rebase master

added set alpha/beta occupancies to play with occupied/empty orbtials
added density results and axes/center optimization results from wfnsympy
modified normal modes to improve the example
updated version

cosymlib/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.8.2'
+__version__ = '0.8.3'
 
 from cosymlib.molecule import Molecule, Geometry
 from cosymlib import file_io

cosymlib/molecule/electronic_structure/__init__.py

@@ -26,6 +26,12 @@ def __init__(self,
             for i in range(self._multiplicity-1):
                 self._beta_occupancy.append(0)
 
+    def set_alpha_occupancy(self, occupancy):
+        self._alpha_occupancy = occupancy
+
+    def set_beta_occupancy(self, occupancy):
+        self._beta_occupancy = occupancy
+
     @property
     def charge(self):
         return self._charge

cosymlib/symmetry/__init__.py

@@ -198,6 +198,18 @@ def wf_ideal_group_table(self, group):
                 'labels': results.SymLab,
                 'table': results.ideal_gt}
 
+    def dens_measure(self, group):
+        results = self._get_wfnsym_results(group)
+        return {'labels': results.SymLab,
+                'csm': results.csm_dens,
+                'csm_coef': results.csm_dens_coef}
+
+    def axes(self, group):
+        results = self._get_wfnsym_results(group)
+        return {'center' : results.center,
+                'axis': results.axis,
+                'axis2': results.axis2}
+
     # Old method to be deleted
     def symmetry_overlap_analysis(self, group, vector_axis1, vector_axis2, center):
         results = self._get_wfnsym_results(group)

examples/normal_modes_api.py

@@ -47,11 +47,12 @@ def get_nm_vibration_path(geometry, normal_mode, points=10, backward=False, k=1.
 molecule = read_generic_structure_file('sf6.fchk')
 freq, nm_martices = read_normal_modes_gaussian('sf6_freq.out')
 k_points = 1.5
-n_freq = 0
-path = get_nm_vibration_path(molecule.geometry.get_positions(), nm_martices[0], k=k_points)
+points = 10
+n_freq = 1
+path = get_nm_vibration_path(molecule.geometry.get_positions(), nm_martices[n_freq - 1], k=k_points)
 
-x = np.linspace(k_points/10, k_points, 10)
-output = open('sf6_freq{}.xyz'.format(n_freq+1), 'w')
+x = np.linspace(k_points/points, k_points, points)
+output = open('sf6_freq{}.xyz'.format(n_freq), 'w')
 for ids, structure in enumerate(path):
     xi = '{:.2f}'.format(x[ids]).replace('.', '')
     txt = get_file_xyz_txt(Geometry(structure, symbols=molecule.geometry.get_symbols(), name='freq : ' + str(freq[0]) +