torchref.base.fourier.grid module

Grid generation functions for crystallographic calculations.

Functions for creating real-space and reciprocal-space grids.

torchref.base.fourier.grid.get_real_grid(cell=None, fractional_matrix=None, max_res=0.8, gridsize=None, device=None)[source]

Generate a real space grid for electron density calculations.

Parameters:

  • cell (torch.Tensor) – Unit cell parameters [a, b, c, alpha, beta, gamma].

  • fractional_matrix (torch.Tensor, optional) – Pre-computed fractionalization matrix.

  • max_res (float, optional) – Maximum resolution for automatic grid sizing. Default is 0.8.

  • gridsize (torch.Tensor or array-like, optional) – Explicit grid dimensions [nx, ny, nz]. If None, calculated from max_res.

  • device (torch.device or str, optional) – Device for tensor placement. If None, inferred from fractional_matrix or cell (whichever tensor is provided); falls back to CPU.

Returns:

Real space grid of shape (nx, ny, nz, 3) containing Cartesian coordinates.

Return type:

torch.Tensor

torchref.base.fourier.grid.find_grid_size(cell, max_res)[source]

Calculate grid size based on unit cell and resolution.

Parameters:

  • cell (torch.Tensor) – Unit cell parameters [a, b, c, alpha, beta, gamma].

  • max_res (float) – Maximum resolution in Angstroms.

Returns:

Grid dimensions [nx, ny, nz] as int32.

Return type:

torch.Tensor

torchref.base.fourier.grid.get_real_grid_numpy(cell, max_res=0.8, gridsize=None)[source]

Generate a real-space grid of Cartesian coordinates (NumPy version).

Creates a 3D grid in fractional coordinates and converts it to Cartesian coordinates. Grid points are placed at cell edges following CCTBX convention.

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.

  • max_res (float, optional) – Maximum resolution in Angstroms for grid spacing. Default is 0.8. Ignored if gridsize is provided.

  • gridsize (list or numpy.ndarray, optional) – Explicit grid dimensions [nx, ny, nz]. If provided, overrides max_res.

Returns:

Real-space grid coordinates with shape (nx, ny, nz, 3).

Return type:

numpy.ndarray

torchref.base.fourier.grid.get_grids(cell, max_res=0.8)[source]

Generate real-space and reciprocal-space grids for Fourier transforms.

Creates a 3D grid in fractional coordinates and converts it to Cartesian coordinates, along with an empty reciprocal space grid.

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.

  • max_res (float, optional) – Maximum resolution in Angstroms for grid spacing. Default is 0.8.

Returns:

  • recgrid (numpy.ndarray) – Empty reciprocal space grid with shape determined by resolution.

  • xyz_real_grid (numpy.ndarray) – Real-space grid coordinates with shape (nx, ny, nz, 3).

torchref.base.fourier.grid.put_hkl_on_grid(real_space_grid, diff, hkl)[source]

Place structure factors on a reciprocal space grid.

Maps structure factor values to their corresponding positions on a 3D reciprocal space grid based on Miller indices.

Parameters:

  • real_space_grid (numpy.ndarray) – Real-space grid used to determine the reciprocal grid dimensions. Shape should be (nx, ny, nz, 3) or similar.

  • diff (numpy.ndarray) – Structure factor values (complex) to place on the grid.

  • hkl (numpy.ndarray) – Miller indices with shape (N, 3), used as grid indices.

Returns:

Complex reciprocal space grid with shape (nx, ny, nz).

Return type:

numpy.ndarray