Add missing orbitals

Updated method of generating charge states in classes_orbtials.py: Atom.assign_charge
Fixes Issue #20

Dans_Diffraction/__init__.py

@@ -31,8 +31,8 @@
 Diamond
 2017
 
-Version 3.2.2
-Last updated: 29/07/24
+Version 3.2.3
+Last updated: 04/09/24
 
 Version History:
 02/03/18 1.0    Version History started.
@@ -78,6 +78,7 @@
 15/05/24 3.2.0  Added "save" and "load" methods to structure factor calculation, improved powder for large calculations
 20/05/24 3.2.1  Added pyproject.toml file for installation, including dansdiffraction script
 29/07/24 3.2.2  Fix for issue #19 in multiple_scattering code, other minor improvements
+04/09/24 3.2.3  Updated method of generating charge states in classes_orbtials.py, Thanks Seonghun!
 
 Acknoledgements:
     2018        Thanks to Hepesu for help with Python3 support and ideas about breaking up calculations
@@ -100,6 +101,8 @@
     Jan 2024    Thanks to Carmelo Prestipino for adding search_distance and plot_distance
     May 2024    Thanks to Innbig for spotting some errors in large liquid crystal powder patterns
     May 2024    Thanks to paul-cares pointing out a silly spelling error in the title!
+    Aug 2024    Thanks to Seonghun for pointing out the error with charge states in Hf
+    Aug 2024    Thanks to MaxPelly for spell checks in examples
 
 -----------------------------------------------------------------------------
    Copyright 2024 Diamond Light Source Ltd.
@@ -149,8 +152,8 @@
 from .functions_crystallography import readcif
 
 
-__version__ = '3.2.2'
-__date__ = '29/07/24'
+__version__ = '3.2.3'
+__date__ = '04/09/24'
 
 
 # Build

Dans_Diffraction/classes_orbitals.py

@@ -33,12 +33,13 @@
 Diamond
 2020
 
-Version 1.0.0
-Last updated: 12/07/20
+Version 1.1.0
+Last updated: 04/09/24
 
 Version History:
 09/05/20 0.1.0  Version History started.
 12/07/20 1.0.0  Program functional, performed some testing
+04/09/24 1.1.0  Added missing orbitals in Atom.assign_charge
 
 @author: DGPorter
 """
@@ -50,7 +51,7 @@
 from . import functions_general as fg
 from . import functions_crystallography as fc
 
-__version__ = '1.0.0'
+__version__ = '1.1.0'
 
 OXIDATION_FILE = os.path.join(fc.datadir, 'Element_OxidationStates.txt')
 
@@ -307,7 +308,20 @@ def assign_charge(self, charge):
         self.charge = charge
         intcharge = np.floor(charge)
         deccharge = charge % 1
-        self.orbitals = [Orbital(s) for s in fc.orbital_configuration(self.element_symbol, intcharge)]
+        # self.orbitals = [Orbital(s) for s in fc.orbital_configuration(self.element_symbol, intcharge)]
+        # # add empty orbitals
+        # for n, orbital in enumerate(self.orbitals[:-1]):
+        #     next_orbital = orbital.next_orbital(fill=0)  # empty orbital
+        #     if next_orbital not in self.orbitals:
+        #         self.orbitals.insert(n + 1, next_orbital)
+        neutral_orbitals = [Orbital(s) for s in fc.orbital_configuration(self.element_symbol, 0)]
+        charge_orbitals = [Orbital(s) for s in fc.orbital_configuration(self.element_symbol, intcharge)]
+        # add missing orbitals
+        for n, orbital in enumerate(neutral_orbitals):
+            if orbital not in charge_orbitals:
+                orbital.fill = 0
+                charge_orbitals.insert(n, orbital)
+        self.orbitals = charge_orbitals
         if deccharge > 0:
             self.orbitals[-1].remove_electron(deccharge)