torchref.base.reciprocal.grid_operations module

Grid operations for reciprocal space.

Functions for placing structure factors on grids and extracting them, which are essential for FFT-based calculations.

torchref.base.reciprocal.grid_operations.place_on_grid(hkls, structure_factor, grid_size, enforce_hermitian=True)

Place structure factors on a reciprocal-space grid.

Vectorized placement of batched structure factors on reciprocal-space grid.

Parameters:

• hkls (torch.Tensor) – Miller indices of shape (N, 3).

• structure_factor (torch.Tensor) – Structure factors of shape (N,) or (B, N) for batched input.

• grid_size (tuple or torch.Tensor) – Grid dimensions (Nx, Ny, Nz).

• enforce_hermitian (bool, optional) – Whether to enforce Hermitian symmetry. Default is True.

Returns:

Complex tensor grid of structure factors of shape (Nx, Ny, Nz) or (B, Nx, Ny, Nz) for batched input.

Return type:

torch.Tensor

torchref.base.reciprocal.grid_operations.extract_structure_factor_from_grid(reciprocal_grid, hkls)

Extract structure factors from reciprocal space grid at given Miller indices.

Parameters:

• reciprocal_grid (torch.Tensor) – Complex tensor of shape (Nx, Ny, Nz) or (B, Nx, Ny, Nz).

• hkls (torch.Tensor) – Miller indices of shape (N, 3).

Returns:

Structure factors of shape (N,) or (B, N) for batched input.

Return type:

torch.Tensor

torchref.base.reciprocal.grid_operations.apply_translation_phase(F_calc, hkl, translation_frac)

Apply translation phase shift to structure factors.

For a translation t in fractional coordinates, the structure factor transforms as: F’(hkl) = F(hkl) * exp(2πi * hkl · t)

Parameters:

• F_calc (torch.Tensor) – Complex structure factors of shape (N,).

• hkl (torch.Tensor) – Miller indices of shape (N, 3).

• translation_frac (torch.Tensor) – Translation vector in fractional coordinates of shape (3,).

Returns:

Phase-shifted structure factors of shape (N,).

Return type:

torch.Tensor