minor cleaning

cosymlib/__init__.py

@@ -57,6 +57,20 @@ def _get_table_format(labels, molecules_names, data):
     return txt
 
 
+def _get_axis_info(molecule, group, axis, axis2, center):
+
+    txt = ''
+    axis_info = molecule.get_symmetry_axes(group, axis=axis, axis2=axis2, center=center)
+    txt += '\nSymmetry axis orientation\n'
+    txt += 'center: ' + '  '.join(['{:12.8f}'.format(s) for s in axis_info['center']])
+    txt += '\n'
+    txt += 'axis  : ' + '  '.join(['{:12.8f}'.format(s) for s in axis_info['axis']])
+    txt += '\n'
+    txt += 'axis2 : ' + '  '.join(['{:12.8f}'.format(s) for s in axis_info['axis2']])
+    txt += '\n'
+    return txt
+
+
 class Cosymlib:
     """
     Main cosymlib class
@@ -336,11 +350,6 @@ def print_chirality_measure(self, labels, central_atom=0, center=None, output=sy
 
         output.write(txt)
 
-    # This should be substituted by calling methods within this class
-    def OLD_print_wnfsym_measure_verbose(self, group, axis=None, axis2=None, center=None, output=sys.stdout):
-        self.print_wnfsym_sym_matrices(group, axis=axis, axis2=axis2, center=center, output=output)
-        self.print_wnfsym_irreducible_repr(group, axis=axis, axis2=axis2, center=center, output=output)
-
     def _print_electronic_symmetry_measure(self, group, axis=None, axis2=None, center=None, output=sys.stdout):
 
         txt = ''
@@ -520,7 +529,7 @@ def print_wnfsym_irreducible_repr(self, group, axis=None, axis2=None, center=Non
             ir_mo = molecule.get_mo_irreducible_representations(group, axis=axis, axis2=axis2, center=center)
             data_wf = molecule.get_wf_irreducible_representations(group, axis=axis, axis2=axis2, center=center)
 
-            txt = '\nMolecule : {}\n'.format(molecule.name)
+            txt += '\nMolecule : {}\n'.format(molecule.name)
             sep_line = '     ' + '---------' * (len(ir_mo['labels'])) + '\n'
 
             txt += '\nWaveFunction: Irred. Rep. Decomposition\n'
@@ -535,14 +544,7 @@ def print_wnfsym_irreducible_repr(self, group, axis=None, axis2=None, center=Non
             txt += 'WFN ' + '  '.join(['{:7.3f}'.format(s) for s in data_wf['total']])
             txt += '\n'
 
-        axes_information = molecule.get_symmetry_axes(group, axis=axis, axis2=axis2, center=center)
-        txt += '\nSymmetry parameters\n'
-        txt += 'center: ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['center']])
-        txt += '\n'
-        txt += 'axis  : ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['axis']])
-        txt += '\n'
-        txt += 'axis2 : ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['axis2']])
-        txt += '\n'
+            txt += _get_axis_info(molecule, group, axis, axis2, center)
 
         output.write(txt)
 
@@ -556,7 +558,7 @@ def print_wnfsym_mo_irreducible_repr(self, group, axis=None, axis2=None, center=
             beta_energies = molecule.electronic_structure.beta_energies
             beta_occupancy = molecule.electronic_structure.beta_occupancy
 
-            txt = '\nMolecule : {}\n'.format(molecule.name)
+            txt += '\nMolecule : {}\n'.format(molecule.name)
 
             sep_line = '     ' + '---------' * (2 + len(ir_mo['labels'])) + '\n'
 
@@ -591,14 +593,8 @@ def print_wnfsym_mo_irreducible_repr(self, group, axis=None, axis2=None, center=
 
             if non_one:
                 warn('The sum of some molecular orbital irreducible represaentations are not equal one (*)')
-        axes_information = molecule.get_symmetry_axes(group, axis=axis, axis2=axis2, center=center)
-        txt += '\nSymmetry parameters\n'
-        txt += 'center: ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['center']])
-        txt += '\n'
-        txt += 'axis  : ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['axis']])
-        txt += '\n'
-        txt += 'axis2 : ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['axis2']])
-        txt += '\n'
+
+            txt += _get_axis_info(molecule, group, axis, axis2, center)
 
         output.write(txt)
 

cosymlib/molecule/__init__.py

@@ -41,7 +41,7 @@ def __init__(self, geometry,
         self._symmetry = geometry._symmetry
         self._shape = geometry._shape
 
