orto 1.3.0__tar.gz → 1.5.0__tar.gz

{orto-1.3.0 → orto-1.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.3.0
+Version: 1.5.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.5.0/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.5.0'

{orto-1.3.0 → orto-1.5.0}/orto/cli.py

@@ -554,6 +554,127 @@ def gen_job_func(uargs):
     return
 
 
+def plot_xes_func(uargs):
+    '''
+    Wrapper for CLI plot xes call
+
+    Parameters
+    ----------
+    uargs : argparser object
+        User arguments
+
+    Returns
+    -------
+    None
+    '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+    from . import plotter
+    from . import extractor as oe
+
+    # Set user specified font name
+    if os.getenv('orto_fontname'):
+        try:
+            plt.rcParams['font.family'] = os.getenv('orto_fontname')
+        except ValueError:
+            ut.cprint('Error in orto_fontname environment variable', 'red')
+            sys.exit(1)
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
+
+    version = oe.OrcaVersionExtractor.extract(uargs.output_file)
+
+    if not len(version):
+        ut.cprint(
+            'Warning: Cannot find version number in Orca output file',
+            'black_yellowbg'
+        )
+        version = [6, 0, 0]
+
+    if version[0] >= 6:
+        if uargs.intensities == 'electric':
+            all_data = oe.XESElectricDipoleExtractor.extract(
+                uargs.output_file
+            )
+        elif uargs.intensities == 'velocity':
+            all_data = oe.XESVelocityDipoleExtractor.extract(
+                uargs.output_file
+            )
+        elif uargs.intensities == 'semi-classical':
+            all_data = oe.XESSemiClassicalDipoleExtractor.extract(
+                uargs.output_file
+            )
+        elif uargs.intensities == 'so_electric':
+            all_data = oe.SOXESElectricDipoleExtractor.extract(
+                uargs.output_file
+            )
+        elif uargs.intensities == 'so_velocity':
+            all_data = oe.SOXESVelocityDipoleExtractor.extract(
+                uargs.output_file
+            )
+        elif uargs.intensities == 'so_semi-classical':
+            all_data = oe.SOXESSemiClassicalDipoleExtractor.extract(
+                uargs.output_file
+            )
+    elif version[0] < 6:
+        ut.cprint('Unsupported version of Orca for XES extraction', 'red')
+
+    ut.cprint('Using intensities: {}'.format(uargs.intensities), 'cyan')
+
+    # Plot each section
+    for it, data in enumerate(all_data):
+
+        if len(all_data) > 1:
+            save_name = f'emission_spectrum_section_{it:d}.png'
+        else:
+            save_name = 'emission_spectrum.png'
+
+        if uargs.x_unit == 'wavenumber':
+            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 == 'energy':
+            x_values = np.asarray(data['energy (ev)'])
+
+        data['fosc'] = np.asarray(data['fosc'])
+
+        # Remove transitions with zero oscillator strength from
+        # beginning and end of spectrum
+        if not uargs.no_trim:
+            # Find first non-zero oscillator strength
+            first_nonzero = np.where(data['fosc'] > 1E-6)[0][0]
+            # Find last non-zero oscillator strength
+            last_nonzero = np.where(data['fosc'] > 1E-6)[0][-1]
+
+            # Trim data
+            x_values = x_values[first_nonzero:last_nonzero + 1]
+            data['fosc'] = data['fosc'][first_nonzero:last_nonzero + 1]
+
+        # Plot emission spectrum
+        fig, ax = plotter.plot_abs(
+            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_shift=uargs.shift,
+            linewidth=uargs.linewidth,
+            lineshape=uargs.lineshape,
+            window_title=f'Emission Spectrum from {uargs.output_file}',
+            osc_style=uargs.osc_style,
+            normalise=uargs.normalise,
+            plot_type='emission'
+        )
+
+        if uargs.x_unit == 'wavenumber':
+            ax[0].set_xlim([0, 50000])
+        plt.show()
+
+
 def plot_abs_func(uargs):
     '''
     Wrapper for CLI plot abs call
@@ -593,28 +714,30 @@ 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):
 
