orto 1.11.1__py3-none-any.whl → 1.11.2__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.11.1'
+__version__ = '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)'])
 
@@ -1202,14 +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):
@@ -1244,7 +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:
@@ -2540,9 +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(

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():
     '''
@@ -282,7 +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
 
@@ -306,6 +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
         -------
@@ -387,7 +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/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-1.11.1.dist-info → orto-1.11.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.1
+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.dist-info/RECORD

@@ -0,0 +1,17 @@
+orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
+orto/__version__.py,sha256=k_9xGm1wdecel8QkX-itmu1beg8G5BX8XXrnN7ZTFjc,23
+orto/cli.py,sha256=Nt6ErYBeU9YX5FGj-cgR7xfekIt4QmDnuaAqjL6ji7A,96715
+orto/constants.py,sha256=anxaiTykO8Q_CXliR7zuOAdnXZrQ2-C4ndaviyl7kGc,419
+orto/data.py,sha256=qs0UsCMOHqhsXYSCT8Kcmq988jQSMuGW4ZceelON0fo,14739
+orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
+orto/extractor.py,sha256=GKCFU7oSawYCYjOizER8e6HSp4bOsyqOxYcTPQHwdjM,84923
+orto/input.py,sha256=uUQV6A-8D0GZpRoY1rKK_aUPmk9kVVTnMzTHuisP5t4,11888
+orto/job.py,sha256=tDiz9omFwinoYJamgz66MZez0Ee9HMhuCIAeHMhXRF8,5916
+orto/plotter.py,sha256=FqeH6xh2MpDmX_n0AtZaIddgNyCcuXwwrDqJBGhQsG4,17837
+orto/utils.py,sha256=GcMZ9uebOSnkPQT_U5O0X49LUtTu8YpXZxEsNKgXNTY,9838
+orto-1.11.2.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
+orto-1.11.2.dist-info/METADATA,sha256=fegThcazVixL23e9n5k_kR6CVOummgf0Eoeui9J6y44,1185
+orto-1.11.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.11.2.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.11.2.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.11.2.dist-info/RECORD,,

orto-1.11.1.dist-info/RECORD

@@ -1,17 +0,0 @@
-orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-orto/__version__.py,sha256=QO79Qbu7GOTJ8NOEAJNkDnn8Y7OBA5xNxoQgCyKm6NU,23
-orto/cli.py,sha256=c9DN29Xn9nxpCzPHHJYo-BirBOviUACsFmIEiJyrGe8,96209
-orto/constants.py,sha256=anxaiTykO8Q_CXliR7zuOAdnXZrQ2-C4ndaviyl7kGc,419
-orto/data.py,sha256=ONG8poKWkJIO1wVfcWh-83zmcy_VxatB0OffaWE_9aI,14911
-orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
-orto/extractor.py,sha256=GKCFU7oSawYCYjOizER8e6HSp4bOsyqOxYcTPQHwdjM,84923
-orto/input.py,sha256=uUQV6A-8D0GZpRoY1rKK_aUPmk9kVVTnMzTHuisP5t4,11888
-orto/job.py,sha256=tDiz9omFwinoYJamgz66MZez0Ee9HMhuCIAeHMhXRF8,5916
-orto/plotter.py,sha256=_t9bow6sUMoRAvD6gVFGJTc-_ifW7RmeR0JAPWK_lm4,17799
-orto/utils.py,sha256=GcMZ9uebOSnkPQT_U5O0X49LUtTu8YpXZxEsNKgXNTY,9838
-orto-1.11.1.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
-orto-1.11.1.dist-info/METADATA,sha256=9IDbC1oGlxYfpGxhcLLxgKEWwKDosU79RZw8ZHNrENA,1185
-orto-1.11.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orto-1.11.1.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
-orto-1.11.1.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
-orto-1.11.1.dist-info/RECORD,,