orto 1.2.0__tar.gz → 1.4.0__tar.gz

{orto-1.2.0 → orto-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.2.0
+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-1.4.0/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.4.0'

{orto-1.2.0 → orto-1.4.0}/orto/cli.py

@@ -593,78 +593,65 @@ 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
             )
-        else:
+        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
             )
-        else:
+        elif uargs.intensities == 'velocity':
             all_data = oe.AbsorptionVelocityDipoleExtractor.extract(
                 uargs.output_file
             )
+        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):
 
-        if uargs.x_lim is None:
-            if uargs.x_unit == 'wavenumber':
-                uargs.x_lim = [0, max(data['energy (cm^-1)'])]
-            if uargs.x_unit == 'wavelength':
-                # 1 to 2000 nm
-                uargs.x_lim = [5000., 10000000.]
-
-        if uargs.x_cut is None:
-            iup = -2
-            ilow = 0
-        else:
-            ilow = min(
-                [
-                    it
-                    for it, val in enumerate(data['energy (cm^-1)'])
-                    if (val - uargs.x_cut[0]) > 0
-                ]
-            )
-            iup = max(
-                [
-                    it
-                    for it, val in enumerate(data['energy (cm^-1)'])
-                    if (uargs.x_cut[1] - val) > 0
-                ]
-            )
-
         if len(all_data) > 1:
             save_name = f'absorption_spectrum_section_{it:d}.png'
         else:
-            save_name = 'absorption_spectrum_section.png'
+            save_name = 'absorption_spectrum.png'
+
+        if uargs.x_unit == 'wavenumber':
+            x_values = data['energy (cm^-1)']
+        elif uargs.x_unit == 'wavelength':
+            x_values = 1E7 / data['energy (cm^-1)']
+        elif uargs.x_unit == 'energy':
+            x_values = data['energy (ev)']
 
         # Plot absorption spectrum
         fig, ax = plotter.plot_abs(
-            data['energy (cm^-1)'][ilow: iup+1],
-            data['fosc'][ilow: iup+1],
+            x_values,
+            uargs.x_unit,
+            data['fosc'],
             show=_SHOW_CONV[uargs.plot],
             save=_SAVE_CONV[uargs.plot],
             save_name=save_name,
             x_lim=uargs.x_lim,
             y_lim=uargs.y_lim,
-            x_unit=uargs.x_unit,
+            x_shift=uargs.shift,
             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
         )
 
         if uargs.x_unit == 'wavenumber':
             ax[0].set_xlim([0, 50000])
-        if uargs.x_unit == 'wavelength':
-            ax[0].set_xlim([0, 2000])
         plt.show()
 
     return
@@ -1621,9 +1608,10 @@ def read_args(arg_list=None):
     )
 
     plot_abs.add_argument(
-        '--intensity_type',
+        '--intensities',
+        '-i',
         type=str,
-        choices=['velocity', 'electric'],
+        choices=['velocity', 'electric', 'semi-classical'],
         default='electric',
         help='Type of intensity to plot (orca_mapspc uses electric)'
     )
@@ -1640,10 +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'
         )
     )
 
@@ -1676,32 +1669,46 @@ def read_args(arg_list=None):
     plot_abs.add_argument(
         '--x_unit',
         type=str,
-        choices=['wavenumber', 'wavelength'],
+        choices=['wavenumber', 'energy', 'wavelength'],
         default='wavenumber',
         help='x units to use for spectrum'
     )
 
     plot_abs.add_argument(
-        '--x_lim',
+        '--shift',
         type=float,
-        nargs=2,
-        help='Wavenumber or Wavelength limits of spectrum'
+        default=0.,
+        help=(
+            'Shift spectrum by this amount in x units\n'
+            'Default: %(default)s'
+        )
     )
 
     plot_abs.add_argument(
-        '--x_cut',
-        type=float,
+        '--x_lim',
         nargs=2,
-        help='Only include signals between these limits'
+        default=['auto', 'auto'],
+        help='x limits of spectrum'
     )
 
     plot_abs.add_argument(
         '--y_lim',
         nargs=2,
-        default=['auto', 'auto'],
+        default=[0., 'auto'],
         help='Epsilon limits of spectrum in cm^-1 mol^-1 L'
     )
 
