orto 1.11.2__tar.gz → 1.12.0__tar.gz

{orto-1.11.2 → orto-1.12.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.2
+Version: 1.12.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.12.0/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.12.0'

{orto-1.11.2 → orto-1.12.0}/orto/cli.py

@@ -537,9 +537,99 @@ def extract_gmatrix_func(uargs, save=True):
     return
 
 
+def gen_orbs_func(uargs):
+    '''
+    Wrapper for CLI gen orbs call
+
+    Parameters
+    ----------
+    uargs: argparser object
+        User arguments
+
+    Returns
+    -------
+    None
+    '''
+    from subto.job import SlurmJob
+
+    # Check orca module
+    if len(uargs.orca_load):
+        orca_load_val = copy.copy(uargs.orca_load)
+    elif os.getenv('orto_orca_load'):
+        try:
+            if len(os.getenv('orto_orca_load')):
+                orca_load_val = os.getenv('orto_orca_load')
+        except ValueError:
+            ut.red_exit(
+                (
+                    'Error in orto_orca_load environment variable'
+                )
+            )
+    else:
+        ut.red_exit(
+            (
+                'Missing orto_orca_load environment variable or '
+                '--orca_load argument'
+            )
+        )
+
+    # Create string of command numbers for orca plot to follow
+    command_nums = '1\\n1\\n4'
+    command_nums += f'\\n{uargs.n_pts:d}'
+    command_nums += '\\n5\\n7'
+
+    if uargs.beta:
+        command_nums += '\\n3\\n1'
+
+    for orbital_number in uargs.orb_numbers:
+        command_nums += '\\n2'
+        command_nums += f'\\n{orbital_number:d}'
+        command_nums += '\\n11'
+    command_nums += '\\n12\\n'
+
+    # Generate job file for orca_plot
+    orb_job = SlurmJob(
+        pathlib.Path(f'{uargs.gbw_file.stem}_orbital_job.sh')
+    )
+
+    # Create content of job
+    orb_job.content_block = ''
+
+    orb_job.content_block += '# Load orca module\n'
+    orb_job.content_block += f'module load {orca_load_val}\n'
+    orb_job.content_block += '# Run orca_plot to generate orbital cube file(s)\n' # noqa
+    orb_job.content_block += f'time mpirun -np {uargs.n_procs:d} $(which orca_plot_mpi) {uargs.gbw_file.name} -i aa <<< $\'{command_nums}\'\n\n' # noqa
+
+    # Set job name
+    orb_job.job_name = f'{uargs.gbw_file.stem}_orbitals'
+
+    orb_job.ntasks_per_node = str(uargs.n_procs)
+    orb_job.mem_per_cpu = str(uargs.memory)
+
+    orb_job.error = f'{uargs.gbw_file.stem}_orbitals.%j.e'
+    orb_job.output = f'{uargs.gbw_file.stem}_orbitals.%j.o'
+
+    # Write job script
+    # with submitter configuration options specified
+    orb_job.write_script(True)
+
+    # Submit to queue
+    if not uargs.no_sub:
+        subprocess.call(
+            'cd {}; {} "{}"; cd ../'.format(
+                uargs.gbw_file.parents[0],
+                orb_job.SUBMIT_COMMAND,
+                orb_job.file_path
+                ),
+            shell=True
+        )
+
+    return
+
+
 def gen_spden_func(uargs):
     '''
-    Wrapper for CLI gen spin density call
+    Wrapper for CLI gen spin_density call
 
     Parameters
     ----------
@@ -868,7 +958,6 @@ def plot_xes_func(uargs):
     None
     '''
     import matplotlib.pyplot as plt
-    import matplotlib as mpl
     from . import plotter
     from . import extractor as oe
 
@@ -876,7 +965,8 @@ def plot_xes_func(uargs):
     ut.check_font_envvar()
 
     # Change matplotlib font size to be larger
-    mpl.rcParams.update({'font.size': 12})
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
 
     version = oe.OrcaVersionExtractor.extract(uargs.output_file)
 
@@ -986,7 +1076,6 @@ def plot_xas_func(uargs):
     None
     '''
     import matplotlib.pyplot as plt
-    import matplotlib as mpl
     from . import plotter
     from . import extractor as oe
 
@@ -994,7 +1083,8 @@ def plot_xas_func(uargs):
     ut.check_font_envvar()
 
     # Change matplotlib font size to be larger
-    mpl.rcParams.update({'font.size': 12})
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
 
     version = oe.OrcaVersionExtractor.extract(uargs.output_file)
 
@@ -1098,42 +1188,11 @@ 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):
@@ -1141,6 +1200,10 @@ 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)
@@ -1152,6 +1215,9 @@ 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(
@@ -1177,6 +1243,9 @@ 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,
@@ -1186,10 +1255,12 @@ 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 '
@@ -1197,9 +1268,11 @@ 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
@@ -1222,7 +1295,8 @@ def plot_abs_func(uargs, save_data_only=False):
             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
@@ -1233,6 +1307,8 @@ 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
@@ -1247,7 +1323,7 @@ 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,
@@ -1255,12 +1331,12 @@ 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
@@ -1286,33 +1362,98 @@ 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
 
-    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')
+    # Plot all spectra
+    import matplotlib.pyplot as plt
+    import matplotlib.colors as mcolors
 
