Separate slddb package

HISTORY.rst

@@ -2,6 +2,14 @@
 History
 =======
 
+1.2.3 (2026-03-16)
+------------------
+* Add ContentHash class for file consistencey validation option in header
+* Improve the documentation, thanks to alexhroom (#133)
+* Switch SLDdb webapi url to new website https://slddb.reflectometry.org
+* Fix export of classes with default parameters to not write the default values to YAML (#149)
+* Fix some issues with build and tests on github
+
 1.2.2 (2025-06-27)
 ------------------
 

MANIFEST.in

@@ -5,7 +5,6 @@ include LICENSE
 include README.rst
 
 recursive-include tests *
-recursive-include orsopy/slddb/element_table/nabs_geant4_data *.npz
 recursive-include orsopy/fileio/schema/ *.json
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

examples/sample_model_complex.yml

@@ -32,3 +32,7 @@ sample:
         composition:
           copper: 0.5
           Si: 0.5
+    test:
+      stacks: 7
+      blocks: 54
+      layers: 253

examples/sample_model_example_1.yml

@@ -2,3 +2,7 @@ sample:
     model:
         origin: guess based on preparation
         stack: air | 10 ( Si 7 | Fe 7 ) | Si
+        test:
+          stacks: 3
+          blocks: 22
+          layers: 22

examples/sample_model_example_2.yml

@@ -15,3 +15,7 @@ sample:
           roughness: {magnitude: 5.0, unit: angstrom}
           sld_unit: 1/angstrom^2
         reference: ORSO model language | 1.0 | http://bla.bli
+        test:
+          stacks: 3
+          blocks: 22
+          layers: 22

examples/sample_model_example_3.yml

@@ -39,4 +39,8 @@ sample:
           length_unit: angstrom
           mass_density_unit: g/cm^3
           sld_unit: 1/angstrom^2
-        reference: ORSO model language | 1.0 | https://www.reflectometry.org/projects/simple_model
+        reference: ORSO model language | 1.0 | https://www.reflectometry.org/projects/simple_model
+        test:
+          stacks: 3
+          blocks: 23
+          layers: 23

examples/sample_model_example_4.yml

@@ -4,29 +4,43 @@ sample:
         stack: Si | LL | rLL | solvent
         sub_stacks:
             LL:
-                sub_stack_class: LipidLeaflet
-                apm: 56.0
-                b_heads: 6.01e-4
-                vm_heads: 319.0
-                b_tails: -2.92e-4
-                vm_tails: 782.0
-                thickness_heads: 9.0
-                head_solvent: solvent
-                tail_solvent: solvent
-                thickness: 23.0
-                comment: Shows the equivalence of using Value or float for apm/vm_heads/vm_tails
+                sequence:
+                - material: {sld: 1.88401254e-06}
+                  thickness: 9.0
+                  roughness: 3.0
+                - material: {sld: -3.73401535e-07}
+                  thickness: 1.4
+                  roughness: 3.0
+                #sub_stack_class: LipidLeaflet - not yet introduced in API
+                #apm: 56.0
+                #b_heads: 6.01e-4
+                #vm_heads: 319.0
+                #b_tails: -2.92e-4
+                #vm_tails: 782.0
+                #thickness_heads: 9.0
+                #head_solvent: solvent
+                #tail_solvent: solvent
+                #thickness: 23.0
+                #comment: Shows the equivalence of using Value or float for apm/vm_heads/vm_tails
             rLL:
-                sub_stack_class: LipidLeaflet
-                apm: {magnitude: 56.0, unit: Angstrom^2}
-                b_heads: 6.01e-4
-                vm_heads: {magnitude: 319.0, unit: Angstrom^3}
-                b_tails: -2.92e-4
-                vm_tails: {magnitude: 782.0, unit: Angstrom^3}
-                thickness_heads: 9.0
-                head_solvent: solvent
-                tail_solvent: solvent
-                thickness: 23.0
-                reverse_monolayer: true
+                sequence:
+                - material: {sld: -3.73401535e-07}
+                  thickness: 1.4
+                  roughness: 0.0
+                - material: {sld: 1.88401254e-06}
+                  thickness: 9.0
+                  roughness: 3.0
+                #sub_stack_class: LipidLeaflet
+                #apm: {magnitude: 56.0, unit: Angstrom^2}
+                #b_heads: 6.01e-4
+                #vm_heads: {magnitude: 319.0, unit: Angstrom^3}
+                #b_tails: -2.92e-4
+                #vm_tails: {magnitude: 782.0, unit: Angstrom^3}
+                #thickness_heads: 9.0
+                #head_solvent: solvent
+                #tail_solvent: solvent
+                #thickness: 23.0
+                #reverse_monolayer: true
         composits:
             solvent:
                 composition:

