orto 1.6.0__py3-none-any.whl → 1.6.1__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.6.0'
+__version__ = '1.6.1'

orto/cli.py

@@ -862,7 +862,7 @@ def plot_abs_func(uargs):
                     output_file
                 )
             elif uargs.intensities == 'semi-classical':
-                all_datasets = oe.AbsorptionSemiClassicalDipoleExtractor.extract(
+                all_datasets = oe.AbsorptionSemiClassicalDipoleExtractor.extract( # noqa
                     output_file
                 )
 
@@ -872,7 +872,7 @@ def plot_abs_func(uargs):
             d.AbsorptionData.from_extractor_dataset(
                 dataset,
                 uargs.intensities,
-                remove_zero_osc=True
+                remove_zero_osc=uargs.zero_osc
             )
             for dataset in all_datasets
         ]
@@ -2023,6 +2023,16 @@ def read_args(arg_list=None):
         )
     )
 
+    plot_abs.add_argument(
+        '--zero_osc',
+        default=1E-5,
+        type=float,
+        help=(
+            'Oscillator strengths below this value are treated as zero\n'
+            'Default: %(default)s'
+        )
+    )
+
     plot_xes = plot_parser.add_parser(
         'xes',
         description='Plots XES from CI calculation output',

orto/data.py

@@ -172,7 +172,7 @@ class AbsorptionData():
 
     @classmethod
     def from_extractor(cls, extractor: oe.AbsorptionExtractor,
-                       remove_zero_osc: bool = True) -> list['AbsorptionData']: # noqa
+                       remove_zero_osc: float = 1E-4) -> list['AbsorptionData']: # noqa
         '''
         Creates AbsorptionData object from data extractor
 
@@ -180,8 +180,8 @@ class AbsorptionData():
         ----------
         extractor: Extractor
             Data extractor object containing transition data
-        remove_zero_osc: bool
-            If True, removes transitions with zero oscillator strength
+        remove_zero_osc: float, default=1E-4
+            Remove transitions with oscillator strength below this value
 
         Returns
         -------
@@ -204,7 +204,7 @@ class AbsorptionData():
     def from_extractor_dataset(cls,
                                dataset: dict[str, list[int | float]],
                                operator: str,
-                               remove_zero_osc: bool = False) -> 'AbsorptionData': # noqa
+                               remove_zero_osc: float = 1E-4) -> 'AbsorptionData': # noqa
         '''
         Creates AbsorptionData object from data extractor
 
@@ -214,8 +214,8 @@ class AbsorptionData():
             Dataset from orto AbsorptionExtractor.data
         operator: str
             Type of operator used to calculate transitions
-        remove_zero_osc: bool
-            If True, removes transitions with zero oscillator strength
+        remove_zero_osc: float, default=1E-4
+            Remove transitions with oscillator strength below this value
 
         Returns
         -------
@@ -228,16 +228,21 @@ class AbsorptionData():
 
         # Remove transitions with zero oscillator strength from
         # beginning and end of spectrum
-        if remove_zero_osc:
-            osc_strengths = np.array(osc_strengths)
-            # Find first non-zero oscillator strength
-            first_nonzero = np.where(osc_strengths > 1E-4)[0][0]
-            # Find last non-zero oscillator strength
-            last_nonzero = np.where(osc_strengths > 1E-4)[0][-1]
-
-            # Trim data
-            energies = energies[first_nonzero:last_nonzero + 1]
-            osc_strengths = osc_strengths[first_nonzero:last_nonzero + 1]
+        osc_strengths = np.array(osc_strengths)
+        # Find first non-zero oscillator strength
+        try:
+            first_nonzero = np.where(osc_strengths > remove_zero_osc)[0][0]
+        except IndexError:
+            raise DataFormattingError(
+                'No transitions with oscillator strength above '
+                f'{remove_zero_osc} found.'
+            )
+        # Find last non-zero oscillator strength
+        last_nonzero = np.where(osc_strengths > remove_zero_osc)[0][-1]
+
+        # Trim data
+        energies = energies[first_nonzero:last_nonzero + 1]
+        osc_strengths = osc_strengths[first_nonzero:last_nonzero + 1]
 
         return cls(energies, osc_strengths, operator)
 

orto/utils.py

@@ -396,6 +396,7 @@ def find_unique_substring(names):
                 break
     return unique_names
 
