
         output_dir: PathLike = ".",
         make_dir_if_not_present: bool = True,
+        cif_name: str | None = None,
+        zip_name: str | None = None,
+        files_to_transfer: dict | None = None,
     ) -> None:
         """
         Write VASP inputs to a directory.
@@ -2802,6 +2812,14 @@ def write_input(
                 Defaults to current directory (".").
             make_dir_if_not_present (bool): Create the directory if not
                 present. Defaults to True.
+            cif_name (str or None): If a str, the name of the CIF file
+                to write the POSCAR to (the POSCAR will also be written).
+            zip_name (str or None): If a str, the name of the zip to
+                archive the VASP input set to.
+            files_to_transfer (dict) : A dictionary of
+                    { < input filename >: < output filepath >}.
+                This allows the transfer of < input filename > files from
+                a previous calculation to < output filepath >.
         """
         if not os.path.isdir(output_dir) and make_dir_if_not_present:
             os.makedirs(output_dir)
@@ -2811,6 +2829,28 @@ def write_input(
                 with zopen(os.path.join(output_dir, key), mode="wt") as file:
                     file.write(str(value))
 
+        if cif_name:
+            self["POSCAR"].structure.to(filename=cif_name)
+
+        if zip_name:
+            files_to_zip = list(self) + ([cif_name] if cif_name else [])
+            with ZipFile(os.path.join(output_dir, zip_name), mode="w") as zip_file:
+                for file in files_to_zip:
+                    try:
+                        zip_file.write(os.path.join(output_dir, file), arcname=file)
+                    except FileNotFoundError:
+                        pass
+
+                    try:
+                        os.remove(os.path.join(output_dir, file))
+                    except (FileNotFoundError, PermissionError, IsADirectoryError):
+                        pass
+
+        files_to_transfer = files_to_transfer or {}
+        for key, val in files_to_transfer.items():
+            with zopen(val, "rb") as fin, zopen(str(Path(output_dir) / key), "wb") as fout:
+                copyfileobj(fin, fout)
+
     @classmethod
     def from_directory(
         cls,
@@ -2884,3 +2924,23 @@ def run_vasp(
             open(err_file, mode="w", encoding="utf-8", buffering=1) as stderr_file,
         ):
             subprocess.check_call(vasp_cmd, stdout=stdout_file, stderr=stderr_file)
+
+    @property
+    def incar(self) -> Incar:
+        """INCAR object."""
+        return Incar(self["INCAR"]) if isinstance(self["INCAR"], dict) else self["INCAR"]
+
+    @property
+    def kpoints(self) -> Kpoints | None:
+        """KPOINTS object."""
+        return self["KPOINTS"]
+
+    @property
+    def poscar(self) -> Poscar:
+        """POSCAR object."""
+        return self["POSCAR"]
+
+    @property
+    def potcar(self) -> Potcar | str | None:
+        """POTCAR or POTCAR.spec object."""
+        return self[self._potcar_filename]