orto 1.5.0__tar.gz → 1.6.1__tar.gz

orto-1.6.1/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
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+other than an Application or a Combined Work as defined below.
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{orto-1.5.0 → orto-1.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.5.0
+Version: 1.6.1
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow
@@ -12,6 +12,7 @@ Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
+License-File: LICENSE
 Requires-Dist: numpy>=2.1.2
 Requires-Dist: xyz_py>=5.13.1
 Requires-Dist: matplotlib>=3.9.2
@@ -25,6 +26,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
+Dynamic: license-file
 Dynamic: project-url
 Dynamic: requires-dist
 Dynamic: requires-python

orto-1.6.1/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.6.1'

{orto-1.5.0 → orto-1.6.1}/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 = {
@@ -573,12 +574,7 @@ def plot_xes_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})
@@ -618,7 +614,7 @@ def plot_xes_func(uargs):
                 uargs.output_file
             )
     elif version[0] < 6:
-        ut.cprint('Unsupported version of Orca for XES extraction', 'red')
+        ut.red_exit('Unsupported version of Orca for XES extraction', 'red')
 
     ut.cprint('Using intensities: {}'.format(uargs.intensities), 'cyan')
 
@@ -675,9 +671,9 @@ def plot_xes_func(uargs):
         plt.show()
 
 
-def plot_abs_func(uargs):
+def plot_xas_func(uargs):
     '''
-    Wrapper for CLI plot abs call
+    Wrapper for CLI plot xas call
 
     Parameters
     ----------
@@ -694,12 +690,7 @@ 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})
@@ -713,28 +704,21 @@ def plot_abs_func(uargs):
         )
         version = [6, 0, 0]
 
-    if version[0] < 6:
-        if uargs.intensities == 'electric':
-            all_data = oe.OldAbsorptionElectricDipoleExtractor.extract(
-                uargs.output_file
-            )
-        elif uargs.intensities == 'velocity':
-            all_data = oe.OldAbsorptionVelocityDipoleExtractor.extract(
-                uargs.output_file
-            )
-    elif version[0] >= 6:
+    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')
 
@@ -792,6 +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( # noqa
+                    output_file
+                )
+
+        ut.cprint('Using intensities: {}'.format(uargs.intensities), 'cyan')
+
+        all_abs_data = [
+            d.AbsorptionData.from_extractor_dataset(
+                dataset,
+                uargs.intensities,
+                remove_zero_osc=uargs.zero_osc
+            )
+            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
@@ -811,12 +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})
@@ -1728,7 +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
     )
@@ -1739,6 +1906,7 @@ def read_args(arg_list=None):
     plot_abs.add_argument(
         'output_file',
         type=pathlib.Path,
+        nargs='+',
         help='Orca output file name'
     )
 
@@ -1755,17 +1923,17 @@ 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' # noqa
@@ -1804,18 +1972,19 @@ 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: %(default)s'
+            'Default: 0.'
         )
     )
 
@@ -1854,6 +2023,16 @@ 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-1.5.0 → orto-1.6.1}/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