orto 1.11.1__tar.gz → 1.11.3__tar.gz

{orto-1.11.1 → orto-1.11.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.1
+Version: 1.11.3
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.11.3/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.11.3'

{orto-1.11.1 → orto-1.11.3}/orto/cli.py

@@ -929,6 +929,8 @@ def plot_xes_func(uargs):
             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 == 'wavelength_rev':
+            x_values = 1E7 / np.asarray(data['energy (cm^-1)'])
         elif uargs.x_unit == 'energy':
             x_values = np.asarray(data['energy (ev)'])
 
@@ -1096,42 +1098,12 @@ def plot_abs_func(uargs, save_data_only=False):
     -------
     None
     '''
-    import matplotlib.pyplot as plt
-    import matplotlib as mpl
-    import matplotlib.colors as mcolors
     from . import plotter
     from . import extractor as oe
     from . import data as d
 
-    # 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:
-        if uargs.unique_names:
-            base_names = [of.stem for of in uargs.output_file]
-            unique_names = ut.find_unique_substring(base_names)
-        else:
-            unique_names = [of.stem for of in uargs.output_file]
-        legend = True
-    else:
-        legend = False
-        unique_names = ['']
 
-    # Handle x_shift argument
+    # Process 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):
@@ -1139,6 +1111,10 @@ def plot_abs_func(uargs, save_data_only=False):
             'Number of x_shift values must match number of output files'
         )
 
+    # Create dictionary to hold absorption data for plotting later
+    spectra_dict = {}
+
+    # Extract data from each output file
     for it, output_file in enumerate(uargs.output_file):
 
         version = oe.OrcaVersionExtractor.extract(output_file)
@@ -1150,6 +1126,9 @@ def plot_abs_func(uargs, save_data_only=False):
             )
             version = [6, 0, 0]
 
+        # Extract absorption data from file
+        # using appropriate extractor for version
+        # and intensity type
         if version[0] < 6:
             if uargs.intensities == 'electric':
                 all_datasets = oe.OldAbsorptionElectricDipoleExtractor.extract(
@@ -1175,6 +1154,9 @@ def plot_abs_func(uargs, save_data_only=False):
 
         ut.cprint('Using intensities: {}'.format(uargs.intensities), 'cyan')
 
+        # Create absorption data object
+        # one per dataset extracted
+        # (doubtful multiple datasets will be present, but just in case)
         all_abs_data = [
             d.AbsorptionData.from_extractor_dataset(
                 dataset,
@@ -1184,10 +1166,12 @@ def plot_abs_func(uargs, save_data_only=False):
             for dataset in all_datasets
         ]
 
+        # Check absorption data was found
         if len(all_abs_data) == 0:
             ut.red_exit(
                 f'No ABSORPTION data found in file {output_file}', 'red'
             )
+        # report if multiple absorption sections found
         elif len(all_abs_data) > 1:
             ut.cprint(
                 f'Found {len(all_abs_data)} ABSORPTION sections in '
@@ -1195,23 +1179,35 @@ def plot_abs_func(uargs, save_data_only=False):
                 f'Plotting final section ONLY',
                 'cyan'
             )
-
+        # and only use final one
+        # (again, doubtful multiple sections will be present, but just in case)
         abs_data = all_abs_data[-1]
 
+        # Determine x values for setting x limits of computed spectrum
         if uargs.x_unit == 'wavenumber':
             x_vals = abs_data.wavenumbers
             min_factor = 0.8
             max_factor = 1.1
+            x_reversed = False
         elif uargs.x_unit == 'wavelength':
             x_vals = abs_data.wavelengths
             max_factor = 1.1
             min_factor = 0.8
+            x_reversed = False
+        elif uargs.x_unit == 'wavelength_rev':
+            x_vals = abs_data.wavelengths
+            max_factor = 1.1
+            min_factor = 0.8
+            x_reversed = True
+            uargs.x_unit = 'wavelength'
         elif uargs.x_unit == 'energy':
             x_vals = abs_data.energies
             min_factor = 0.9995
             max_factor = 1.0005
+            x_reversed = False
 
-        # Set x_min and x_max
+        # Set x_min
+        # based on user arguments
         if isinstance(uargs.x_lim[0], str):
             if uargs.x_lim[0] == 'auto':
                 x_min = min(x_vals) * min_factor
@@ -1222,6 +1218,8 @@ def plot_abs_func(uargs, save_data_only=False):
         else:
             x_min = uargs.x_lim[0]
 
+        # Set x_max
+        # based on user arguments
         if isinstance(uargs.x_lim[1], str):
             if uargs.x_lim[1] == 'auto':
                 x_max = max(x_vals) * max_factor
@@ -1236,7 +1234,7 @@ def plot_abs_func(uargs, save_data_only=False):
         if uargs.trim_transitions is not None:
             abs_data.trim_to_n(uargs.trim_transitions)
 