+
 def is_floatable(string: str) -> bool:
     '''
     Checks if string can be converted to float
@@ -415,4 +416,4 @@ def is_floatable(string: str) -> bool:
         float(string)
         return True
     except ValueError:
-        return False
+        return False

{orto-1.6.0.dist-info → orto-1.6.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.6.0
+Version: 1.6.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.6.1.dist-info/RECORD

@@ -0,0 +1,17 @@
+orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
+orto/__version__.py,sha256=purtuLvskAhEdNLSjxoYqUibNFbOHk0IB5Wc4KCA7l4,22
+orto/cli.py,sha256=K3qJzw1stIff3YW88h7MLZuTVFIWGfnw7RaTFLRyhrk,76740
+orto/constants.py,sha256=anxaiTykO8Q_CXliR7zuOAdnXZrQ2-C4ndaviyl7kGc,419
+orto/data.py,sha256=YsfSD3yaebPmaGweeR0o-hBxN0Xi7WZ1PlWv-vnhnJc,11416
+orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
+orto/extractor.py,sha256=d2_pGQeIjK_JbsMINTawUgcO2vcPq0b9uQj9VKuI720,75953
+orto/input.py,sha256=N8JbySSVEC_qmXZ7ppJsZ7Z1qel6PfalGYRtnX1hJ6U,9900
+orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
+orto/plotter.py,sha256=-8Lgv-kDjw_wHZrDrQzQGT521gSZ3IJdIeLqzdQgflQ,17656
+orto/utils.py,sha256=GcMZ9uebOSnkPQT_U5O0X49LUtTu8YpXZxEsNKgXNTY,9838
+orto-1.6.1.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
+orto-1.6.1.dist-info/METADATA,sha256=Gxi6rsbFM8jx-4YxqII-Pb1fNE1FSPEdIZeHUfBMnDU,1184
+orto-1.6.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.6.1.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.6.1.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.6.1.dist-info/RECORD,,

orto-1.6.0.dist-info/RECORD

@@ -1,17 +0,0 @@
-orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-orto/__version__.py,sha256=bYN93DTWr8alkTnO3wj31CU5gqTshxIcsbXUcJcUAc8,22
-orto/cli.py,sha256=AH9Cnfu21XGTs2ygLZGb8yxzJPe1gxxnF9qOsm_H1II,76491
-orto/constants.py,sha256=anxaiTykO8Q_CXliR7zuOAdnXZrQ2-C4ndaviyl7kGc,419
-orto/data.py,sha256=r6Ht1X0-FhjUbEAAi3a9F2R2_QG3QFElaAAcZNz4GRQ,11213
-orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
-orto/extractor.py,sha256=d2_pGQeIjK_JbsMINTawUgcO2vcPq0b9uQj9VKuI720,75953
-orto/input.py,sha256=N8JbySSVEC_qmXZ7ppJsZ7Z1qel6PfalGYRtnX1hJ6U,9900
-orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
-orto/plotter.py,sha256=-8Lgv-kDjw_wHZrDrQzQGT521gSZ3IJdIeLqzdQgflQ,17656
-orto/utils.py,sha256=fghKZnrO1HTtOZPZRbNK6QTgUOXiIQ6NEFvesDSoY0o,9836
-orto-1.6.0.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
-orto-1.6.0.dist-info/METADATA,sha256=zfjB9HzSeKgJKRlTqLMw2AmqspP1nyYAlJZDa_vS3kE,1184
-orto-1.6.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orto-1.6.0.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
-orto-1.6.0.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
-orto-1.6.0.dist-info/RECORD,,