orto 1.6.0__py3-none-any.whl → 1.7.0__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.6.0'
+__version__ = '1.7.0'

orto/cli.py

@@ -776,7 +776,7 @@ def plot_xas_func(uargs):
     return
 
 
-def plot_abs_func(uargs):
+def plot_abs_func(uargs, save_data_only=False):
     '''
     Wrapper for CLI plot abs call\n\n
 
@@ -789,6 +789,9 @@ def plot_abs_func(uargs):
     uargs : argparser object
         User arguments
 
+    save_data_only : bool, default=False
+        If True, saves generated spectrum data to file only.
+
     Returns
     -------
     None
@@ -862,7 +865,7 @@ def plot_abs_func(uargs):
                     output_file
                 )
             elif uargs.intensities == 'semi-classical':
-                all_datasets = oe.AbsorptionSemiClassicalDipoleExtractor.extract(
+                all_datasets = oe.AbsorptionSemiClassicalDipoleExtractor.extract( # noqa
                     output_file
                 )
 
@@ -872,7 +875,7 @@ def plot_abs_func(uargs):
             d.AbsorptionData.from_extractor_dataset(
                 dataset,
                 uargs.intensities,
-                remove_zero_osc=True
+                remove_zero_osc=uargs.zero_osc
             )
             for dataset in all_datasets
         ]
@@ -936,30 +939,60 @@ def plot_abs_func(uargs):
             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_data_only:
+            # Save spectrum data to file
+            abs_data.save_spectrum_data(
+                f'absorption_spectrum_{output_file}.csv',
+                comments='Data from {}\nfwhm={}, lineshape={}\nintensities={}'.format( # noqa
+                    output_file,
+                    uargs.linewidth,
+                    uargs.lineshape,
+                    uargs.intensities
+                )
+            )
+            abs_data.save_transition_data(
+                f'transition_data_{output_file}.csv',
+                comments='Data from {}\nintensities={}'.format(
+                    output_file,
+                    uargs.intensities
+                )
+            )
+            ut.cprint(
+                f'Saved absorption data to absorption_spectrum_{output_file}.csv', # noqa
+                'cyan'
+            )
+            ut.cprint(
+                f'Saved absorption spectrum data to transition_data_{output_file}.csv', # noqa
+                '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
+            )
 
-    if _SAVE_CONV[uargs.plot]:
-        plt.savefig('absorption_spectrum.png', dpi=500)
+    if not save_data_only:
+        if _SAVE_CONV[uargs.plot]:
+            savename = f'absorption_spectrum_{output_file}.png'
+            plt.savefig(savename, dpi=500)
+            ut.cprint(f'Saved image to {savename}', 'cyan')
 
-    if _SHOW_CONV[uargs.plot]:
-        plt.show()
+        if _SHOW_CONV[uargs.plot]:
+            plt.show()
 
     return
 
@@ -1880,6 +1913,109 @@ def read_args(arg_list=None):
         )
     )
 
