orto 0.26.2__tar.gz → 0.27.0__tar.gz

{orto-0.26.2 → orto-0.27.0}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 0.26.2
+Version: 0.27.0
 Summary: A package to make life easier when performing Orca calculations.
-Home-page: https://gitlab.com/kragskow-group/orto
+Home-page: https://orto.kragskow.group
 Author: Jon Kragskow
 Author-email: jgck20@bath.ac.uk
 Project-URL: Bug Tracker, https://gitlab.com/kragskow-group/orto/issues
-Project-URL: Documentation, https://www.kragskow.dev/orto/index.html
+Project-URL: Documentation, https://orto.kragskow.group
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent

orto-0.27.0/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '0.27.0'

{orto-0.26.2 → orto-0.27.0}/orto/cli.py

@@ -108,7 +108,7 @@ def extract_sf_energies_func(uargs):
                 if len(all_data) > 1:
                     f.write(f'# Section {it + 1:d}\n')
 
-                f.write('State, Root, Multiplicity, Relative Energy (cm^-1)\n')
+                f.write('State, Root, Multiplicity, Relative Energy (cm⁻¹)\n')
 
                 f.write(
                     f'1, {data['root'][0]:d}, {data['multiplicity'][0]:d}, 0\n' # noqa
@@ -190,7 +190,7 @@ def extract_so_energies_func(uargs):
             if len(all_energies) > 1:
                 f.write(f'# Section {it + 1:d}\n')
 
-            f.write('State, Relative Energy (cm^-1)\n')
+            f.write('State, Relative Energy (cm⁻¹)\n')
 
             for eit, energy in enumerate(energies):
                 f.write(
@@ -242,7 +242,7 @@ def extract_gmatrix_func(uargs, save=True):
         with open(out_name, 'w') as f:
             for it, data in enumerate(all_data):
                 if len(all_data) > 1:
-                    f.write(f'Section {it + 1:d}')
+                    f.write(f'Section {it + 1:d}\n')
                 for key, val in data.items():
                     f.write(f'{key}:\n')
                     f.write(str(val).replace('[', '').replace(']', ''))
@@ -701,7 +701,7 @@ def distort_func(uargs):
     data = oe.FrequencyExtractor.extract(uargs.output_file)
 
     ut.cprint(
-        'Distorting along mode #{}:  {: .2f} cm^-1'.format(
+        'Distorting along mode #{}:  {: .2f} cm⁻¹'.format(
             uargs.mode_number,
             data[0]['energy (cm^-1)'][uargs.mode_number]
             ),
@@ -907,7 +907,7 @@ def extract_freq_func(uargs, save=True):
         uargs.num = len(data[0]['energy (cm^-1)'])
 
     if not save:
-        print('Frequencies (cm^-1) and intensities (km/mol)')
+        print('Frequencies (cm⁻¹) and intensities (km/mol)')
         for frq, inty in zip(
             data[0]['energy (cm^-1)'][:uargs.num],
             data[0]['IR Intensity (km mol^-1)'][:uargs.num]
@@ -919,7 +919,7 @@ def extract_freq_func(uargs, save=True):
         with open(out_name, 'w') as f:
             f.write(
                 f'# Frequencies and intensities from {uargs.output_file}\n')
-            f.write('# Frequency (cm^-1), Intensity (km/mol)\n')
+            f.write('# Frequency (cm⁻¹), Intensity (km/mol)\n')
             for frq, inty in zip(
                 data[0]['energy (cm^-1)'][:uargs.num],
                 data[0]['IR Intensity (km mol^-1)'][:uargs.num]

{orto-0.26.2 → orto-0.27.0}/orto/extractor.py

@@ -424,8 +424,8 @@ class AILFTOrbEnergyExtractor(extto.BetweenExtractor):
 
 class FrequencyExtractor(extto.BetweenExtractor):
     '''
-    Extracts Vibrational mode energies, eigenvectors, and intensity \n
-    information from output file
+    Extracts Vibrational mode energies, eigenvectors, intensities, \n
+    and irreps from output file
     '''
 
     # Regex Start Pattern
@@ -448,6 +448,7 @@ class FrequencyExtractor(extto.BetweenExtractor):
          - tx\n
          - ty\n
          - tz\n
+         - irrep\n
         and all values are numpy arrays.\n
         Dimensions are n_atoms*3, 1 for all arrays other than displacements.
         '''
@@ -477,37 +478,51 @@ class FrequencyExtractor(extto.BetweenExtractor):
             [float(val) for val in freq_pattern.findall(block)]
         )
 
+        # Check if symmetry is enabled by searching for 
+        # "Point group" in block
+        if re.search(r'Point group', block):
+            symmetry = True
+        else:
+            symmetry = False
+
         n_atoms = len(wavenumbers) // 3
 
