SOF-7915: refactor espresso structure parser, support for non-zero ibrav

.github/workflows/cicd.yml

@@ -16,12 +16,12 @@ jobs:
 
     steps:
       - name: Checkout this repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           lfs: true
 
       - name: Checkout actions repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           repository: Exabyte-io/actions
           token: ${{ secrets.BOT_GITHUB_TOKEN }}
@@ -43,12 +43,12 @@ jobs:
 
     steps:
       - name: Checkout this repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           lfs: true
 
       - name: Checkout actions repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           repository: Exabyte-io/actions
           token: ${{ secrets.BOT_GITHUB_TOKEN }}
@@ -71,13 +71,13 @@ jobs:
 
     steps:
       - name: Checkout this repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           lfs: true
           fetch-tags: true
 
       - name: Checkout actions repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           repository: Exabyte-io/actions
           token: ${{ secrets.BOT_GITHUB_TOKEN }}

express/parsers/apps/espresso/pw_input_file.py

@@ -0,0 +1,79 @@
+import math
+from typing import List
+
+from mat3ra.esse.models.properties_directory.structural.lattice import LatticeSchema
+from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config
+from mat3ra.utils.constants import COEFFICIENTS
+from mat3ra.utils.string import remove_comments_from_source_code
+from mat3ra.parsers.applications.espresso.pw_x.stdin.parser import EspressoPwxStdinParser
+
+# Maps QE ibrav codes → made/esse Bravais type strings
+IBRAV_TO_LATTICE_TYPE = {
+    1:  "CUB",
+    2:  "FCC",
+    3:  "BCC",  -3: "BCC",
+    4:  "HEX",
+    5:  "RHL",  -5: "RHL",
+    6:  "TET",
+    7:  "BCT",
+    8:  "ORC",
+    9:  "ORCC", -9: "ORCC",
+    10: "ORCF",
+    11: "ORCI",
+    12: "MCL",  -12: "MCL",
+    13: "MCLC",
+    14: "TRI",
+}
+
+
+def _get_cell_from_ibrav(system: dict) -> List[List[float]]:
+    ibrav = int(system.get("ibrav", 0))
+    lattice_type = IBRAV_TO_LATTICE_TYPE.get(ibrav)
+    if lattice_type is None:
+        raise ValueError(f"Unsupported ibrav={ibrav}")
+
+    has_celldm = "celldm1" in system
+
+    if has_celldm:
+        a = float(system["celldm1"]) * COEFFICIENTS["BOHR_TO_ANGSTROM"]
+        b = a * float(system.get("celldm2", 1))
+        c = a * float(system.get("celldm3", 1))
+        # celldm(4,5,6) are cosines → convert to degrees
+        alpha = math.degrees(math.acos(float(system.get("celldm4", 0))))
+        beta  = math.degrees(math.acos(float(system.get("celldm5", 0))))
+        gamma = math.degrees(math.acos(float(system.get("celldm6", 0))))
+    else:
+        a = float(system.get("a", 1))
+        b = float(system.get("b", a))
+        c = float(system.get("c", a))
+        alpha = math.degrees(math.acos(float(system["cosbc"]))) if "cosbc" in system else float(system.get("alpha", 90))
+        beta  = math.degrees(math.acos(float(system["cosac"]))) if "cosac" in system else float(system.get("beta",  90))
+        gamma = math.degrees(math.acos(float(system["cosab"]))) if "cosab" in system else float(system.get("gamma", 90))
+
+    lattice_config = LatticeSchema(type=lattice_type, a=a, b=b, c=c, alpha=alpha, beta=beta, gamma=gamma)
+
+    return get_primitive_lattice_vectors_from_config(lattice_config)
+
+
+class PwInputFile:
+    def __init__(self, input_text: str):
+        text = remove_comments_from_source_code(
+            remove_comments_from_source_code(input_text, language="fortran"), language="python"
+        )
+        parser = EspressoPwxStdinParser(text)
+
+        system = parser.get_namelist("SYSTEM")
+        ibrav = int(system.get("ibrav", 0))
+
+        celldm1_angstrom = float(system["celldm1"]) * COEFFICIENTS["BOHR_TO_ANGSTROM"] if "celldm1" in system else None
+
+        # Delegate crystal lattice calculation based on ibrav value
+        cell = parser.get_card_cell_parameters(celldm1_angstrom) if ibrav == 0 else _get_cell_from_ibrav(system)
+
+        atom_names, positions = parser.get_card_atomic_positions(cell, celldm1_angstrom)
+
+        self.structure = {
+            "cell": cell,
+            "atom_names": atom_names,
+            "positions": positions,
+        }

express/parsers/structure.py

@@ -1,9 +1,8 @@
-import io
 import json
 
 import pymatgen as mg
 from pymatgen.core.structure import Structure
-from ase.io import read, write
+from express.parsers.apps.espresso.pw_input_file import PwInputFile
 from jarvis.core.atoms import Atoms
 from jarvis.io.vasp.inputs import Poscar
 
