Simplify get_cross_section from an established AtomInfo

Author: ajjackson

Framework/PythonInterface/plugins/algorithms/Abins.py

@@ -230,13 +230,7 @@ def _fill_s_1d_workspace(self, *, s_points: np.ndarray, workspace: str, species:
         :param species: atom/isotope identity and data
         """
         if species is not None:
-            s_points = (
-                s_points
-                * self._scale
-                * self.get_cross_section(
-                    scattering=self._scale_by_cross_section, protons_number=species.z_number, nucleons_number=species.nucleons_number
-                )
-            )
+            s_points = s_points * self._scale * self.get_cross_section(scattering=self._scale_by_cross_section, species=species)
         dim = 1
         length = s_points.size
 

scripts/abins/abins2.py

@@ -217,9 +217,7 @@ def _fill_s_1d_workspace(self, s_points=None, workspace=None, species: AtomInfo
         :param workspace: workspace to be filled with S
         """
         if species is not None:
-            s_points = s_points * self.get_cross_section(
-                scattering=self._scale_by_cross_section, protons_number=species.z_number, nucleons_number=species.nucleons_number
-            )
+            s_points = s_points * self.get_cross_section(scattering=self._scale_by_cross_section, species=species)
         dim = 1
         length = s_points.size
 

scripts/abins/abinsalgorithm.py

@@ -13,7 +13,7 @@
 import os
 from pathlib import Path
 import re
-from typing import Dict, Iterable, List, Optional, Tuple, Union
+from typing import Dict, Iterable, List, Literal, Tuple, Union
 
 import yaml
 
@@ -664,29 +664,18 @@ def write_workspaces_to_ascii(scale: float = 1.0, *, ws_name: str) -> None:
             )
 
     @staticmethod
-    def get_cross_section(scattering: str = "Total", nucleons_number: Optional[int] = None, *, protons_number: int) -> float:
+    def get_cross_section(scattering: Literal["Total", "Incoherent", "Coherent"], species: AtomInfo) -> float:
         """
         Calculates cross section for the given element.
         :param scattering: Type of cross-section: 'Incoherent', 'Coherent' or 'Total'
-        :param protons_number: number of protons in the given type fo atom
-        :param nucleons_number: number of nucleons in the given type of atom
+        :param species: Data for atom/isotope type
         :returns: cross section for that element
         """
-        if nucleons_number is not None:
-            try:
-                atom = Atom(a_number=nucleons_number, z_number=protons_number)
-            # isotopes are not implemented for all elements so use different constructor in that cases
-            except RuntimeError:
-                logger.warning(f"Could not find data for isotope {nucleons_number}, " f"using default values for {protons_number} protons.")
-                atom = Atom(z_number=protons_number)
-        else:
-            atom = Atom(z_number=protons_number)
-
         scattering_keys = {"Incoherent": "inc_scatt_xs", "Coherent": "coh_scatt_xs", "Total": "tot_scatt_xs"}
-        cross_section = atom.neutron()[scattering_keys[scattering]]
+        cross_section = species.neutron_data[scattering_keys[scattering]]
 
         if isnan(cross_section):
-            raise ValueError(f"Found NaN cross-section for {atom.symbol} with {nucleons_number} nucleons.")
+            raise ValueError(f"Found NaN cross-section for {species.symbol} with {species.nucleons_number} nucleons.")
 
         return cross_section
 

scripts/test/Abins/AbinsAlgorithmTest.py

@@ -10,7 +10,7 @@
 # Import mantid.simpleapi first, otherwise we get circular import
 import mantid.simpleapi  # noqa: F401
 
-from abins.abinsalgorithm import AbinsAlgorithm
+from abins.abinsalgorithm import AbinsAlgorithm, AtomInfo
 
 
 class AtomsDataTest(unittest.TestCase):
@@ -19,16 +19,12 @@ class AtomsDataTest(unittest.TestCase):
     def test_cross_section(self):
         """Get cross section from nucleus information"""
 
-        for scattering, nucleons_number, protons_number, expected in [
-            ("Incoherent", 67, 30, 0.28),
-            ("Coherent", None, 30, 4.054),
-            ("Total", None, 1, 82.02),
+        for scattering, nucleons_number, symbol, expected in [
+            ("Incoherent", 67, "Zn", 0.28),
+            ("Coherent", 0, "Zn", 4.054),
+            ("Total", 0, "H", 82.02),
         ]:
-            xc = AbinsAlgorithm.get_cross_section(
-                scattering=scattering,
-                nucleons_number=nucleons_number,
-                protons_number=protons_number,
-            )
+            xc = AbinsAlgorithm.get_cross_section(scattering=scattering, species=AtomInfo(mass=float(nucleons_number), symbol=symbol))
 
             self.assertAlmostEqual(xc, expected)
 
@@ -37,4 +33,4 @@ def test_get_bad_cross_section(self):
 
         with self.assertRaisesRegex(ValueError, "Found NaN cross-section for Zn with 65 nucleons"):
             # Zn65 is unstable and has no recorded cross section values
-            AbinsAlgorithm.get_cross_section(nucleons_number=65, protons_number=30)
+            AbinsAlgorithm.get_cross_section("Total", AtomInfo(symbol="Zn", mass=65.0))