orto 1.0.6__py3-none-any.whl → 1.2.0__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.0.6'
+__version__ = '1.2.0'

orto/cli.py

@@ -464,7 +464,7 @@ def gen_job_func(uargs):
 
         # Check xyz file is present
         try:
-            inp.check_xyz(oj.input_file, uargs.skip_xyz)
+            inp.check_coord(oj.input_file, uargs.skip_xyz)
         except (DataNotFoundError, DataFormattingError) as e:
             ut.red_exit(str(e))
 
@@ -504,6 +504,28 @@ def gen_job_func(uargs):
             # Use orca file value
             config['mem_per_cpu'] = maxcore
 
+        # Check if NBO is requested
+        if inp.get_nbo(oj.input_file):
+            # Check if NBO module has been provided to orto
+            try:
+                if os.getenv('orto_nbo_load') is not None:
+                    nbo_module = os.getenv('orto_nbo_load')
+                else:
+                    ut.red_exit(
+                        'Missing orto_nbo_load environment variable'
+                    )
+            except ValueError:
+                ut.red_exit(
+                    (
+                        'Missing or malformed orto_nbo_load'
+                        'environment variable'
+                    )
+                )
+            oj.pre_orca += f'module load {nbo_module}\n'
+            oj.pre_orca += f'export NBOFIL={oj.input_file.stem}\n'
+        else:
+            nbo_module = None
+
         # Set SLURM error and output file names
         config['error'] = 'slurm.%j.e'
         config['output'] = 'slurm.%j.o'
@@ -835,9 +857,22 @@ def extract_orbs_func(uargs, save=True) -> None:
                 dtype=int
             )
         ])
+    elif uargs.num is not None:
+        keep = uargs.num
     else:
         keep = range(len(contributions))
 
+    # Remove orbital indices which do not exist
+    keep = [val for val in keep if val < len(contributions)]
+
+    if not len(keep):
+        ut.red_exit(
+            (
+                r'Selected orbital indices do not exist!'
+                f'\nNORBS = {len(contributions):d}'
+            )
+        )
+
     contributions = contributions.loc[:, keep]
 
     # Remove contributions from unwanted orbitals
@@ -2058,13 +2093,37 @@ def read_args(arg_list=None):
         )
     )
 
+    def gte_zero(x):
+        '''
+        Custom type for argparse to ensure that the input
+        \nis greater than or equal to zero
+        '''
+        value = int(x)
+        if value < 0:
+            raise argparse.ArgumentTypeError(
+                f'{x} is not a valid index (must be >= 0)'
+            )
+        return value
+
+    orb_group.add_argument(
+        '-n',
+        '--num',
+        nargs='+',
+        type=gte_zero,
+        metavar='NUMBER',
+        default=None,
+        help=(
+            'Print specified orbitals using index starting from 0\n'
+            '(same as Orca)\n'
+        )
+    )
+
     orb_group.add_argument(
         '-hl',
         '--homo_lumo',
         nargs='?',
         type=int,
         metavar='NUMBER',
-        const=0,
         default=None,
         help=(
             'Print specified number of orbitals either side of HOMO and LUMO'

orto/extractor.py

@@ -1880,7 +1880,7 @@ class MOInpExtractor(extto.LineExtractor):
 
 class XYZInputExtractor(extto.LineExtractor):
     '''
-    Extracts .xyz line of an input file
+    Extracts *xyz line of an input file
 
     *xyz charge multiplicity
     '''
@@ -1936,6 +1936,26 @@ class XYZInputExtractor(extto.LineExtractor):
         return _ext.data
 
 
+class IntInputExtractor(XYZInputExtractor):
+    '''
+    Extracts *int line of an input file
+
+    *int charge multiplicity
+    '''
+
+    # Regex pattern for line
+    PATTERN = rb'\* *int *-?\d+ *\d'
+
+    MODIFIERS = [re.IGNORECASE]
+
+    @property
+    def data(self) -> list[str]:
+        '''
+        *int line, one entry per match
+        '''
+        return self._data
+
+
 class MaxCoreInputExtractor(extto.LineExtractor):
     '''
     Extracts maxcore from input file\n
@@ -2006,7 +2026,7 @@ class SimpleInputExtractor(extto.LineExtractor):
     # Regex pattern for line
     PATTERN = rb'^ *!.*'
 