@@ -38,22 +37,22 @@ def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.structure_string = kwargs.get("structure_string")
         self.structure_format = kwargs.get("structure_format")
+        self.cell_type = kwargs.get("cell_type", "original")  # original, primitive or conventional
 
-        # convert espresso input into poscar
+        # convert espresso input into pymatgen.core.structure
         if self.structure_format == "espresso-in":
-            self.structure_format = "poscar"
-            self.structure_string = self.espresso_input_to_poscar(self.structure_string)
-
+            parsed = PwInputFile(self.structure_string)
+            self.structure = Structure(
+                lattice=parsed.structure["cell"],
+                species=parsed.structure["atom_names"],
+                coords=parsed.structure["positions"],
+                coords_are_cartesian=True,
+            )
         # convert jarvis-db-entry JSON into poscar
-        if self.structure_format == "jarvis-db-entry":
-            self.structure_format = "poscar"
+        elif self.structure_format == "jarvis-db-entry":
             self.structure_string = self.jarvis_db_entry_json_to_poscar(self.structure_string)
-
-        # cell_type is either original, primitive or conventional
-        self.cell_type = kwargs.get("cell_type", "original")
-
-        # Initialize structure class
-        if self.structure_format == "pymatgen.core.structure":
+            self.structure = Structure.from_str(self.structure_string, "poscar")
+        elif self.structure_format == "pymatgen.core.structure":
             structure_as_dict = json.loads(self.structure_string)
             self.structure = Structure.from_dict(structure_as_dict)
         else:
@@ -63,7 +62,7 @@ def __init__(self, *args, **kwargs):
             self.structure = STRUCTURE_MAP[self.cell_type](self.structure)
 
         # keep only one atom inside the basis in order to have the original lattice type
-        self.lattice_only_structure = self.structure.copy() # deepcopy
+        self.lattice_only_structure = self.structure.copy()  # deepcopy
         self.lattice_only_structure.remove_sites(range(1, len(self.structure.sites)))
 
     def lattice_vectors(self):
@@ -178,16 +177,15 @@ def basis(self):
         for i, site in enumerate(self.structure.sites):
             if not site.is_ordered:
                 raise ValueError(
-                   f"Disordered site at {site.frac_coords.tolist()} with "
-                   f"occupancy {site.species} is not supported."
+                    f"Disordered site at {site.frac_coords.tolist()} with "
+                    f"occupancy {site.species} is not supported."
                 )
 
             # Use specie.symbol to strip oxidation state (e.g. "Li0+" → "Li", "O2-" → "O")
             elements.append({"id": i, "value": site.specie.symbol})
-            coordinates.append({
-                "id": i,
-                "value": self._round(site.frac_coords.tolist(), PRECISION_MAP["coordinates_crystal"])
-            })
+            coordinates.append(
+                {"id": i, "value": self._round(site.frac_coords.tolist(), PRECISION_MAP["coordinates_crystal"])}
+            )
         return {"units": "crystal", "elements": elements, "coordinates": coordinates}
 
     def space_group_symbol(self):
@@ -240,27 +238,6 @@ def atomic_constraints(self):
         """
         return self.structure.site_properties.get("selective_dynamics")
 
-    def espresso_input_to_poscar(self, espresso_input):
-        """
-        Extracts structure from espresso input file and returns in poscar format.
-
-        Args:
-            espresso_input (str): input file content
-
-        Returns:
-            str: poscar
-        """
-        input_ = io.StringIO()
-        input_.write(espresso_input)
-        input_.seek(0)
-        atoms = read(input_, format="espresso-in")
-        output_ = io.StringIO()
-        write(output_, atoms, format="vasp", vasp5=True)
-        content = output_.getvalue()
-        input_.close()
-        output_.close()
-        return content
-
     def jarvis_db_entry_json_to_poscar(self, jarvis_db_entry_json_str):
         """
         Extracts structure from jarvis atoms dictionary and returns in poscar format.

pyproject.toml

@@ -15,9 +15,9 @@ classifiers = [
     "Topic :: Software Development",
 ]
 dependencies = [
-    "pymatgen>=2023.8.10",
-    "ase>=3.17.0",
     "mat3ra-esse>=2026.6.12",
+    "mat3ra-made[tools] @ git+https://github.com/exabyte-io/made.git@bdfa37a451f0364cee1602bcec723fb878fdfc0a",
+    "mat3ra-parsers @ git+https://github.com/exabyte-io/parsers.git@30182b7f967024d31ff03dc39dcbdc33faf89722",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     "numpy>=1.24.4,<2",

tests/.gitattributes

@@ -5,3 +5,4 @@ fixtures/vasp/** filter=lfs diff=lfs merge=lfs -text
 fixtures/data.py filter=lfs diff=lfs merge=lfs -text
 fixtures/pyML/test-001/*.JSON filter=lfs diff=lfs merge=lfs -text
 *.cif filter=lfs diff=lfs merge=lfs -text
+fixtures/structural/test-005/*.in filter=lfs diff=lfs merge=lfs -text