+    plot_abs.add_argument(
+        '--normalise_absorption',
+        '-na',
+        action='store_true',
+        default=False,
+        help=(
+            'Normalises absorption spectrum to maximum value\n'
+            'Default: %(default)s'
+        )
+    )
+
     plot_ailft = plot_parser.add_parser(
         'ailft_orbs',
         description='Plots AI-LFT orbital energies from output file',
@@ -1911,7 +1918,7 @@ def read_args(arg_list=None):
         default=5,
         help=(
             'Width of signal (FWHM for Gaussian, Width for Lorentzian),'
-            ' in Wavenumbers'
+            ' in same unit as plot x unit'
         )
     )
 

{orto-1.2.0 → orto-1.4.0}/orto/extractor.py

@@ -1359,7 +1359,7 @@ class AbsorptionElectricDipoleExtractor(extto.BetweenExtractor):
         '''
 
         result = re.findall(
-            r'\s+(\d+-\d+[A-Z]\s+->\s+\d+-\d+[A-Z])\s+(\d\.\d*)\s+(\d*\.\d)\s+(\d*\.\d)\s+(\d\.\d{9})\s+(\d\.\d{5})\s+(-*\d\.\d{5})\s+(-*\d\.\d{5})\s+(-*\d\.\d{5})', # noqa
+            r'\s+(\d+[A-Za-z]*-\d*[A-Za-z]\s+->\s+\d+[A-Za-z]*-\d*[A-Za-z])\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d\.\d{5})\s+(-*\d\.\d{5})\s+(-*\d\.\d{5})\s+(-*\d\.\d{5})', # noqa
             block
         )
 
@@ -1415,6 +1415,67 @@ class AbsorptionVelocityDipoleExtractor(AbsorptionElectricDipoleExtractor):
     END_PATTERN = rb'(?=-{77})'
 
 
+class AbsorptionSemiClassicalDipoleExtractor(AbsorptionElectricDipoleExtractor): # noqa
+    '''
+    Extracts ABSORPTION SPECTRUM VIA FULL SEMI-CLASSICAL FORMULATION table
+    from ORCA output file for versions newer than 6.
+    '''
+
+    # Regex Start Pattern
+    START_PATTERN = rb'(?<=ABSORPTION SPECTRUM VIA FULL SEMI-CLASSICAL FORMULATION\s[\S\s]{408}\s)' # noqa
+
+    # Regex End Pattern
+    END_PATTERN = rb'(?=-{77})'
+
+    @property
+    def data(self) -> dict[str, list[str | float]]:
+        '''
+        Absorption spectrum data:\n
+        A dictionary with keys:\n
+            transition\n
+            energy (cm^-1)\n
+            energy (ev)\n
+            wavelength (nm)\n
+            fosc\n
+        All values are list[float], but 'transition' entries are list[str]
+        '''
+        return self._data
+
+    @staticmethod
+    def _process_block(block: str) -> dict[str, list[int | float]]: # noqa
+        '''
+        Converts single block into data entries described in self.data
+
+        Parameters
+        ----------
+        block: str
+            String block extracted from file
+
+        Returns
+        -------
+        dict[str, list[float]]
+        '''
+
+        result = re.findall(
+            r'\s+(\d+[A-Za-z]*-\d*[A-Za-z]\s+->\s+\d+[A-Za-z]*-\d*[A-Za-z])\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)', # noqa
+            block
+        )
+
+        result = np.asarray(result, dtype=str).T
+
+        fresult = result[1:].astype(float)
+
+        data = {
+            'state': result[0].tolist(),
+            'energy (ev)': fresult[0].tolist(),
+            'energy (cm^-1)': fresult[1].tolist(),
+            'wavelength (nm)': fresult[2].tolist(),
+            'fosc': fresult[3].tolist(),
+        }
+
+        return data
+
+
 class OldAbsorptionElectricDipoleExtractor(extto.BetweenExtractor):
     '''
     Extracts ABSORPTION SPECTRUM VIA TRANSITION ELECTRIC DIPOLE MOMENTS table