@@ -624,11 +747,25 @@ def plot_abs_func(uargs):
             save_name = 'absorption_spectrum.png'
 
         if uargs.x_unit == 'wavenumber':
-            x_values = data['energy (cm^-1)']
+            x_values = np.asarray(data['energy (cm^-1)'])
         elif uargs.x_unit == 'wavelength':
-            x_values = 1E7 / data['energy (cm^-1)']
+            x_values = 1E7 / np.asarray(data['energy (cm^-1)'])
         elif uargs.x_unit == 'energy':
-            x_values = data['energy (ev)']
+            x_values = np.asarray(data['energy (ev)'])
+
+        data['fosc'] = np.asarray(data['fosc'])
+
+        # Remove transitions with zero oscillator strength from
+        # beginning and end of spectrum
+        if not uargs.no_trim:
+            # Find first non-zero oscillator strength
+            first_nonzero = np.where(data['fosc'] > 1E-6)[0][0]
+            # Find last non-zero oscillator strength
+            last_nonzero = np.where(data['fosc'] > 1E-6)[0][-1]
+
+            # Trim data
+            x_values = x_values[first_nonzero:last_nonzero + 1]
+            data['fosc'] = data['fosc'][first_nonzero:last_nonzero + 1]
 
         # Plot absorption spectrum
         fig, ax = plotter.plot_abs(
@@ -644,8 +781,8 @@ 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,
-            normalise=uargs.normalise_absorption
+            osc_style=uargs.osc_style,
+            normalise=uargs.normalise
         )
 
         if uargs.x_unit == 'wavenumber':
@@ -1606,7 +1743,7 @@ def read_args(arg_list=None):
     )
 
     plot_abs.add_argument(
-        '--intensity_type',
+        '--intensities',
         '-i',
         type=str,
         choices=['velocity', 'electric', 'semi-classical'],
@@ -1626,10 +1763,15 @@ 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' # noqa
+            ' - \'combined\' plots oscillator strengths on intensity axis\n'
+            ' - \'off\' does not plot oscillator strengths\n'
+            'Default: %(default)s'
         )
     )
 
@@ -1677,6 +1819,16 @@ 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_abs.add_argument(
         '--x_lim',
         nargs=2,
@@ -1692,12 +1844,147 @@ def read_args(arg_list=None):
     )
 