-    MODIFIERS = [re.IGNORECASE]
+    MODIFIERS = [re.IGNORECASE, re.MULTILINE]
 
     @property
     def data(self) -> list[str]:

orto/input.py

@@ -9,6 +9,45 @@ from . import extractor as oe
 from . import utils as ut
 
 
+def get_nbo(file_name: str | Path) -> bool:
+    '''
+    Check if NBO is present in the simple input line.\n
+
+    Parameters
+    ----------
+    file_name: str | Path
+        Orca input file as either name or Path object
+
+    Returns
+    -------
+    bool
+        True if NBO is present, False otherwise
+    '''
+    # Check for simple input line beginning with !
+    try:
+        simple = oe.SimpleInputExtractor.extract(file_name)
+    except DataNotFoundError:
+        ut.red_exit(
+            'Error: Missing simple input line (or !) in input file'
+        )
+    # Check for NBO in simple input
+    nbo_simple = re.findall(
+        r'NBO',
+        simple[0],
+        flags=re.IGNORECASE
+    )
+    if len(nbo_simple):
+        # Set to True if found
+        if nbo_simple is None:
+            _nbo = True
+        else:
+            _nbo = True
+    else:
+        _nbo = False
+
+    return _nbo
+
+
 def get_nprocs(file_name: str | Path) -> int:
     '''
     Get the number of processors from the input file.\n
@@ -124,6 +163,81 @@ def get_maxcore(file_name: str | Path) -> int:
     return maxcore
 
 
+def check_coord(file_name: str | Path, skip_check) -> None:
+    '''
+    Check *xyz, *xyzfile, or *int line is present in input file.\n
+    If xyzfile is given, then also checks if this exists and is formatted \n
+    correctly.\n
+
+    Parameters
+    ----------
+    file_name: str | Path
+        Orca input file as either name or Path object
+    skip_check: bool
+        If True, skip the xyz file check
+
+    Returns
+    -------
+    None
+
+    Raises
+    ------
+    DataNotFoundError
+        If neither *xyzfile, *xyz, nor *int are present in the input file
+    DataFormattingError
+        If xyz file is not formatted correctly
+    '''
+
+    # Get xyz file name and check it exists and is formatted correctly
+    try:
+        xyz_file = oe.XYZFileInputExtractor.extract(file_name)
+    except DataNotFoundError:
+        xyz_file = []
+
+    try:
+        xyzline = oe.XYZInputExtractor.extract(file_name)
+    except DataNotFoundError:
+        xyzline = []
+
+    try:
+        intline = oe.IntInputExtractor.extract(file_name)
+    except DataNotFoundError:
+        intline = []
+
+    lens = [len(xyz_file), len(xyzline), len(intline)]
+
+    if not sum(lens):
+        ut.red_exit(
+            'Error: missing or incorrect *xyzfile or *xyz line in input'
+        )
+    elif sum(lens) > 1:
+        ut.red_exit(
+            (
+                'Error: multiple *xyzfile or *xyz lines in input.\n'
+                'Only one can be present'
+            )
+        )
+
+    if len(xyz_file):
+        xyz_file = Path(xyz_file[0])
+        if not xyz_file.is_file():
+            ut.red_exit(
+                'Error: xyz file specified in input cannot be found'
+            )
+
+        if not skip_check:
+            try:
+                xyzp.check_xyz(
+                    xyz_file.absolute(),
+                    allow_indices=False
+                )
+            except xyzp.XYZError as e:
+                raise DataFormattingError(
+                    f'{e}\n Use -sx to skip this check at your peril'
+                )
+    return
+
+
 def check_xyz(file_name: str | Path, skip_check) -> None:
     '''
     Check *xyz or *xyzfile line is present in input file.\n

