braggcalculator 0.1.0__tar.gz

braggcalculator-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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braggcalculator-0.1.0/PKG-INFO

@@ -0,0 +1,207 @@
+Metadata-Version: 2.4
+Name: braggcalculator
+Version: 0.1.0
+Summary: Fast, validated and differentiable Bragg powder diffraction
+License: Apache-2.0
+License-File: LICENSE
+Keywords: crystallography,diffraction,PXRD,neutron,PyTorch
+Author: Frederik Lizak Johansen
+Author-email: fupjohansen@gmail.com
+Requires-Python: >=3.12,<3.14
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Provides-Extra: all
+Provides-Extra: ase
+Provides-Extra: torch
+Requires-Dist: ase (>=3.23,<4) ; extra == "ase" or extra == "all"
+Requires-Dist: numpy (>=2.3.2,<3.0.0)
+Requires-Dist: pymatgen (>=2025.6.14,<2027)
+Requires-Dist: spglib (>=2.6.0,<3.0.0)
+Requires-Dist: torch (>=2.2,<3) ; extra == "torch" or extra == "all"
+Project-URL: Documentation, https://github.com/FrederikLizakJohansen/BraggCalculator/blob/main/docs/api.md
+Project-URL: Issues, https://github.com/FrederikLizakJohansen/BraggCalculator/issues
+Project-URL: Repository, https://github.com/FrederikLizakJohansen/BraggCalculator
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/FrederikLizakJohansen/BraggCalculator/main/assets/braggcalculator-logo.png" width="650" alt="BraggCalculator logo">
+</p>
+
+# BraggCalculator
+
+BraggCalculator is a fast, validated powder X-ray and neutron diffraction
+engine for ideal periodic crystals. It evaluates reciprocal-space Bragg
+diffraction with NumPy or optional PyTorch kernels.
+
+The current scientific scope is monochromatic, kinematic powder diffraction.
+It includes neutral-atom X-ray form factors, coherent elemental neutron
+scattering lengths, occupancies, isotropic Debye-Waller factors, the standard
+powder Lorentz or Lorentz-polarization correction, and area-normalized Gaussian
+profiles. It does not model diffuse scattering, finite-particle shape, preferred
+orientation, microstrain, absorption, background, anomalous X-ray terms, or
+instrumental wavelength distributions.
+
+## Installation
+
+```bash
+python -m pip install braggcalculator
+python -m pip install "braggcalculator[torch]"  # Torch/autograd/CUDA backend
+python -m pip install "braggcalculator[ase]"    # ASE structure input
+```
+
+Python 3.12 and 3.13 are supported. To work from a source checkout, use
+`python -m pip install -e ".[all]"`.
+
+The [API reference](https://github.com/FrederikLizakJohansen/BraggCalculator/blob/main/docs/api.md)
+documents the public configuration, methods, and result conventions.
+
+## Quick start
+
+```python
+from braggcalculator import BraggCalculator
+
+calculator = BraggCalculator(mode="xray", wavelength="CuKa1")
+calculator.load("structure.cif")
+
+two_theta, integrated_intensity = calculator.line_pattern(scaled=True)
+grid, profile = calculator.pattern()
+```
+
+`line_pattern()` returns the conventional merged powder lines. `pattern()`
+returns an area-normalized Gaussian profile on a regular grid.
+`reflection_table()` provides the corresponding HKLs, d-spacings, Q values,
+scattering angles, structure factors, and corrected intensities. The
+[API reference](https://github.com/FrederikLizakJohansen/BraggCalculator/blob/main/docs/api.md)
+documents lower-level reciprocal-point output and the rules for differentiable
+lattice changes.
+
+The Q-space API uses inverse angstroms:
+
+```python
+q, intensity = calculator.line_pattern(domain="q")
+q_grid, profile_q = calculator.pattern(domain="q")
+```
+
+## Torch and autograd
+
+Symmetry detection and HKL enumeration are discrete preprocessing operations.
+Autograd therefore operates on a fixed reflection topology. Rebuild the
+calculator if a lattice change is large enough that reflections can enter or
+leave the configured Q range.
+
+```python
+from braggcalculator import BraggCalculator
+from braggcalculator.backends import TorchBackend
+
+calculator = BraggCalculator(backend=TorchBackend(device="cpu")).load(
+    "structure.cif"
+)
+parameters = calculator.tensor_parameters(
+    requires_grad=["lattice", "frac_coords", "occupancies", "b_iso"]
+)