examples/sample_model_example_5.yml

@@ -6,4 +6,8 @@ sample:
           Fe:
             magnetic_moment: 2.5
           Si:
-            relative_density: 0.9
+            relative_density: 0.9
+        test:
+          stacks: 3
+          blocks: 22
+          layers: 22

examples/sample_model_example_6.yml

@@ -17,4 +17,8 @@ sample:
             but:
               roughness: 15.0
         globals:
-            slice_resolution: {magnitude: 10.0, unit: nm}
+            slice_resolution: {magnitude: 10.0, unit: nm}
+        test:
+          stacks: 4
+          blocks: 13
+          layers: 57

examples/sample_model_example_7.yml

@@ -8,3 +8,7 @@ sample:
             material1: Ni
             material2: Ti
             function: 0.5+0.5*sin(x*2*pi)
+        test:
+          stacks: 3
+          blocks: 7
+          layers: 52

examples/sample_model_example_8.yml

@@ -8,3 +8,7 @@ sample:
             material1: Ni
             material2: Ti
             function: (0.5+0.5*sin(x*20.0*2*pi))*exp(-(x-0.5)**2/0.25**2)
+        test:
+          stacks: 3
+          blocks: 3
+          layers: 202

examples/sample_model_example_9.yml

@@ -0,0 +1,14 @@
+sample:
+    model:
+        comment: Material from SLD db Bio Blender mixture
+        stack: air | dna1 50 | RNA=AUGUUUAGUUAA 50 | protein1 100 | Si
+        layers:
+            dna1:
+                material: DNA=ATTAG
+            protein1:
+                material: Protein=MAHAGRTGYDNREIVMKYIHYKLSQRGYEWDAGDVGAAPPGAAPAPGIFSSQPGHTPHPAASRDPVARTSPLQTPAAPGAAAGPALSPVPPVVHLTLRQAGDDFSRRYRRDFAEMSSQLHLTPFTARGRFATVVEELFRDGVNWGRIVAFFEFGGVMCVESVNREMSPLVDNIALWMTEYLNRHLHTWIQDNGGWDAFVELYGPSMRPLFDFSWLSLKTLLSLALVGACITLGAYLGHK
+                comment: Bcl-2
+        test:
+          stacks: 5
+          blocks: 5
+          layers: 5

examples/sample_model_export_genx.yml

@@ -1,4 +1,4 @@
-stack: ambient | top | ML | buffer | substrate
+stack: Amb | top | ML | buffer | Sub
 origin: GenX model "X-ray_Reflectivity.hgx"
 sub_stacks:
   top:
@@ -11,45 +11,58 @@ sub_stacks:
     repetitions: 1
     stack: bufPt | bufFe
 layers:
+  Amb:
+    material:
+      sld: {real: 1.0e-25, imag: 1.0e-25, unit: 1/angstrom^2}
   topPt:
     thickness: 11.0
     roughness: 3.0
     material:
-      sld: {real: 4.864311704082625e-06, imag: -4.533346598101179e-07}
+      formula: Pt
+      number_density: 0.06640515431495381
   TopFe:
     thickness: 11.0
     roughness: 2.0
     material:
-      sld: {real: 2.1041406836134337e-06, imag: -2.7004929545359514e-07}
+      formula: Fe
+      number_density: 0.08495744391749196
   Pt:
-    thickness: 11.0
+    thickness: 18.0
     roughness: 2.0
     material:
-      sld: {real: 4.864311704082625e-06, imag: -4.533346598101179e-07}
+      formula: Pt
+      number_density: 0.06640515431495381
   Fe:
     thickness: 11.0
     roughness: 2.0
     material:
-      sld: {real: 2.1041406836134337e-06, imag: -2.7004929545359514e-07}
+      formula: Fe
+      number_density: 0.08495744391749196
   bufPt:
     thickness: 45.0
     roughness: 2.0
     material:
-      sld: {real: 4.864311704082625e-06, imag: -4.533346598101179e-07}
+      formula: Pt
+      number_density: 0.06640515431495381
   bufFe:
     thickness: 2.0
     roughness: 2.0
     material:
-      sld: {real: 2.1041406836134337e-06, imag: -2.7004929545359514e-07}
-materials:
-  ambient:
-    sld: {real: 9.999999999999999e-27, imag: 9.999999999999999e-27}
-  substrate:
-    sld: {real: 5.456591989186995e-07, imag: -5.636808187886301e-09}
+      formula: Fe
+      number_density: 0.08495744391749196
+  Sub:
+    roughness: 4.0
+    material:
+      formula: MgO
+      number_density: 0.026994924954108625
 globals:
   roughness: {magnitude: 0.3, unit: nm}
   length_unit: angstrom
-  mass_density_unit: g/cm^3
-  number_density_unit: 1/nm^3
+  number_density_unit: 1/angstrom^3
   sld_unit: 1/angstrom^2
   magnetic_moment_unit: muB
+test:
+  stacks: 5
+  # 1 + 2 + 19*2 + 2 + 1 = 44
+  blocks: 44
+  layers: 44