{orto-1.2.0 → orto-1.4.0}/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
 
@@ -75,45 +76,60 @@ def lorentzian(p: ArrayLike, fwhm, p0, area) -> NDArray:
     return lor
 
 
-def plot_abs(wavenumbers: ArrayLike, foscs: ArrayLike,
+def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
              lineshape: str = 'gaussian', linewidth: float = 100.,
-             x_lim: list[float] = 0., x_unit: str = 'wavenumber',
-             abs_type: str = 'napierian', y_lim: list[float] = 'auto',
-             show_osc: bool = True, save: bool = False,
+             x_lim: list[float] = ['auto', 'auto'],
+             abs_type: str = 'napierian',
+             y_lim: list[float] = [0., 'auto'],
+             x_shift: float = 0., normalise: 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 oscillator strengths specifying intensity
+    Plots absorption spectrum with intensity specified by oscillator strength.\n # noqa
+    Spectrum is computed as a sum of Gaussian or Lorentzian lineshapes.\n
+    The x_values can be either wavenumbers [cm^-1], wavelengths [nm] or\n
+    energies [eV].\n
 
     Parameters
     ----------
-    wavenumbers: array_like
-        Wavenumber of eac transition [cm^-1]
+    x_values: array_like
+        x_values for each transition, either wavenumber, wavelength or energy\n
+        with unit type specified by x_type
+    x_type: str {'wavenumber', 'wavelength', 'energy'}
+        Type of x_values, either wavenumber [cm^-1], wavelength [nm] or\n
+        energy [eV].
     foscs: array_like
         Oscillator strength of each transition
     lineshape: str {'gaussian', 'lorentzian'}
         Lineshape function to use for each transition/signal
     linewidth: float
         Linewidth used in lineshape [cm^-1]
-    x_lim: list[float], default [0., 2000]
+    x_lim: list[float], default ['auto', 'auto']
         Minimum and maximum x-values to plot [cm^-1 or nm]
-    y_lim: list[float | str], default 'auto'
+    y_lim: list[float | str], default [0., 'auto']
         Minimum and maximum y-values to plot [cm^-1 mol^-1 L]
-    x_unit: str {'wavenumber', 'wavelength'}
-        X-unit to use, data will be converted internally.\n
-        Assumes cm^-1 for wavenumber and nm for wavelength.
     abs_type: str {'napierian', 'logarithmic'}
         Absorbance (and epsilon) type to use. Orca_mapspc uses napierian
-    show_osc: bool, default True
-        If True, show oscillator strength stemplots
+    normalise: bool, default False
+        If True, normalise the absorption spectrum to the maximum value.
+    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
+
     Returns
     -------
     plt.Figure
@@ -123,6 +139,13 @@ def plot_abs(wavenumbers: ArrayLike, 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):
+        raise ValueError('x_values and foscs must have the same length')
+
     fig, ax = plt.subplots(1, 1, num=window_title)
 
     ls_func = {
@@ -130,7 +153,38 @@ def plot_abs(wavenumbers: ArrayLike, foscs: ArrayLike,
         'lorentzian': lorentzian
     }
 
