Merge pull request #10 from Quantum-Accelerators/cifcharge

Add support for framework charges

Author: Andrew-S-Rosen

pyproject.toml

@@ -25,7 +25,7 @@ classifiers = [
     "Operating System :: MacOS",
 ]
 requires-python = ">=3.9, <3.13"
-dependencies = ["ase", "numpy", "pymatgen"]
+dependencies = ["ase", "numpy", "pymatgen>=2024.2.8"]
 
 [project.optional-dependencies]
 dev = ["black>=23.7.0", "docformatter>=1.7.5", "isort>=5.12.0", "pytest>=7.4.0", "pytest-cov>=3.0.0", "ruff>=0.0.285"]

src/raspa_ase/utils/io.py

@@ -71,7 +71,7 @@ def write_frameworks(frameworks: list[Atoms], directory: str | Path) -> None:
         name = f"framework{i}"
 
         structure = AseAtomsAdaptor.get_structure(framework)
-        structure.to(str(Path(directory, name + ".cif")))
+        structure.to(str(Path(directory, name + ".cif")), write_site_properties=True)
 
 
 def parse_output(filepath: str | Path) -> dict[str, Any]:

src/raspa_ase/utils/params.py

@@ -25,8 +25,7 @@ def get_framework_params(frameworks: list[Atoms]) -> dict[str, Any]:
     dict
         The framework-related parameters.
     """
-    # TODO: Add support for writing charges to CIF
-    # with _atom_site_charge and in RASPA set UseChargesFromCIFFile yes
+
     parameters = {}
     for i, framework in enumerate(frameworks):
         if framework == Atoms():
@@ -36,13 +35,21 @@ def get_framework_params(frameworks: list[Atoms]) -> dict[str, Any]:
         cutoff = get_parameter(parameters, "CutOff", default=12.0)
         n_cells = get_suggested_cells(framework, cutoff)
 
+        framework_params = {
+            "FrameworkName": name,
+            "UnitCells": n_cells,
+        }
+
+        if framework.has("initial_charges"):
+            framework_params = merge_parameters(
+                framework_params, {"UseChargesFromCIFFile": True}
+            )
+
         parameters[f"Framework {i}"] = merge_parameters(
-            {
-                "FrameworkName": name,
-                "UnitCells": n_cells,
-            },
+            framework_params,
             framework.info,
         )
+
     return parameters
 
 

tests/requirements.txt

@@ -1,3 +1,3 @@
 https://gitlab.com/ase/ase/-/archive/master/ase-master.zip
 numpy==1.26.3
-pymatgen==2023.12.18
+pymatgen==2024.2.23

tests/test_calculator.py

@@ -128,6 +128,7 @@ def test_raspa_functional1(tmp_path):
 
 def test_raspa_functional2(tmp_path):
     atoms = bulk("Cu")
+    atoms.set_initial_charges([1.0] * len(atoms))
     atoms.calc = Raspa(
         directory=tmp_path,
         boxes=[{"BoxLengths": [1, 2, 3]}, {"BoxLengths": [4, 5, 6]}],
@@ -145,7 +146,7 @@ def test_raspa_functional2(tmp_path):
     assert Path(tmp_path, "simulation.input").exists()
     assert (
         Path(tmp_path / "simulation.input").read_text()
-        == "CutOff 12.8\nComponent 0 MoleculeName N2\n    MoleculeDefinition ExampleDefinition\nComponent 1 MoleculeName CO2\n    MoleculeDefinition ExampleDefinition\n    TranslationProbability 1.0\nBox 0\n    BoxLengths 1 2 3\nBox 1\n    BoxLengths 4 5 6\nFramework 0\n    FrameworkName framework0\n    UnitCells 12 12 12\n"
+        == "CutOff 12.8\nComponent 0 MoleculeName N2\n    MoleculeDefinition ExampleDefinition\nComponent 1 MoleculeName CO2\n    MoleculeDefinition ExampleDefinition\n    TranslationProbability 1.0\nBox 0\n    BoxLengths 1 2 3\nBox 1\n    BoxLengths 4 5 6\nFramework 0\n    FrameworkName framework0\n    UnitCells 12 12 12\n    UseChargesFromCIFFile Yes\n"
     )