Publications and references

Publications using diffBloch

• Colmey, B., Doherty, T. A. S., Malik, S. A. & Midgley, P. A. (2026). The role of absorption in three-dimensional electron diffraction dynamical structure refinement. Submitted to Acta Crystallographica A. https://arxiv.org/abs/2602.08935

• Malik, S. A., Doherty, T. A. S., Colmey, B., Roberts, S. J., Gal, Y. & Midgley, P. A. (2026). Hybrid physics-machine learning models for quantitative electron diffraction refinements. Nature Communications. https://www.nature.com/articles/s41467-026-71673-9

General references

diffBloch stands on published science and several open-source projects. This section records the sources used throughout the codebase.

• Electron scattering factors (Lobato parametrization). Lobato, I. & Van Dyck, D. (2014). An accurate parameterization for scattering factors, electron densities and electrostatic potentials for neutral atoms that obey all physical constraints. Acta Crystallographica A70(6), 636–649. DOI: 10.1107/S205327331401643X — open access (PDF).

• Dynamical electron diffraction (Bloch-wave method). Spence, J. C. H. & Zuo, J. M. (1992). Electron Microdiffraction. Plenum Press, New York.

• Bloch-wave matrix-exponential propagation (GPU-accelerated). Pennington, R. S., Wang, F. & Koch, C. T. (2014). Stacked-Bloch-wave electron diffraction simulations using GPU acceleration. Ultramicroscopy 141, 32–37. https://www.sciencedirect.com/science/article/pii/S0304399114000485

• Dynamical refinement of 3D electron diffraction data (rocking-curve integration framework). Palatinus, L., Petříček, V. & Corrêa, C. A. (2015). Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. Acta Crystallographica A71, 235–244. DOI: 10.1107/S2053273315001266; with the companion tests paper Palatinus, L. et al. (2015). …: tests on experimental data. Acta Crystallographica B71, 740–751. DOI: 10.1107/S2052520615017023.

• Orientation refinement (hexagonal modified-simplex search). Palatinus, L., Jacob, D., Cuvillier, P., Klementová, M., Sinkler, W. & Marks, L. D. (2013). Structure refinement from precession electron diffraction data. Acta Crystallographica A69, 171–188. DOI: 10.1107/S010876731204946X.

Software we depend on, extract from, or verify against

Runtime dependencies

• gemmi — CIF/mmCIF and PETS parsing, unit-cell handling, and space-group symmetry operations (the blessed parser behind io/). Wojdyr, M. (2022), GEMMI: A library for structural biology, Journal of Open Source Software 7(73), 4200. DOI: 10.21105/joss.04200 · https://github.com/project-gemmi/gemmi

• PyTorch — differentiable tensor backend (core/ constraints, ADP, symmetry expansion onward). https://github.com/pytorch/pytorch

• NumPy — array backend for the pure planning/geometry helpers. https://github.com/numpy/numpy

• pydantic — boundary validation for config and IO records. https://github.com/pydantic/pydantic

• PyYAML — experiment/config and lock parsing. https://github.com/yaml/pyyaml

Planned dependencies (seams already in place)

• diffpy.structure — special-position and ADP symmetry-constraint expansion, behind the io.symmetry_setup seam (lands with the constraints/symmetry stage). https://github.com/diffpy/diffpy.structure

Development & verification oracles (not runtime dependencies)

• abTEM — Madsen, J. & Susi, T. (2021), The abTEM code: transmission electron microscopy from first principles, Open Research Europe 1:24. https://open-research-europe.ec.europa.eu/articles/1-24

Citing diffBloch

@misc{diffBloch,
  author  = {Doherty, Tiarnan and Malik, Shreshth and Colmey, Benjamin and Maitland, Iain, and Midgley, Paul},
  title   = {diffBloch},
  version = {0.2.0},
  year = {2026},
  url     = {https://github.com/Differentiable-Electron-Crystallography/diffBloch}
}