Merge remote-tracking branch 'origin/development' into development

abelcarreras · Jul 27, 2023 · 9fcc21f · 9fcc21f
2 parents 2d8d5a7 + 4dec145
commit 9fcc21f
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Showing 16 changed files with 926 additions and 921 deletions.
diff --git a/pyqchem/file_io.py b/pyqchem/file_io.py
@@ -146,7 +146,11 @@ def build_fchk(parsed_data):
     # txt_fchk += get_array_txt('Beta Orbital Energies', 'R', beta_mo_energies)
 
     if 'scf_density' in parsed_data:
-        total_density = np.array(parsed_data['scf_density']['alpha']) + np.array(parsed_data['scf_density']['beta'])
+        if 'beta' in parsed_data['scf_density']:
+            total_density = np.array(parsed_data['scf_density']['alpha']) + np.array(parsed_data['scf_density']['beta'])
+        else:
+            total_density = np.array(parsed_data['scf_density']['alpha'])
+
         scf_density = mat_to_vect(total_density)
         txt_fchk += get_array_txt('Total SCF Density', 'R', scf_density)
 

diff --git a/pyqchem/parsers/parser_fchk.py b/pyqchem/parsers/parser_fchk.py
@@ -230,8 +230,9 @@ def _get_all_tdm(output):
     for i, m in enumerate(re.finditer('Transition density', output)):
         indices = np.array(output[m.end() :m.end() + 100].replace('\n', ' ').split(')')[0].split('(')[1].split(','), dtype=int)
         n_elements = int(output[m.end() :m.end() + 100].replace('\n', ' ').split(')')[1].split()[2])
+        nbas = int(np.sqrt(n_elements))
         data = output[m.end(): m.end() + n_elements*50].split(')')[1].split()[3:n_elements+3]
-        tdm_data_dict[tuple(indices)] = np.array(data, dtype=float).tolist()
+        tdm_data_dict[tuple(indices)] = np.array(data, dtype=float).reshape(nbas, nbas).tolist()
 
     return tdm_data_dict
 

diff --git a/pyqchem/parsers/parser_rasci.py b/pyqchem/parsers/parser_rasci.py
@@ -298,7 +298,7 @@ def parser_rasci(output):
                       'dipole_moment_units': 'ua',
                       'oscillator_strength': strength,
                       'configurations': table,
-                      'contributions_fwn': contributions}
+                      'contributions_wfn': contributions}
 
         if nato_occ is not None:
             state_dict.update({'natural_occupation_numbers': nato_occ})