TiO2 tests and tutorial

cspell.json

@@ -24,6 +24,7 @@
         "newaxis",
         "NIONS",
         "outcar",
+        "outcars",
         "pathify",
         "phonopy",
         "polarizabilities",

ramannoodle/polarizability/interpolation/__init__.py

@@ -174,7 +174,7 @@ def add_dof(  # pylint: disable=too-many-locals
                     f"due to symmetry, amplitude {duplicate} should not be specified"
                 )
 
-            if len(interpolation_x) <= interpolation_order:
+            if len(interpolation_x) - 1 <= interpolation_order:
                 raise InvalidDOFException(
                     f"insufficient amplitudes ({len(interpolation_x)}) available for"
                     f"{interpolation_order}-order interpolation"

test/tests/test_polarizability.py

@@ -11,8 +11,6 @@
 from ramannoodle.polarizability.interpolation import InterpolationPolarizabilityModel
 from ramannoodle.io.vasp import read_structural_symmetry_from_outcar
 from ramannoodle.exceptions import InvalidDOFException
-from ramannoodle.symmetry import StructuralSymmetry
-from ramannoodle import io
 
 # pylint: disable=protected-access
 
@@ -33,7 +31,7 @@ def test_find_duplicates(vectors: list[NDArray[np.float64]], known: bool) -> Non
     "outcar_path_fixture,displaced_atom_index, amplitudes, known_dof_added",
     [
         ("test/data/STO_RATTLED_OUTCAR", 0, np.array([-0.05, 0.05, 0.01, -0.01]), 1),
-        ("test/data/TiO2/PHONON_OUTCAR", 0, np.array([0.01]), 72),
+        ("test/data/TiO2/phonons_OUTCAR", 0, np.array([0.01]), 72),
     ],
     indirect=["outcar_path_fixture"],
 )
@@ -58,7 +56,7 @@ def test_add_dof(
     "outcar_path_fixture,displaced_atom_index, amplitudes",
     [
         ("test/data/STO_RATTLED_OUTCAR", 0, np.array([0.01, 0.01])),
-        ("test/data/TiO2/PHONON_OUTCAR", 0, np.array([-0.01, 0.01])),
+        ("test/data/TiO2/phonons_OUTCAR", 0, np.array([-0.01, 0.01])),
     ],
     indirect=["outcar_path_fixture"],
 )
@@ -77,71 +75,3 @@ def test_overspecified_dof(
         model.add_dof(displacement, amplitudes, polarizabilities, 1)
 
     assert "should not be specified" in str(error.value)
-
-
-@pytest.mark.parametrize(
-    "outcar_symmetry_fixture,ref_eps,to_add,additional_references",
-    [
-        (
-            "test/data/TiO2/PHONON_OUTCAR",
-            "test/data/TiO2/ref_OUTCAR",
-            [
-                ["test/data/TiO2/Ti5_0.1z_OUTCAR", "test/data/TiO2/Ti5_0.2z_OUTCAR"],
-                ["test/data/TiO2/Ti5_0.1x_OUTCAR", "test/data/TiO2/Ti5_0.2x_OUTCAR"],
-                [
-                    "test/data/TiO2/O43_0.1z_OUTCAR",
-                    "test/data/TiO2/O43_0.2z_OUTCAR",
-                    "test/data/TiO2/O43_m0.1z_OUTCAR",
-                    "test/data/TiO2/O43_m0.2z_OUTCAR",
-                ],
-                [
-                    "test/data/TiO2/O43_0.1x_OUTCAR",
-                    "test/data/TiO2/O43_0.2x_OUTCAR",
-                ],
-                [
-                    "test/data/TiO2/O43_0.1y_OUTCAR",
-                    "test/data/TiO2/O43_0.2y_OUTCAR",
-                ],
-            ],
-            [
-                "test/data/TiO2/Ti5_m0.2z_OUTCAR",
-                "test/data/TiO2/Ti5_m0.1z_OUTCAR",
-                "test/data/TiO2/O43_m0.1x_OUTCAR",
-                "test/data/TiO2/O43_m0.2x_OUTCAR",
-                "test/data/TiO2/O43_m0.1y_OUTCAR",
-                "test/data/TiO2/O43_m0.2y_OUTCAR",
-            ],
-        ),
-    ],
-    indirect=["outcar_symmetry_fixture"],
-)
-def test_get_polarizability(
-    outcar_symmetry_fixture: StructuralSymmetry,
-    ref_eps: str,
-    to_add: list[str],
-    additional_references: list[str],
-) -> None:
-    """Test."""
-    symmetry = outcar_symmetry_fixture
-    _, polarizability = io.read_positions_and_polarizability(
-        ref_eps, file_format="outcar"
-    )
-    model = InterpolationPolarizabilityModel(symmetry, polarizability)
-    for outcar_path_list in to_add:
-        model.add_dof_from_files(
-            outcar_path_list, file_format="outcar", interpolation_order=2
-        )
-
-    # Tests
-    total_outcar_paths = additional_references
-    for outcar_path in to_add:
-        total_outcar_paths += outcar_path
-    for outcar_path in total_outcar_paths:
-        positions, known_polarizability = io.read_positions_and_polarizability(
-            outcar_path, file_format="outcar"
-        )
-        cartesian_displacement = symmetry.get_cartesian_displacement(
-            positions - symmetry.get_fractional_positions()
-        )
-        model_polarizability = model.get_polarizability(cartesian_displacement)
-        assert np.isclose(model_polarizability, known_polarizability, atol=1e-4).all()

