orto 1.4.0__py3-none-any.whl → 1.5.0__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.4.0'
+__version__ = '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
@@ -626,11 +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(
@@ -647,7 +782,7 @@ def plot_abs_func(uargs):
             lineshape=uargs.lineshape,
             window_title=f'Absorption Spectrum from {uargs.output_file}',
             osc_style=uargs.osc_style,
-            normalise=uargs.normalise_absorption
+            normalise=uargs.normalise
         )
 
         if uargs.x_unit == 'wavenumber':
@@ -1633,7 +1768,7 @@ def read_args(arg_list=None):
         default='combined',
         help=(
             'Style of oscillators to plot\n'
-            ' - \'separate\' plots oscillator strengths as stems on separate axis\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'
@@ -1684,6 +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,
@@ -1699,12 +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/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/plotter.py

@@ -85,7 +85,8 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
              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
+             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
@@ -129,6 +130,8 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
         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
     -------
@@ -204,7 +207,11 @@ 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
 
@@ -213,11 +220,11 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
         _txt_save_name,
         np.vstack([x_grid, spectrum]).T,
         fmt='%.5f',
-        header='Absorption spectrum data\nx (wavenumber, wavelength or energy), y (absorbance)' # noqa
+        header=f'{plot_type.capitalize()} spectrum data\nx (wavenumber, wavelength or energy), y (absorbance)' # noqa
     )
     if verbose:
         ut.cprint(
-            f'\nAbsorption spectrum data saved to\n {_txt_save_name}',
+            f'\n{plot_type.capitalize()} spectrum data saved to\n {_txt_save_name}', # noqa
             'cyan'
         )
 
@@ -278,8 +285,11 @@ def plot_abs(x_values: ArrayLike, x_type: str, foscs: ArrayLike,
     if save:
         plt.savefig(save_name, dpi=500)
         if verbose:
-            ut.cprint(f'\nAbsorption spectrum saved to\n {save_name}', 'cyan')
-    
+            ut.cprint(
+                f'\n{plot_type.capitalize()} spectrum saved to\n {save_name}',
+                'cyan'
+            )
+
     if show:
         plt.show()
 

{orto-1.4.0.dist-info → orto-1.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.4.0
+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.dist-info/RECORD

@@ -0,0 +1,15 @@
+orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
+orto/__version__.py,sha256=wShy9YfBfroz0HjRH_aNNehkEu1_PLsd_GjTU5aCDPk,22
+orto/cli.py,sha256=D7UIJbMlLERhOUwg4Fm2QEeejvU_NKfVvSzcXZ8ards,71649
+orto/constants.py,sha256=2obWYg306Lce4U9Qs4MHg1yZq7SHFkazG-cnkD5svpo,343
+orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
+orto/extractor.py,sha256=4n996-cZ_mLT65fheaou2zA3TiOAcOnClEUQa9-c8lE,72030
+orto/input.py,sha256=N8JbySSVEC_qmXZ7ppJsZ7Z1qel6PfalGYRtnX1hJ6U,9900
+orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
+orto/plotter.py,sha256=5QbLnrWzITuSWRklhmHvYnb8NfAPTdGevB3g1WzTjCY,19136
+orto/utils.py,sha256=gVfGplkfc6xGYgLMi_7I_yAdWG-QKRaqQdy9v5F4Mck,7279
+orto-1.5.0.dist-info/METADATA,sha256=_d4YzeA-fveynM-q4t0-6X2MoinbvEsH1qnc03bX2cM,1140
+orto-1.5.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.5.0.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.5.0.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.5.0.dist-info/RECORD,,

orto-1.4.0.dist-info/RECORD

@@ -1,15 +0,0 @@
-orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-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=onvevzjbhsb18DY8DiMGuDOLOjQ-Ore6eBybMkIUs7U,18817
-orto/utils.py,sha256=gVfGplkfc6xGYgLMi_7I_yAdWG-QKRaqQdy9v5F4Mck,7279
-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,,