+    gen_abs = gen_parser.add_parser(
+        'abs',
+        description='Generates absorption spectrum data from TDDFT/CI calculation output', # noqa
+        usage=ut.cstring('orto gen abs <output_file> [options]', 'cyan'), # noqa
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+    gen_abs._positionals.title = 'Mandatory Arguments'
+
+    gen_abs.set_defaults(func=lambda x: plot_abs_func(x, save_data_only=True))
+
+    gen_abs.add_argument(
+        'output_file',
+        type=pathlib.Path,
+        nargs='+',
+        help='Orca output file name'
+    )
+
+    gen_abs.add_argument(
+        '--intensities',
+        '-i',
+        type=str,
+        choices=['velocity', 'electric', 'semi-classical'],
+        default='electric',
+        help='Type of intensity to plot (orca_mapspc uses electric)'
+    )
+
+    gen_abs.add_argument(
+        '--linewidth',
+        '-lw',
+        type=float,
+        default=1,
+        help=(
+            'Width of signal (FWHM for Gaussian, Width for Lorentzian),'
+            ' in same unit as x axis'
+        )
+    )
+
+    gen_abs.add_argument(
+        '--lineshape',
+        '-ls',
+        type=str,
+        choices=['gaussian', 'lorentzian'],
+        default='lorentzian',
+        help='Lineshape to use for each signal'
+    )
+
+    gen_abs.add_argument(
+        '--x_unit',
+        type=str,
+        choices=['energy', 'wavelength', 'wavenumber'],
+        default='energy',
+        help='x units to use for spectrum'
+    )
+
+    gen_abs.add_argument(
+        '--x_shift',
+        type=float,
+        default=None,
+        nargs='+',
+        help=(
+            'Shift spectrum by this amount in x units\n'
+            'Default: 0.'
+        )
+    )
+
+    gen_abs.add_argument(
+        '--no_trim',
+        action='store_true',
+        default=False,
+        help=(
+            'Do not trim spectrum to non-zero oscillator strength\n'
+            'Default: %(default)s'
+        )
+    )
+
+    gen_abs.add_argument(
+        '--x_lim',
+        nargs=2,
+        default=['auto', 'auto'],
+        help='x limits of spectrum'
+    )
+
+    gen_abs.add_argument(
+        '--normalise',
+        '-n',
+        action='store_true',
+        default=False,
+        help=(
+            'Normalises spectrum to maximum value\n'
+            'Default: %(default)s'
+        )
+    )
+
+    gen_abs.add_argument(
+        '--zero_osc',
+        default=1E-5,
+        type=float,
+        help=(
+            'Oscillator strengths below this value are treated as zero\n'
+            'Default: %(default)s'
+        )
+    )
+
     plot_subprog = all_subparsers.add_parser(
         'plot',
         description='Plot data from orca file',
@@ -1988,16 +2124,6 @@ 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,
@@ -2023,6 +2149,16 @@ def read_args(arg_list=None):
         )
     )
 
+    plot_abs.add_argument(
+        '--zero_osc',
+        default=1E-5,
+        type=float,
+        help=(
+            'Oscillator strengths below this value are treated as zero\n'
+            'Default: %(default)s'
+        )
+    )
+
     plot_xes = plot_parser.add_parser(
         'xes',
         description='Plots XES from CI calculation output',

orto/data.py

@@ -18,11 +18,15 @@ class AbsorptionSpectrum():
     x_unit: str
         Unit of x values: 'eV', 'nm', or 'cm^-1'
     x_label: str
-        Label for x axis using LaTeX formatting
+        Label for x axis
+    x_label_mathmode: str
+        Label for x axis using LaTeX mathmode formatting
     y_unit: str
         Unit of y values, e.g. 'cm^-1 mol^-1 L'
     y_label: str
-        Label for y axis using LaTeX formatting
+        Label for y axis
+    y_label_mathmode: str
+        Label for y axis using LaTeX mathmode formatting
     spectrum: NDArray
         Absorption spectrum values at each point in x_grid
     fwhm: float
@@ -37,11 +41,15 @@ class AbsorptionSpectrum():
     x_unit: str
         Unit of x values: 'eV', 'nm', or 'cm^-1'
     x_label: str
-        Label for x axis using LaTeX formatting
+        Label for x axis
+    x_label_mathmode: str
+        Label for x axis using LaTeX mathmode formatting
     y_unit: str
         Unit of y values, e.g. 'cm^-1 mol^-1 L'
     y_label: str
-        Label for y axis using LaTeX formatting
+        Label for y axis
+    y_label_mathmode: str
+        Label for y axis using LaTeX mathmode formatting
     y_values: NDArray
         Absorption spectrum values at each point in x_grid
     fwhm: float
@@ -50,14 +58,17 @@ class AbsorptionSpectrum():
         Comment or metadata for the spectrum
     '''
 
-    def __init__(self, x_grid: NDArray, x_unit: str, x_label: str, y_unit: str,
-                 y_label: str, y_values: NDArray, fwhm: float,
+    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:
         self.x_grid = x_grid
         self.x_unit = x_unit
         self.x_label = x_label
+        self.x_label_mathmode = x_label_mathmode
         self.y_unit = y_unit
         self.y_label = y_label
+        self.y_label_mathmode = y_label_mathmode
         self.fwhm = fwhm
         self.y_values = y_values
         self.comment = comment
@@ -172,7 +183,7 @@ class AbsorptionData():
 
