orto 0.27.0__tar.gz → 1.0.0__tar.gz

{orto-0.27.0 → orto-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 0.27.0
+Version: 1.0.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.0.0/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.0.0'

{orto-0.27.0 → orto-1.0.0}/orto/cli.py

@@ -912,7 +912,7 @@ def extract_freq_func(uargs, save=True):
             data[0]['energy (cm^-1)'][:uargs.num],
             data[0]['IR Intensity (km mol^-1)'][:uargs.num]
         ):
-            print(f'{frq:.2f} {inty:.2f}')
+            print(f'{frq:.5f} {inty:.5f}')
     else:
         # Save to new .csv file
         out_name = f'{uargs.output_file.stem}_frequencies.csv'
@@ -924,7 +924,7 @@ def extract_freq_func(uargs, save=True):
                 data[0]['energy (cm^-1)'][:uargs.num],
                 data[0]['IR Intensity (km mol^-1)'][:uargs.num]
             ):
-                f.write(f'{frq:.2f}, {inty:.2f}\n')
+                f.write(f'{frq:.5f}, {inty:.5f}\n')
 
         ut.cprint(f'Data written to {out_name}', 'cyan')
 
@@ -1379,7 +1379,7 @@ def read_args(arg_list=None):
         '--output_file',
         type=pathlib.Path,
         help=(
-            'Name of truncated molden file',
+            'Name of truncated molden file\n'
             'If not specified, molden file will be truncated in place'
         ),
         default=None

{orto-0.27.0 → orto-1.0.0}/orto/extractor.py

@@ -478,7 +478,7 @@ class FrequencyExtractor(extto.BetweenExtractor):
             [float(val) for val in freq_pattern.findall(block)]
         )
 
-        # Check if symmetry is enabled by searching for 
+        # Check if symmetry is enabled by searching for
         # "Point group" in block
         if re.search(r'Point group', block):
             symmetry = True
@@ -538,25 +538,23 @@ class FrequencyExtractor(extto.BetweenExtractor):
         tz_pattern = re.compile(
             r'\([ -]?\d\.\d{6} *-?\d\.\d{6} *(-?\d\.\d{6})\)'
         )
-        # t2_pattern = re.compile(
-        #     r'(\d\.\d{6}) *\([ -]?\d\.\d{6} *-?\d\.\d{6} *-?\d\.\d{6}\)'
-        # )
-        # eps_pat = re.compile(
-        #     r'\d{,4}: * \d{,4}.\d{2} * (\d.\d{6})'
-        # )
+
         tx = np.asarray(
-            [0] * 6 + [float(val) for val in tx_pattern.findall(block)]
+            [float(val) for val in tx_pattern.findall(block)]
         )
         ty = np.asarray(
-            [0] * 6 + [float(val) for val in ty_pattern.findall(block)]
+            [float(val) for val in ty_pattern.findall(block)]
         )
         tz = np.asarray(
-            [0] * 6 + [float(val) for val in tz_pattern.findall(block)]
+            [float(val) for val in tz_pattern.findall(block)]
         )
 
-        # epso = np.asarray(
-        #     [0] * 6 + [float(val) for val in eps_pat.findall(block)]
-        # )
+        # t values are missing for first n_zero modes and for imaginary modes
+        n_missing = len(wavenumbers) - len(tx)
+        z_arr = np.zeros(n_missing)
+        tx = np.concatenate((z_arr, tx))
+        ty = np.concatenate((z_arr, ty))
+        tz = np.concatenate((z_arr, tz))
 
         # This is the T2 printed by ORCA
         # (Dipole derivative wrt to MWC)**2 * vibrational overlap**2
@@ -574,11 +572,10 @@ class FrequencyExtractor(extto.BetweenExtractor):
         icm2eh = 100 / sc.physical_constants['hartree-inverse meter relationship'][0] # noqa
         #
         b2 = np.zeros_like(wavenumbers)
-        n_zero = np.where(wavenumbers > 1E-4)[0][0]
-        b2[n_zero:] = 1 / (2 * icm2eh * wavenumbers[n_zero:])
+        b2[n_missing:] = 1 / (2 * icm2eh * wavenumbers[n_missing:])
         # divide by sqrt(b2)
         # to give units of e m_e^-1/2
-        t[n_zero:] /= np.sqrt(b2[n_zero:])
+        t[n_missing:] /= np.sqrt(b2[n_missing:])
 
         # Convert to SI
         # First convert electrons to coulombs
@@ -588,12 +585,13 @@ class FrequencyExtractor(extto.BetweenExtractor):
         t *= (sc.m_e)**-0.5
 
         # Calculate A_e in units of m mol^-1
+        # this is "Intensity" in Orca
         ae = np.ones_like(wavenumbers)
-        ae[:n_zero] = 0
+        ae[:n_missing] = 0
         ae *= sc.Avogadro / (12 * sc.epsilon_0 * sc.speed_of_light**2)
-        ae[n_zero:] *= t[n_zero:] ** 2
+        ae[n_missing:] *= t[n_missing:] ** 2
         # and convert to km mol^-1
-        ae[n_zero:] /= 1000
+        ae[n_missing:] /= 1000
 
         # Convert absorbance to linear
         alin = ae / np.log(10)
@@ -613,7 +611,7 @@ class FrequencyExtractor(extto.BetweenExtractor):
             irreps = np.concatenate([
                 [
                     irrep
-                    for irrep in iblock.replace('\n','').split()
+                    for irrep in iblock.replace('\n', '').split()
                 ]
                 for iblock in irrep_blocks
             ])

{orto-0.27.0 → orto-1.0.0}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 0.27.0
+Version: 1.0.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-0.27.0 → orto-1.0.0}/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__ = '0.27.0'
+__version__ = '1.0.0'
 
 setuptools.setup(
     name='orto',

orto-0.27.0/orto/__version__.py

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