     plot_abs.add_argument(
-        '--normalise_absorption',
-        '-na',
+        '--normalise',
+        '-n',
+        action='store_true',
+        default=False,
+        help=(
+            'Normalises spectrum to maximum value\n'
+            'Default: %(default)s'
+        )
+    )
+
+    plot_xes = plot_parser.add_parser(
+        'xes',
+        description='Plots XES from CI calculation output',
+        usage=ut.cstring('orto plot xes <output_file>', 'cyan'),
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+    plot_xes._positionals.title = 'Mandatory Arguments'
+
+    plot_xes.set_defaults(func=plot_xes_func)
+
+    plot_xes.add_argument(
+        'output_file',
+        type=pathlib.Path,
+        help='Orca output file name'
+    )
+
+    plot_xes.add_argument(
+        '--intensities',
+        '-i',
+        type=str,
+        choices=[
+            'velocity',
+            'electric',
+            'semi-classical',
+            'so_velocity',
+            'so_electric',
+            'so_semi-classical',
+        ],
+        default='electric',
+        help='Type of intensity to plot (orca_mapspc uses electric)'
+    )
+
+    plot_xes.add_argument(
+        '--linewidth',
+        '-lw',
+        type=float,
+        default=2000,
+        help=(
+            'Width of signal (FWHM for Gaussian, Width for Lorentzian),'
+            ' in Wavenumbers'
+        )
+    )
+
+    plot_xes.add_argument(
+        '--osc_style',
+        type=str,
+        default='combined',
+        help=(
+            'Style of oscillators to plot\n'
+            ' - \'separate\' plots oscillator strengths as stems on separate axis\n' # noqa
+            ' - \'combined\' plots oscillator strengths on intensity axis\n'
+            ' - \'off\' does not plot oscillator strengths\n'
+            'Default: %(default)s'
+        )
+    )
+
+    plot_xes.add_argument(
+        '--plot',
+        '-p',
+        choices=['on', 'show', 'save', 'off'],
+        metavar='<str>',
+        type=str,
+        default='on',
+        help=(
+            'Controls plot appearance/save \n'
+            ' - \'on\' shows and saves the plots\n'
+            ' - \'show\' shows the plots\n'
+            ' - \'save\' saves the plots\n'
+            ' - \'off\' neither shows nor saves\n'
+            'Default: %(default)s'
+        )
+    )
+
+    plot_xes.add_argument(
+        '--lineshape',
+        '-ls',
+        type=str,
+        choices=['gaussian', 'lorentzian'],
+        default='lorentzian',
+        help='Lineshape to use for each signal'
+    )
+
+    plot_xes.add_argument(
+        '--x_unit',
+        type=str,
+        choices=['wavenumber', 'energy', 'wavelength'],
+        default='wavenumber',
+        help='x units to use for spectrum'
+    )
+
+    plot_xes.add_argument(
+        '--shift',
+        type=float,
+        default=0.,
+        help=(
+            'Shift spectrum by this amount in x units\n'
+            'Default: %(default)s'
+        )
+    )
+
+    plot_xes.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.add_argument(
+        '--x_lim',
+        nargs=2,
+        default=['auto', 'auto'],
+        help='x limits of spectrum'
+    )
+
+    plot_xes.add_argument(
+        '--y_lim',
+        nargs=2,
+        default=[0., 'auto'],
+        help='Epsilon limits of spectrum in cm^-1 mol^-1 L'
+    )
+
+    plot_xes.add_argument(
+        '--normalise',
+        '-n',
         action='store_true',
         default=False,
         help=(
-            'Normalises absorption spectrum to maximum value\n'
+            'Normalises spectrum to maximum value\n'
             'Default: %(default)s'
         )
     )

{orto-1.3.0 → orto-1.5.0}/orto/extractor.py

@@ -1575,6 +1575,72 @@ class OldAbsorptionVelocityDipoleExtractor(OldAbsorptionElectricDipoleExtractor)
     END_PATTERN = rb'(?=-{77})'
 