-        if _SHOW_CONV[uargs.plot]:
-            plt.show()
+    # Set font name and size
+    ut.check_font_envvar()
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
+    plt.rcParams['legend.loc'] = 'center right'
+
+    # 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()
 
     return
 
@@ -1330,7 +1471,7 @@ def plot_ir_func(uargs):
     -------
     None
     '''
-    import matplotlib as mpl
+    import matplotlib.pyplot as plt
     from . import plotter
     from . import extractor as oe
 
@@ -1338,7 +1479,8 @@ def plot_ir_func(uargs):
     ut.check_font_envvar()
 
     # Change matplotlib font size to be larger
-    mpl.rcParams.update({'font.size': 12})
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
 
     # Extract frequency information
     data = oe.FrequencyExtractor.extract(uargs.output_file)
@@ -1725,12 +1867,14 @@ def plot_susc_func(uargs) -> 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})
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
 
     # Extract data from file
     data = oe.SusceptibilityExtractor.extract(uargs.output_file)
@@ -1754,7 +1898,8 @@ def plot_susc_func(uargs) -> None:
         exp_data = {'Temperature (K)': [], 'chi*T (cm3*K/mol)': []}
         with open(uargs.exp_file, newline='') as csvfile:
             reader = csv.DictReader(
-                row for row in csvfile if not row.startswith('#')
+                [row for row in csvfile if not row.startswith('#')],
+                skipinitialspace=True
             )
             for row in reader:
                 exp_data['Temperature (K)'].append(
@@ -1836,12 +1981,14 @@ def plot_ailft_func(uargs) -> None:
         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})
+    plt.rcParams['font.size'] = 10
+    plt.rcParams['legend.fontsize'] = 9
 
     # Create extractor
     data = oe.AILFTOrbEnergyExtractor.extract(uargs.output_file)
@@ -2151,6 +2298,89 @@ def read_args(arg_list=None):
         )
     )
 
+    gen_orbs = gen_parser.add_parser(
+        'orbs',
+        aliases=['orbitals', 'mos', 'mo'],
+        description='Generate molecular orbital cube file(s) from gbw file', # noqa
+        usage=ut.cstring(
+            'orto gen orbs <gbw_file> <orbs> <n_procs> [options]',
+            'cyan'
+        ),
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+    gen_orbs._positionals.title = 'Mandatory Arguments'
+    gen_orbs.set_defaults(func=gen_orbs_func)
+
+    gen_orbs.add_argument(
+        'gbw_file',
+        type=pathlib.Path,
+        help='Orca gbw file name'
+    )
+
+    gen_orbs.add_argument(
+        'orb_numbers',
+        type=int,
+        nargs='+',
+        help=(
+            'Orbital number(s) to generate cube file for'
+            '(these are alpha spin by default)'
+        )
+    )
+
+    gen_orbs.add_argument(
+        'n_procs',
+        type=int,
+        help='Number of processors/cores used in calculation',
+        default=1
+    )
+
+    gen_orbs.add_argument(
+        '--n_pts',
+        '-n',
+        type=int,
+        default=100,
+        help=(
+            'Number of points in each dimension of cube file\n'
+            'Default: %(default)s'
+        )
+    )
+
+    gen_orbs.add_argument(
+        '--memory',
+        '-mem',
+        type=int,
+        default=500,
+        help=(
+            'Per-core Memory to use in MB\n'
+            'Default: %(default)s'
+        )
+    )
+
+    gen_orbs.add_argument(
+        '-om',
+        '--orca_load',
+        type=str,
+        default='',
+        help='Orca environment module (overrides ORTO_ORCA_LOAD envvar)'
+    )
+
+    gen_orbs.add_argument(
+        '--beta',
+        action='store_true',
+        help=(
+            'Plot beta orbitals instead of alpha (for open shell calculations)'
+        )
+    )
+
+    gen_orbs.add_argument(
+        '--no_sub',
+        '-ns',
+        action='store_true',
+        help=(
+            'Disables submission of job to queue'
+        )
+    )
+
     gen_spden = gen_parser.add_parser(
         'spdens',
         aliases=['spin_density', 'spden'],
@@ -2604,12 +2834,13 @@ 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-1.11.2 → orto-1.12.0}/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()
@@ -143,18 +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 $f_\mathregular{osc}$')
@@ -218,6 +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()
@@ -261,13 +278,18 @@ def plot_chit(chit: ArrayLike, temps: ArrayLike, fields: ArrayLike = None,
     Returns
     -------
     plt.Figure
-        Matplotlib Figure object
+        Matplotlib Figure objectwidth
     plt.Axes
         Matplotlib Axis object for plot
     ''' # noqa
 
     # Create figure and axes
-    fig, ax = plt.subplots(1, 1, figsize=(5, 4), num=window_title)
+    fig, ax = plt.subplots(
+        1,
+        1,
+        figsize=(4 * (1 + np.sqrt(5))/2, 4),
+        num=window_title
+    )
 
     if fields is None:
         # Plot data as it is

{orto-1.11.2 → orto-1.12.0}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.2
+Version: 1.12.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.11.2 → orto-1.12.0}/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__ = '1.11.2'
+__version__ = '1.12.0'
 
 setuptools.setup(
     name='orto',

orto-1.11.2/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '1.11.2'