test/tests/test_spectrum.py

@@ -0,0 +1,96 @@
+"""Testing for spectra."""
+
+from pathlib import Path
+
+import numpy as np
+
+import pytest
+
+from ramannoodle.polarizability.interpolation import InterpolationPolarizabilityModel
+from ramannoodle.symmetry import StructuralSymmetry
+from ramannoodle import io
+
+# pylint: disable=protected-access
+
+
+def _get_all_eps_outcars(directory: str) -> list[str]:
+    """Return name of all eps OUTCARs in a directory."""
+    path = Path(directory)
+    return [str(item) for item in path.glob("*eps_OUTCAR")]
+
+
+def _validate_polarizabilities(
+    model: InterpolationPolarizabilityModel, data_directory: str
+) -> None:
+    for outcar_path in _get_all_eps_outcars(data_directory):
+        positions, known_polarizability = io.read_positions_and_polarizability(
+            f"{outcar_path}", file_format="outcar"
+        )
+        cartesian_displacement = model._structural_symmetry.get_cartesian_displacement(
+            positions - model._structural_symmetry.get_fractional_positions()
+        )
+        model_polarizability = model.get_polarizability(cartesian_displacement)
+        assert np.isclose(model_polarizability, known_polarizability, atol=1e-4).all()
+
+
+@pytest.mark.parametrize(
+    "outcar_symmetry_fixture,data_directory,dof_eps_outcars",
+    [
+        (
+            "test/data/TiO2/phonons_OUTCAR",
+            "test/data/TiO2/",
+            [
+                ["Ti5_0.1z_eps_OUTCAR", "Ti5_0.2z_eps_OUTCAR"],
+                ["Ti5_0.1x_eps_OUTCAR", "Ti5_0.2x_eps_OUTCAR"],
+                [
+                    "O43_0.1z_eps_OUTCAR",
+                    "O43_0.2z_eps_OUTCAR",
+                    "O43_m0.1z_eps_OUTCAR",
+                    "O43_m0.2z_eps_OUTCAR",
+                ],
+                ["O43_0.1x_eps_OUTCAR", "O43_0.2x_eps_OUTCAR"],
+                ["O43_0.1y_eps_OUTCAR", "O43_0.2y_eps_OUTCAR"],
+            ],
+        ),
+    ],
+    indirect=["outcar_symmetry_fixture"],
+)
+def test_spectrum(
+    outcar_symmetry_fixture: StructuralSymmetry,
+    data_directory: str,
+    dof_eps_outcars: list[str],
+) -> None:
+    """Test a spectrum calculation."""
+    # Setup model
+    symmetry = outcar_symmetry_fixture
+    _, polarizability = io.read_positions_and_polarizability(
+        f"{data_directory}/ref_eps_OUTCAR", file_format="outcar"
+    )
+    model = InterpolationPolarizabilityModel(symmetry, polarizability)
+    for outcar_names in dof_eps_outcars:
+        model.add_dof_from_files(
+            [f"{data_directory}/{name}" for name in outcar_names],
+            file_format="outcar",
+            interpolation_order=2,
+        )
+
+    _validate_polarizabilities(model, data_directory)
+
+    # Spectrum test
+    with np.load(f"{data_directory}/known_spectrum.npz") as known_spectrum:
+        phonons = io.read_phonons(
+            f"{data_directory}/phonons_OUTCAR", file_format="outcar"
+        )
+        spectrum = phonons.get_raman_spectrum(model)
+        wavenumbers, intensities = spectrum.measure(
+            laser_correction=True,
+            laser_wavelength=532,
+            bose_einstein_correction=True,
+            temperature=300,
+        )
+
+        known_wavenumbers = known_spectrum["wavenumbers"]
+        known_intensities = known_spectrum["intensities"]
+
+        assert np.isclose(wavenumbers, known_wavenumbers).all()
+        assert np.isclose(intensities, known_intensities, atol=1e-4).all()

test/tests/test_symmetry.py

@@ -51,7 +51,7 @@ def test_check_orthogonal(
     "outcar_symmetry_fixture, known_nonequivalent_atoms,"
     "known_orthogonal_displacements, known_displacements_shape",
     [
-        ("test/data/TiO2/PHONON_OUTCAR", 2, 36, [2] * 36),
+        ("test/data/TiO2/phonons_OUTCAR", 2, 36, [2] * 36),
         ("test/data/STO_RATTLED_OUTCAR", 135, 1, [1]),
         ("test/data/LLZO_OUTCAR", 9, 32, [1] * 32),
     ],

test/tests/test_vasp.py

@@ -19,7 +19,7 @@
     "known_first_displacement, known_last_displacement",
     [
         (
-            "test/data/TiO2/PHONON_OUTCAR",
+            "test/data/TiO2/phonons_OUTCAR",
             PHONONS_OUTCAR_NUM_ATOMS,
             np.array([811.691808, 811.691808, 811.691808, 811.691808]),
             np.array([-0.068172, 0.046409, 0.000000]) / np.sqrt(ATOMIC_WEIGHTS["Ti"]),

test/tests/test_vasp_utils.py

@@ -43,7 +43,7 @@ def test_fail_get_atomic_symbol_from_potcar_line(potcar_line: str) -> None:
 
 @pytest.mark.parametrize(
     "outcar_file_fixture, known",
-    [("test/data/TiO2/PHONON_OUTCAR", ["Ti"] * 36 + ["O"] * 72)],
+    [("test/data/TiO2/phonons_OUTCAR", ["Ti"] * 36 + ["O"] * 72)],
     indirect=["outcar_file_fixture"],
 )
 def test_read_atomic_symbols_from_outcar(
@@ -137,7 +137,7 @@ def test_read_polarizability_from_outcar(
     "outcar_file_fixture, known_lattice",
     [
         (
-            "test/data/TiO2/PHONON_OUTCAR",
+            "test/data/TiO2/phonons_OUTCAR",
             np.array(
                 [
                     [11.3768434223, 0.0000000000, 0.0000000000],