orto 1.4.0__py3-none-any.whl → 1.6.0__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.4.0'
+__version__ = '1.6.0'

orto/cli.py

@@ -15,6 +15,7 @@ from shutil import move as shutilmove
 from . import job
 from . import utils as ut
 from . import constants as cst
+from . import data as d
 from .exceptions import DataNotFoundError, DataFormattingError
 
 _SHOW_CONV = {
@@ -554,9 +555,9 @@ def gen_job_func(uargs):
     return
 
 
-def plot_abs_func(uargs):
+def plot_xes_func(uargs):
     '''
-    Wrapper for CLI plot abs call
+    Wrapper for CLI plot xes call
 
     Parameters
     ----------
@@ -573,12 +574,7 @@ def plot_abs_func(uargs):
     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)
+    ut.check_font_envvar()
 
     # Change matplotlib font size to be larger
     mpl.rcParams.update({'font.size': 12})
@@ -592,28 +588,137 @@ def plot_abs_func(uargs):
         )
         version = [6, 0, 0]
 
-    if version[0] < 6:
+    if version[0] >= 6:
         if uargs.intensities == 'electric':
-            all_data = oe.OldAbsorptionElectricDipoleExtractor.extract(
+            all_data = oe.XESElectricDipoleExtractor.extract(
                 uargs.output_file
             )
         elif uargs.intensities == 'velocity':
-            all_data = oe.OldAbsorptionVelocityDipoleExtractor.extract(
+            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:
+    elif version[0] < 6:
+        ut.red_exit('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_xas_func(uargs):
+    '''
+    Wrapper for CLI plot xas 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
+    ut.check_font_envvar()
+
+    # 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.AbsorptionElectricDipoleExtractor.extract(
+            all_data = oe.XASElectricDipoleExtractor.extract(
                 uargs.output_file
             )
         elif uargs.intensities == 'velocity':
-            all_data = oe.AbsorptionVelocityDipoleExtractor.extract(
+            all_data = oe.XASVelocityDipoleExtractor.extract(
                 uargs.output_file
             )
         elif uargs.intensities == 'semi-classical':
-            all_data = oe.AbsorptionSemiClassicalDipoleExtractor.extract(
+            all_data = oe.XASSemiClassicalDipoleExtractor.extract(
                 uargs.output_file
             )
+    elif version[0] < 6:
+        ut.red_exit('Unsupported version of Orca for XAS extraction', 'red')
 
     ut.cprint('Using intensities: {}'.format(uargs.intensities), 'cyan')
 
@@ -626,11 +731,25 @@ 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 +766,7 @@ 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':
@@ -657,6 +776,194 @@ def plot_abs_func(uargs):
     return
 
