added convolution, naming: read->load

docs/source/api.rst

@@ -4,7 +4,7 @@ API
 .. autosummary::
    :toctree: generated
 
-   ramannoodle.io.vasp
+   ramannoodle.io
    ramannoodle.dynamics
    ramannoodle.polarizability
    ramannoodle.spectrum

docs/source/generated/ramannoodle.io.rst

@@ -0,0 +1,13 @@
+ramannoodle.io
+==============
+
+.. automodule:: ramannoodle.io
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      read_phonons
+      read_positions_and_polarizability
+      read_structural_symmetry

docs/source/generated/ramannoodle.io.vasp.rst

@@ -8,6 +8,6 @@
 
    .. autosummary::
 
-      load_phonons_from_outcar
-      load_positions_and_polarizability_from_outcar
-      load_structural_symmetry_from_outcar
+      read_phonons_from_outcar
+      read_positions_and_polarizability_from_outcar
+      read_structural_symmetry_from_outcar

docs/source/generated/ramannoodle.polarizability.rst

@@ -8,5 +8,4 @@
 
    .. autosummary::
 
-      InterpolationPolarizabilityModel
       PolarizabilityModel

docs/source/ramannoodle.polarizability.interpolation.rst

@@ -0,0 +1,10 @@
+ramannoodle.polarizability.interpolation package
+================================================
+
+Module contents
+---------------
+
+.. automodule:: ramannoodle.polarizability.interpolation
+   :members:
+   :undoc-members:
+   :show-inheritance:

ramannoodle/io/__init__.py

@@ -9,15 +9,15 @@
 from . import vasp
 
 # These dictionaries map between file_format's and appropriate loading functions.
-_PHONON_LOADERS = {"outcar": vasp.load_phonons_from_outcar}
+_PHONON_LOADERS = {"outcar": vasp.read_phonons_from_outcar}
 _POSITION_AND_POLARIZABILITY_LOADERS = {
-    "outcar": vasp.load_positions_and_polarizability_from_outcar
+    "outcar": vasp.read_positions_and_polarizability_from_outcar
 }
-_STRUCTURAL_SYMMETRY_LOADERS = {"outcar": vasp.load_structural_symmetry_from_outcar}
+_STRUCTURAL_SYMMETRY_LOADERS = {"outcar": vasp.read_structural_symmetry_from_outcar}
 
 
-def load_phonons(filepath: str | Path, file_format: str) -> Phonons:
-    """Extract phonons from a file.
+def read_phonons(filepath: str | Path, file_format: str) -> Phonons:
+    """Read phonons from a file.
 
     Parameters
     ----------
@@ -39,11 +39,11 @@ def load_phonons(filepath: str | Path, file_format: str) -> Phonons:
         raise ValueError(f"unsupported format: {file_format}") from exc
 
 
-def load_positions_and_polarizability(
+def read_positions_and_polarizability(
     filepath: str | Path,
     file_format: str,
 ) -> tuple[NDArray[np.float64], NDArray[np.float64]]:
-    """Extract fractional positions and polarizability from a file.
+    """Read fractional positions and polarizability from a file.
 
     Parameters
     ----------
@@ -67,10 +67,10 @@ def load_positions_and_polarizability(
         raise ValueError(f"unsupported format: {file_format}") from exc
 
 
-def load_structural_symmetry(
+def read_structural_symmetry(
     filepath: str | Path, file_format: str
 ) -> StructuralSymmetry:
-    """Extract structural symmetry from a file.
+    """Read structural symmetry from a file.
 
     Parameters
     ----------

ramannoodle/io/vasp/__init__.py

@@ -18,7 +18,7 @@
 from ...exceptions import NoMatchingLineFoundException, InvalidFileException
 
 
-def load_phonons_from_outcar(filepath: str | Path) -> Phonons:
+def read_phonons_from_outcar(filepath: str | Path) -> Phonons:
     """Extract phonons from a VASP OUTCAR file.
 
     Parameters
@@ -76,7 +76,7 @@ def load_phonons_from_outcar(filepath: str | Path) -> Phonons:
         return Phonons(wavenumbers, cartesian_displacements)
 
 
-def load_positions_and_polarizability_from_outcar(
+def read_positions_and_polarizability_from_outcar(
     filepath: str | Path,
 ) -> tuple[NDArray[np.float64], NDArray[np.float64]]:
     """Extract fractional positions and polarizability from a VASP OUTCAR file.
@@ -107,7 +107,7 @@ def load_positions_and_polarizability_from_outcar(
         return positions, polarizability
 
 
-def load_structural_symmetry_from_outcar(
+def read_structural_symmetry_from_outcar(
     filepath: str | Path,
 ) -> StructuralSymmetry:
     """Extract structural symmetry from a VASP OUTCAR file.