     @classmethod
     def from_extractor(cls, extractor: oe.AbsorptionExtractor,
-                       remove_zero_osc: bool = True) -> list['AbsorptionData']: # noqa
+                       remove_zero_osc: float = 1E-4) -> list['AbsorptionData']: # noqa
         '''
         Creates AbsorptionData object from data extractor
 
@@ -180,8 +191,8 @@ class AbsorptionData():
         ----------
         extractor: Extractor
             Data extractor object containing transition data
-        remove_zero_osc: bool
-            If True, removes transitions with zero oscillator strength
+        remove_zero_osc: float, default=1E-4
+            Remove transitions with oscillator strength below this value
 
         Returns
         -------
@@ -204,7 +215,7 @@ class AbsorptionData():
     def from_extractor_dataset(cls,
                                dataset: dict[str, list[int | float]],
                                operator: str,
-                               remove_zero_osc: bool = False) -> 'AbsorptionData': # noqa
+                               remove_zero_osc: float = 1E-4) -> 'AbsorptionData': # noqa
         '''
         Creates AbsorptionData object from data extractor
 
@@ -214,8 +225,8 @@ class AbsorptionData():
             Dataset from orto AbsorptionExtractor.data
         operator: str
             Type of operator used to calculate transitions
-        remove_zero_osc: bool
-            If True, removes transitions with zero oscillator strength
+        remove_zero_osc: float, default=1E-4
+            Remove transitions with oscillator strength below this value
 
         Returns
         -------
@@ -228,16 +239,21 @@ class AbsorptionData():
 
         # Remove transitions with zero oscillator strength from
         # beginning and end of spectrum
-        if remove_zero_osc:
-            osc_strengths = np.array(osc_strengths)
-            # Find first non-zero oscillator strength
-            first_nonzero = np.where(osc_strengths > 1E-4)[0][0]
-            # Find last non-zero oscillator strength
-            last_nonzero = np.where(osc_strengths > 1E-4)[0][-1]
+        osc_strengths = np.array(osc_strengths)
+        # Find first non-zero oscillator strength
+        try:
+            first_nonzero = np.where(osc_strengths > remove_zero_osc)[0][0]
+        except IndexError:
+            raise DataFormattingError(
+                'No transitions with oscillator strength above '
+                f'{remove_zero_osc} found.'
+            )
+        # Find last non-zero oscillator strength
+        last_nonzero = np.where(osc_strengths > remove_zero_osc)[0][-1]
 
-            # Trim data
-            energies = energies[first_nonzero:last_nonzero + 1]
-            osc_strengths = osc_strengths[first_nonzero:last_nonzero + 1]
+        # Trim data
+        energies = energies[first_nonzero:last_nonzero + 1]
+        osc_strengths = osc_strengths[first_nonzero:last_nonzero + 1]
 
         return cls(energies, osc_strengths, operator)
 
@@ -287,20 +303,24 @@ class AbsorptionData():
         if x_type == 'energy':
             x_unit = 'eV'
             x_label = 'Energy (eV)'
+            x_label_mathmode = 'Energy (eV)'
             x_vals = self.energies
         elif x_type == 'wavelength':
             x_unit = 'nm'
             x_label = 'Wavelength (nm)'
+            x_label_mathmode = 'Wavelength (nm)'
             x_vals = self.wavelengths
         elif x_type == 'wavenumber':
             x_unit = 'cm^-1'
-            x_label = r'Wavenumber (cm$\mathregular{^{-1}}$)'
+            x_label = r'Wavenumber (cm⁻¹)'
+            x_label_mathmode = r'Wavenumber (cm$\mathregular{^{-1}}$)'
             x_vals = self.wavenumbers
         else:
             raise DataFormattingError(f'Invalid x_type: {x_type}')
 
         y_unit = 'cm mol^-1 eV^-1'
-        y_label = r'$\epsilon$ (cm$^\mathregular{-1}$ mol$^\mathregular{-1}$ L)'  # noqa
+        y_label = r'ε (cm⁻¹ mol⁻¹ L))'
+        y_label_mathmode = r'$\epsilon$ (cm$^\mathregular{-1}$ mol$^\mathregular{-1}$ L)'  # noqa
 
