JDFTXStructure - partial fix for special case lattice tags (#4401)

* Adding `NotImplementedError` for Structure <-> JDFTXInfile conversion for JDFTXInfile with special case lattices (aka lattices not provided as a 3x3 matrix)

* Adding partial implementation of JDFTXStructure <-> JDFTXInfile special case lattice

Author: benrich37

src/pymatgen/io/jdftx/inputs.py

@@ -20,7 +20,7 @@ class is written.
 import scipy.constants as const
 from monty.json import MSONable
 
-from pymatgen.core import Structure
+from pymatgen.core import Lattice, Structure
 from pymatgen.core.periodic_table import Element
 from pymatgen.core.units import bohr_to_ang
 from pymatgen.io.jdftx.generic_tags import AbstractTag, BoolTagContainer, DumpTagContainer, MultiformatTag, TagContainer
@@ -788,17 +788,8 @@ def from_jdftxinfile(cls, jdftxinfile: JDFTXInfile, sort_structure: bool = False
         Returns:
             JDFTXStructure: The created JDFTXStructure object.
         """
-        jl = jdftxinfile["lattice"]
-        lattice = np.zeros([3, 3])
-        for i in range(3):
-            for j in range(3):
-                lattice[i][j] += float(jl[f"R{i}{j}"])
-        if "latt-scale" in jdftxinfile:
-            latt_scale = np.array([jdftxinfile["latt-scale"][x] for x in ["s0", "s1", "s2"]])
-            lattice *= latt_scale
-        lattice = lattice.T  # convert to row vector format
-        lattice *= const.value("Bohr radius") * 10**10  # Bohr radius in Ang; convert to Ang
 
+        lattice = _infile_to_pmg_lattice(jdftxinfile)
         atomic_symbols = [x["species-id"] for x in jdftxinfile["ion"]]
         coords = np.array([[x["x0"], x["x1"], x["x2"]] for x in jdftxinfile["ion"]])
         coords *= const.value("Bohr radius") * 10**10  # Bohr radius in Ang; convert to Ang
@@ -1016,3 +1007,58 @@ def _multi_getattr(varbase: Any, varname: str):
     for var in varlist:
         varbase = getattr(varbase, var)
     return varbase
+
+
+def _infile_to_pmg_lattice(jdftxinfile: JDFTXInfile) -> Lattice:
+    jl = jdftxinfile["lattice"]
+    if "R00" not in jl:
+        return _infile_special_format_to_pmg_lattice(jdftxinfile)
+    return _infile_matrix_format_to_pmg_lattice(jdftxinfile)
+
+
+def _infile_special_format_to_pmg_lattice(jdftxinfile: JDFTXInfile) -> Lattice:
+    jl = jdftxinfile["lattice"]
+    if "modification" in jl:
+        raise NotImplementedError("Special case lattices with modification not implemented yet")
+    # Second boolean to check if latt-scale was passed but does nothing
+    if ("latt-scale" in jl) and (not all(np.isclose(float(x), 1) in jl for x in ["s0", "s1", "s2"])):
+        raise NotImplementedError("latt-scale for special case lattices not implemented yet")
+    if "Monoclinic" in jl:
+        lattice = Lattice.monoclinic(jl["a"], jl["b"], jl["c"], jl["beta"])
+    elif "Orthorhombic" in jl:
+        lattice = Lattice.orthorhombic(jl["a"], jl["b"], jl["c"])
+    elif "Cubic" in jl:
+        lattice = Lattice.cubic(jl["a"])
+    elif "Hexagonal" in jl:
+        lattice = Lattice.hexagonal(jl["a"], jl["c"])
+    elif "Rhombohedral" in jl:
+        lattice = Lattice.rhombohedral(jl["a"], jl["alpha"])
+    elif "Tetragonal" in jl:
+        lattice = Lattice.tetragonal(jl["a"], jl["c"])
+    elif "Triclinic" in jl:
+        lattice = Lattice.from_parameters(jl["a"], jl["b"], jl["c"], jl["alpha"], jl["beta"], jl["gamma"])
+    else:
+        raise ValueError(f"Unable to convert JDFTX lattice tag {jl} to pymatgen Lattice object")
+    return lattice
+
+
+def _infile_matrix_format_to_pmg_lattice(jdftxinfile: JDFTXInfile) -> Lattice:
+    """Convert JDFTX lattice tag to pymatgen Lattice object.
+
+    Args:
+        jl (dict[str, Any]): JDFTX lattice tag.
+
+    Returns:
+        Lattice: Pymatgen Lattice object.
+    """
+    _lattice = np.zeros([3, 3])
+    jl = jdftxinfile["lattice"]
+    for i in range(3):
+        for j in range(3):
+            _lattice[i][j] += float(jl[f"R{i}{j}"])
+    if "latt-scale" in jdftxinfile:
+        latt_scale = np.array([jdftxinfile["latt-scale"][x] for x in ["s0", "s1", "s2"]])
+        _lattice *= latt_scale
+    _lattice = _lattice.T  # convert to row vector format
+    _lattice *= const.value("Bohr radius") * 10**10  # Bohr radius in Ang; convert to Ang
+    return Lattice(_lattice)

tests/io/jdftx/test_jdftxinfile.py

@@ -487,6 +487,40 @@ def test_lattice_writing(value_str: str):
     )
 
 
+@pytest.mark.parametrize(
+    ("value_str"),
+    [
+        ("Rhombohedral 1.0 1.0"),
+        ("Triclinic 1.0 1.0 1.0 1.0 1.0 1.0"),
+        ("Hexagonal 1.0 1.0"),
+        ("Body-Centered Cubic 1.0"),
+        ("Cubic 1.0"),
+        ("Orthorhombic 1.0 1.0 1.0"),
+        ("Base-Centered Orthorhombic 1.0 1.0 1.0"),
+        ("Monoclinic 1.0 1.0 1.0 1.0"),
+        ("Base-Centered Monoclinic 1.0 1.0 1.0 1.0"),
+        ("Tetragonal 1.0 1.0"),
+        ("Body-Centered Tetragonal 1.0 1.0"),
+    ],
+)
+def test_jdftxstructure_lattice_conversion(value_str: str):
+    test_vars = ["a", "b", "c", "alpha", "beta", "gamma"]
+    mft_lattice_tag = get_tag_object("lattice")
+    assert mft_lattice_tag is not None
+    i = mft_lattice_tag.get_format_index_for_str_value("lattice", value_str)
+    tag_object = mft_lattice_tag.format_options[i]
+    parsed_tag = tag_object.read("lattice", value_str)
+    infile = JDFTXInfile.from_str("lattice " + value_str + "\n ion H 0.0 0.0 0.0 0", dont_require_structure=True)
+    if "modification" in parsed_tag:
+        with pytest.raises(NotImplementedError):
+            _ = infile.to_pmg_structure(infile)
+    else:
+        structure = infile.to_pmg_structure(infile)
+        for var in test_vars:
+            if var in parsed_tag:
+                assert_same_value(float(getattr(structure.lattice, var)), float(parsed_tag[var]))
+
+
 # This fails, but I don't think we need to support this
 # @pytest.mark.parametrize(
 #     ("unordered_dict", "expected_out"),