ipyvasp 0.9.89__tar.gz → 0.9.91__tar.gz

{ipyvasp-0.9.89 → ipyvasp-0.9.91}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.89
+Version: 0.9.91
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -20,7 +20,7 @@ Requires-Dist: scipy==1.9.1
 Requires-Dist: ipywidgets>=8.0.4
 Requires-Dist: pillow>=9.3.0
 Requires-Dist: pandas==1.4.4
-Requires-Dist: plotly==5.14.1
+Requires-Dist: plotly==6.0.1
 Requires-Dist: requests==2.28.1
 Requires-Dist: typer==0.9.0
 Provides-Extra: extra

ipyvasp-0.9.91/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.9.91"

{ipyvasp-0.9.89 → ipyvasp-0.9.91}/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-0.9.89 → ipyvasp-0.9.91}/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-0.9.89 → ipyvasp-0.9.91}/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-0.9.89 → ipyvasp-0.9.91}/ipyvasp/widgets.py

@@ -100,6 +100,7 @@ def fix_signature(cls):
     cls.__signature__ = inspect.signature(cls.__init__)
     return cls
 
+@fix_signature
 class Files:
     """Creates a Batch of files in a directory recursively based on glob pattern or given list of files.
     This is a boilerplate abstraction to do analysis in multiple calculations simultaneously.
@@ -675,8 +676,9 @@ class BandsWidget(VBox):
             description="Style", options=["plotly_white", "plotly_dark"]
         )
         self._click = Dropdown(description="Click", options=["None", "vbm", "cbm"])
-        self._ktcicks = Text(description="kticks")
+        self._ktcicks = Text(description="kticks", tooltip="0 index maps to minimum value of kpoints slider.")
         self._brange = ipw.IntRangeSlider(description="bands",min=1, max=1) # number, not index
+        self._krange = ipw.IntRangeSlider(description="kpoints",min=0, max=1,value=[0,1], tooltip="Includes non-zero weight kpoints") 
         self._ppicks = PropsPicker(
             on_button_click=self._update_graph, on_selection_changed=self._warn_update
         )
@@ -690,6 +692,7 @@ class BandsWidget(VBox):
             free_widgets=[
                 self._tsd,
                 self._brange,
+                self._krange,
                 self._ktcicks,
                 ipw.HTML("<hr/>"),
                 self._ppicks,
@@ -702,6 +705,7 @@ class BandsWidget(VBox):
         self._tsd.observe(self._change_theme, "value")
         self._click.observe(self._click_save_data, "value")
         self._ktcicks.observe(self._warn_update, "value")
+        self._krange.observe(self._set_krange, "value")
         self._brange.observe(self._warn_update, "value")
 
     @property
@@ -722,9 +726,17 @@ class BandsWidget(VBox):
                 vp.Vasprun(path) if path.parts[-1].endswith('xml') else vp.Vaspout(path)
             ).bands
             self._ppicks.update(self.bands.source.summary)
-            self._ktcicks.value = ", ".join(
+
+            self._krange.max = self.bands.source.summary.NKPTS - 1
+            self._krange.tooltip = f"Includes {self.bands.source.get_skipk()} non-zero weight kpoints"
+            self.bands.source.set_skipk(0) # full range to view for slider flexibility after fix above
+
+            self._kwargs['kpairs'] = [self._krange.value,]
+            if (ticks := ", ".join(
                 f"{k}:{v}" for k, v in self.bands.get_kticks()
-            )
+            )): # Do not overwrite if empty
+                self._ktcicks.value = ticks
+            
             self._brange.max = self.bands.source.summary.NBANDS
             if self.bands.source.summary.LSORBIT:
                 self._click.options = ["None", "vbm", "cbm", "so_max", "so_min"]
@@ -781,7 +793,7 @@ class BandsWidget(VBox):
                 for vs in self._ktcicks.value.split(",")
             ]
             kticks = [(int(vs[0]), vs[1]) for vs in hsk if len(vs) == 2] or None
-            self._kwargs = {"kticks": kticks, # below numbers instead of index and full shown range
+            self._kwargs = {**self._kwargs, "kticks": kticks, # below numbers instead of index and full shown range
                 "bands": range(self._brange.value[0] - 1, self._brange.value[1]) if self._brange.value else None}
 
             if self._ppicks.projections:
@@ -814,6 +826,10 @@ class BandsWidget(VBox):
     def _change_theme(self, change):
         self._fig.layout.template = self._tsd.value
 
+    def _set_krange(self, change):
+        self._kwargs["kpairs"] = [self._krange.value,]
+        self._warn_update(None)  # Update warning
+
     def _click_save_data(self, change=None):
         def _show_and_save(data_dict):
             self._interact.output_widget.clear_output(wait=True)  # Why need again?

{ipyvasp-0.9.89 → ipyvasp-0.9.91}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.89
+Version: 0.9.91
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -20,7 +20,7 @@ Requires-Dist: scipy==1.9.1
 Requires-Dist: ipywidgets>=8.0.4
 Requires-Dist: pillow>=9.3.0
 Requires-Dist: pandas==1.4.4
-Requires-Dist: plotly==5.14.1
+Requires-Dist: plotly==6.0.1
 Requires-Dist: requests==2.28.1
 Requires-Dist: typer==0.9.0
 Provides-Extra: extra

{ipyvasp-0.9.89 → ipyvasp-0.9.91}/ipyvasp.egg-info/requires.txt

@@ -4,7 +4,7 @@ scipy==1.9.1
 ipywidgets>=8.0.4
 pillow>=9.3.0
 pandas==1.4.4
-plotly==5.14.1
+plotly==6.0.1
 requests==2.28.1
 typer==0.9.0
 

{ipyvasp-0.9.89 → ipyvasp-0.9.91}/setup.py

@@ -25,7 +25,7 @@ REQUIRED = [
     "ipywidgets>=8.0.4",
     "pillow>=9.3.0",
     "pandas==1.4.4",
-    "plotly==5.14.1",
+    "plotly==6.0.1",
     "requests==2.28.1",
     "typer==0.9.0",
 ]

ipyvasp-0.9.89/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.9.89"