orto 1.11.0__tar.gz → 1.11.1__tar.gz

{orto-1.11.0 → orto-1.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.0
+Version: 1.11.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.11.1/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.11.1'

{orto-1.11.0 → orto-1.11.1}/orto/cli.py

@@ -1040,6 +1040,7 @@ def plot_xas_func(uargs):
 
         # Remove transitions with zero oscillator strength from
         # beginning and end of spectrum
+        print(data['fosc'], x_values)
         if not uargs.no_trim:
             # Find first non-zero oscillator strength
             first_nonzero = np.where(data['fosc'] > 1E-6)[0][0]
@@ -2417,7 +2418,7 @@ def read_args(arg_list=None):
 
     gen_abs.add_argument(
         '--zero_osc',
-        default=1E-5,
+        default=1E-7,
         type=float,
         help=(
             'Oscillator strengths below this value are treated as zero\n'
@@ -2582,7 +2583,7 @@ def read_args(arg_list=None):
 
     plot_abs.add_argument(
         '--zero_osc',
-        default=1E-5,
+        default=1E-7,
         type=float,
         help=(
             'Oscillator strengths below this value are treated as zero\n'
@@ -2612,6 +2613,16 @@ def read_args(arg_list=None):
         )
     )
 
+    plot_abs.add_argument(
+        '--no_trim',
+        action='store_true',
+        default=False,
+        help=(
+            'Do not trim spectrum to non-zero oscillator strength\n'
+            'Default: %(default)s'
+        )
+    )
+
     plot_xes = plot_parser.add_parser(
         'xes',
         description='Plots XES from CI calculation output',

{orto-1.11.0 → orto-1.11.1}/orto/data.py

@@ -236,7 +236,7 @@ class AbsorptionData():
     def from_extractor_dataset(cls,
                                dataset: dict[str, list[int | float]],
                                operator: str,
-                               remove_zero_osc: float = 1E-4) -> 'AbsorptionData': # noqa
+                               remove_zero_osc: float = 1E-7) -> 'AbsorptionData': # noqa
         '''
         Creates AbsorptionData object from data extractor
 
@@ -246,7 +246,7 @@ class AbsorptionData():
             Dataset from orto AbsorptionExtractor.data
         operator: str
             Type of operator used to calculate transitions
-        remove_zero_osc: float, default=1E-4
+        remove_zero_osc: float, default=1E-7
             Remove transitions with oscillator strength below this value
 
         Returns
@@ -261,6 +261,7 @@ class AbsorptionData():
         # Remove transitions with zero oscillator strength from
         # beginning and end of spectrum
         osc_strengths = np.array(osc_strengths)
+
         # Find first non-zero oscillator strength
         try:
             first_nonzero = np.where(osc_strengths > remove_zero_osc)[0][0]

{orto-1.11.0 → orto-1.11.1}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.0
+Version: 1.11.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.11.0 → orto-1.11.1}/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__ = '1.11.0'
+__version__ = '1.11.1'
 
 setuptools.setup(
     name='orto',

orto-1.11.0/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '1.11.0'