{orto-1.0.6.dist-info → orto-1.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.0.6
+Version: 1.2.0
 Summary: A package to make life easier when performing Orca calculations.
 Home-page: https://orto.kragskow.group
 Author: Jon Kragskow
@@ -15,7 +15,7 @@ Description-Content-Type: text/markdown
 Requires-Dist: numpy>=2.1.2
 Requires-Dist: xyz_py>=5.13.1
 Requires-Dist: matplotlib>=3.9.2
-Requires-Dist: extto>=0.5.0
+Requires-Dist: extto>=1.0.1
 Requires-Dist: pandas>=2.2.3
 Requires-Dist: subto>=0.1.1
 Requires-Dist: python-docx>=1.1.2

orto-1.2.0.dist-info/RECORD

@@ -0,0 +1,15 @@
+orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
+orto/__version__.py,sha256=U3f_Jgr3zpgiYG2kLcvcT05TQsVzN9Kktg_f3Q9OZFA,22
+orto/cli.py,sha256=AJEQtMXw4uODLZpTgiBu3jz5l6VDU9kSWc5r3e0Zxss,63122
+orto/constants.py,sha256=2obWYg306Lce4U9Qs4MHg1yZq7SHFkazG-cnkD5svpo,343
+orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
+orto/extractor.py,sha256=aeZK130lBIERS4Pj1jvTlxCwVB_AhFLUB16zQrDhcbM,67767
+orto/input.py,sha256=N8JbySSVEC_qmXZ7ppJsZ7Z1qel6PfalGYRtnX1hJ6U,9900
+orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
+orto/plotter.py,sha256=ICrO03T_HGe-H1XKZ2qzsKYdPY44E0PKiXqIQQawd7I,15633
+orto/utils.py,sha256=gVfGplkfc6xGYgLMi_7I_yAdWG-QKRaqQdy9v5F4Mck,7279
+orto-1.2.0.dist-info/METADATA,sha256=rH_vzAEMyJpQc9mJ_3T_q8OeielkInXjdfxrQwIWGdE,1140
+orto-1.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+orto-1.2.0.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
+orto-1.2.0.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
+orto-1.2.0.dist-info/RECORD,,

orto-1.0.6.dist-info/RECORD

@@ -1,15 +0,0 @@
-orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-orto/__version__.py,sha256=iNeZ6LZ9iCV_ugsqAh5K1fFqbKkfU8o3NbLYBWI3m1I,22
-orto/cli.py,sha256=S05ypFp4NEv1ZVaa4xTSz_oTrAeVwpL1rd8qNRviz8A,61349
-orto/constants.py,sha256=2obWYg306Lce4U9Qs4MHg1yZq7SHFkazG-cnkD5svpo,343
-orto/exceptions.py,sha256=D7oNeAEGeJNt5thzt6PaCn5FY6JcbJOWUE1N1LVhhuE,159
-orto/extractor.py,sha256=tO2oFf6Cgwdnh_m1v8r1rXQO2_FL7s-1KBqLPy6zNco,67384
-orto/input.py,sha256=DGWG0IQ_QS9RCm4BlgFPyt4_WW6Tz9k2Mybwd1O9SJo,7003
-orto/job.py,sha256=SM0nlc_bqhhPvfuuykhMvaUnkwC3Gp-6RvYw_a0TyGc,5855
-orto/plotter.py,sha256=ICrO03T_HGe-H1XKZ2qzsKYdPY44E0PKiXqIQQawd7I,15633
-orto/utils.py,sha256=gVfGplkfc6xGYgLMi_7I_yAdWG-QKRaqQdy9v5F4Mck,7279
-orto-1.0.6.dist-info/METADATA,sha256=CxH6biskRO90R3ezsXOGAQiViTuYV0uRWnoTQ6PrnYw,1140
-orto-1.0.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orto-1.0.6.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
-orto-1.0.6.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
-orto-1.0.6.dist-info/RECORD,,