+grid, profile = calculator.pattern(parameters=parameters)
+loss = profile.square().sum()
+loss.backward()
+```
+
+Use `TorchBackend(device="cuda")` with a CUDA-enabled PyTorch installation to
+run the continuous diffraction and profile kernels on a GPU.
+
+Species identities and reflection indices are intentionally not differentiable.
+Isotope-specific neutron samples can select a tabulated isotope through
+`neutron_scattering_lengths={"H": "2H"}` (or supply a measured/custom length)
+because pymatgen structures do not retain isotope identity.
+
+By default, `qmax` is derived from the requested 2-theta and Q ranges and the
+physical Ewald limit. An explicit `qmax` that would truncate either output range
+is rejected instead of silently dropping reflections.
+
+## Scientific conventions
+
+- Direct lattice vectors are rows in angstroms.
+- `g = 1 / d`, `Q = 2 pi / d`, and `s = sin(theta) / wavelength = g / 2`.
+- Isotropic displacement amplitudes use `exp(-B s^2)`.
+- Line intensities are `|F|^2` times the powder Lorentz-polarization factor.
+- Gaussian profile amplitudes are integrated areas, not peak heights.
+- Every reciprocal point is evaluated explicitly. This makes systematic
+  absences emerge from the full structure factor and avoids multiplicity
+  double-counting.
+
+X-ray coefficients, radiation wavelengths, and coherent elemental neutron
+lengths are read from the required pymatgen dependency. This keeps the source
+of physical values explicit and versioned rather than duplicating an
+unmaintained local table.
+
+## Validation and performance
+
+BraggCalculator evaluates the same kinematic equations as pymatgen and does
+not prune the reciprocal set. In pymatgen 2026.5.4, each pattern rebuilds the
+reciprocal points and flattened site arrays, then a Python loop processes one
+reflection at a time; the site sum inside that reflection is vectorized.
+BraggCalculator reduces the primitive cell and constructs the exact reflection
+topology during `load()`. Its numerical kernel processes reflection-by-site
+chunks and merges equal-spacing lines with indexed reductions. Repeated calls
+reuse the topology, and reducible supercells perform numerical work on the
+primitive sites. These two savings are reported separately as cached and
+end-to-end timings.
+
+Run the unit and analytical test suite:
+
+```bash
+python -m pytest -q
+```
+
+Validate X-ray and neutron peak positions and normalized intensities against
+pymatgen across cubic, diamond, perovskite, triclinic, disordered, and 40-atom
+P1 cells:
+
+```bash
+python scripts/validate_against_pymatgen.py
+```
+
+Run the reproducible performance comparison. The command fails if either the
+cached or end-to-end calculation is not faster for every case:
+
+```bash
+python benchmarks/benchmark_against_pymatgen.py \
+    --number 20 --repeat 7 --require-speedup 1 --json benchmark.json
+```
+
+Performance is machine- and dependency-version-specific, so benchmark JSON
+records the exact environment and all timing samples. The versioned scaling
+data, plotting commands, and CPU/CUDA protocol are documented in
+[the paper README](https://github.com/FrederikLizakJohansen/BraggCalculator/blob/main/paper/README.md).
+
+## Demonstration
+
+The [NaCl demonstration](https://github.com/FrederikLizakJohansen/BraggCalculator/tree/main/demo)
+loads a CIF, verifies the calculated powder lines against pymatgen, and writes
+an overlay with a residual panel:
+
+```bash
+python -m pip install -e . matplotlib
+python demo/compare_with_pymatgen.py
+```
+
+The script stops if either implementation departs from the stated numerical
+tolerances.
+
+## Data and model references
+
+- P. A. Doyle and P. S. Turner, *Acta Crystallographica A* **24**, 390–397
+  (1968), DOI: [10.1107/S0567739468000756](https://doi.org/10.1107/S0567739468000756).
+- V. F. Sears, *Neutron News* **3**(3), 26–37 (1992), DOI:
+  [10.1080/10448639208218770](https://doi.org/10.1080/10448639208218770).
+- The [pymatgen diffraction documentation](https://pymatgen.org/pymatgen.analysis.diffraction.html)
+  describes the independent oracle implementation used in validation.
+
+## License
+
+Apache License 2.0. See `LICENSE`.
+