-    def molecule_copy(self):
+    def get_copy(self):
         return deepcopy(self)
 
     def set_name(self, name):
@@ -70,7 +70,7 @@ def electronic_structure(self):
         :rtype: ElectronicStructure
         """
         if self._electronic_structure is None:
-            warn('Warning: Electronic structure auto generated from Extended-Huckel calculation')
+            warn('Electronic structure auto generated from Extended-Huckel calculation')
             eh = ExtendedHuckel(self.geometry)
             self._electronic_structure = ElectronicStructure(basis=eh.get_basis(),
                                                              orbital_coefficients=[eh.get_mo_coefficients(), []],
@@ -82,8 +82,8 @@ def electronic_structure(self):
 
         return self._electronic_structure
 
-    # TODO: 'symmetry' and 'shape' properties should be removed. All methods inside these
-    # TODO: classes should be mirrored in geometry/molecule class
+    # TODO: 'symmetry' and 'shape' properties may be removed. All methods inside these
+    # TODO: classes may be mirrored in geometry/molecule class? [idea]
     @property
     def symmetry(self):
         return self._symmetry

cosymlib/molecule/electronic_structure/__init__.py

@@ -1,3 +1,6 @@
+HARTREE_TO_EV = 27.21139563180092
+
+
 class ElectronicStructure:
     """
     Main Electronic structure class
@@ -10,13 +13,13 @@ class ElectronicStructure:
     # :type charge: int
     :param multiplicity: The multiplicity
     :type multiplicity: int
-    :param alpha_energies: Alpha molecular orbital energies
+    :param alpha_energies: Alpha molecular orbital energies in Hartree
     :type alpha_energies: list
-    :param beta_energies: Beta molecular orbital energies
+    :param beta_energies: Beta molecular orbital energies in Hartree
     :type beta_energies: list
-    :param alpha_occupancy: List of alpha electrons
+    :param alpha_occupancy: Occupancy of alpha orbitals
     :type alpha_occupancy: list
-    :param beta_occupancy: List of beta electrons
+    :param beta_occupancy: Occupancy of beta orbitals
     :type beta_occupancy: list
 
     """
@@ -39,12 +42,11 @@ def __init__(self,
         else:
             self._Cb = orbital_coefficients[1]
 
-        ha_eV = 27.21139563180092
-        self._alpha_energies = [energy*ha_eV for energy in alpha_energies]
+        self._alpha_energies = [energy * HARTREE_TO_EV for energy in alpha_energies]
         if len(beta_energies) == 0:
-            self._beta_energies = [energy*ha_eV for energy in alpha_energies]
+            self._beta_energies = [energy * HARTREE_TO_EV for energy in alpha_energies]
         else:
-            self._beta_energies = [energy*ha_eV for energy in beta_energies]
+            self._beta_energies = [energy * HARTREE_TO_EV for energy in beta_energies]
 
         self._alpha_occupancy = alpha_occupancy
         self._beta_occupancy = beta_occupancy
@@ -61,14 +63,14 @@ def set_occupancy(self, occupancy):
 
     def set_alpha_occupancy(self, occupancy):
         if len(occupancy) > len(self._Ca):
-            raise IndexError('Lenght of alpha occupancy list is longer than the molecular orbitals provided')
+            raise IndexError('Alpha occupancy list do not match with molecular orbitals')
         self._alpha_occupancy = occupancy
         self._occupancy_consistency()
         self._recalculate_spin()
 
     def set_beta_occupancy(self, occupancy):
         if len(occupancy) > len(self._Cb):
-            raise IndexError('Lenght of beta occupancy list is longer than the molecular orbitals provided')
+            raise IndexError('Beta occupancy list do not match with molecular orbitals')
         self._beta_occupancy = occupancy
         self._occupancy_consistency()
         self._recalculate_spin()