Examples

Runnable examples are provided in examples/. Each experiment directory contains an experiment.yaml, a starting structure .cif, and experimental .cif_pets data.

Colmey et al. (2026)

The examples in examples/Colmey_et_al_2026 reproduce the refinements from Colmey et al. (2026), The role of absorption in three-dimensional electron diffraction dynamical structure refinement (arXiv:2602.08935).

Six experiments compare refinements with and without absorption:

Material	Without absorption	With absorption
Alpha-quartz	quartz-no-abs	quartz-absorption
Borane	borane-no-abs	borane-absorption
CsPbBr₃	cspbbr3-no-abs	cspbbr3-absorption

The experimental data were originally published by Suresh et al. (2024), Ionisation of atoms determined by kappa refinement against 3D electron diffraction data (Nature Communications 15, 9066).

Running an example

For example, run the absorptive quartz refinement with:

uv run diffbloch preprocess examples/Colmey_et_al_2026/data/quartz-absorption
uv run diffbloch refine examples/Colmey_et_al_2026/data/quartz-absorption

Replace quartz-absorption with any directory listed above. Add --refresh to the refine command to rebuild preprocessing before refinement:

uv run diffbloch refine examples/Colmey_et_al_2026/data/quartz-absorption --refresh

Results

Each refinement writes a refined CIF, a text report, and a thickness plot in its experiment directory. Reproducibility records are written under reproducibility/.

The current code has changed since the calculations reported in the paper, so the examples repeat the same experiments but are not expected to reproduce the published values exactly. The original published values and full data provenance are given in the example directory’s README.md.