braggcalculator-0.1.0/README.md

@@ -0,0 +1,175 @@
+<p align="center">
+  <img src="https://raw.githubusercontent.com/FrederikLizakJohansen/BraggCalculator/main/assets/braggcalculator-logo.png" width="650" alt="BraggCalculator logo">
+</p>
+
+# BraggCalculator
+
+BraggCalculator is a fast, validated powder X-ray and neutron diffraction
+engine for ideal periodic crystals. It evaluates reciprocal-space Bragg
+diffraction with NumPy or optional PyTorch kernels.
+
+The current scientific scope is monochromatic, kinematic powder diffraction.
+It includes neutral-atom X-ray form factors, coherent elemental neutron
+scattering lengths, occupancies, isotropic Debye-Waller factors, the standard
+powder Lorentz or Lorentz-polarization correction, and area-normalized Gaussian
+profiles. It does not model diffuse scattering, finite-particle shape, preferred
+orientation, microstrain, absorption, background, anomalous X-ray terms, or
+instrumental wavelength distributions.
+
+## Installation
+
+```bash
+python -m pip install braggcalculator
+python -m pip install "braggcalculator[torch]"  # Torch/autograd/CUDA backend
+python -m pip install "braggcalculator[ase]"    # ASE structure input
+```
+
+Python 3.12 and 3.13 are supported. To work from a source checkout, use
+`python -m pip install -e ".[all]"`.
+
+The [API reference](https://github.com/FrederikLizakJohansen/BraggCalculator/blob/main/docs/api.md)
+documents the public configuration, methods, and result conventions.
+
+## Quick start
+
+```python
+from braggcalculator import BraggCalculator
+
+calculator = BraggCalculator(mode="xray", wavelength="CuKa1")
+calculator.load("structure.cif")
+
+two_theta, integrated_intensity = calculator.line_pattern(scaled=True)
+grid, profile = calculator.pattern()
+```
+
+`line_pattern()` returns the conventional merged powder lines. `pattern()`
+returns an area-normalized Gaussian profile on a regular grid.
+`reflection_table()` provides the corresponding HKLs, d-spacings, Q values,
+scattering angles, structure factors, and corrected intensities. The
+[API reference](https://github.com/FrederikLizakJohansen/BraggCalculator/blob/main/docs/api.md)
+documents lower-level reciprocal-point output and the rules for differentiable
+lattice changes.
+
+The Q-space API uses inverse angstroms:
+
+```python
+q, intensity = calculator.line_pattern(domain="q")
+q_grid, profile_q = calculator.pattern(domain="q")
+```
+
+## Torch and autograd
+
+Symmetry detection and HKL enumeration are discrete preprocessing operations.
+Autograd therefore operates on a fixed reflection topology. Rebuild the
+calculator if a lattice change is large enough that reflections can enter or
+leave the configured Q range.
+
+```python
+from braggcalculator import BraggCalculator
+from braggcalculator.backends import TorchBackend
+
+calculator = BraggCalculator(backend=TorchBackend(device="cpu")).load(
+    "structure.cif"
+)
+parameters = calculator.tensor_parameters(
+    requires_grad=["lattice", "frac_coords", "occupancies", "b_iso"]
+)
+grid, profile = calculator.pattern(parameters=parameters)
+loss = profile.square().sum()
+loss.backward()
+```
+
+Use `TorchBackend(device="cuda")` with a CUDA-enabled PyTorch installation to
+run the continuous diffraction and profile kernels on a GPU.
+
+Species identities and reflection indices are intentionally not differentiable.
+Isotope-specific neutron samples can select a tabulated isotope through
+`neutron_scattering_lengths={"H": "2H"}` (or supply a measured/custom length)
+because pymatgen structures do not retain isotope identity.
+
+By default, `qmax` is derived from the requested 2-theta and Q ranges and the
+physical Ewald limit. An explicit `qmax` that would truncate either output range
+is rejected instead of silently dropping reflections.
+
+## Scientific conventions
+
+- Direct lattice vectors are rows in angstroms.