tests/fixtures/structural/references.py

@@ -29,3 +29,14 @@
         {"id": 8, "value": [0.333333330, 0.666666670, 0.666666670]},
     ],
 }
+
+SI_IBRAV_BASIS = {
+    "units": "crystal",
+    "elements": [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}],
+    "coordinates": [
+        {"id": 0, "value": [0.0, 0.0, 0.0]},
+        {"id": 1, "value": [0.25, 0.25, 0.25]},
+    ],
+}
+
+SI_PRIMITIVE_LATTICE_A = 3.867  # Angstrom

tests/unit/parsers/test_structure_parser.py

@@ -1,7 +1,7 @@
 import os
 
 from tests.unit import UnitTestBase
-from tests.fixtures.structural.references import LI_CIF_BASIS
+from tests.fixtures.structural.references import LI_CIF_BASIS, SI_IBRAV_BASIS, SI_PRIMITIVE_LATTICE_A
 from express.parsers.structure import StructureParser
 
 LI_CIF_PATH = os.path.join(os.path.dirname(__file__), "..", "..", "fixtures", "structural", "test-004", "Li.cif")
@@ -10,6 +10,14 @@
     os.path.dirname(__file__), "..", "..", "fixtures", "structural", "test-004", "SrLaCoO4.cif"
 )
 
+SI_IBRAV0_PATH = os.path.join(
+    os.path.dirname(__file__), "..", "..", "fixtures", "structural", "test-005", "pw_si_ibrav0.in"
+)
+
+SI_IBRAV2_PATH = os.path.join(
+    os.path.dirname(__file__), "..", "..", "fixtures", "structural", "test-005", "pw_si_ibrav2.in"
+)
+
 
 def _read_file(path):
     with open(path) as f:
@@ -46,12 +54,12 @@ class DisorderedStructureParserTest(UnitTestBase):
     when basis() is called on a structure with disordered (mixed-occupancy) sites.
 
     The SrLaCoO4 CIF has Sr2+ and La3+ sharing the same Wyckoff 4e site
-    with occupancy 0.5 each — a canonical disordered case.
+    with occupancy 0.5 each, a disordered case.
     """
 
     def setUp(self):
         super().setUp()
-        # Parsing itself succeeds — pymatgen can load disordered structures.
+        # Parsing itself succeeds as pymatgen can load disordered structures.
         # The error is raised lazily when basis() is called.
         self.parser = StructureParser(
             structure_string=_read_file(DISORDERED_CIF_PATH),
@@ -72,3 +80,59 @@ def test_basis_raises_for_disordered_site(self):
         self.assertIn("is not supported", error)
         self.assertIn("occupancy", error)
         self.assertIn("0.361", error)
+
+
+class EspressoInIbrav0StructureParserTest(UnitTestBase):
+    """Tests that StructureParser correctly parses espresso-in files with ibrav=0
+    and explicit CELL_PARAMETERS.
+    The primitive lattice constant is 3.867 Angstrom."""
+
+    def setUp(self):
+        super().setUp()
+        self.parser = StructureParser(
+            structure_string=_read_file(SI_IBRAV0_PATH),
+            structure_format="espresso-in",
+        )
+
+    def tearDown(self):
+        super().tearDown()
+
+    def test_basis(self):
+        self.assertDeepAlmostEqual(self.parser.basis(), SI_IBRAV_BASIS, places=5)
+
+    def test_formula(self):
+        self.assertEqual(self.parser.formula(), "Si2")
+
+    def test_lattice_bravais_type(self):
+        self.assertEqual(self.parser.lattice_bravais()["type"], "FCC")
+
+    def test_lattice_parameter_a(self):
+        self.assertAlmostEqual(self.parser.lattice_bravais()["a"], SI_PRIMITIVE_LATTICE_A, places=3)
+
+
+class EspressoInIbrav2StructureParserTest(UnitTestBase):
+    """Tests that StructureParser correctly parses espresso-in files with ibrav=2
+    (FCC) defined via celldm(1), without explicit CELL_PARAMETERS.
+    The primitive lattice constant is 3.867 Angstrom."""
+
+    def setUp(self):
+        super().setUp()
+        self.parser = StructureParser(
+            structure_string=_read_file(SI_IBRAV2_PATH),
+            structure_format="espresso-in",
+        )
+
+    def tearDown(self):
+        super().tearDown()
+
+    def test_basis(self):
+        self.assertDeepAlmostEqual(self.parser.basis(), SI_IBRAV_BASIS, places=5)
+
+    def test_formula(self):
+        self.assertEqual(self.parser.formula(), "Si2")
+
+    def test_lattice_bravais_type(self):
+        self.assertEqual(self.parser.lattice_bravais()["type"], "FCC")
+
+    def test_lattice_parameter_a(self):
+        self.assertAlmostEqual(self.parser.lattice_bravais()["a"], SI_PRIMITIVE_LATTICE_A, places=3)