orto 1.8.3__py3-none-any.whl → 1.10.0__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.8.3'
+__version__ = '1.10.0'

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
@@ -216,9 +217,16 @@ def extract_gmatrix_func(uargs, save=True):
         'L': oe.GMatrixLExtractor,
         'S': oe.GMatrixSExtractor,
         'eff': oe.GMatrixEffectiveExtractor,
+        'dft': oe.GMatrixDFTExtractor
     }
 
-    all_data = choices[uargs.type]().extract(uargs.output_file)
+    if oe.EPRNMRDetector(uargs.output_file):
+        uargs.type = 'dft'
+
+    try:
+        all_data = choices[uargs.type]().extract(uargs.output_file)
+    except (DataFormattingError, ValueError) as e:
+        ut.red_exit(str(e))
 
     if not save:
         for it, data in enumerate(all_data):
@@ -329,6 +337,86 @@ 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 +1737,7 @@ 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 +1907,71 @@ 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 +2518,7 @@ 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/extractor.py

@@ -14,6 +14,19 @@ from .exceptions import DataFormattingError
 from . import constants as const
 
 
+def EPRNMRDetector(file_name: str | pathlib.Path) -> bool:
+    '''
+    Detects if Orca output file is from EPR/NMR calculation
+    '''
+    with open(file_name, 'rb') as f:
+        file_content = f.read()
+
+    if re.search(rb'%EPRNMR', file_content):
+        return True
+    else:
+        return False
+
+
 class OrcaVersionExtractor(extto.LineExtractor):
     '''
     Extracts Orca version from output file
@@ -2421,6 +2434,100 @@ class SimpleInputExtractor(extto.LineExtractor):
         return _ext.data
 
 
+class GMatrixDFTExtractor(extto.BetweenExtractor):
+    '''
+    Extracts DFT ELECTRONIC G-MATRIX block from output file
+    '''
+
+    # Regex Start Pattern
+    START_PATTERN = rb'(?<=ELECTRONIC G-MATRIX\s[\S\s]{19}\s)'
+
+    # Regex End Pattern
+    END_PATTERN = rb'(?=EPR g-tensor done in)'
+
+    @property
+    def data(self) -> dict[str, NDArray]:
+        '''
+        G Matrix data:\n
+        A dictionary with keys:\n
+            matrix\n
+            values\n
+            vectors
+        All values are ndarray of floats
+        '''
+        return self._data
+
+    @staticmethod
+    def _process_block(block: str) -> dict[str, NDArray]:
+        '''
+        Converts single block into data entries described in self.data
+
+        Parameters
+        ----------
+        block: str
+            String block extracted from file
+
+        Returns
+        -------
+        dict[str, NDArray]
+        '''
+
+        # Trim block to lines after Orientation:
+
+        block = block.split('The g-matrix:')[-1]
+
+        # Get Matrix
+        _matrix = re.findall(
+            r'(\s-?\d\.\d{7}\s+-?\d\.\d{7}\s+-?\d\.\d{7})',
+            block
+        )[:3]
+
+        # Convert to matrix of floats
+        matrix = np.asarray([
+            [float(v) for v in val.split()]
+            for val in _matrix
+        ])
+
+        if matrix.shape != (3, 3):
+            raise DataFormattingError(
+                'G-matrix is not the correct shape (3x3)'
+            )
+
+        # Diagonalise g.g^T
+        vals, vecs = la.eigh(matrix @ matrix.T)
+
+        # get g values as sqrt of eigenvalues of g.g^T
+        vals = np.sqrt(vals)
+
+        data = {
+            'matrix': matrix,
+            'values': vals,
+            'vectors': vecs
+        }
+
+        return data
+
+    @classmethod
+    def extract(cls, file_name: str | pathlib.Path) -> list[dict[str, NDArray]]: # noqa
+        '''
+        Convenience method which instantiates class, extracts blocks, and
+        returns processed datasets
+
+        Parameters
+        ----------
+        file_name: str | pathlib.Path
+            File to parse
+
+        Returns
+        -------
+        list[dict[str, NDArray]]
+            Each entry contains processed data, as defined in cls.data
+        '''
+        _ext = cls()
+        _ext(file_name, process=True)
+        return _ext.data
+
+
 class GMatrixExtractor(extto.BetweenExtractor):
     '''
     Extracts ELECTRONIC G-MATRIX block from output file
@@ -2471,6 +2578,11 @@ class GMatrixExtractor(extto.BetweenExtractor):
             for val in _matrix
         ])
 
