orto 1.11.3__tar.gz → 1.12.0__tar.gz

{orto-1.11.3 → orto-1.12.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.3
+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-1.11.3 → 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)
 
@@ -1102,7 +1192,6 @@ def plot_abs_func(uargs, save_data_only=False):
     from . import extractor as oe
     from . import data as d
 
-
     # Process x_shift argument
     if uargs.x_shift is None:
         uargs.x_shift = [0.0 for _ in uargs.output_file]
@@ -1280,12 +1369,12 @@ def plot_abs_func(uargs, save_data_only=False):
     if save_data_only:
         return
 
-    ## Plot all spectra
+    # Plot all spectra
     import matplotlib.pyplot as plt
     import matplotlib.colors as mcolors
 
     # Set font name and size
-    plt.rcParams['font.family'] = 'Arial'
+    ut.check_font_envvar()
     plt.rcParams['font.size'] = 10
     plt.rcParams['legend.fontsize'] = 9
     plt.rcParams['legend.loc'] = 'center right'
@@ -1382,7 +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
 
@@ -1390,7 +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)
@@ -1777,12 +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)
@@ -1806,7 +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(
@@ -1888,12 +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)
@@ -2203,6 +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'],

{orto-1.11.3 → orto-1.12.0}/orto/plotter.py

@@ -278,13 +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-1.11.3 → orto-1.12.0}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.11.3
+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-1.11.3 → 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__ = '1.11.3'
+__version__ = '1.12.0'
 
 setuptools.setup(
     name='orto',

orto-1.11.3/orto/__version__.py

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