orsopy/__init__.py

@@ -1,3 +1,3 @@
 """Top-level package for orsopy."""
 
-__version__ = "1.2.2"
+__version__ = "1.2.3"

orsopy/fileio/model_building_blocks.py

@@ -2,7 +2,7 @@
 from dataclasses import dataclass, field
 from typing import Dict, List, Optional, Union
 
-from ..utils.chemical_formula import Formula
+from slddb.chemical_formula import Formula
 from ..utils.density_resolver import MaterialResolver
 from .base import ComplexValue, Header, Value
 
@@ -122,7 +122,7 @@ def get_sld(self, xray_energy=None) -> complex:
         if self.sld is not None:
             return rel * self.sld.as_unit("1/angstrom^2") + 0j
 
-        from orsopy.slddb.material import Material, get_element
+        from slddb.material import Material, get_element
 
         formula = Formula(self.formula, strict=True)
         if self.mass_density is not None:
@@ -247,7 +247,29 @@ def resolve_names(self, resolvable_items):
             elif self.material in SPECIAL_MATERIALS:
                 self.material = SPECIAL_MATERIALS[self.material]
             else:
-                self.material = Material(formula=self.material)
+                try:
+                    Formula(self.material, strict=True)
+                except ValueError:
+                    # try to resolve name directly with databse
+                    res = None
+                    if len(DENSITY_RESOLVERS) == 0:
+                        from ..utils.resolver_slddb import ResolverSLDDB
+
+                        DENSITY_RESOLVERS.append(ResolverSLDDB())
+                    for resolver in DENSITY_RESOLVERS:
+                        res = resolver.resolve_item(self.material)
+                        if res is not None:
+                            break
+                    if res:
+                        # could resolve the string to an actual material
+                        self.material = Material(
+                            formula=res["formula"], number_density=res["number_density"], comment=res["comment"]
+                        )
+                    else:
+                        # will lead to errors later but keep string as formula
+                        self.material = Material(formula=self.material)
+                else:
+                    self.material = Material(formula=self.material)
         elif self.composition is not None:
             self._composition_materials = {}
             for key, value in self.composition.items():

orsopy/fileio/model_language.py

@@ -10,7 +10,7 @@
 from dataclasses import dataclass
 from typing import Dict, List, Optional, Union
 
-from ..utils.chemical_formula import Formula
+from slddb.chemical_formula import Formula
 from . import model_complex
 from .base import Header, Literal
 from .model_building_blocks import (DENSITY_RESOLVERS, SPECIAL_MATERIALS, Composit, Layer, Material, ModelParameters,
@@ -169,7 +169,7 @@ def resolve_to_blocks(self) -> List[Union[Layer, SubStackType]]:
                 sub_blocks = obj.resolve_to_blocks()
                 blocks = blocks[: i + added] + sub_blocks + blocks[i + added :]
                 added += len(sub_blocks) - 1
-        return blocks
+        return blocks * self.repetitions
 
     def resolve_to_layers(self) -> List[Layer]:
         layers = list(self.sequence)
@@ -304,6 +304,10 @@ def resolve_stack(self):
                     except ValueError:
                         # try to resolve name directly with databse
                         res = None
+                        if len(DENSITY_RESOLVERS) == 0:
+                            from ..utils.resolver_slddb import ResolverSLDDB
+
+                            DENSITY_RESOLVERS.append(ResolverSLDDB())
                         for resolver in DENSITY_RESOLVERS:
                             res = resolver.resolve_item(item)
                             if res is not None:
@@ -336,7 +340,7 @@ def resolve_stack(self):
         return output
 
     def resolve_to_blocks(self) -> List[Union[Layer, SubStackType]]:
-        # like resovle_to_layers but keeping SubStackType classes in tact
+        # like resovle_to_layers but keeping SubStackType classes intact
         blocks = self.resolve_stack()
         added = 0
         for i in range(len(blocks)):