Optical wave field calculation, resolution correction, and CTR performance work

.github/workflows/build-wheels.yml

@@ -16,15 +16,21 @@ concurrency:
 env:
   CIBW_SKIP: "*-musllinux_*"
   CIBW_BUILD_FRONTEND: "build"
-  CIBW_CONFIG_SETTINGS_WINDOWS: "setup-args=--vsenv"
+  CIBW_CONFIG_SETTINGS: "setup-args=-Dstatic_xxhash=true"
+  CIBW_CONFIG_SETTINGS_WINDOWS: 'setup-args="--vsenv -Dstatic_xxhash=true"'
   CIBW_TEST_ENVIRONMENT: "PYTEST_DISABLE_PLUGIN_AUTOLOAD=1 MPLBACKEND=Agg QT_QPA_PLATFORM=minimal"
   CIBW_TEST_REQUIRES: pytest
+  CIBW_TEST_EXTRAS: extendedfilesupport,symmetry
   CIBW_TEST_COMMAND: >-
     python -c "from orgui.datautils.xrayutils import CTRuc;
     assert CTRuc.HAS_CPP_ACCEL;
     CTRuc.set_accel_backend('cpp');
     print('CTR_ACCEL_BACKEND=', CTRuc.CTR_ACCEL_BACKEND)" &&
     pytest --pyargs orgui.datautils.xrayutils.test.test_CTRcalc
+    orgui.datautils.xrayutils.test.test_CTRsymmetry
+    orgui.datautils.xrayutils.test.test_CTRresolution
+    orgui.datautils.xrayutils.test.test_CTRoptical_profile
+    orgui.datautils.xrayutils.test.test_scattering_factor_cache
   CIBW_TEST_SKIP: "*-manylinux_aarch64"
 
 jobs:

.github/workflows/release.yml

@@ -121,15 +121,21 @@ jobs:
           CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-* cp314-*"
           CIBW_SKIP: "*-musllinux_*"
           CIBW_BUILD_FRONTEND: "build"
-          CIBW_CONFIG_SETTINGS_WINDOWS: "setup-args=--vsenv"
+          CIBW_CONFIG_SETTINGS: "setup-args=-Dstatic_xxhash=true"
+          CIBW_CONFIG_SETTINGS_WINDOWS: 'setup-args="--vsenv -Dstatic_xxhash=true"'
           CIBW_TEST_ENVIRONMENT: "PYTEST_DISABLE_PLUGIN_AUTOLOAD=1 MPLBACKEND=Agg QT_QPA_PLATFORM=minimal"
           CIBW_TEST_REQUIRES: pytest
+          CIBW_TEST_EXTRAS: extendedfilesupport,symmetry
           CIBW_TEST_COMMAND: >-
             python -c "from orgui.datautils.xrayutils import CTRuc;
             assert CTRuc.HAS_CPP_ACCEL;
             CTRuc.set_accel_backend('cpp');
             print('CTR_ACCEL_BACKEND=', CTRuc.CTR_ACCEL_BACKEND)" &&
             pytest --pyargs orgui.datautils.xrayutils.test.test_CTRcalc
+            orgui.datautils.xrayutils.test.test_CTRsymmetry
+            orgui.datautils.xrayutils.test.test_CTRresolution
+            orgui.datautils.xrayutils.test.test_CTRoptical_profile
+            orgui.datautils.xrayutils.test.test_scattering_factor_cache
           CIBW_TEST_SKIP: "*-manylinux_aarch64"
         with:
           output-dir: wheelhouse

.github/workflows/tests.yml

@@ -55,11 +55,15 @@ jobs:
         run: python -m pip install --upgrade pip pytest
 
       - name: Install package
-        run: python -m pip install ".[speedup]"
+        run: python -m pip install ".[speedup,extendedfilesupport,symmetry]"
 
       - name: Run xrayutils tests
         run: >-
           pytest --pyargs
           orgui.datautils.xrayutils.test.test_HKLcalc
           orgui.datautils.xrayutils.test.test_DetectorCalibration
           orgui.datautils.xrayutils.test.test_CTRcalc
+          orgui.datautils.xrayutils.test.test_CTRsymmetry
+          orgui.datautils.xrayutils.test.test_CTRresolution
+          orgui.datautils.xrayutils.test.test_CTRoptical_profile
+          orgui.datautils.xrayutils.test.test_scattering_factor_cache

.gitignore

@@ -10,6 +10,8 @@
 __pycache__/
 dist/
 build/
+subprojects/xxHash-0.8.2/
+subprojects/.wraplock
 orgui.egg-info/
 orgui/_version.py
 benchmarks/roi_sum_results.json

