torchref.base.scattering.anomalous_table module

Anomalous scattering factor lookup (f’ and f’’).

Uses gemmi for wavelength-dependent f’/f’’ values via the Cromer-Liberman calculation. These corrections account for the dispersive (f’) and absorptive (f’’) components of X-ray scattering near atomic absorption edges.

The complete scattering factor is: f(s, lambda) = f0(s) + f’(lambda) + i*f’’(lambda)

where f0 is the normal (Thomson) scattering factor and f’/f’’ are the wavelength-dependent anomalous corrections.

torchref.base.scattering.anomalous_table.wavelength_to_energy_ev(wavelength)[source]

Convert X-ray wavelength in Angstroms to energy in eV.

Uses the gemmi.hc constant (hc in eV*Angstrom).

Parameters:

wavelength (float) – Wavelength in Angstroms

Returns:

Energy in eV

Return type:

float

torchref.base.scattering.anomalous_table.get_anomalous_correction(element, wavelength)[source]

Get f’ and f’’ for a single element at given wavelength.

Uses the Cromer-Liberman calculation via gemmi. Returns the standard crystallographic f’ and f’’ values as used in International Tables.

Parameters:

  • element (str) – Element symbol (e.g., ‘Fe’, ‘Hg’, ‘Se’)

  • wavelength (float) – X-ray wavelength in Angstroms

Returns:

  • f_prime (float) – Real anomalous correction (electrons)

  • f_double_prime (float) – Imaginary anomalous correction (electrons)

Return type:

Tuple[float, float]

Examples

>>> f_prime, f_double_prime = get_anomalous_correction('Se', 0.9792)
>>> print(f"Se at Se K-edge: f'={f_prime:.2f}, f''={f_double_prime:.2f}")

Notes

The gemmi.cromer_liberman function expects energy in eV, not keV.

torchref.base.scattering.anomalous_table.get_significant_elements(elements, wavelength, threshold=0.5)[source]

Find elements with significant anomalous scattering.

An element is considered significant if |f'| > threshold OR |f''| > threshold. This filtering avoids unnecessary computation for light atoms (C, N, O, H) which have negligible anomalous contributions at typical wavelengths.

Parameters:

  • elements (list of str) – List of unique element symbols

  • wavelength (float) – X-ray wavelength in Angstroms

  • threshold (float, optional) – Significance threshold in electrons (default: 0.5)

Returns:

{element: (f_prime, f_double_prime)} for significant elements only

Return type:

dict

Examples

>>> elements = ['C', 'N', 'O', 'S', 'Fe', 'Zn']
>>> significant = get_significant_elements(elements, wavelength=1.0)
>>> print(f"Significant anomalous scatterers: {list(significant.keys())}")
torchref.base.scattering.anomalous_table.get_anomalous_corrections_by_indices(element_list, significant_elements, device, dtype)[source]

Get anomalous corrections and mask for atoms needing correction.

This function creates tensors suitable for vectorized computation of the anomalous correction to structure factors.

Parameters:

  • element_list (list of str) – Element symbols for all atoms (length n_atoms)

  • significant_elements (dict) – {element: (f_prime, f_double_prime)} from get_significant_elements()

  • device (torch.device) – Device for output tensors

  • dtype (torch.dtype) – Data type for output tensors

Returns:

  • mask (torch.Tensor) – Boolean mask of shape (n_atoms,) - True for atoms needing correction

  • f_prime (torch.Tensor) – f’ values for significant atoms only (n_significant,)

  • f_double_prime (torch.Tensor) – f’’ values for significant atoms only (n_significant,)

Return type:

Tuple[Tensor, Tensor, Tensor]

Examples

>>> elements = ['C', 'C', 'N', 'Fe', 'O', 'Fe']
>>> significant = {'Fe': (-1.2, 3.1)}
>>> mask, fp, fdp = get_anomalous_corrections_by_indices(
...     elements, significant, torch.device('cpu'), torch.float32
... )
>>> print(f"Atoms needing correction: {mask.sum().item()}")  # 2 (two Fe atoms)