orto 1.8.3__tar.gz → 1.9.0__tar.gz

{orto-1.8.3 → orto-1.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.8.3
+Version: 1.9.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.9.0/orto/__version__.py

@@ -0,0 +1 @@
+__version__ = '1.9.0'

{orto-1.8.3 → orto-1.9.0}/orto/cli.py

@@ -11,6 +11,7 @@ import numpy as np
 import re
 from mmap import mmap, ACCESS_READ
 from shutil import move as shutilmove
+from subto.job import SlurmJob
 
 from . import job
 from . import utils as ut
@@ -329,6 +330,86 @@ def extract_gmatrix_func(uargs, save=True):
     return
 
 
+def gen_spden_func(uargs):
+    '''
+    Wrapper for CLI gen spin density call
+
+    Parameters
+    ----------
+    uargs : argparser object
+        User arguments
+
+    Returns
+    -------
+    None
+    '''
+
+    # 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\\n3\\ny\\n4'
+    command_nums += f'\\n{uargs.n_pts:d}'
+    command_nums += '\\n5\\n7\\n11\\n12\\n'
+
+    # Generate job file for orca_plot
+    spin_job = SlurmJob(
+        pathlib.Path(f'{uargs.gbw_file.stem}_spin_density_job.sh')
+    )
+
+    # Create content of job
+    spin_job.content_block = ''
+
+    spin_job.content_block += '# Load orca module\n'
+    spin_job.content_block += f'module load {orca_load_val}\n'
+    spin_job.content_block += '# Run orca_plot to generate spin density cube file\n' # noqa
+    spin_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
+    spin_job.job_name = f'{uargs.gbw_file.stem}_spin_density'
+
+    spin_job.ntasks_per_node = str(uargs.n_procs)
+    spin_job.mem_per_cpu = str(uargs.memory)
+
+    spin_job.error = f'{uargs.gbw_file.stem}_spin_density.%j.e'
+    spin_job.output = f'{uargs.gbw_file.stem}_spin_density.%j.o'
+
+    # Write job script
+    # with submitter configuration options specified
+    spin_job.write_script(True)
+
+    # Submit to queue
+    if not uargs.no_sub:
+        subprocess.call(
+            'cd {}; {} "{}"; cd ../'.format(
+                uargs.gbw_file.parents[0],
+                spin_job.SUBMIT_COMMAND,
+                spin_job.file_path
+                ),
+            shell=True
+        )
+
+    return
+
+
 def gen_trunc_molden_func(uargs):
     '''
     Wrapper for CLI gen truncmolden call
@@ -1649,6 +1730,7 @@ def read_args(arg_list=None):
 
     extract_coords = extract_parser.add_parser(
         'coords',
+        aliases=['coord'],
         description='Extracts coordinates from Orca output file',
         formatter_class=argparse.RawTextHelpFormatter,
         usage=ut.cstring('orto extract coords <output_file> [options]', 'cyan')
@@ -1818,6 +1900,71 @@ def read_args(arg_list=None):
         )
     )
 
+    gen_spden = gen_parser.add_parser(
+        'spdens',
+        aliases=['spin_density', 'spden'],
+        description='Generate spin density cube file from gbw file', # noqa
+        usage=ut.cstring(
+            'orto gen spdens <gbw_file> <n_procs> [options]',
+            'cyan'
+        ),
+        formatter_class=argparse.RawTextHelpFormatter
+    )
+    gen_spden._positionals.title = 'Mandatory Arguments'
+    gen_spden.set_defaults(func=gen_spden_func)
+
+    gen_spden.add_argument(
+        'gbw_file',
+        type=pathlib.Path,
+        help='Orca gbw file name'
+    )
+
+    gen_spden.add_argument(
+        'n_procs',
+        type=int,
+        help='Number of processors/cores used in calculation',
+        default=1
+    )
+
+    gen_spden.add_argument(
+        '--n_pts',
+        '-n',
+        type=int,
+        default=100,
+        help=(
+            'Number of points in each dimension of cube file\n'
+            'Default: %(default)s'
+        )
+    )
+
+    gen_spden.add_argument(
+        '--memory',
+        '-mem',
+        type=int,
+        default=500,
+        help=(
+            'Per-core Memory to use in MB\n'
+            'Default: %(default)s'
+        )
+    )
+
+    gen_spden.add_argument(
+        '-om',
+        '--orca_load',
+        type=str,
+        default='',
+        help='Orca environment module (overrides ORTO_ORCA_LOAD envvar)'
+    )
+
+    gen_spden.add_argument(
+        '--no_sub',
+        '-ns',
+        action='store_true',
+        help=(
+            'Disables submission of job to queue'
+        )
+    )
+
     gen_job = gen_parser.add_parser(
         'job',
         description=(
@@ -2364,6 +2511,7 @@ def read_args(arg_list=None):
 
     plot_ailft = plot_parser.add_parser(
         'ailft_orbs',
+        aliases=['ailft_orb'],
         description='Plots AI-LFT orbital energies from output file',
         usage=ut.cstring(
             'orto plot ailft_orbs <output_file> [options]',

{orto-1.8.3 → orto-1.9.0}/orto/job.py

@@ -29,7 +29,7 @@ class OrcaJob():
         Orca output file name. Default is same as input with extension \n
         replaced by .out
     job_file: pathlib.Path
-        Submission script name. Default is same as input with extension \n
+        Submission script file path. Default is same as input with extension \n
         replaced by scheduler job file extension e.g. '.slm'
     job_name: str
         Job name. Default is same as input without extension
@@ -99,6 +99,9 @@ class OrcaJob():
 
     @property
     def job_file(self) -> pathlib.Path:
+        '''
+        The submission script file path
+        '''
         return self._job_file
 
     @job_file.setter
@@ -164,7 +167,7 @@ class OrcaJob():
         verbose: bool, default True
             If True, jobscript location is written to screen
         **kwargs
-            The keyword arguments are passed to `subto.job.Job` constructor
+            Keyword arguments passed to `subto.job.Job` constructor
         '''
 
         if len(self.load):

{orto-1.8.3 → orto-1.9.0}/orto.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.8.3
+Version: 1.9.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

{orto-1.8.3 → orto-1.9.0}/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__ = '1.8.3'
+__version__ = '1.9.0'
 
 setuptools.setup(
     name='orto',

orto-1.8.3/orto/__version__.py

@@ -1 +0,0 @@
-__version__ = '1.8.3'