orto 1.1.0__py3-none-any.whl → 1.3.0__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.1.0'
+__version__ = '1.3.0'

orto/cli.py

@@ -597,7 +597,7 @@ def plot_abs_func(uargs):
             all_data = oe.OldAbsorptionElectricDipoleExtractor.extract(
                 uargs.output_file
             )
-        else:
+        elif uargs.intensity_type == 'velocity':
             all_data = oe.OldAbsorptionVelocityDipoleExtractor.extract(
                 uargs.output_file
             )
@@ -606,65 +606,50 @@ def plot_abs_func(uargs):
             all_data = oe.AbsorptionElectricDipoleExtractor.extract(
                 uargs.output_file
             )
-        else:
+        elif uargs.intensity_type == 'velocity':
             all_data = oe.AbsorptionVelocityDipoleExtractor.extract(
                 uargs.output_file
             )
+        elif uargs.intensity_type == 'semi-classical':
+            all_data = oe.AbsorptionSemiClassicalDipoleExtractor.extract(
+                uargs.output_file
+            )
 
     # 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
+            show_osc=not uargs.no_osc,
+            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
@@ -857,9 +842,22 @@ def extract_orbs_func(uargs, save=True) -> None:
                 dtype=int
             )
         ])
+    elif uargs.num is not None:
+        keep = uargs.num
     else:
         keep = range(len(contributions))
 
+    # Remove orbital indices which do not exist
+    keep = [val for val in keep if val < len(contributions)]
+
+    if not len(keep):
+        ut.red_exit(
+            (
+                r'Selected orbital indices do not exist!'
+                f'\nNORBS = {len(contributions):d}'
+            )
+        )
+
     contributions = contributions.loc[:, keep]
 
     # Remove contributions from unwanted orbitals
@@ -1609,8 +1607,9 @@ def read_args(arg_list=None):
 
     plot_abs.add_argument(
         '--intensity_type',
+        '-i',
         type=str,
-        choices=['velocity', 'electric'],
+        choices=['velocity', 'electric', 'semi-classical'],
         default='electric',
         help='Type of intensity to plot (orca_mapspc uses electric)'
     )
@@ -1663,32 +1662,46 @@ 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',
@@ -1898,7 +1911,7 @@ 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'
         )
     )
 
@@ -2080,13 +2093,37 @@ def read_args(arg_list=None):
         )
     )
 
+    def gte_zero(x):
+        '''
+        Custom type for argparse to ensure that the input
+        \nis greater than or equal to zero
+        '''
+        value = int(x)
+        if value < 0:
+            raise argparse.ArgumentTypeError(
+                f'{x} is not a valid index (must be >= 0)'
+            )
+        return value
+
+    orb_group.add_argument(
+        '-n',
+        '--num',
+        nargs='+',
+        type=gte_zero,
+        metavar='NUMBER',
+        default=None,
+        help=(
+            'Print specified orbitals using index starting from 0\n'
+            '(same as Orca)\n'
+        )
+    )
+
     orb_group.add_argument(
         '-hl',
         '--homo_lumo',
         nargs='?',
         type=int,
         metavar='NUMBER',
-        const=0,
         default=None,
         help=(
             'Print specified number of orbitals either side of HOMO and LUMO'

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/plotter.py

@@ -75,35 +75,43 @@ 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',
+             x_lim: list[float] = ['auto', 'auto'],
+             abs_type: str = 'napierian',
+             y_lim: list[float] = [0., 'auto'],
+             x_shift: float = 0., normalise: bool = False,
              show_osc: bool = True, save: bool = False,
              save_name: str = 'absorption_spectrum.png', show: bool = False,
              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
+    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
     save: bool, default False
@@ -114,6 +122,7 @@ def plot_abs(wavenumbers: ArrayLike, foscs: ArrayLike,
         If True, plot is shown on screen
     window_title: str, default 'UV-Visible Absorption Spectrum'
         Title of figure window, not of plot
+
     Returns
     -------
     plt.Figure
@@ -123,6 +132,11 @@ def plot_abs(wavenumbers: ArrayLike, foscs: ArrayLike,
         Matplotlib Axis object for twinx oscillator strength axis
     '''
 
+    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 +144,38 @@ 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
@@ -143,26 +188,29 @@ 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')
+    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
 
-    # Convert values to wavelength
-    if x_unit == 'wavelength':
-        x_range = 1E7 / x_range
-        wavenumbers = [1E7 / wn for wn in wavenumbers]
+    np.savetxt('spectrum.txt', np.vstack([x_grid, spectrum]).T, fmt='%.5f')
 
     # Main spectrum
-    ax.plot(x_range, spectrum, color='k')
+    ax.plot(x_grid, spectrum, color='k')
 
     if show_osc:
         fax = ax.twinx()
         # Oscillator strength twin axis
-        plt.stem(wavenumbers, foscs, basefmt=' ')
+        plt.stem(x_values, foscs, basefmt=' ')
         fax.yaxis.set_minor_locator(AutoMinorLocator())
         fax.set_ylabel(r'$f_\mathregular{osc}$')
+        fax.set_ylim([0., fax.get_ylim()[1]])
     else:
         fax = None
         plt.subplots_adjust(right=0.2)
@@ -171,21 +219,27 @@ def plot_abs(wavenumbers: ArrayLike, foscs: ArrayLike,
 
     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()
 

{orto-1.1.0.dist-info → orto-1.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.1.0
+Version: 1.3.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow
@@ -15,7 +15,7 @@ Description-Content-Type: text/markdown
 Requires-Dist: numpy>=2.1.2
 Requires-Dist: xyz_py>=5.13.1
 Requires-Dist: matplotlib>=3.9.2
-Requires-Dist: extto>=1.0.0
+Requires-Dist: extto>=1.0.1
 Requires-Dist: pandas>=2.2.3
 Requires-Dist: subto>=0.1.1
 Requires-Dist: python-docx>=1.1.2

orto-1.3.0.dist-info/RECORD

@@ -0,0 +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/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/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-1.1.0.dist-info/RECORD

@@ -1,15 +0,0 @@
-orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-orto/__version__.py,sha256=b6-WiVk0Li5MaV2rBnHYl104TsouINojSWKqHDas0js,22
-orto/cli.py,sha256=ywJuTP9X_hyD4bEwxU5vVkLDQm4YJGsWaLZ8TFCNxeo,62167
-orto/constants.py,sha256=2obWYg306Lce4U9Qs4MHg1yZq7SHFkazG-cnkD5svpo,343
-orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
-orto/extractor.py,sha256=aeZK130lBIERS4Pj1jvTlxCwVB_AhFLUB16zQrDhcbM,67767
-orto/input.py,sha256=N8JbySSVEC_qmXZ7ppJsZ7Z1qel6PfalGYRtnX1hJ6U,9900
-orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
-orto/plotter.py,sha256=ICrO03T_HGe-H1XKZ2qzsKYdPY44E0PKiXqIQQawd7I,15633
-orto/utils.py,sha256=gVfGplkfc6xGYgLMi_7I_yAdWG-QKRaqQdy9v5F4Mck,7279
-orto-1.1.0.dist-info/METADATA,sha256=TfXaxaTmcxbT1fbq5yQI9r24aV_1g7P0cj4g9mZlxic,1140
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