orto 1.9.0__py3-none-any.whl → 1.10.0__py3-none-any.whl

orto/__version__.py

@@ -1 +1 @@
-__version__ = '1.9.0'
+__version__ = '1.10.0'

orto/cli.py

@@ -217,9 +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):

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-1.9.0.dist-info → orto-1.10.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orto
-Version: 1.9.0
+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-1.9.0.dist-info/RECORD

@@ -1,17 +0,0 @@
-orto/__init__.py,sha256=IedlltYr3qYZxChNUdz62qogXA9Pos_MUvXdGXqAa0E,41
-orto/__version__.py,sha256=w-88NSa4AsKUbL8rYWL8WNyh9CtUgEFkmfF69cJJ9ic,22
-orto/cli.py,sha256=i59s8-WthfZPYsHJDPWdMQfZ8ABCJJ8n5loieLeJVCA,86106
-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=tDiz9omFwinoYJamgz66MZez0Ee9HMhuCIAeHMhXRF8,5916
-orto/plotter.py,sha256=_t9bow6sUMoRAvD6gVFGJTc-_ifW7RmeR0JAPWK_lm4,17799
-orto/utils.py,sha256=GcMZ9uebOSnkPQT_U5O0X49LUtTu8YpXZxEsNKgXNTY,9838
-orto-1.9.0.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
-orto-1.9.0.dist-info/METADATA,sha256=v6KwljenLuZNETfGZexfXCkb7ECRGHFK2N7tJoat6bs,1184
-orto-1.9.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-orto-1.9.0.dist-info/entry_points.txt,sha256=HXenCglMp_03JkN34pK2phkjXK9CFcXTGHKv5QaVY8I,39
-orto-1.9.0.dist-info/top_level.txt,sha256=hQ-z28gTN_FZ2B5Kiwxr_9cUTcCoib9W5HjbkceDXw4,5
-orto-1.9.0.dist-info/RECORD,,