+- `g = 1 / d`, `Q = 2 pi / d`, and `s = sin(theta) / wavelength = g / 2`.
+- Isotropic displacement amplitudes use `exp(-B s^2)`.
+- Line intensities are `|F|^2` times the powder Lorentz-polarization factor.
+- Gaussian profile amplitudes are integrated areas, not peak heights.
+- Every reciprocal point is evaluated explicitly. This makes systematic
+  absences emerge from the full structure factor and avoids multiplicity
+  double-counting.
+
+X-ray coefficients, radiation wavelengths, and coherent elemental neutron
+lengths are read from the required pymatgen dependency. This keeps the source
+of physical values explicit and versioned rather than duplicating an
+unmaintained local table.
+
+## Validation and performance
+
+BraggCalculator evaluates the same kinematic equations as pymatgen and does
+not prune the reciprocal set. In pymatgen 2026.5.4, each pattern rebuilds the
+reciprocal points and flattened site arrays, then a Python loop processes one
+reflection at a time; the site sum inside that reflection is vectorized.
+BraggCalculator reduces the primitive cell and constructs the exact reflection
+topology during `load()`. Its numerical kernel processes reflection-by-site
+chunks and merges equal-spacing lines with indexed reductions. Repeated calls
+reuse the topology, and reducible supercells perform numerical work on the
+primitive sites. These two savings are reported separately as cached and
+end-to-end timings.
+
+Run the unit and analytical test suite:
+
+```bash
+python -m pytest -q
+```
+
+Validate X-ray and neutron peak positions and normalized intensities against
+pymatgen across cubic, diamond, perovskite, triclinic, disordered, and 40-atom
+P1 cells:
+
+```bash
+python scripts/validate_against_pymatgen.py
+```
+
+Run the reproducible performance comparison. The command fails if either the
+cached or end-to-end calculation is not faster for every case:
+
+```bash
+python benchmarks/benchmark_against_pymatgen.py \
+    --number 20 --repeat 7 --require-speedup 1 --json benchmark.json
+```
+
+Performance is machine- and dependency-version-specific, so benchmark JSON
+records the exact environment and all timing samples. The versioned scaling
+data, plotting commands, and CPU/CUDA protocol are documented in
+[the paper README](https://github.com/FrederikLizakJohansen/BraggCalculator/blob/main/paper/README.md).
+
+## Demonstration
+
+The [NaCl demonstration](https://github.com/FrederikLizakJohansen/BraggCalculator/tree/main/demo)
+loads a CIF, verifies the calculated powder lines against pymatgen, and writes
+an overlay with a residual panel:
+
+```bash
+python -m pip install -e . matplotlib
+python demo/compare_with_pymatgen.py
+```
+
+The script stops if either implementation departs from the stated numerical
+tolerances.
+
+## Data and model references
+
+- P. A. Doyle and P. S. Turner, *Acta Crystallographica A* **24**, 390–397
+  (1968), DOI: [10.1107/S0567739468000756](https://doi.org/10.1107/S0567739468000756).
+- V. F. Sears, *Neutron News* **3**(3), 26–37 (1992), DOI:
+  [10.1080/10448639208218770](https://doi.org/10.1080/10448639208218770).
+- The [pymatgen diffraction documentation](https://pymatgen.org/pymatgen.analysis.diffraction.html)
+  describes the independent oracle implementation used in validation.
+
+## License
+
+Apache License 2.0. See `LICENSE`.

braggcalculator-0.1.0/braggcalculator/__init__.py

@@ -0,0 +1,5 @@
+from .core import BraggCalculator
+from .results import ReflectionTable
+from ._version import __version__
+
+__all__ = ["BraggCalculator", "ReflectionTable", "__version__"]

braggcalculator-0.1.0/braggcalculator/_version.py

@@ -0,0 +1 @@
+__version__ = "0.1.0"

braggcalculator-0.1.0/braggcalculator/backends/__init__.py

@@ -0,0 +1,8 @@
+from .numpy_backend import NumpyBackend
+
+try:
+    from .torch_backend import TorchBackend
+except ImportError:  # pragma: no cover
+    TorchBackend = None
+
+__all__ = ["NumpyBackend", "TorchBackend"]