CHANGELOG.md

@@ -3,6 +3,70 @@
 This is the changelog for the software orGUI, written by Timo Fuchs
 
 
+## [Unreleased] (2026-07-19)
+
+Scientific and analysis additions:
+
+- Added interface-based optical ``delta``/``beta`` profiles and layered
+  wavefield calculations for s- and p-polarized X-rays. Scalar and
+  multidimensional angle inputs are supported, and specular reflectivity can
+  be calculated for s, p, or unpolarized incidence. This provides the optical
+  wavefield foundation for future distorted-wave Born approximation (DWBA)
+  calculations; the full distorted-wave scattering amplitude is not included
+  yet.
+- Added optional CTR intensity-resolution modeling with constant or
+  gamma-dependent box and Gaussian functions. Calculations can convolve
+  irregular existing L points or sample the crystal structure factor with
+  deterministic quadrature.
+- Added Poisson-distributed surface occupancies and coherent out-of-plane
+  epitaxy/strain coupling for film-interface models.
+- Added py3Dmol atom-sphere rendering for Jupyter notebooks. ``plot3d`` now
+  selects py3Dmol automatically in a notebook, can be directed to either
+  py3Dmol or Mayavi explicitly, and can incrementally add unit cells to a
+  shared viewer. Covalent radii are interpreted consistently by both backends
+  and can be adjusted with the dimensionless ``radius_scale`` parameter.
+- ``PoissonSurface``'s basis now requires three parameters (``W``, ``alpha``,
+  ``offset``) instead of two. The previous two-parameter form was only ever
+  used in test code, so no migration path is provided; a saved ``.xtal``/
+  ``.xpr`` file with a two-parameter ``PoissonSurface`` basis will fail to
+  load.
+- Wyckoff-parameterized fit values are now interpreted as absolute atomic
+  positions instead of deltas relative to the Wyckoff position. Wyckoff
+  parameter fitting was development-only and never part of a release, so no
+  migration is provided.
+
+Scientific correctness and performance fixes:
+
+- Optical profiles now preserve areal optical content under surface-normal
+  strain, keep ionic forward scattering factors for charged species, avoid
+  merging layers beyond the requested z tolerance, and remain finite at the
+  exact p-polarized critical-angle limit.
+- Optical reflectivity and full wavefield calculations now evaluate angle
+  arrays with NumPy-vectorized kernels while preserving the caller's input
+  shape.
+- Corrected film and epitaxy-interface anchoring, stacking, and support
+  ownership across strained interfaces.
+- Fixed missing support in one-dimensional electron-density calculations and
+  corrected atomic-coordinate stacking when splitting unit cells into layers.
+- Added a C++ electron-density backend and bounded caches for atomic form
+  factors, anomalous scattering factors, and accelerated form-factor lookup.
+
+A ***critical bug*** was fixed that affects bulk CTR calculations:
+
+- ``UnitCell.F_bulk``'s semi-infinite geometric lattice sum used the raw,
+  untransformed ``l`` index instead of the index converted by
+  ``refHKLTransform`` when computing the out-of-plane attenuation phase. This
+  was only correct for the default case where a component uses its own bulk
+  cell as the reference (no ``reference_uc`` set); any explicit
+  ``reference_uc`` whose out-of-plane reciprocal axis differs from the
+  bulk's — including a plain scale difference between the reference and bulk
+  out-of-plane axis length, not only a rotated or reindexed reference — gave
+  incorrect bulk structure-factor amplitudes. This bug was present in both
+  the accelerated (numba/C++) and plain-Python code paths in all previous
+  released versions, up to and including v1.5.0. See the CTR structure-factor
+  documentation for details.
+
+
 ## [1.5.0] (2026-06-07)
 
 [532b60b](https://github.com/tifuchs/orGUI/commit/532b60bab3073ae9f0ff063a0e119aa9e9957857)...[c574bdf](https://github.com/tifuchs/orGUI/commit/c574bdf0bd5af6fa8258d108e7355c579bfef857)

THIRD_PARTY_LICENSES/pybind11-BSD-3-Clause.txt

@@ -0,0 +1,29 @@
+Copyright (c) 2016 Wenzel Jakob <wenzel.jakob@epfl.ch>, All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Please also refer to the file .github/CONTRIBUTING.md, which clarifies licensing of
+external contributions to this project including patches, pull requests, etc.

THIRD_PARTY_LICENSES/xxHash-BSD-2-Clause.txt

@@ -0,0 +1,26 @@
+xxHash Library
+Copyright (c) 2012-2021 Yann Collet
+All rights reserved.
+
+BSD 2-Clause License (https://www.opensource.org/licenses/bsd-license.php)
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.