Fix Cryspy recalculation for wrapped Wyckoff coordinates

docs/docs/tutorials/ed-15.ipynb

@@ -229,8 +229,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "project.analysis.fit.show_minimizer_types()\n",
-    "project.analysis.fit.minimizer_type = 'lmfit'"
+    "project.analysis.fit.show_minimizer_types()"
    ]
   },
   {
@@ -239,6 +238,16 @@
    "id": "22",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "project.analysis.fit.minimizer_type = 'bumps'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "23",
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# Start refinement. All parameters, which have standard uncertainties\n",
     "# in the input CIF files, are refined by default.\n",
@@ -248,7 +257,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -259,7 +268,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -269,7 +278,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -279,7 +288,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "27",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -288,7 +297,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "27",
+   "id": "28",
    "metadata": {},
    "source": [
     "## Step 5: Perform Analysis (ADP aniso)"
@@ -297,7 +306,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "29",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -308,7 +317,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29",
+   "id": "30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -321,7 +330,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "31",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -331,7 +340,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -341,7 +350,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "33",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -351,7 +360,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33",
+   "id": "34",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -361,7 +370,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34",
+   "id": "35",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -371,7 +380,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35",
+   "id": "36",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -381,7 +390,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36",
+   "id": "37",
    "metadata": {},
    "outputs": [],
    "source": [

docs/docs/tutorials/ed-15.py

@@ -75,7 +75,9 @@
 
 # %%
 project.analysis.fit.show_minimizer_types()
-project.analysis.fit.minimizer_type = 'lmfit'
+
+# %%
+project.analysis.fit.minimizer_type = 'bumps'
 
 # %%
 # Start refinement. All parameters, which have standard uncertainties

src/easydiffraction/analysis/calculators/cryspy.py

@@ -110,9 +110,19 @@ def calculate_structure_factors(
             else:
                 cryspy_obj = self._recreate_cryspy_obj(structure, experiment)
                 cryspy_dict = cryspy_obj.get_dictionary()
+                self._update_structure_in_cryspy_dict(
+                    cryspy_dict[f'crystal_{structure.name}'],
+                    structure,
+                )
+                self._update_experiment_in_cryspy_dict(cryspy_dict, experiment)
         else:
             cryspy_obj = self._recreate_cryspy_obj(structure, experiment)
             cryspy_dict = cryspy_obj.get_dictionary()
+            self._update_structure_in_cryspy_dict(
+                cryspy_dict[f'crystal_{structure.name}'],
+                structure,
+            )
+            self._update_experiment_in_cryspy_dict(cryspy_dict, experiment)
 
         self._cryspy_dicts[combined_name] = copy.deepcopy(cryspy_dict)
 
@@ -182,9 +192,19 @@ def calculate_pattern(
             else:
                 cryspy_obj = self._recreate_cryspy_obj(structure, experiment)
                 cryspy_dict = cryspy_obj.get_dictionary()
+                self._update_structure_in_cryspy_dict(
+                    cryspy_dict[f'crystal_{structure.name}'],
+                    structure,
+                )
+                self._update_experiment_in_cryspy_dict(cryspy_dict, experiment)
         else:
             cryspy_obj = self._recreate_cryspy_obj(structure, experiment)
             cryspy_dict = cryspy_obj.get_dictionary()
+            self._update_structure_in_cryspy_dict(
+                cryspy_dict[f'crystal_{structure.name}'],
+                structure,
+            )
+            self._update_experiment_in_cryspy_dict(cryspy_dict, experiment)
 
         self._cryspy_dicts[combined_name] = copy.deepcopy(cryspy_dict)
 
@@ -290,6 +310,13 @@ def _update_structure_in_cryspy_dict(
         for idx, atom_site in enumerate(structure.atom_sites):
             cryspy_occ[idx] = atom_site.occupancy.value
 
