Move JDFTx sets from atomate2 to pymatgen (#4479)

* Addition of JDFTx set to pymatgen from atomate2.

* None structure handling in input set generation

---------

Signed-off-by: Cooper <[email protected]>
Co-authored-by: cote3804 <[email protected]>

Author: cote3804

src/pymatgen/io/jdftx/BaseJdftxSet.yaml

@@ -0,0 +1,67 @@
+# Default JDFTx settings for atomate2 calculations.
+### Functional ###
+elec-ex-corr: gga
+van-der-waals: D3
+
+### Electronic Parameters ###
+elec-cutoff:
+  Ecut: 20
+  EcutRho: 100
+electronic-minimize:
+  nIterations: 100
+  energyDiffThreshold: 1.0e-07
+elec-smearing:
+  smearingType: Fermi
+  smearingWidth: 0.001
+# elec-initial-magnetization:
+#   M: 0
+#   constrain: False
+spintype: z-spin
+core-overlap-check: none
+converge-empty-states: True
+band-projection-params:
+  ortho: True
+  norm: False
+
+### Lattice / Unit Cell ###
+latt-move-scale:
+  s0: 0
+  s1: 0
+  s2: 0
+lattice-minimize:
+  nIterations: 00
+symmetries: none
+#coulomb-interaction: slab 001
+#coords-type Lattice
+
+### Solvation & Bias ###
+# fluid: LinearPCM
+# pcm-variant: CANDLE
+# fluid-solvent: H2O
+# fluid-cation:
+#   name: Na+
+#   concentration: 0.5
+# fluid-anion:
+#   name: F-
+#   concentration: 0.5
+
+### Pseudopotential ###
+ion-species: GBRV_v1.5/$ID_pbe_v1.uspp
+
+
+### Output Files ###
+dump-name: jdftx.$VAR
+dump:
+  - End:
+      Dtot: True
+      State: True
+      BoundCharge: True
+      Forces: True
+      Ecomponents: True
+      VfluidTot: True
+      ElecDensity: True
+      KEdensity: True
+      EigStats: True
+      BandEigs: True
+      BandProjections: True
+      DOS: True

src/pymatgen/io/jdftx/sets.py

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+from __future__ import annotations
+
+import os
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+from pymatgen.io.core import InputSet
+from pymatgen.io.jdftx.inputs import JDFTXInfile, JDFTXStructure
+
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+    from pymatgen.util.typing import PathLike
+
+FILE_NAMES = {"in": "init.in", "out": "jdftx.out"}
+
+
+class JdftxInputSet(InputSet):
+    """
+    A class to represent a JDFTx input file as a JDFTx InputSet.
+
+    Parameters
+    ----------
+    jdftxinput
+        A JdftxInput object
+    """
+
+    def __init__(self, jdftxinput: JDFTXInfile, structure: Structure) -> None:
+        self.structure = structure
+        self.jdftxinput = jdftxinput
+
+    def write_input(
+        self,
+        directory: str | Path,
+        infile: PathLike = FILE_NAMES["in"],
+        make_dir: bool = True,
+        overwrite: bool = True,
+    ) -> None:
+        """Write JDFTx input file to a directory.
+
+        Parameters
+        ----------
+        directory
+            Directory to write input files to.
+        make_dir
+            Whether to create the directory if it does not already exist.
+        overwrite
+            Whether to overwrite an input file if it already exists.
+        """
+        directory = Path(directory)
+        if make_dir:
+            os.makedirs(directory, exist_ok=True)
+
+        if not overwrite and (directory / infile).exists():
+            raise FileExistsError(f"{directory / infile} already exists.")
+        jdftx_structure = JDFTXStructure(structure=self.structure)
+        jdftxinput = condense_jdftxinputs(self.jdftxinput, jdftx_structure)
+
+        jdftxinput.write_file(filename=(directory / infile))
+
+    @staticmethod
+    def from_file(
+        file: PathLike,
+    ) -> JdftxInputSet:
+        """Load a set of JDFTx inputs from a filename.
+
+        Parameters
+        ----------
+        directory
+            Input file to read JDFTx inputs from.
+        """
+        jdftxinput = JDFTXInfile.from_file(file)
+        structure = jdftxinput.structure
+        if structure is None:
+            raise ValueError(f"Structure not defined in file {file}.")
+        return JdftxInputSet(jdftxinput=jdftxinput, structure=structure)
+
+
+def condense_jdftxinputs(jdftxinput: JDFTXInfile, jdftxstructure: JDFTXStructure) -> JDFTXInfile:
+    """
+    Combine JDFTXInfile and JDFTxStructure into complete JDFTXInfile.
+
+    Function combines a JDFTXInfile class with calculation
+    settings and a JDFTxStructure that defines the structure
+    into one JDFTXInfile instance.
+
+    Parameters
+    ----------
+        jdftxinput: JDFTXInfile
+            A JDFTXInfile object with calculation settings.
+
+        jdftxstructure: JDFTXStructure
+            A JDFTXStructure object that defines the structure.
+
+    Returns
+    -------
+        JDFTXInfile
+            A JDFTXInfile that includes the calculation
+            parameters and input structure.
+    """
+    # force Cartesian coordinates
+    coords_type = jdftxinput.get("coords-type")
+    return jdftxinput + JDFTXInfile.from_str(jdftxstructure.get_str(in_cart_coords=(coords_type == "Cartesian")))

tests/io/jdftx/test_sets.py

@@ -0,0 +1,29 @@
+"""Tests for JDFTx input sets."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from pymatgen.io.jdftx.inputs import JDFTXInfile
+from pymatgen.io.jdftx.sets import JdftxInputSet
+from pymatgen.util.testing import TEST_FILES_DIR
+
+from .inputs_test_utils import assert_idential_jif, ex_infile1_fname
+
+ex_files_dir = Path(TEST_FILES_DIR) / "io" / "jdftx" / "example_files"
+
+
+def test_jdftxinputset_from_directory():
+    input_set = JdftxInputSet.from_file(ex_infile1_fname)
+    jdftx_inputfile = JDFTXInfile.from_file(ex_infile1_fname)
+    assert_idential_jif(input_set.jdftxinput, jdftx_inputfile)
+
+
+def test_jdftxinputset_write_file(tmp_path):
+    jdftx_inputfile = JDFTXInfile.from_file(ex_infile1_fname)
+    input_set = JdftxInputSet(jdftx_inputfile, jdftx_inputfile.structure)
+    input_set.write_input(tmp_path, infile="test.in")
+    written_file = tmp_path / "test.in"
+    read_jdftx_inputfile = JDFTXInfile.from_file(written_file)
+    assert written_file.exists()
+    assert_idential_jif(read_jdftx_inputfile, jdftx_inputfile)