 
+def plot_abs_func(uargs):
+    '''
+    Wrapper for CLI plot abs call\n\n
+
+    Plots ABSORPTION blocks from orca output\n
+        - UVVIS (TDDFT)\n
+        - XAS (TDDFT)\n\n
+
+    Parameters
+    ----------
+    uargs : argparser object
+        User arguments
+
+    Returns
+    -------
+    None
+    '''
+    import matplotlib.pyplot as plt
+    import matplotlib as mpl
+    import matplotlib.colors as mcolors
+    from . import plotter
+    from . import extractor as oe
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
+    # Set user specified font name
+    ut.check_font_envvar()
+
+    # Change matplotlib font size to be larger
+    mpl.rcParams.update({'font.size': 12})
+
+    if len(uargs.output_file) == 1:
+        colours = ['black']
+    else:
+        colours = list(mcolors.TABLEAU_COLORS.values())
+
+    fig, ax = plt.subplots(1, 1,  figsize=(6, 4))
+    oax = ax.twinx()
+
+    # Find unique name from multiple file names
+    if len(uargs.output_file) > 1:
+        base_names = [of.stem for of in uargs.output_file]
+        unique_names = ut.find_unique_substring(base_names)
+        legend = True
+    else:
+        legend = False
+        unique_names = ['']
+
+    # Handle x_shift argument
+    if uargs.x_shift is None:
+        uargs.x_shift = [0.0 for _ in uargs.output_file]
+    elif len(uargs.x_shift) != len(uargs.output_file):
+        ut.red_exit(
+            'Number of x_shift values must match number of output files'
+        )
+
+    for it, output_file in enumerate(uargs.output_file):
+
+        version = oe.OrcaVersionExtractor.extract(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_datasets = oe.OldAbsorptionElectricDipoleExtractor.extract(
+                    output_file
+                )
+            elif uargs.intensities == 'velocity':
+                all_datasets = oe.OldAbsorptionVelocityDipoleExtractor.extract(
+                    output_file
+                )
+        elif version[0] >= 6:
+            if uargs.intensities == 'electric':
+                all_datasets = oe.AbsorptionElectricDipoleExtractor.extract(
+                    output_file
+                )
+            elif uargs.intensities == 'velocity':
+                all_datasets = oe.AbsorptionVelocityDipoleExtractor.extract(
+                    output_file
+                )
+            elif uargs.intensities == 'semi-classical':
+                all_datasets = oe.AbsorptionSemiClassicalDipoleExtractor.extract(
+                    output_file
+                )
+
+        ut.cprint('Using intensities: {}'.format(uargs.intensities), 'cyan')
+
+        all_abs_data = [
+            d.AbsorptionData.from_extractor_dataset(
+                dataset,
+                uargs.intensities,
+                remove_zero_osc=True
+            )
+            for dataset in all_datasets
+        ]
+
+        if len(all_abs_data) == 0:
+            ut.red_exit(
+                f'No ABSORPTION data found in file {output_file}', 'red'
+            )
+        elif len(all_abs_data) > 1:
+            ut.cprint(
+                f'Found {len(all_abs_data)} ABSORPTION sections in '
+                f'file {output_file}\n'
+                f'Plotting final section ONLY',
+                'cyan'
+            )
+
+        abs_data = all_abs_data[-1]
+
+        if uargs.x_unit == 'wavenumber':
+            x_vals = abs_data.wavenumbers
+            min_factor = 0.8
+            max_factor = 1.1
+        elif uargs.x_unit == 'wavelength':
+            x_vals = abs_data.wavelengths
+            max_factor = 1.1
+            min_factor = 0.8
+        elif uargs.x_unit == 'energy':
+            x_vals = abs_data.energies
+            min_factor = 0.9995
+            max_factor = 1.0005
+
+        # Set x_min and x_max
+        if isinstance(uargs.x_lim[0], str):
+            if uargs.x_lim[0] == 'auto':
+                x_min = min(x_vals) * min_factor
+            elif ut.is_floatable(uargs.x_lim[0]):
+                x_min = float(uargs.x_lim[0])
+            else:
+                raise ValueError(f'Invalid x_min value: {uargs.x_lim[0]}')
+        else:
+            x_min = uargs.x_lim[0]
+
+        if isinstance(uargs.x_lim[1], str):
+            if uargs.x_lim[1] == 'auto':
+                x_max = max(x_vals) * max_factor
+            elif ut.is_floatable(uargs.x_lim[1]):
+                x_max = float(uargs.x_lim[1])
+            else:
+                raise ValueError(f'Invalid x_max value: {uargs.x_lim[1]}')
+        else:
+            x_max = uargs.xlim[1]
+
+        # Generate spectrum
+        abs_data.generate_spectrum(
+            fwhm=uargs.linewidth,
+            lineshape=uargs.lineshape,
+            x_type=uargs.x_unit,
+            num_points=10000,
+            x_min=x_min,
+            x_max=x_max,
+            comment=unique_names[it]
+        )
+
+        # Plot absorption spectrum
+        plotter.plot_absorption_spectrum(
+            abs_data,
+            linecolor=colours[it],
+            stickcolour=colours[it],
+            osc_style=uargs.osc_style,
+            normalise=uargs.normalise,
+            window_title='',
+            fig=fig,
+            ax=ax,
+            oax=oax,
+            show=False,
+            save=False,
+            x_lim=[x_min, x_max],
+            y_lim=uargs.y_lim,
+            x_shift=uargs.x_shift[it],
+            legend=legend
+        )
+
+    if _SAVE_CONV[uargs.plot]:
+        plt.savefig('absorption_spectrum.png', dpi=500)
+
+    if _SHOW_CONV[uargs.plot]:
+        plt.show()
+
+    return
+
+
 def plot_ir_func(uargs):
     '''
     Wrapper for CLI plot_ir call
@@ -676,12 +983,7 @@ def plot_ir_func(uargs):
     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)
+    ut.check_font_envvar()
 
     # Change matplotlib font size to be larger
     mpl.rcParams.update({'font.size': 12})
@@ -1593,7 +1895,7 @@ def read_args(arg_list=None):
 
     plot_abs = plot_parser.add_parser(
         'abs',
-        description='Plots absorption spectrum from CI calculation output',
+        description='Plots absorption spectrum from TDDFT/CI calculation output', # noqa
         usage=ut.cstring('orto plot abs <output_file> [options]', 'cyan'),
         formatter_class=argparse.RawTextHelpFormatter
     )
@@ -1604,6 +1906,7 @@ def read_args(arg_list=None):
     plot_abs.add_argument(
         'output_file',
         type=pathlib.Path,
+        nargs='+',
         help='Orca output file name'
     )
 
@@ -1620,20 +1923,20 @@ def read_args(arg_list=None):
         '--linewidth',
         '-lw',
         type=float,
-        default=2000,
+        default=1,
         help=(
             'Width of signal (FWHM for Gaussian, Width for Lorentzian),'
-            ' in Wavenumbers'
+            ' in same unit as x axis'
         )
     )
 
     plot_abs.add_argument(
         '--osc_style',
         type=str,
-        default='combined',
+        default='separate',
         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'
@@ -1669,17 +1972,28 @@ def read_args(arg_list=None):
     plot_abs.add_argument(
         '--x_unit',
         type=str,
-        choices=['wavenumber', 'energy', 'wavelength'],
-        default='wavenumber',
+        choices=['energy', 'wavelength', 'wavenumber'],
+        default='energy',
         help='x units to use for spectrum'
     )
 
     plot_abs.add_argument(
-        '--shift',
+        '--x_shift',
         type=float,
-        default=0.,
+        default=None,
+        nargs='+',
         help=(
             'Shift spectrum by this amount in x units\n'
+            'Default: 0.'
+        )
+    )
+
+    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'
         )
     )
@@ -1699,12 +2013,147 @@ 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/constants.py

@@ -6,3 +6,5 @@ ELECTRON_MASS = 9.10938215E-31  # kg
 EPSILON_0 = 8.8541878128E-12  # F m^-1
 SPEED_OF_LIGHT_M_S = 299792458.0  # m s^-1
 SPEED_OF_LIGHT_CM_S = SPEED_OF_LIGHT_M_S * 100.0  # cm s^-1
+EV_TO_NM = 1239.84193  # eV nm
+EV_TO_WAVENUMBER = 8065.54429  # eV^-1 cm^-1