ipyvasp 0.9.88__tar.gz → 0.9.90__tar.gz

{ipyvasp-0.9.88 → ipyvasp-0.9.90}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.88
+Version: 0.9.90
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

ipyvasp-0.9.90/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.9.90"

{ipyvasp-0.9.88 → ipyvasp-0.9.90}/ipyvasp/bsdos.py

@@ -200,6 +200,14 @@ class _BandsDosBase:
     def data(self):
         "Returns a dictionary of information about the picked data after a plotting function called."
         return self._data
+    
+    def get_skipk(self):
+        "Returns number of first few skipped kpoints in bandstructure plot in case of HSE calculations."
+        return self.source.get_skipk()
+    
+    def set_skipk(self, skipk):
+        "Set/reset to skip first kpoints in bandstructure plot in case of HSE calculations."
+        self.source.set_skipk(skipk)
 
     def _fix_projections(self, projections):
         labels, spins, atoms, orbs, uspins, uatoms, uorbs = (

{ipyvasp-0.9.88 → ipyvasp-0.9.90}/ipyvasp/core/parser.py

@@ -16,8 +16,11 @@ class DataSource:
     """Base class for all data sources. It provides a common interface to access data from different sources.
     Subclass it to get data from a source and implement the abstract methods."""
 
-    def __init__(self, path):
+    def __init__(self, path, skipk=None):
         self._path = Path(path).absolute()
+        self._skipk = (
+            skipk if isinstance(skipk, (int, np.integer)) else self._read_skipk()
+        )
         if not self._path.is_file():
             raise FileNotFoundError("File: '{}'' does not exist!".format(path))
         self._summary = self.get_summary()  # summary data is read only once
@@ -76,7 +79,23 @@ class DataSource:
         raise NotImplementedError(
             "`get_structure` should be implemented in a subclass. See Vasprun.get_structure as example."
         )
-
+    
+    def _read_skipk(self):
+        raise NotImplementedError(
+            "`_read_skipk` should be implemented in a subclass. See Vasprun._read_skipk as example."
+        )
+    
+    def get_skipk(self):
+        "Returns the number of first few k-points to skip in band structure plot in case of HSE calculation."
+        return self._skipk
+    
+    def set_skipk(self, skipk):
+        "Set the number of first few k-points to skip in band structure plot in case of HSE calculation."
+        if isinstance(skipk, (int, np.integer)):
+            self._skipk = skipk
+        else:
+            raise TypeError("skipk should be an integer to skip first few random kpoints.")
+        
     def get_kpoints(self):
         raise NotImplementedError(
             "`get_kpoints` should be implemented in a subclass. See Vasprun.get_kpoints as example."
@@ -111,7 +130,8 @@ class Vaspout(DataSource):
     dos = DataSource.dos
     bands = DataSource.bands
 
-    def __init__(self, path):
+    def __init__(self, path, skipk=None):
+        # super().__init__(path, skipk)
         raise NotImplementedError("Vaspout is not implemented yet.")
 
 def read(file, start_match, stop_match=r'\n', nth_match=1, skip_last=False,apply=None):
@@ -153,10 +173,7 @@ class Vasprun(DataSource):
     bands = DataSource.bands
 
     def __init__(self, path="./vasprun.xml", skipk=None):
-        super().__init__(path)
-        self._skipk = (
-            skipk if isinstance(skipk, (int, np.integer)) else self.get_skipk()
-        )
+        super().__init__(path, skipk)
 
     def read(self, start_match, stop_match=r'\n', nth_match=1, skip_last=False,apply=None):
         """Reads a part of the file between start_match and stop_match and returns a generator. It is lazy and fast.
@@ -167,7 +184,7 @@ class Vasprun(DataSource):
         kws = {k:v for k,v in locals().items() if k !='self'}
         return read(self.path,**kws)
 
-    def get_skipk(self):
+    def _read_skipk(self):
         "Returns the number of k-points to skip in band structure plot in case of HSE calculation."
         weights = np.fromiter(
             (
@@ -199,8 +216,9 @@ class Vasprun(DataSource):
                 ).iter("v")
             ]
         )
-        info_dict["NBANDS"] = int( # Bad initializations, read last one
-            ET.fromstring(list(self.read("<i.*NBANDS", "</i>"))[-1]).text 
+        _nbands = [*self.read("<i.*NBANDS[\"\']", "</i>"),*self.read("<i.*NBANDS[\"\']", "</i>",nth_match=2)]
+        info_dict["NBANDS"] = int( # Bad initializations of NBANDS, read last one
+            ET.fromstring(_nbands[-1]).text 
         )
         info_dict["NELECTS"] = int(
             float(ET.fromstring(next(self.read("<i.*NELECT", "</i>"))).text)

{ipyvasp-0.9.88 → ipyvasp-0.9.90}/ipyvasp/evals_dataframe.py

@@ -66,7 +66,7 @@ class EvalsDataFrame(pd.DataFrame):
     source : DataSource
         Data source to collect data from. Could be ``ipyvasp.Vasprun`` or ``ipyvasp.Vaspout``.  Alternatively you can use ``DataSource.get_dataframe`` method to get dataframe directly.
     spins : list
-
+        of spin indices [zero based here], In output data frame you will see corresponding spin number based on full data.
     bands : list
         of band indices [zero based here], In output data frame you will see corresponding band number based on full data.
     atoms : list

{ipyvasp-0.9.88 → ipyvasp-0.9.90}/ipyvasp/utils.py

@@ -42,7 +42,7 @@ def take(f, rows, cols=None, dtype=None, exclude=None,sep=None):
     Negative indexing is not supported in cols because of variable length of each line.
     If `cols=None`, returns a single str of line if one integer given, otherwise a list of lines.
     If `cols` is int ot sequence of int, each line is splitted by `sep` (default all whitespaces) and `dtype` is applied over resulting fields.
-    `exclude` should be regex. It removes lines after selection by `rows`.
+    `exclude` should be regex. It removes matching lines after selection by `rows`. Empty lines are also discarded if `cols` is given.
 
     Returns list (nested or plain) or single value or None based on `rows` and `cols` selection.
 
@@ -86,7 +86,7 @@ def take(f, rows, cols=None, dtype=None, exclude=None,sep=None):
     if exclude:
         lines = (l for l in lines if not re.search(exclude,l))
     
-    if cols:
+    if cols is not None:
         conv = dtype if callable(dtype) else (lambda v: v)
         return_col = False
         if isinstance(cols, int):
@@ -96,6 +96,7 @@ def take(f, rows, cols=None, dtype=None, exclude=None,sep=None):
         if not isinstance(cols, (list,tuple, range)):
             raise TypeError(f"cols should be a sequce of integers or single int, got {type(cols)}")
         
+        lines = (l for l in lines if l.strip()) # remove empty lines after indexing and only if cols are given
         lines = ([conv(v) for i, v in enumerate(l.split(sep)) if i in cols] for l in lines)
         
         if return_col:

{ipyvasp-0.9.88 → ipyvasp-0.9.90}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.88
+Version: 0.9.90
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

ipyvasp-0.9.88/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.9.88"