         # Create grid for spectrum
         x_grid = np.linspace(x_min, x_max, num_points)
@@ -339,8 +359,10 @@ class AbsorptionData():
             x_grid=x_grid,
             x_unit=x_unit,
             x_label=x_label,
+            x_label_mathmode=x_label_mathmode,
             y_unit=y_unit,
             y_label=y_label,
+            y_label_mathmode=y_label_mathmode,
             y_values=y_vals,
             fwhm=fwhm,
             comment=comment
@@ -349,3 +371,81 @@ class AbsorptionData():
         self.spectrum = spectrum
 
         return
+
+    def save_spectrum_data(self, filename: str, comments: str = '') -> None:
+        '''
+        Saves absorption spectrum data to CSV file
+
+        Parameters
+        ----------
+        filename: str
+            Name of output CSV file
+        comments: str
+            Comments to add at the top of the file
+
+        Returns
+        -------
+        None
+        '''
+
+        if self.spectrum is None:
+            raise ValueError(
+                'Spectrum has not been generated yet\n'
+                'Call generate_spectrum() first.'
+            )
+
+        # Select x values based on x_type
+        if self.spectrum.x_label.split()[0].lower() == 'energy':
+            x_vals = self.spectrum.x_grid
+        elif self.spectrum.x_label.split()[0].lower() == 'wavelength':
+            x_vals = const.EV_TO_NM / self.spectrum.x_grid
+        elif self.spectrum.x_label.split()[0].lower() == 'wavenumber':
+            x_vals = self.spectrum.x_grid * const.EV_TO_WAVENUMBER
+
+        if len(comments):
+            header = comments + f'\n{self.spectrum.x_label}, ε (cm⁻¹ mol⁻¹ L))'
+        else:
+            header = f'{self.spectrum.x_label}, ε (cm⁻¹ mol⁻¹ L))'
+
+        # Save to CSV
+        np.savetxt(
+            filename,
+            np.column_stack((x_vals, self.spectrum.y_values)),
+            delimiter=',',
+            header=header,
+            comments='#',
+        )
+
+    def save_transition_data(self, filename: str, comments: str = '') -> None:
+        '''
+        Saves transition data to CSV file
+
+        Parameters
+        ----------
+        filename: str
+            Name of output CSV file
+        comments: str
+            Comments to add at the top of the file
+
+        Returns
+        -------
+        None
+        '''
+
+        if len(comments):
+            header = comments + '\nEnergy (eV),Wavelength (nm),Wavenumber (cm⁻¹),Oscillator Strength'  # noqa
+        else:
+            header = 'Energy (eV),Wavelength (nm),Wavenumber (cm⁻¹),Oscillator Strength'  # noqa
+
+        np.savetxt(
+            filename,
+            np.column_stack((
+                self.energies,
+                self.wavelengths,
+                self.wavenumbers,
+                self.osc_strengths
+            )),
+            delimiter=',',
+            header=header,
+            comments='#',
+        )

orto/plotter.py

@@ -115,20 +115,20 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
     else:
         _y_values = abs_data.spectrum.y_values
         _osc = abs_data.osc_strengths
-        ax.set_ylabel(abs_data.spectrum.y_label)
+        ax.set_ylabel(abs_data.spectrum.y_label_mathmode)
 