+        if matrix.shape != (3, 3):
+            raise DataFormattingError(
+                'G-matrix is not the correct shape (3x3)'
+            )
+
         # Diagonalise g.g^T
         vals, vecs = la.eigh(matrix @ matrix.T)
 

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.dist-info → orto-1.10.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.8.3
+Version: 1.10.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow

orto-1.10.0.dist-info/RECORD

@@ -0,0 +1,17 @@
+orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
+orto/__version__.py,sha256=ZXE8njb1SRoMJuadNA6KRGRdfAFsM49XLsgr_fSOXts,23
+orto/cli.py,sha256=XBeO5dTWaZP_mnNA5IR2eZBcnhHEtwW6IuFtLgUPMkA,86309
+orto/constants.py,sha256=anxaiTykO8Q_CXliR7zuOAdnXZrQ2-C4ndaviyl7kGc,419
+orto/data.py,sha256=960LHFeG7l626X_WA-8YxvG2toNAsgNvLo86OoYAmBY,14910
+orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
+orto/extractor.py,sha256=oqRdDWLaVPIwB4aZ5nrITWexx60hKn0zghACmymwVfM,80618
+orto/input.py,sha256=uUQV6A-8D0GZpRoY1rKK_aUPmk9kVVTnMzTHuisP5t4,11888
+orto/job.py,sha256=tDiz9omFwinoYJamgz66MZez0Ee9HMhuCIAeHMhXRF8,5916
+orto/plotter.py,sha256=_t9bow6sUMoRAvD6gVFGJTc-_ifW7RmeR0JAPWK_lm4,17799
+orto/utils.py,sha256=GcMZ9uebOSnkPQT_U5O0X49LUtTu8YpXZxEsNKgXNTY,9838
+orto-1.10.0.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
+orto-1.10.0.dist-info/METADATA,sha256=2qdWW5pyurXxTVD-6GXUSvuxZhLJ2BTbkGUtDdPJVoQ,1185
+orto-1.10.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.10.0.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.10.0.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.10.0.dist-info/RECORD,,

orto-1.8.3.dist-info/RECORD

@@ -1,17 +0,0 @@
-orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-orto/__version__.py,sha256=U3WnIim1rPfsaJ6EKERUuRl6DH-DG8tqNKxxzBZArOA,22
-orto/cli.py,sha256=DIEcU9jMP5BPtItaDmb6vS00GJa8amoBxUwUsu6nhrQ,82209
-orto/constants.py,sha256=anxaiTykO8Q_CXliR7zuOAdnXZrQ2-C4ndaviyl7kGc,419
-orto/data.py,sha256=960LHFeG7l626X_WA-8YxvG2toNAsgNvLo86OoYAmBY,14910
-orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
-orto/extractor.py,sha256=S27297-gasqLaLbMOqW9sj1X0U0mr3OjikxHcz9Es3o,77867
-orto/input.py,sha256=uUQV6A-8D0GZpRoY1rKK_aUPmk9kVVTnMzTHuisP5t4,11888
-orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
-orto/plotter.py,sha256=_t9bow6sUMoRAvD6gVFGJTc-_ifW7RmeR0JAPWK_lm4,17799
-orto/utils.py,sha256=GcMZ9uebOSnkPQT_U5O0X49LUtTu8YpXZxEsNKgXNTY,9838
-orto-1.8.3.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
-orto-1.8.3.dist-info/METADATA,sha256=fokjznTSffyKFIn8KxX5G3iItEjjDqMNvbsacMNAukY,1184
-orto-1.8.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orto-1.8.3.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
-orto-1.8.3.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
-orto-1.8.3.dist-info/RECORD,,