ramannoodle/polarizability/interpolation/__init__.py

@@ -222,7 +222,7 @@ def add_dof_from_files(
         polarizabilities = []
         filepaths = pathify_as_list(filepaths)
         for filepath in filepaths:
-            fractional_positions, polarizability = io.load_positions_and_polarizability(
+            fractional_positions, polarizability = io.read_positions_and_polarizability(
                 filepath, file_format
             )
             displacement = calculate_displacement(

ramannoodle/spectrum/spectrum_utils.py

@@ -44,3 +44,40 @@ def get_laser_correction(
 
     """
     return ((wavenumbers - laser_wavenumber) / 10000) ** 4 / wavenumbers
+
+
+def convolve_intensities(
+    wavenumbers: NDArray[np.float64],
+    intensities: NDArray[np.float64],
+    function: str = "gaussian",
+    width: float = 5,
+    out_wavenumbers: NDArray[np.float64] | None = None,
+) -> tuple[NDArray[np.float64], NDArray[np.float64]]:
+    """Convolves and smooths intensities."""
+    if out_wavenumbers is None:
+        out_wavenumbers = np.linspace(np.min(wavenumbers), np.max(wavenumbers), 1000)
+
+    out_wavenumbers = np.array(out_wavenumbers)
+    convolved_intensities = out_wavenumbers * 0
+    for wavenumber, intensity in zip(wavenumbers, intensities):
+        factor = 0
+        if function == "gaussian":
+            factor = (
+                1
+                / width
+                * 1
+                / np.sqrt(2 * np.pi)
+                * np.exp(-((wavenumber - out_wavenumbers) ** 2) / (2 * width**2))
+            )
+        elif function == "lorentzian":
+            factor = (
+                1
+                / np.pi
+                * 0.5
+                * width
+                / ((wavenumber - out_wavenumbers) ** 2 + (0.5 * width) ** 2)
+            )
+        else:
+            raise ValueError(f"unsupported convolution type: {type}")
+        convolved_intensities += factor * intensity
+    return (out_wavenumbers, convolved_intensities)

test/tests/test_polarizability.py

@@ -9,7 +9,7 @@
 
 from ramannoodle.polarizability.polarizability_utils import find_duplicates
 from ramannoodle.polarizability.interpolation import InterpolationPolarizabilityModel
-from ramannoodle.io.vasp import load_structural_symmetry_from_outcar
+from ramannoodle.io.vasp import read_structural_symmetry_from_outcar
 from ramannoodle.exceptions import InvalidDOFException
 
 # pylint: disable=protected-access
@@ -42,7 +42,7 @@ def test_add_dof(
     known_dof_added: int,
 ) -> None:
     """Test."""
-    symmetry = load_structural_symmetry_from_outcar(outcar_path_fixture)
+    symmetry = read_structural_symmetry_from_outcar(outcar_path_fixture)
     model = InterpolationPolarizabilityModel(symmetry, np.zeros((3, 3)))
     displacement = symmetry._fractional_positions * 0
     displacement[displaced_atom_index][0] = 1.0
@@ -66,7 +66,7 @@ def test_overspecified_dof(
     amplitudes: NDArray[np.float64],
 ) -> None:
     """Test."""
-    symmetry = load_structural_symmetry_from_outcar(outcar_path_fixture)
+    symmetry = read_structural_symmetry_from_outcar(outcar_path_fixture)
     model = InterpolationPolarizabilityModel(symmetry, np.zeros((3, 3)))
     displacement = symmetry._fractional_positions * 0
     displacement[displaced_atom_index][0] = 1.0
@@ -79,7 +79,7 @@ def test_overspecified_dof(
 
 def test_get_polarizability() -> None:
     """Test."""
-    symmetry = load_structural_symmetry_from_outcar(
+    symmetry = read_structural_symmetry_from_outcar(
         Path("test/data/TiO2/PHONON_OUTCAR")
     )
     model = InterpolationPolarizabilityModel(symmetry, np.diag([2, 2, 2]))

test/tests/test_symmetry.py

@@ -12,7 +12,7 @@
     is_orthogonal_to_all,
     get_fractional_positions_permutation_matrix,
 )
-from ramannoodle.io.vasp import load_structural_symmetry_from_outcar
+from ramannoodle.io.vasp import read_structural_symmetry_from_outcar
 
 
 @pytest.mark.parametrize(
@@ -67,7 +67,7 @@ def test_structural_symmetry(
 ) -> None:
     """Test."""
     # Equivalent atoms test
-    symmetry = load_structural_symmetry_from_outcar(outcar_path_fixture)
+    symmetry = read_structural_symmetry_from_outcar(outcar_path_fixture)
     assert symmetry.get_num_nonequivalent_atoms() == known_nonequivalent_atoms
 
     # Equivalent displacement test

test/tests/test_vasp.py

@@ -7,7 +7,7 @@
 import pytest
 
 from ramannoodle.io import (
-    load_phonons,
+    read_phonons,
 )
 from ramannoodle.globals import ATOMIC_WEIGHTS
 
@@ -28,15 +28,15 @@
     ],
     indirect=["outcar_path_fixture"],
 )
-def test_load_phonons_from_outcar(
+def test_read_phonons_from_outcar(
     outcar_path_fixture: Path,
     known_num_atoms: int,
     known_wavenumbers: NDArray[np.float64],
     known_first_displacement: NDArray[np.float64],
     known_last_displacement: NDArray[np.float64],
 ) -> None:
     """Test."""
-    phonons = load_phonons(outcar_path_fixture, file_format="outcar")
+    phonons = read_phonons(outcar_path_fixture, file_format="outcar")
 
     known_degrees_of_freedom = known_num_atoms * 3
     assert phonons.get_wavenumbers().shape == (known_degrees_of_freedom,)