Merge pull request #11 from Quantum-Accelerators/Andrew-S-Rosen-patch-1

Use the actual RASPA executable in the GitHub Actions test suite

.github/workflows/tests.yaml

@@ -39,8 +39,14 @@ jobs:
           pip install -r tests/requirements.txt
           pip install .[dev]
 
+      - name: Install conda packages
+        run: conda install -c conda-forge raspa2
+
+      - name: Set up environment
+        run: echo "RASPA_DIR=/usr/share/miniconda" >> "$GITHUB_ENV"
+
       - name: Run tests with pytest
-        run: pytest --cov=raspa_ase --cov-report=xml
+        run: pytest --noconftest --cov=raspa_ase --cov-report=xml
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3

src/raspa_ase/calculator.py

@@ -55,7 +55,7 @@ def __init__(self, argv: list[str] | None = None) -> None:
     def run(
         self,
         directory: Path | str,
-        output_filename: Path | str,
+        output_filename: str,
     ) -> None:
         """
         Run the RASPA calculation.
@@ -80,10 +80,16 @@ class RaspaTemplate(CalculatorTemplate):
     RASPA template, used to define how to read and write RASPA files.
     """
 
-    def __init__(self) -> None:
+    def __init__(self, frameworks: list[Atoms] | None = None) -> None:
         """
         Initialize the RASPA template.
 
+        Parameters
+        ----------
+        frameworks
+            The frameworks to use, to be used in place of the `Atoms` object
+            the calculator is applied to.
+
         Returns
         -------
         None
@@ -96,6 +102,7 @@ def __init__(self) -> None:
 
         self.input_file = SIMULATION_INPUT
         self.output_file = f"{label}.out"
+        self.frameworks = frameworks
 
     def execute(self, directory: Path | str, profile: RaspaProfile) -> None:
         """
@@ -114,8 +121,8 @@ def execute(self, directory: Path | str, profile: RaspaProfile) -> None:
         """
         profile.run(directory, self.output_file)
 
-    @staticmethod
     def write_input(
+        self,
         directory: Path | str,
         atoms: Atoms,
         parameters: dict[str, Any],
@@ -142,7 +149,7 @@ def write_input(
         -------
         None
         """
-        frameworks = [atoms]
+        frameworks = self.frameworks if self.frameworks else [atoms]
         parameters = merge_parameters(parameters, get_framework_params([atoms]))
 
         write_simulation_input(parameters, directory / SIMULATION_INPUT)
@@ -369,7 +376,7 @@ def __init__(
             parameters = merge_parameters(parameters, {f"Box {i}": box})
 
         super().__init__(
-            template=RaspaTemplate(),
+            template=RaspaTemplate(frameworks=multiple_frameworks),
             profile=profile,
             directory=directory,
             parameters=parameters,

tests/test_calculator.py

@@ -1,8 +1,10 @@
+import os
 from pathlib import Path
 
 import pytest
 from ase import Atoms
 from ase.build import bulk
+from ase.io import read
 
 from raspa_ase.calculator import Raspa, RaspaProfile, RaspaTemplate
 
@@ -15,7 +17,10 @@ def test_profile_bad(monkeypatch):
 
 def test_profile():
     profile = RaspaProfile()
-    assert profile.argv == ["./bin/simulate", "simulation.input"]
+    assert profile.argv == [
+        f"{os.getenv('RASPA_DIR')}/bin/simulate",
+        "simulation.input",
+    ]
 
 
 def test_profile2():
@@ -25,7 +30,6 @@ def test_profile2():
 
 def test_run(monkeypatch, tmp_path):
     monkeypatch.chdir(tmp_path)
-    monkeypatch.setenv("RASPA_DIR", "bad_dir")
     RaspaProfile().run(tmp_path, tmp_path / "simulation.input")
 
 
@@ -37,8 +41,10 @@ def test_template():
 
 def test_template_execute(monkeypatch, tmp_path):
     monkeypatch.chdir(tmp_path)
+    with Path(tmp_path / "simulation.input").open(mode="w") as fd:
+        fd.write("")
     template = RaspaTemplate()
-    template.execute("bad_dir", RaspaProfile())
+    template.execute(tmp_path, RaspaProfile())
 
 
 def test_template_write_input(monkeypatch, tmp_path):
@@ -134,10 +140,32 @@ def test_multi_frameworks(tmp_path):
     atoms1.info = {"HeliumVoidFraction": 0.75}
     atoms2 = bulk("Fe")
     atoms = Atoms()
-    atoms.calc = Raspa(directory=tmp_path, multiple_frameworks=[atoms1, atoms2])
+    atoms.calc = Raspa(
+        directory=tmp_path,
+        multiple_frameworks=[atoms1, atoms2],
+        boxes=[{"BoxLengths": [1, 2, 3]}, {"BoxLengths": [4, 5, 6]}],
+        parameters={"CutOff": 12.8},
+        components=[
+            {"MoleculeName": "N2", "MoleculeDefinition": "ExampleDefinition"},
+            {
+                "MoleculeName": "CO2",
+                "MoleculeDefinition": "ExampleDefinition",
+                "TranslationProbability": 1.0,
+            },
+        ],
+    )
     atoms.get_potential_energy()
     assert Path(tmp_path, "simulation.input").exists()
+    input_str = Path(tmp_path / "simulation.input").read_text()
     assert (
-        Path(tmp_path / "simulation.input").read_text()
-        == "Framework 0\n    FrameworkName framework0\n    UnitCells 12 12 12\n    HeliumVoidFraction 0.75\nFramework 1\n    FrameworkName framework1\n    UnitCells 12 12 12\n"
+        "Framework 0\n    FrameworkName framework0\n    UnitCells 12 12 12\n    HeliumVoidFraction 0.75\n"
+        in input_str
+    )
+    assert (
+        "Framework 1\n    FrameworkName framework1\n    UnitCells 12 12 12\n"
+        in input_str
     )
+    assert Path(tmp_path / "framework0.cif").exists()
+    assert Path(tmp_path / "framework1.cif").exists()
+    assert read(tmp_path / "framework0.cif")[0].symbol == "Cu"
+    assert read(tmp_path / "framework1.cif")[0].symbol == "Fe"