orto 1.11.0__tar.gz → 1.11.2__tar.gz

{orto-1.11.0 → orto-1.11.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.0
+Version: 1.11.2
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.11.2/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.11.2'

{orto-1.11.0 → orto-1.11.2}/orto/cli.py

@@ -929,6 +929,8 @@ def plot_xes_func(uargs):
             x_values = np.asarray(data['energy (cm^-1)'])
         elif uargs.x_unit == 'wavelength':
             x_values = 1E7 / np.asarray(data['energy (cm^-1)'])
+        elif uargs.x_unit == 'wavelength_rev':
+            x_values = 1E7 / np.asarray(data['energy (cm^-1)'])
         elif uargs.x_unit == 'energy':
             x_values = np.asarray(data['energy (ev)'])
 
@@ -1040,6 +1042,7 @@ 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]
@@ -1201,14 +1204,23 @@ def plot_abs_func(uargs, save_data_only=False):
             x_vals = abs_data.wavenumbers
             min_factor = 0.8
             max_factor = 1.1
+            x_reversed = False
         elif uargs.x_unit == 'wavelength':
             x_vals = abs_data.wavelengths
             max_factor = 1.1
             min_factor = 0.8
+            x_reversed = False
+        elif uargs.x_unit == 'wavelength_rev':
+            x_vals = abs_data.wavelengths
+            max_factor = 1.1
+            min_factor = 0.8
+            x_reversed = True
+            uargs.x_unit = 'wavelength'
         elif uargs.x_unit == 'energy':
             x_vals = abs_data.energies
             min_factor = 0.9995
             max_factor = 1.0005
+            x_reversed = False
 
         # Set x_min and x_max
         if isinstance(uargs.x_lim[0], str):
@@ -1243,7 +1255,8 @@ def plot_abs_func(uargs, save_data_only=False):
             num_points=10000,
             x_min=x_min,
             x_max=x_max,
-            comment=unique_names[it]
+            comment=unique_names[it],
+            x_reversed=x_reversed
         )
 
         if save_data_only:
@@ -2417,7 +2430,7 @@ 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'
@@ -2539,9 +2552,9 @@ def read_args(arg_list=None):
     plot_abs.add_argument(
         '--x_unit',
         type=str,
-        choices=['energy', 'wavelength', 'wavenumber'],
+        choices=['energy', 'wavelength', 'wavelength_rev', 'wavenumber'],
         default='energy',
-        help='x units to use for spectrum'
+        help='x units to use for spectrum (rev = reversed axis direction)'
     )
 
     plot_abs.add_argument(
@@ -2582,7 +2595,7 @@ 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 +2625,16 @@ 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-1.11.2}/orto/data.py

@@ -33,6 +33,9 @@ class AbsorptionSpectrum():
         Full width at half maximum used in spectrum generation
     comment: str, default=''
         Comment or metadata for the spectrum
+    x_reversed: bool, default False
+        Whether the x axis is reversed (e.g. for wavelength spectra)\n
+        By default, False - increasing x values from left to right
 
     Attributes
     ----------
@@ -61,7 +64,7 @@ class AbsorptionSpectrum():
     def __init__(self, x_grid: NDArray, x_unit: str, x_label: str,
                  x_label_mathmode: str, y_unit: str, y_label: str,
                  y_label_mathmode: str, y_values: NDArray, fwhm: float,
-                 comment: str = '') -> None:
+                 comment: str = '', x_reversed: bool = False) -> None:
         self.x_grid = x_grid
         self.x_unit = x_unit
         self.x_label = x_label
@@ -72,30 +75,9 @@ class AbsorptionSpectrum():
         self.fwhm = fwhm
         self.y_values = y_values
         self.comment = comment
+        self.x_reversed = x_reversed
         return
 
-    @classmethod
-    def from_data(cls, x_grid: NDArray, y_values: NDArray,
-                  fwhm: float) -> 'AbsorptionSpectrum':
-        '''
-        Creates AbsorptionSpectrum object from data
-
-        Parameters
-        ----------
-        x_grid: NDArray
-            Grid of x values (energies, wavelengths, or wavenumbers)
-        y_values: NDArray
-            Absorption spectrum values at each point in x_grid
-        fwhm: float
-            Full width at half maximum used in spectrum generation
-
-        Returns
-        -------
-        AbsorptionSpectrum
-            Created AbsorptionSpectrum object
-        '''
-        return cls(x_grid, y_values, fwhm)
-
 
 class AbsorptionData():
     '''
@@ -236,7 +218,7 @@ 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 +228,7 @@ 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 +243,7 @@ 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]
@@ -281,7 +264,8 @@ class AbsorptionData():
     def generate_spectrum(self, fwhm: float, lineshape: str, x_min: float,
                           x_max: float, num_points: int,
                           x_type: str = 'energy',
-                          comment: str = '') -> AbsorptionSpectrum:
+                          comment: str = '',
+                          x_reversed: bool = False) -> AbsorptionSpectrum:
         '''
         Generates absorption spectrum using Gaussian broadening
 
@@ -305,6 +289,9 @@ class AbsorptionData():
               'wavenumber' (cm^-1)
         comment: str
             Comment to add to spectrum metadata
+        x_reversed: bool
+            Whether to reverse the x axis (e.g. for wavelength spectra)\n
+            By default, False - increasing x values from left to right
 
         Returns
         -------
@@ -386,7 +373,8 @@ class AbsorptionData():
             y_label_mathmode=y_label_mathmode,
             y_values=y_vals,
             fwhm=fwhm,
-            comment=comment
+            comment=comment,
+            x_reversed=x_reversed
         )
 
         self.spectrum = spectrum

{orto-1.11.0 → orto-1.11.2}/orto/plotter.py

@@ -118,7 +118,6 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
         ax.set_ylabel(abs_data.spectrum.y_label_mathmode)
 
     if abs_data.spectrum.x_label.split()[0].lower() == 'wavelength':
-        ax.invert_xaxis()
         stick_x_values = [
             wavelength + x_shift
             for wavelength in abs_data.wavelengths
@@ -134,6 +133,9 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
             for wavenumber in abs_data.wavenumbers
         ]
 
+    if abs_data.spectrum.x_reversed:
+        ax.invert_xaxis()
+
     x_values = abs_data.spectrum.x_grid + x_shift
 
     # Main spectrum

{orto-1.11.0 → orto-1.11.2}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.0
+Version: 1.11.2
 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-1.11.2}/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__ = '1.11.2'
 
 setuptools.setup(
     name='orto',

orto-1.11.0/orto/__version__.py

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