-    x_range = np.linspace(x_lim[0], x_lim[1], 100000)
+    if not isinstance(x_lim, list):
+        raise ValueError('`x_lim` must be a list of values')
+
+    if x_lim[0] != x_lim[1]:
+        if isinstance(x_lim[0], str):
+            if x_lim[0] == 'auto':
+                x_lim[0] = ax.get_ylim()[0]
+            else:
+                x_lim[0] = float(x_lim[0])
+        if isinstance(x_lim[1], str):
+            if x_lim[1] == 'auto':
+                x_lim[1] = ax.get_ylim()[1]
+            else:
+                x_lim[1] = float(x_lim[1])
+    else:
+        x_lim = [np.min(x_values), np.max(x_values)]
+
+    # Set limits and range of continuous variable
+    ax.set_xlim([x_lim[0], x_lim[1]])
+    x_grid = np.linspace(x_lim[0], x_lim[1], 100000)
+
+    # Exclude values of x_values out of the range of x_lim
+    x_values = np.asarray(
+        [val for val in x_values if x_lim[0] <= val <= x_lim[1]]
+    )
+    # Exclude oscillator strengths for those values
+    foscs = np.asarray(
+        [
+            fosc
+            for val, fosc in zip(x_values, foscs)
+            if x_lim[0] <= val <= x_lim[1]]
+    )
 
     # Conversion from oscillator strength to napierian integrated absorption
     # coefficient
@@ -143,55 +197,89 @@ def plot_abs(wavenumbers: ArrayLike, foscs: ArrayLike,
 
     # Spectrum as sum of signals. Always computed in wavenumbers.
     spectrum = np.sum([
-        ls_func[lineshape](x_range, linewidth, x_value, A_log)
-        for x_value, A_log in zip(wavenumbers, A_logs)
+        ls_func[lineshape](x_grid, linewidth, x_value, A_log)
+        for x_value, A_log in zip(x_values, A_logs)
     ], axis=0)
 
-    np.savetxt('spectrum.txt', np.vstack([x_range, spectrum]).T, fmt='%.5f')
-
-    # Convert values to wavelength
-    if x_unit == 'wavelength':
-        x_range = 1E7 / x_range
-        wavenumbers = [1E7 / wn for wn in wavenumbers]
+    if normalise:
+        # Normalise the spectrum to the maximum value
+        spectrum /= np.max(spectrum)
+        ax.set_ylabel('Normalised Absorbance (arbitrary units)')  # noqa
+    else:
+        ax.set_ylabel(r'$\epsilon$ (cm$^\mathregular{-1}$ mol$^\mathregular{-1}$ L)') # noqa
+
+    _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_range, spectrum, color='k')
+    ax.plot(x_grid, spectrum, color='k')
 
-    if show_osc:
+    if osc_style == 'separate':
         fax = ax.twinx()
         # Oscillator strength twin axis
-        plt.stem(wavenumbers, 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)
 
     if y_lim[0] != y_lim[1]:
         if isinstance(y_lim[0], str):
-            y_lim[0] = ax.get_ylim()[0]
+            if y_lim[0] == 'auto':
+                y_lim[0] = ax.get_ylim()[0]
+            else:
+                y_lim[0] = float(y_lim[0])
         if isinstance(y_lim[1], str):
-            y_lim[1] = ax.get_ylim()[1]
+            if y_lim[1] == 'auto':
+                y_lim[1] = ax.get_ylim()[1]
+            else:
+                y_lim[1] = float(y_lim[1])
         ax.set_ylim([y_lim[0], y_lim[1]])
 
     ax.xaxis.set_minor_locator(AutoMinorLocator())
     ax.yaxis.set_minor_locator(AutoMinorLocator())
 
-    xunit_to_label = {
+    xtype_to_label = {
         'wavenumber': r'Wavenumber (cm$^\mathregular{-1}$)',
         'wavelength': 'Wavelength (nm)',
+        'energy': r'Energy (eV)'
     }
 
-    ax.set_xlabel(xunit_to_label[x_unit.lower()])
-    ax.set_ylabel(r'$\epsilon$ (cm$^\mathregular{-1}$ mol$^\mathregular{-1}$ L)') # noqa
+    ax.set_xlabel(xtype_to_label[x_type.lower()])
 
     fig.tight_layout()
 
     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-1.2.0 → orto-1.4.0}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.2.0
+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-1.2.0 → orto-1.4.0}/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__ = '1.2.0'
+__version__ = '1.4.0'
 
 setuptools.setup(
     name='orto',

orto-1.2.0/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '1.2.0'