orto 1.3.0__py3-none-any.whl → 1.4.0__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.3.0'
+__version__ = '1.4.0'

orto/cli.py

@@ -593,28 +593,30 @@ def plot_abs_func(uargs):
         version = [6, 0, 0]
 
     if version[0] < 6:
-        if uargs.intensity_type == 'electric':
+        if uargs.intensities == 'electric':
             all_data = oe.OldAbsorptionElectricDipoleExtractor.extract(
                 uargs.output_file
             )
-        elif uargs.intensity_type == 'velocity':
+        elif uargs.intensities == 'velocity':
             all_data = oe.OldAbsorptionVelocityDipoleExtractor.extract(
                 uargs.output_file
             )
     elif version[0] >= 6:
-        if uargs.intensity_type == 'electric':
+        if uargs.intensities == 'electric':
             all_data = oe.AbsorptionElectricDipoleExtractor.extract(
                 uargs.output_file
             )
-        elif uargs.intensity_type == 'velocity':
+        elif uargs.intensities == 'velocity':
             all_data = oe.AbsorptionVelocityDipoleExtractor.extract(
                 uargs.output_file
             )
-        elif uargs.intensity_type == 'semi-classical':
+        elif uargs.intensities == 'semi-classical':
             all_data = oe.AbsorptionSemiClassicalDipoleExtractor.extract(
                 uargs.output_file
             )
 
+    ut.cprint('Using intensities: {}'.format(uargs.intensities), 'cyan')
+
     # Plot each section
     for it, data in enumerate(all_data):
 
@@ -644,7 +646,7 @@ def plot_abs_func(uargs):
             linewidth=uargs.linewidth,
             lineshape=uargs.lineshape,
             window_title=f'Absorption Spectrum from {uargs.output_file}',
-            show_osc=not uargs.no_osc,
+            osc_style=uargs.osc_style,
             normalise=uargs.normalise_absorption
         )
 
@@ -1606,7 +1608,7 @@ def read_args(arg_list=None):
     )
 
     plot_abs.add_argument(
-        '--intensity_type',
+        '--intensities',
         '-i',
         type=str,
         choices=['velocity', 'electric', 'semi-classical'],
@@ -1626,10 +1628,15 @@ def read_args(arg_list=None):
     )
 
     plot_abs.add_argument(
-        '--no_osc',
-        action='store_true',
+        '--osc_style',
+        type=str,
+        default='combined',
         help=(
-            'Disables oscillator strength stem plots'
+            'Style of oscillators to plot\n'
+            ' - \'separate\' plots oscillator strengths as stems on separate axis\n'
+            ' - \'combined\' plots oscillator strengths on intensity axis\n'
+            ' - \'off\' does not plot oscillator strengths\n'
+            'Default: %(default)s'
         )
     )
 

orto/plotter.py

@@ -4,6 +4,7 @@ from matplotlib.ticker import AutoMinorLocator
 import numpy as np
 from numpy.typing import ArrayLike, NDArray
 import itertools
+import pathlib
 
 from . import utils as ut
 
@@ -81,8 +82,9 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
              abs_type: str = 'napierian',
              y_lim: list[float] = [0., 'auto'],
              x_shift: float = 0., normalise: bool = False,
-             show_osc: bool = True, save: bool = False,
+             osc_style: str = 'separate', save: bool = False,
              save_name: str = 'absorption_spectrum.png', show: bool = False,
+             verbose: bool = True,
              window_title: str = 'Absorption Spectrum') -> tuple[plt.Figure, list[plt.Axes]]: # noqa
     '''
     Plots absorption spectrum with intensity specified by oscillator strength.\n # noqa
@@ -112,14 +114,19 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
         Absorbance (and epsilon) type to use. Orca_mapspc uses napierian
     normalise: bool, default False
         If True, normalise the absorption spectrum to the maximum value.
-    show_osc: bool, default True
-        If True, show oscillator strength stemplots
+    osc_style: str, default 'separate'
+        Style of oscillator strength plots:
+        - 'separate': plots oscillator strengths as stems on separate axis
+        - 'combined': plots oscillator strengths on intensity axis
+        - 'off': does not plot oscillator strengths
     save: bool, default False
         If True, plot is saved to save_name
-    save_name: str
+    save_name: str | pathlib.Path, default 'absorption_spectrum.png'
         If save is True, plot is saved to this location/filename
     show: bool, default False
         If True, plot is shown on screen
+    verbose: bool, default True
+        If True, plot file location is written to terminal
     window_title: str, default 'UV-Visible Absorption Spectrum'
         Title of figure window, not of plot
 
@@ -132,6 +139,8 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
         Matplotlib Axis object for twinx oscillator strength axis
     '''
 