-        # Generate spectrum
+        # Generate spectrum data
         abs_data.generate_spectrum(
             fwhm=uargs.linewidth,
             lineshape=uargs.lineshape,
@@ -1244,11 +1242,12 @@ def plot_abs_func(uargs, save_data_only=False):
             num_points=10000,
             x_min=x_min,
             x_max=x_max,
-            comment=unique_names[it]
+            comment=output_file,
+            x_reversed=x_reversed
         )
 
+        # Save spectrum data to file
         if save_data_only:
-            # Save spectrum data to file
             abs_data.save_spectrum_data(
                 f'absorption_spectrum_{output_file.stem}.csv',
                 comments='Data from {}\nfwhm={}, lineshape={}\nintensities={}'.format( # noqa
@@ -1274,33 +1273,98 @@ def plot_abs_func(uargs, save_data_only=False):
                 'cyan'
             )
         else:
-            # 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
-            )
+            # Add to dictionary of spectra for plotting later
+            spectra_dict[output_file] = abs_data
+
+    # Exit if only saving data
+    if save_data_only:
+        return
+
+    ## Plot all spectra
+    import matplotlib.pyplot as plt
+    import matplotlib.colors as mcolors
+
+    # Set font name and size
+    plt.rcParams['font.family'] = 'Arial'
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
+    plt.rcParams['legend.loc'] = 'center right'
 
-    if not save_data_only:
-        if _SAVE_CONV[uargs.plot]:
-            savename = f'absorption_spectrum_{output_file.stem}.png'
-            plt.savefig(savename, dpi=500)
-            ut.cprint(f'Saved image to {savename}', 'cyan')
+    # Create list of colours for plotting
+    if len(uargs.output_file) == 1:
+        colours = ['black']
+    else:
+        colours = list(mcolors.TABLEAU_COLORS.values())
+
+    # Width of figure in inches
+    # Make wider if multiple spectra to plot
+    # to include legend
+    if len(spectra_dict) > 1:
+        width = 6.
+    else:
+        width = 4
+    # width in cm
+    width_cm = 2.54 * width
+
+    # Create figure and axis with
+    # height based on golden ratio
+    golden = (1 + np.sqrt(5))/2
+    fig, ax = plt.subplots(
+        1,
+        1,
+        num='Absorption Spectrum',
+        figsize=(width, 4. / golden)
+    )
+    # Secondary axis for oscillator strength sticks
+    oax = ax.twinx()
+
+    # Plot absorption spectrum for each file
+    for it, (output_file, abs_data) in enumerate(spectra_dict.items()): # noqa
+
+        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=False
+        )
+
+    if uargs.x_lim != ['auto', 'auto']:
+        ax.set_xlim(float(uargs.x_lim[0]), float(uargs.x_lim[1]))
+
+    fig.tight_layout()
+
+    if len(spectra_dict) > 1:
+        fig.subplots_adjust(right=3.3/6.)
+        if uargs.legend is None:
+            legend_labels = [
+                f'{output_file.stem}' for output_file in spectra_dict.keys()
+            ]
+            fig.legend(legend_labels, loc=7)
+        else:
+            fig.legend(uargs.legend, loc=7)
+
+    if _SAVE_CONV[uargs.plot]:
+        savename = f'absorption_spectrum_{output_file.stem}.png'
+        plt.savefig(savename, dpi=500)
+        ut.cprint(f'Saved image to {savename}', 'cyan')
+        ut.cprint(
+            f'Use width={width:.1f} in. or {width_cm:.1f} cm',
+            'cyan'
+        )
 
-        if _SHOW_CONV[uargs.plot]:
-            plt.show()
+    if _SHOW_CONV[uargs.plot]:
+        plt.show()
 
     return
 
@@ -2540,9 +2604,9 @@ def read_args(arg_list=None):
     plot_abs.add_argument(
         '--x_unit',
         type=str,
-        choices=['energy', 'wavelength', 'wavenumber'],
+        choices=['energy', 'wavelength', 'wavelength_rev', 'wavenumber'],
         default='energy',
-        help='x units to use for spectrum'
+        help='x units to use for spectrum (rev = reversed axis direction)'
     )
 
     plot_abs.add_argument(
@@ -2592,12 +2656,13 @@ def read_args(arg_list=None):
     )
 
     plot_abs.add_argument(
-        '--unique_names',
-        action='store_true',
-        default=False,
+        '--legend',
+        type=str,
+        nargs='+',
+        default=None,
         help=(
-            'Attempt to shorten file names in plot legend\n'
-            'Default: %(default)s'
+            'Legend labels for each spectrum plotted\n'
+            'If not provided, file names are used\n'
         )
     )
 

{orto-1.11.1 → orto-1.11.3}/orto/data.py

@@ -33,6 +33,9 @@ class AbsorptionSpectrum():
         Full width at half maximum used in spectrum generation
     comment: str, default=''
         Comment or metadata for the spectrum
+    x_reversed: bool, default False
+        Whether the x axis is reversed (e.g. for wavelength spectra)\n
+        By default, False - increasing x values from left to right
 
