torchref.base.coordinates.transforms_numpy module
NumPy implementations of coordinate transformation functions.
These functions provide CPU-based coordinate transformations for use when GPU acceleration is not needed or available.
- torchref.base.coordinates.transforms_numpy.get_fractional_matrix(cell)[source]
Calculate the fractional-to-Cartesian transformation matrix.
Constructs the matrix B that transforms fractional coordinates to Cartesian coordinates based on the unit cell parameters.
- Parameters:
cell (numpy.ndarray or list) – Unit cell parameters [a, b, c, alpha, beta, gamma] where lengths are in Angstroms and angles are in degrees.
- Returns:
3x3 transformation matrix B such that cart = frac @ B.T.
- Return type:
- torchref.base.coordinates.transforms_numpy.get_inv_fractional_matrix(cell)[source]
Calculate the Cartesian-to-fractional transformation matrix.
Computes the inverse of the fractional matrix for converting Cartesian coordinates to fractional coordinates.
- Parameters:
cell (numpy.ndarray or list) – Unit cell parameters [a, b, c, alpha, beta, gamma] where lengths are in Angstroms and angles are in degrees.
- Returns:
3x3 inverse transformation matrix B_inv such that frac = cart @ B_inv.T.
- Return type:
- torchref.base.coordinates.transforms_numpy.cartesian_to_fractional(xyz, cell)[source]
Convert Cartesian coordinates to fractional coordinates.
- Parameters:
xyz (numpy.ndarray) – Cartesian coordinates with shape (N, 3).
cell (numpy.ndarray or list) – Unit cell parameters [a, b, c, alpha, beta, gamma] where lengths are in Angstroms and angles are in degrees.
- Returns:
Fractional coordinates with shape (N, 3).
- Return type:
- torchref.base.coordinates.transforms_numpy.fractional_to_cartesian(xyz_fractional, cell)[source]
Convert fractional coordinates to Cartesian coordinates.
- Parameters:
xyz_fractional (numpy.ndarray) – Fractional coordinates with shape (N, 3).
cell (numpy.ndarray or list) – Unit cell parameters [a, b, c, alpha, beta, gamma] where lengths are in Angstroms and angles are in degrees.
- Returns:
Cartesian coordinates with shape (N, 3).
- Return type:
- torchref.base.coordinates.transforms_numpy.convert_coords_to_fractional(df, cell)[source]
Convert coordinates from a DataFrame to fractional coordinates.
Extracts x, y, z columns from a DataFrame and converts them from Cartesian to fractional coordinates.
- Parameters:
df (pandas.DataFrame) – DataFrame containing ‘x’, ‘y’, ‘z’ columns with Cartesian coordinates.
cell (numpy.ndarray or list) – Unit cell parameters [a, b, c, alpha, beta, gamma] where lengths are in Angstroms and angles are in degrees.
- Returns:
Fractional coordinates with shape (N, 3).
- Return type: