midas-hkls 0.5.0

Pure-Python crystallography, CIF I/O, and differentiable structure factors for X-ray diffraction.

midas-hkls

Crystallography toolkit for MIDAS: HKL list generation (sginfo-equivalent), CIF I/O, and differentiable structure factors in PyTorch for intensity-aware peak fitting in pf-HEDM, ff-HEDM, and powder diffraction.

What it provides

Always-on (numpy only)

• SpaceGroup — load by number, Hermann-Mauguin symbol, or Hall symbol; expose symmetry operations, systematic absences, equivalent reflections, multiplicities, Laue class, centering. All 230 SGs.
• Lattice — direct/reciprocal metric tensors, d-spacings, Bragg 2θ, with per-crystal-system convenience constructors.
• generate_hkls() — enumerate Laue-unique allowed reflections within a d-spacing or 2θ cutoff, sorted by d-descending, with multiplicities.
• Atom, Crystal — asymmetric-unit description with symmetry expansion to the full unit cell (special-position dedupe).
• Cromer-Mann (IT92) form factors f(s) for 98 neutral elements.
• CLI: midas-hkls gen|info|list (drop-in for GetHKLList).

Optional: [cif] (gemmi) or [cif-pure] (pycifrw)

• read_cif(path) -> Crystal and write_cif(crystal, path) — full CIF1.1 with anisotropic ADPs (gemmi) or isotropic-only (pycifrw fallback).
• Origin-choice and rhombohedral/hexagonal settings handled correctly via the resolved Hall symbol.

Optional: [torch] — differentiable structure factors

• structure_factors(crystal_t, hkl, *, anomalous=False) returns complex F_hkl tensor, differentiable through:
  • atomic fractional coordinates,
  • occupancies,
  • isotropic B-factors and anisotropic U-tensors,
  • the six lattice parameters,
  • wavelength (when anomalous=True).
• intensity_from_crystal(...) and powder_intensity(F, m, 2θ) for Lorentz-polarization-weighted powder I_hkl.
• anomalous_correction(elements, wavelength_A) for f', f'' (Cromer-Liberman tables, 92 elements × 401 log-spaced energies, 100 eV–200 keV).
• Symmetry expansion is exact integer arithmetic; the autograd graph is rebuilt each forward call so gradients flow through ASU handles to UC atoms.

Quick start

1. Generate HKL list

from midas_hkls import SpaceGroup, Lattice, generate_hkls

sg  = SpaceGroup.from_number(225)              # CeO₂ / Cu / Au / NaCl  (Fm-3m)
lat = Lattice.for_system("cubic", a=5.411)
refs = generate_hkls(sg, lat, wavelength_A=0.173, two_theta_max_deg=15.0)
for r in refs:
    print(r.ring_nr, (r.h, r.k, r.l), r.d_spacing, r.two_theta_deg, r.multiplicity)

2. Read a structure & compute differentiable F_hkl

import torch
from midas_hkls import read_cif, generate_hkls, structure_factors, intensity_from_crystal

xt = read_cif("ceo2.cif")
xt_t = xt.to_torch(requires_grad={"B_iso": True})         # mark B-factors trainable
refs = generate_hkls(xt.space_group, xt.lattice,
                     wavelength_A=0.173, two_theta_max_deg=20.0)

F, I = intensity_from_crystal(xt_t, refs, wavelength_A=0.173, polarization=0.5)

# Fit B-factors against an experimental I_obs (log-space residual)
opt = torch.optim.Adam([xt_t.B_iso_asu], lr=0.05)
for _ in range(300):
    opt.zero_grad()
    _, I = intensity_from_crystal(xt_t, refs, wavelength_A=0.173)
    loss = ((torch.log(I + 1e-3) - torch.log(I_obs + 1e-3)) ** 2).mean()
    loss.backward()
    opt.step()

3. Anomalous scattering (resonant f', f'')

from midas_hkls import structure_factors, anomalous_correction

# Add f', f'' from Cromer-Liberman tables at the experimental wavelength
F_anomalous = structure_factors(xt_t, hkls,
                                wavelength_A=1.5418, anomalous=True)

# Or get f', f'' directly per element
fp, fpp = anomalous_correction(["Fe", "O"], wavelength_A=1.5418)

CLI

midas-hkls gen --sg 225 --lat 5.411 5.411 5.411 90 90 90 --wavelength 0.173 \
               --two-theta-max 15.0 -o ceo2.csv
midas-hkls info --sg "Fm-3m" --ops
midas-hkls list

Install

pip install midas-hkls                       # base: numpy only
pip install "midas-hkls[cif]"                # + gemmi (CIF I/O)
pip install "midas-hkls[torch]"              # + torch (structure factors)
pip install "midas-hkls[all]"                # all of the above

Parity & validation

• HKL generation: byte-for-byte parity vs. MIDAS's GetHKLList (sginfo) on CeO₂, LaB₆, Si, α-Fe, α-Ti, calcite, Pnma, P21/c.
• Structure factors: |F| matches gemmi.StructureFactorCalculatorX to <0.01% on CeO₂, Si, α-Fe, LaB₆, calcite (after applying gemmi's change_occupancies_to_crystallographic to align conventions).
• Anomalous f', f'' matches gemmi.cromer_liberman exactly on grid energies and within 0.05 between grid points.
• torch.autograd.gradcheck verified on |F|² w.r.t. lattice parameters and atomic positions in float64.

Conventions

• Lengths in Å; angles in degrees.
• B-factor B = 8π² U (Ų); CIF U_ij stored in fractional basis.
• Wavelengths in Å; energies in eV (E_eV = 12398.4 / λ_Å).
• Symmetry operations stored as integer Seitz matrices over translation base STBF=12 — exact-arithmetic absence detection, no float fuzz.
• Equivalent HKLs include Friedel pairs (centric structure factor under X-ray Laue symmetry).

Roadmap (post v0.4.0)

• Wyckoff special-position constraints during refinement.
• Aspherical / multipole atomic form factors.
• Magnetic structure factors.
• Expanded ion form factors (currently only neutral atoms).

Origin

The 530-entry Hall-symbol table is extracted verbatim from sginfo (© 1994-96 Ralf W. Grosse-Kunstleve, public domain). IT92 form factors and Cromer-Liberman anomalous tables are exported from gemmi at packaging time and ship as JSON.