     Attributes
     ----------
@@ -61,7 +64,7 @@ class AbsorptionSpectrum():
     def __init__(self, x_grid: NDArray, x_unit: str, x_label: str,
                  x_label_mathmode: str, y_unit: str, y_label: str,
                  y_label_mathmode: str, y_values: NDArray, fwhm: float,
-                 comment: str = '') -> None:
+                 comment: str = '', x_reversed: bool = False) -> None:
         self.x_grid = x_grid
         self.x_unit = x_unit
         self.x_label = x_label
@@ -72,30 +75,9 @@ class AbsorptionSpectrum():
         self.fwhm = fwhm
         self.y_values = y_values
         self.comment = comment
+        self.x_reversed = x_reversed
         return
 
-    @classmethod
-    def from_data(cls, x_grid: NDArray, y_values: NDArray,
-                  fwhm: float) -> 'AbsorptionSpectrum':
-        '''
-        Creates AbsorptionSpectrum object from data
-
-        Parameters
-        ----------
-        x_grid: NDArray
-            Grid of x values (energies, wavelengths, or wavenumbers)
-        y_values: NDArray
-            Absorption spectrum values at each point in x_grid
-        fwhm: float
-            Full width at half maximum used in spectrum generation
-
-        Returns
-        -------
-        AbsorptionSpectrum
-            Created AbsorptionSpectrum object
-        '''
-        return cls(x_grid, y_values, fwhm)
-
 
 class AbsorptionData():
     '''
@@ -282,7 +264,8 @@ class AbsorptionData():
     def generate_spectrum(self, fwhm: float, lineshape: str, x_min: float,
                           x_max: float, num_points: int,
                           x_type: str = 'energy',
-                          comment: str = '') -> AbsorptionSpectrum:
+                          comment: str = '',
+                          x_reversed: bool = False) -> AbsorptionSpectrum:
         '''
         Generates absorption spectrum using Gaussian broadening
 
@@ -306,6 +289,9 @@ class AbsorptionData():
               'wavenumber' (cm^-1)
         comment: str
             Comment to add to spectrum metadata
+        x_reversed: bool
+            Whether to reverse the x axis (e.g. for wavelength spectra)\n
+            By default, False - increasing x values from left to right
 
         Returns
         -------
@@ -387,7 +373,8 @@ class AbsorptionData():
             y_label_mathmode=y_label_mathmode,
             y_values=y_vals,
             fwhm=fwhm,
-            comment=comment
+            comment=comment,
+            x_reversed=x_reversed
         )
 
         self.spectrum = spectrum

{orto-1.11.1 → orto-1.11.3}/orto/plotter.py

@@ -79,7 +79,18 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
         raise ValueError('AbsorptionData object does not contain spectrum')
 
     if fig is None or ax is None:
-        fig, ax = plt.subplots(1, 1, num=window_title)
+        width = 4
+        width_cm = 10.4
+        golden = (1 + np.sqrt(5))/2
+        fig, ax = plt.subplots(
+            1,
+            1,
+            num=window_title,
+            figsize=(width, width / golden)
+        )
+    else:
+        width = fig.get_size_inches()[0]
+        width_cm = width * 2.54
 
     if oax is None and osc_style == 'separate':
         oax = ax.twinx()
@@ -118,7 +129,6 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
         ax.set_ylabel(abs_data.spectrum.y_label_mathmode)
 
     if abs_data.spectrum.x_label.split()[0].lower() == 'wavelength':
-        ax.invert_xaxis()
         stick_x_values = [
             wavelength + x_shift
             for wavelength in abs_data.wavelengths
@@ -134,6 +144,9 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
             for wavenumber in abs_data.wavenumbers
         ]
 
+    if abs_data.spectrum.x_reversed:
+        ax.invert_xaxis()
+
     x_values = abs_data.spectrum.x_grid + x_shift
 
     # Main spectrum
@@ -141,18 +154,20 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
         x_values,
         _y_values,
         color=linecolor,
+        lw=1.1,
         label=abs_data.spectrum.comment
     )
 
     if osc_style == 'separate':
         # Oscillator strength twin axis
-        oax.stem(
+        _, stemlines, _ = oax.stem(
             stick_x_values,
             _osc,
             basefmt=' ',
             markerfmt=' ',
             linefmt=stickcolour
         )
+        plt.setp(stemlines, 'linewidth', 1.1)
         oax.yaxis.set_minor_locator(AutoMinorLocator())
         if normalise:
             oax.set_ylabel(r'Normalised $f_\mathregular{osc}$')
@@ -216,6 +231,10 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
                 f'\nSpectrum saved to\n {save_name}',
                 'cyan'
             )
+            ut.cprint(
+                f'Use width={width:.1f} in. or {width_cm:.1f} cm',
+                'cyan'
+            )
 
     if show:
         plt.show()

{orto-1.11.1 → orto-1.11.3}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.1
+Version: 1.11.3
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.11.1 → orto-1.11.3}/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__ = '1.11.1'
+__version__ = '1.11.3'
 
 setuptools.setup(
     name='orto',

orto-1.11.1/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '1.11.1'