minor format details

added coors_2.xyz example for autogenerated electronic structure

cosymlib/__init__.py

@@ -271,29 +271,28 @@ def print_symmetry_nearest_structure(self, label, multi=1, central_atom=0, conne
 
             output.write(file_io.get_file_xyz_txt(geometry))
 
-    # This should just call methos within this class
+    # 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=None, axis2=None, center=None, output=sys.stdout)
-        self.print_wnfsym_irreducible_repr(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 = ''
         first = True
         for molecule in self._molecules:
             wf_measure = molecule.get_wf_symmetry(group, axis=axis, axis2=axis2, center=center)
-            wf_ir = molecule.get_wf_irreducible_representations(group, axis=axis, axis2=axis2, center=center)
 
             if first:
-                sep_line = '        ' + '---------' * len(wf_measure['labels']) + '\n'
+                sep_line = '          ' + '---------' * len(wf_measure['labels']) + '\n'
 
                 txt += '\nWaveFunction: CSM-like values\n'
                 txt += sep_line
-                txt += '        ' + '  '.join(['{:^7}'.format(s) for s in wf_measure['labels']])
+                txt += '           ' + '  '.join(['{:^7}'.format(s) for s in wf_measure['labels']])
                 txt += '\n'
                 txt += sep_line
 
-            txt += '{:.10} '.format(molecule.name) + '  '.join(['{:7.3f}'.format(s) for s in wf_measure['csm']])
+            txt += '{:<9} '.format(molecule.name) + '  '.join(['{:7.3f}'.format(s) for s in wf_measure['csm']])
             txt += '\n'
             first = False
 

examples/coord_2.xyz

@@ -0,0 +1,18 @@
+ 5
+ Methane
+   C      0.0000      0.0000      0.0000
+   H      0.6252      0.6252      0.6252
+   H     -0.6252     -0.6252      0.6252
+   H     -0.6252      0.6252     -0.6252
+   H      0.6252     -0.6252     -0.6252
+ 4
+ Ammonia
+   N      0.0000      0.0000      0.1000
+   H      0.5288      0.1610      0.9359
+   H      0.2051      0.8240     -0.6786
+   H      0.3345     -0.9314     -0.4496
+3
+ Water
+   O      0.0000      0.0000      0.1140
+   H      0.0000      0.7808     -0.4562
+   H      0.0000     -0.7808     -0.4561

examples/python_api.py

@@ -66,7 +66,6 @@ def print_csm(data):
 
 
 molecule = file_io.get_molecule_from_file_fchk('pirrol.fchk')
-molecules_set = file_io.read_generic_structure_file('pirrol.fchk', read_multiple=True)
 
 data = molecule.get_wf_symmetry('C2v',
                                 axis=[0.000000, 0.000000, 1.000000],  # valor defecte
@@ -77,12 +76,23 @@ def print_csm(data):
 print_csm(data)
 
 print('\nCOSYMLIB\n--------')
-
+molecules_set = file_io.get_geometry_from_file_xyz('coord_2.xyz', read_multiple=True)
 molecules_group = Cosymlib(molecules_set)
+print('\n\n***********{}************'.format('print_electronic_symmetry_measure()'))
 molecules_group.print_electronic_symmetry_measure('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
+
+
+molecules_set = file_io.read_generic_structure_file('pirrol.fchk', read_multiple=True)
+molecules_group = Cosymlib(molecules_set)
+print('\n\n***********{}************'.format('print_info()'))
 molecules_group.print_info()
+print('\n\n***********{}************'.format('print_wnfsym_irreducible_repr()'))
 molecules_group.print_wnfsym_irreducible_repr('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
+print('\n\n***********{}************'.format('print_wnfsym_sym_ovelap()'))
 molecules_group.print_wnfsym_sym_ovelap('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
+print('\n\n***********{}************'.format('print_wnfsym_sym_matrices()'))
 molecules_group.print_wnfsym_sym_matrices('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
+print('\n\n***********{}************'.format('plot_mo_diagram()'))
 molecules_group.plot_mo_diagram('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])
+print('\n\n***********{}************'.format('plot_sym_energy_evolution()'))
 molecules_group.plot_sym_energy_evolution('C2v', axis=[0, 0, 1], center=[0.0, 0.0, 0.0])