+        # Displacements section can be different depending on symmetry
+        if symmetry:
+            displacement_pattern = re.compile(
+                r'(?: +\d+){1,10}\s(?: +\d+\-[A-Za-z]+[0-9]*[A-Za-z]*){1,10}\s((?: +\d+ +(?: +-?\d\.\d{6}){1,10}\s)*)' # noqa
+            )
+        else:
+            displacement_pattern = re.compile(
+                r'(?: +\d+){1,6} +\s((?: +\d+ +(?: +-?\d\.\d{6}){1,6}\s)*)'
+            )
+
         # Extract Displacements
         disp_table = re.findall(
-            r'((?: +\d+){1,6} +\s(?: +\d+ +(?: +-?\d\.\d{6}){1,6}\s)*)',
+            displacement_pattern,
             block
         )
 
         # and combine in a single dataframe
-        master = pd.read_csv(
-                StringIO(disp_table[0]),
-                sep=r'\s{2,}',
-                engine='python',
-                index_col=0
-            )
-
-        for chunk in disp_table[1:]:
-            _df = pd.read_csv(
-                StringIO(chunk),
-                sep=r'\s{2,}',
-                engine='python',
-                index_col=0
+        all_df = [
+            pd.read_csv(
+                StringIO(dt),
+                sep=r'\s+',
+                index_col=[0],
+                header=None,
+                skipinitialspace=True,
             )
-            master = master.join(_df)
+            for dt in disp_table
+        ]
+        # Combine list of dataframe chunks into a single dataframe
+        combined_df = pd.concat(all_df, axis=1, join='outer')
 
         # convert to numpy array
-        disp_table = master.to_numpy()
+        disp_array = combined_df.to_numpy()
         # and reshape
-        disp_x = disp_table[0::3, :]
-        disp_y = disp_table[1::3, :]
-        disp_z = disp_table[2::3, :]
+        disp_x = disp_array[0::3, :]
+        disp_y = disp_array[1::3, :]
+        disp_z = disp_array[2::3, :]
         disp = np.zeros((n_atoms, n_atoms * 3, 3))
         disp[:, :, 0] = disp_x
         disp[:, :, 1] = disp_y
@@ -586,6 +601,25 @@ class FrequencyExtractor(extto.BetweenExtractor):
         # Convert to units of 1000 cm mol^-1
         eps = alin * 100
 
+        # Get irreducible representations
+        if symmetry:
+            irrep_pattern = re.compile(
+                r'(?: +\d+){1,10}\s((?: +\d+\-[A-Za-z]+[0-9]*[A-Za-z]*){1,10}\s)(?: +\d+ +(?: +-?\d\.\d{6}){1,10}\s)*' # noqa
+            )
+            irrep_blocks = re.findall(
+                irrep_pattern,
+                block
+            )
+            irreps = np.concatenate([
+                [
+                    irrep
+                    for irrep in iblock.replace('\n','').split()
+                ]
+                for iblock in irrep_blocks
+            ])
+        else:
+            irreps = np.array([''] * len(wavenumbers))
+
         data = {
             'energy (cm^-1)': wavenumbers,
             'displacements': disp,
@@ -594,7 +628,8 @@ class FrequencyExtractor(extto.BetweenExtractor):
             't2 (a.u.^2)': t2,
             'tx (a.u.)': tx,
             'ty (a.u.)': ty,
-            'tz (a.u.)': tz
+            'tz (a.u.)': tz,
+            'irrep': irreps
         }
 
         return data

{orto-0.26.2 → orto-0.27.0}/orto.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 0.26.2
+Version: 0.27.0
 Summary: A package to make life easier when performing Orca calculations.
-Home-page: https://gitlab.com/kragskow-group/orto
+Home-page: https://orto.kragskow.group
 Author: Jon Kragskow
 Author-email: jgck20@bath.ac.uk
 Project-URL: Bug Tracker, https://gitlab.com/kragskow-group/orto/issues
-Project-URL: Documentation, https://www.kragskow.dev/orto/index.html
+Project-URL: Documentation, https://orto.kragskow.group
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent

{orto-0.26.2 → orto-0.27.0}/setup.py

@@ -8,7 +8,7 @@ Please see the `orto` documentation for more details.
 
 # DO NOT EDIT THIS NUMBER!
 # IT IS AUTOMATICALLY CHANGED BY python-semantic-release
-__version__ = '0.26.2'
+__version__ = '0.27.0'
 
 setuptools.setup(
     name='orto',
@@ -18,10 +18,10 @@ setuptools.setup(
     description='A package to make life easier when performing Orca calculations.', # noqa
     long_description=long_description,
     long_description_content_type='text/markdown',
-    url='https://gitlab.com/kragskow-group/orto',
+    url='https://orto.kragskow.group',
     project_urls={
         'Bug Tracker': 'https://gitlab.com/kragskow-group/orto/issues',
-        'Documentation': 'https://www.kragskow.dev/orto/index.html'
+        'Documentation': 'https://orto.kragskow.group'
     },
     classifiers=[
         'Programming Language :: Python :: 3',

orto-0.26.2/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '0.26.2'