+    save_name = pathlib.Path(save_name)
+
     x_values = np.asarray(x_values) + x_shift
     foscs = np.asarray(foscs)
     if len(x_values) != len(foscs):
@@ -199,20 +208,43 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
     else:
         ax.set_ylabel(r'$\epsilon$ (cm$^\mathregular{-1}$ mol$^\mathregular{-1}$ L)') # noqa
 
-    np.savetxt('spectrum.txt', np.vstack([x_grid, spectrum]).T, fmt='%.5f')
+    _txt_save_name = save_name.with_suffix('.txt')
+    np.savetxt(
+        _txt_save_name,
+        np.vstack([x_grid, spectrum]).T,
+        fmt='%.5f',
+        header='Absorption spectrum data\nx (wavenumber, wavelength or energy), y (absorbance)' # noqa
+    )
+    if verbose:
+        ut.cprint(
+            f'\nAbsorption spectrum data saved to\n {_txt_save_name}',
+            'cyan'
+        )
 
     # Main spectrum
     ax.plot(x_grid, spectrum, color='k')
 
-    if show_osc:
+    if osc_style == 'separate':
         fax = ax.twinx()
         # Oscillator strength twin axis
-        plt.stem(x_values, foscs, basefmt=' ')
+        fax.stem(x_values, foscs, basefmt=' ', markerfmt=' ')
         fax.yaxis.set_minor_locator(AutoMinorLocator())
         fax.set_ylabel(r'$f_\mathregular{osc}$')
         fax.set_ylim([0., fax.get_ylim()[1]])
+    elif osc_style == 'combined':
+        fax = None
+        plt.subplots_adjust(right=0.2)
+        ax.stem(
+            x_values,
+            foscs/np.max(foscs) * np.max(spectrum),
+            basefmt=' ',
+            markerfmt=' '
+        )
+        ax.spines['right'].set_visible(False)
+        ax.spines['top'].set_visible(False)
     else:
         fax = None
+        # No oscillator strength plot
         plt.subplots_adjust(right=0.2)
         ax.spines['right'].set_visible(False)
         ax.spines['top'].set_visible(False)
@@ -245,7 +277,9 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
 
     if save:
         plt.savefig(save_name, dpi=500)
-
+        if verbose:
+            ut.cprint(f'\nAbsorption spectrum saved to\n {save_name}', 'cyan')
+    
     if show:
         plt.show()
 

{orto-1.3.0.dist-info → orto-1.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.3.0
+Version: 1.4.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.3.0.dist-info → orto-1.4.0.dist-info}/RECORD

@@ -1,15 +1,15 @@
 orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-orto/__version__.py,sha256=zi_LaUT_OsChAtsPXbOeRpQkCohSsOyeXfavQPM0GoE,22
-orto/cli.py,sha256=_PVQjeH1mIy_P-WegHllvpGWzhNaEpQuAA8Ht-PkLKQ,63161
+orto/__version__.py,sha256=EyMGX1ADFzN6XVXHWbJUtKPONYKeFkvWoKIFPDDB2I8,22
+orto/cli.py,sha256=CvRhsHcUs0PjoxqqxKiCkqNZySn8z1HfbBBoi9JbLDc,63487
 orto/constants.py,sha256=2obWYg306Lce4U9Qs4MHg1yZq7SHFkazG-cnkD5svpo,343
 orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
 orto/extractor.py,sha256=NJaqpH6iLtzEMuYGJrpbZ5vKJrtE5rQOXLLPjm0acGQ,69536
 orto/input.py,sha256=N8JbySSVEC_qmXZ7ppJsZ7Z1qel6PfalGYRtnX1hJ6U,9900
 orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
-orto/plotter.py,sha256=vXEfFLxdejt0YbKgCI4PUgBBX3a7SfGlqOQY0Mh4Wak,17562
+orto/plotter.py,sha256=onvevzjbhsb18DY8DiMGuDOLOjQ-Ore6eBybMkIUs7U,18817
 orto/utils.py,sha256=gVfGplkfc6xGYgLMi_7I_yAdWG-QKRaqQdy9v5F4Mck,7279
-orto-1.3.0.dist-info/METADATA,sha256=1fJYXo4-HhO0oB_CPjen8HldS-iatuOeSzm7KDiHLB0,1140
-orto-1.3.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orto-1.3.0.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
-orto-1.3.0.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
-orto-1.3.0.dist-info/RECORD,,
+orto-1.4.0.dist-info/METADATA,sha256=TFoHVG_EWEI1lBEltHKXyQ7AnUw3b5yYZeT6MJq8JyU,1140
+orto-1.4.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.4.0.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.4.0.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.4.0.dist-info/RECORD,,