-    if abs_data.spectrum.x_label == 'Wavelength (nm)':
+    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
         ]
-    elif abs_data.spectrum.x_label == 'Energy (eV)':
+    elif abs_data.spectrum.x_label.split()[0].lower() == 'energy':
         stick_x_values = [
             energy + x_shift
             for energy in abs_data.energies
         ]
-    elif abs_data.spectrum.x_label == r'Wavenumber (cm$\mathregular{^{-1}}$)':
+    elif abs_data.spectrum.x_label.split()[0].lower() == r'wavenumber':
         stick_x_values = [
             wavenumber + x_shift
             for wavenumber in abs_data.wavenumbers
@@ -199,7 +199,7 @@ def plot_absorption_spectrum(abs_data: data.AbsorptionData,
     ax.xaxis.set_minor_locator(AutoMinorLocator())
     ax.yaxis.set_minor_locator(AutoMinorLocator())
 
-    ax.set_xlabel(abs_data.spectrum.x_label)
+    ax.set_xlabel(abs_data.spectrum.x_label_mathmode)
 
     fig.tight_layout()
 

orto/utils.py

@@ -396,6 +396,7 @@ def find_unique_substring(names):
                 break
     return unique_names
 
+
 def is_floatable(string: str) -> bool:
     '''
     Checks if string can be converted to float
@@ -415,4 +416,4 @@ def is_floatable(string: str) -> bool:
         float(string)
         return True
     except ValueError:
-        return False
+        return False

{orto-1.6.0.dist-info → orto-1.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.6.0
+Version: 1.7.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.7.0.dist-info/RECORD

@@ -0,0 +1,17 @@
+orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
+orto/__version__.py,sha256=ZKj0X3okn4mK4HiX_1UKKuGOzcIskftLiHEMJogbUYY,22
+orto/cli.py,sha256=uiEr5CfGoZ9dalSjExw-6RxMDcODKtzwkWdrYMB0t88,80401
+orto/constants.py,sha256=anxaiTykO8Q_CXliR7zuOAdnXZrQ2-C4ndaviyl7kGc,419
+orto/data.py,sha256=cNO8gQj6aZP-xriWUY2HchZ6iWZxVZnlrvAD4qhWT_o,14436
+orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
+orto/extractor.py,sha256=d2_pGQeIjK_JbsMINTawUgcO2vcPq0b9uQj9VKuI720,75953
+orto/input.py,sha256=N8JbySSVEC_qmXZ7ppJsZ7Z1qel6PfalGYRtnX1hJ6U,9900
+orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
+orto/plotter.py,sha256=IATM7vBauT3StFXqk_4DKzCSiTnUunrCeNYRBKM3eUE,17695
+orto/utils.py,sha256=GcMZ9uebOSnkPQT_U5O0X49LUtTu8YpXZxEsNKgXNTY,9838
+orto-1.7.0.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
+orto-1.7.0.dist-info/METADATA,sha256=qkvcsk4bG2bdtxhiFCUKHj9cA_s0QEn3pShfEIrc6X0,1184
+orto-1.7.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.7.0.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.7.0.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.7.0.dist-info/RECORD,,

orto-1.6.0.dist-info/RECORD

@@ -1,17 +0,0 @@
-orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-orto/__version__.py,sha256=bYN93DTWr8alkTnO3wj31CU5gqTshxIcsbXUcJcUAc8,22
-orto/cli.py,sha256=AH9Cnfu21XGTs2ygLZGb8yxzJPe1gxxnF9qOsm_H1II,76491
-orto/constants.py,sha256=anxaiTykO8Q_CXliR7zuOAdnXZrQ2-C4ndaviyl7kGc,419
-orto/data.py,sha256=r6Ht1X0-FhjUbEAAi3a9F2R2_QG3QFElaAAcZNz4GRQ,11213
-orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
-orto/extractor.py,sha256=d2_pGQeIjK_JbsMINTawUgcO2vcPq0b9uQj9VKuI720,75953
-orto/input.py,sha256=N8JbySSVEC_qmXZ7ppJsZ7Z1qel6PfalGYRtnX1hJ6U,9900
-orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
-orto/plotter.py,sha256=-8Lgv-kDjw_wHZrDrQzQGT521gSZ3IJdIeLqzdQgflQ,17656
-orto/utils.py,sha256=fghKZnrO1HTtOZPZRbNK6QTgUOXiIQ6NEFvesDSoY0o,9836
-orto-1.6.0.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
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