+        # Atomic multiplicities
+        if 'atom_multiplicity' in cryspy_model_dict:
+            CryspyCalculator._update_atom_multiplicity(
+                cryspy_model_dict,
+                structure,
+            )
+
         # Atomic ADPs - isotropic
         # For anisotropic atoms the full ADP lives in the β tensor;
         # setting b_iso to zero avoids double-counting in cryspy's DWF
@@ -313,6 +340,43 @@ def _update_structure_in_cryspy_dict(
                 structure,
             )
 
+    @staticmethod
+    def _update_atom_multiplicity(
+        cryspy_model_dict: dict[str, Any],
+        structure: Structure,
+    ) -> None:
+        """
+        Update cryspy atom multiplicities.
+
+        CrysPy normalizes fractional coordinates into the ``[0, 1)``
+        interval while parsing CIF.  For sites such as ``(x, -x, z)``,
+        that can turn ``-x`` into ``1 - x`` before the Wyckoff
+        multiplicity is inferred, making special positions look like
+        general positions.  EasyDiffraction already stores the intended
+        Wyckoff letter, so keep the calculator dictionary aligned with
+        that model state.
+        """
+        if cryspy is None:
+            return
+
+        from cryspy.A_functions_base.function_2_space_group import (  # noqa: PLC0415
+            get_it_number_by_name_hm_short,
+        )
+
+        from easydiffraction.crystallography.space_groups import SPACE_GROUPS  # noqa: PLC0415
+
+        it_number = get_it_number_by_name_hm_short(structure.space_group.name_h_m.value)
+        coord_code = structure.space_group.it_coordinate_system_code.value
+        if it_number is None or (it_number, coord_code) not in SPACE_GROUPS:
+            return
+
+        positions = SPACE_GROUPS[it_number, coord_code]['Wyckoff_positions']
+        multiplicity = cryspy_model_dict['atom_multiplicity']
+        for idx, atom_site in enumerate(structure.atom_sites):
+            wyckoff_letter = atom_site.wyckoff_letter.value
+            if wyckoff_letter in positions:
+                multiplicity[idx] = positions[wyckoff_letter]['multiplicity']
+
     @staticmethod
     def _update_aniso_beta(
         cryspy_model_dict: dict[str, Any],

tests/unit/easydiffraction/analysis/calculators/test_cryspy.py

@@ -78,3 +78,39 @@ def test_update_structure_zeroes_biso_for_anisotropic_atoms():
     CryspyCalculator._update_structure_in_cryspy_dict(cryspy_model_dict, structure)
 
     assert cryspy_model_dict['atom_b_iso'][0] == 0.0
+
+
+def test_update_structure_restores_wyckoff_multiplicity_after_coordinate_wrapping():
+    import numpy as np
+    import pytest
+
+    pytest.importorskip('cryspy')
+
+    from easydiffraction.analysis.calculators.cryspy import CryspyCalculator
+    from easydiffraction.datablocks.structure.item.base import Structure
+
+    structure = Structure(name='hs')
+    structure.space_group.name_h_m = 'R -3 m'
+    structure.space_group.it_coordinate_system_code = 'h'
+    structure.atom_sites.create(
+        label='O',
+        type_symbol='O',
+        fract_x=0.20587714,
+        fract_y=-0.20587714,
+        fract_z=0.06271739,
+        wyckoff_letter='h',
+        adp_iso=0.5,
+    )
+
+    cryspy_model_dict = {
+        'unit_cell_parameters': [6.86, 6.86, 14.14, np.pi / 2, np.pi / 2, 2 * np.pi / 3],
+        'atom_fract_xyz': np.array([[0.20587714], [0.79412286], [0.06271739]]),
+        'atom_occupancy': np.array([1.0]),
+        'atom_multiplicity': np.array([36]),
+        'atom_b_iso': np.array([0.5]),
+    }
+
+    CryspyCalculator._update_structure_in_cryspy_dict(cryspy_model_dict, structure)
+
+    assert cryspy_model_dict['atom_fract_xyz'][1][0] == -0.20587714
+    assert cryspy_model_dict['atom_multiplicity'][0] == 18