 
+class XESElectricDipoleExtractor(AbsorptionElectricDipoleExtractor):
+    '''
+    Extracts X-RAY EMISSION SPECTRUM VIA TRANSITION ELECTRIC DIPOLE MOMENTS table\n # noqa
+    from ORCA output file for versions newer than 6.
+    '''
+
+    # Regex Start Pattern
+    START_PATTERN = rb'(?<=              X-RAY   EMISSION SPECTRUM VIA TRANSITION VELOCITY DIPOLE MOMENTS\s[\S\s]{408}\s)' # noqa
+
+    # Regex End Pattern
+    END_PATTERN = rb'(?=-{77})'
+
+
+class XESVelocityDipoleExtractor(AbsorptionElectricDipoleExtractor):
+    '''
+    Extracts X-RAY EMISSION SPECTRUM VIA TRANSITION VELOCITY DIPOLE MOMENTS table\n # noqa
+    from ORCA output file for versions newer than 6.
+    '''
+
+    # Regex Start Pattern
+    START_PATTERN = rb'(?<=              X-RAY   EMISSION SPECTRUM VIA TRANSITION VELOCITY DIPOLE MOMENTS\s[\S\s]{415}\s)' # noqa
+
+
+class SOXESElectricDipoleExtractor(AbsorptionElectricDipoleExtractor):
+    '''
+    Extracts SPIN-ORBIT X-RAY EMISSION SPECTRUM VIA TRANSITION ELECTRIC DIPOLE MOMENTS table\n # noqa
+    from ORCA output file for versions newer than 6.
+    '''
+
+    # Regex Start Pattern
+    START_PATTERN = rb'(?<=SPIN-ORBIT X-RAY   EMISSION SPECTRUM VIA TRANSITION ELECTRIC DIPOLE MOMENTS\s[\S\s]{415}\s)' # noqa
+
+    # Regex End Pattern
+    END_PATTERN = rb'(?=-{77})'
+
+
+class SOXESVelocityDipoleExtractor(AbsorptionElectricDipoleExtractor):
+    '''
+    Extracts SPIN-ORBIT X-RAY EMISSION SPECTRUM VIA TRANSITION VELOCITY DIPOLE MOMENTS table\n # noqa
+    from ORCA output file for versions newer than 6.
+    ''' 
+
+    # Regex Start Pattern
+    START_PATTERN = rb'(?<=SPIN-ORBIT X-RAY   EMISSION SPECTRUM VIA TRANSITION VELOCITY DIPOLE MOMENTS\s[\S\s]{408}\s)' # noqa
+
+
+class XESSemiClassicalDipoleExtractor(AbsorptionSemiClassicalDipoleExtractor):
+    '''
+    Extracts X-RAY EMISSION SPECTRUM VIA FULL SEMI-CLASSICAL FORMULATION table\n # noqa
+    from ORCA output file for versions newer than 6.
+    '''
+
+    # Regex Start Pattern
+    START_PATTERN = rb'(?<=              X-RAY   EMISSION SPECTRUM VIA FULL SEMI-CLASSICAL FORMULATION\s[\S\s]{408}\s)' # noqa
+
+
+class SOXESSemiClassicalDipoleExtractor(AbsorptionSemiClassicalDipoleExtractor): # noqa
+    '''
+    Extracts SPIN-ORBIT X-RAY EMISSION SPECTRUM VIA TRANSITION VELOCITY DIPOLE MOMENTS table\n # noqa
+    from ORCA output file for versions newer than 6.
+    '''
+
+    # Regex Start Pattern
+    START_PATTERN = rb'(?<=   SPIN-ORBIT X-RAY   EMISSION SPECTRUM VIA FULL SEMI-CLASSICAL FORMULATION\s[\S\s]{408}\s)' # noqa
+
+
 class HessNameInputExtractor(extto.LineExtractor):
     '''
     Extracts Hessian file name from %mtr block of input file

{orto-1.3.0 → orto-1.5.0}/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
 
@@ -81,9 +82,11 @@ 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,
-             window_title: str = 'Absorption Spectrum') -> tuple[plt.Figure, list[plt.Axes]]: # noqa
+             verbose: bool = True,
+             window_title: str = 'Absorption Spectrum',
+             plot_type: str = 'absorption') -> tuple[plt.Figure, list[plt.Axes]]: # noqa
     '''
     Plots absorption spectrum with intensity specified by oscillator strength.\n # noqa
     Spectrum is computed as a sum of Gaussian or Lorentzian lineshapes.\n
@@ -112,16 +115,23 @@ 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
+    plot_type: str, default 'absorption'
+        Type of plot to create, either 'absorption' or 'emission'.
 
     Returns
     -------
@@ -132,6 +142,8 @@ 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):
@@ -195,24 +207,51 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
     if normalise:
         # Normalise the spectrum to the maximum value
         spectrum /= np.max(spectrum)
-        ax.set_ylabel('Normalised Absorbance (arbitrary units)')  # noqa
+        ax.set_ylabel(
+            'Normalised {} (arbitrary units)'.format(
+                plot_type.capitalize()
+            )
+        )  # noqa
     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=f'{plot_type.capitalize()} spectrum data\nx (wavenumber, wavelength or energy), y (absorbance)' # noqa
+    )
+    if verbose:
+        ut.cprint(
+            f'\n{plot_type.capitalize()} spectrum data saved to\n {_txt_save_name}', # noqa
+            '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)
@@ -245,6 +284,11 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
 
     if save:
         plt.savefig(save_name, dpi=500)
+        if verbose:
+            ut.cprint(
+                f'\n{plot_type.capitalize()} spectrum saved to\n {save_name}',
+                'cyan'
+            )
 
     if show:
         plt.show()

{orto-1.3.0 → orto-1.5.0}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.3.0
+Version: 1.5.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.3.0 → orto-1.5.0}/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__ = '1.3.0'
+__version__ = '1.5.0'
 
 setuptools.setup(
     name='orto',

orto-1.3.0/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '1.3.0'