ipyvasp 0.9.91__tar.gz → 0.9.93__tar.gz

{ipyvasp-0.9.91 → ipyvasp-0.9.93}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.91
+Version: 0.9.93
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -23,6 +23,7 @@ Requires-Dist: pandas==1.4.4
 Requires-Dist: plotly==6.0.1
 Requires-Dist: requests==2.28.1
 Requires-Dist: typer==0.9.0
+Requires-Dist: einteract
 Provides-Extra: extra
 Requires-Dist: jupyterlab>=3.5.2; extra == "extra"
 Requires-Dist: ipython>=8.7; extra == "extra"
@@ -30,7 +31,10 @@ Requires-Dist: ase>=3.22.1; extra == "extra"
 Requires-Dist: nglview>=3.0.4; extra == "extra"
 
 
-# ipyvasp
+# IPyVASP
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15482350.svg)](https://doi.org/10.5281/zenodo.15482350)
+[![PyPI Downloads](https://static.pepy.tech/badge/ipyvasp)](https://pepy.tech/projects/ipyvasp)
 
 An VASP-based DFT pre and post processing tool.
 

{ipyvasp-0.9.91 → ipyvasp-0.9.93}/README.md

@@ -1,4 +1,7 @@
-# ipyvasp
+# IPyVASP
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15482350.svg)](https://doi.org/10.5281/zenodo.15482350)
+[![PyPI Downloads](https://static.pepy.tech/badge/ipyvasp)](https://pepy.tech/projects/ipyvasp)
 
 An VASP-based DFT pre and post processing tool.
 
@@ -41,4 +44,4 @@ Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget`
 ![snip](op.png)
 
 
-More coming soon!
+More coming soon!

{ipyvasp-0.9.91 → ipyvasp-0.9.93}/ipyvasp/__init__.py

@@ -31,7 +31,7 @@ from .bsdos import *
 from .potential import *
 from .evals_dataframe import *
 from .utils import *
-from .widgets import Files, BandsWidget, KpathWidget, summarize, load_results
+from .widgets import Files, BandsWidget, KPathWidget, summarize, load_results
 from .core import plot_toolkit, spatial_toolkit
 from .core.spatial_toolkit import to_basis, to_R3, get_TM, get_bz, rotation
 from .core.plot_toolkit import (

{ipyvasp-0.9.91 → ipyvasp-0.9.93}/ipyvasp/_enplots.py

@@ -774,7 +774,7 @@ def _format_rgb_data(
 
     # Now process data to make single data for faster plotting.
     txt = "Projection: [{}]</br>Value:".format(", ".join(labels))
-    K, E, C, S, PT, OT, KT, ET = [], [], [], [], [], [], [], []
+    K, E, C, S, PT, OT, KT, ET, jKbop = [], [], [], [], [], [], [], [], []
     for i, b in enumerate(indices):
         K = [*K, *data["kpath"], np.nan]
         E = [*E, *data["evals"][:, i], np.nan]
@@ -800,6 +800,19 @@ def _format_rgb_data(
             "",
         ]  # Add bands subscripts to labels.
 
+        jKbop = [*jKbop, *[
+            {
+                "nk":j+1,
+                **{f"k{u}":v for u,v in zip("xyz",xyz)},
+                "nb":b+1,
+                "occ":occ,
+                **{c:v for c,v in zip("rgb",rgb)}
+            } 
+            for (j, xyz), occ,rgb  in zip(
+                enumerate(data["kpoints"]), data["occs"][:, i],data["norms"][:, i]
+            )
+        ], {k:np.nan for k in ("nk","kx","ky","kz","nb","occ","r","g","b")}]
+
     T = [
         f"</br>{p} </br></br>Band: {e}  {o}</br>{k}"
         for (p, e, o, k) in zip(PT, ET, OT, KT)
@@ -810,6 +823,7 @@ def _format_rgb_data(
         "C": C,
         "S": S,
         "T": T,
+        "jKbop": jKbop,
         "labels": labels,
     }  # K, energy, marker color, marker size, text, labels that get changed
 
@@ -833,7 +847,7 @@ def _fmt_labels(ticklabels):
 
 @gu._fmt_doc(_docs)
 def iplot_bands(
-    K, E, fig=None, elim=None, kticks=None, interp=None, title=None, **kwargs
+    K, E, occs = None, fig=None, elim=None, kticks=None, interp=None, title=None, **kwargs
 ):
     """Plot band structure using plotly.
     {params}\n    {K}\n    {E}
@@ -854,10 +868,10 @@ def iplot_bands(
     data = _format_rgb_data(
         K,
         E,
-        [E],
+        [E], # don't let it fail if no projections
         ["X"],
         interp,
-        E,
+        E if occs is None else occs,
         np.array([K, K, K]).reshape((-1, 3)),
         maxwidth=1,
         indices=indices,
@@ -873,6 +887,7 @@ def iplot_bands(
     kwargs = {
         "mode": "markers + lines",
         "marker": dict(size=0.1),
+        "customdata": [{k:v for k,v in d.items() if not k in 'rgb'} for d in data["jKbop"]], # useless rgb data to skip
         **kwargs,
     }  # marker so that it is selectable by box, otherwise it does not
     fig.add_trace(go.Scatter(x=K, y=E, hovertext=T, **kwargs))
@@ -955,6 +970,7 @@ def iplot_rgb_lines(
                 "color": C,
                 "size": S,
             },
+            "customdata": data["jKbop"], # need for selection and hover template
         }
     )  # marker edge should be free
 

{ipyvasp-0.9.91 → ipyvasp-0.9.93}/ipyvasp/_lattice.py

@@ -232,7 +232,7 @@ def periodic_table(selection=None):
     return ax
 
 
-def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=False, comment=""):
+def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=False, comment="", scale=None):
     """Writes POSCAR data to a file or returns string
 
     Parameters
@@ -246,6 +246,8 @@ def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=F
         If file already exists, overwrite=True changes it.
     comment: str
         Add comment, previous comment will be there too.
+    scale: float
+        Scale factor for the basis vectors. Default is provided by loaded data.
 
 
     .. note::
@@ -253,7 +255,14 @@ def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=F
     """
     _comment = poscar_data.metadata.comment + comment
     out_str = f"{poscar_data.SYSTEM}  # " + (_comment or "Created by ipyvasp")
-    scale = poscar_data.metadata.scale
+
+    if scale is None:
+        scale = poscar_data.metadata.scale
+    elif not isinstance(scale, (int, float)):
+        raise TypeError("scale must be a number or None.")
+    elif scale == 0:
+        raise ValueError("scale can not be zero.")
+    
     out_str += "\n  {:<20.14f}\n".format(scale)
     out_str += "\n".join(
         ["{:>22.16f}{:>22.16f}{:>22.16f}".format(*a) for a in poscar_data.basis / scale]
@@ -550,9 +559,9 @@ class InvokeMaterialsProject:
                 else:
                     print(self._cif)
 
-            def write_poscar(self, outfile=None, overwrite=False, comment=""):
+            def write_poscar(self, outfile=None, overwrite=False, comment="",scale=None):
                 "Use `ipyvasp.lattice.POSCAR.write` if you need extra options."
-                write_poscar(self.export_poscar(), outfile=outfile, overwrite=overwrite, comment=comment)
+                write_poscar(self.export_poscar(), outfile=outfile, overwrite=overwrite, comment=comment, scale=scale)
 
             def export_poscar(self):
                 "Export poscar data form cif content."

ipyvasp-0.9.93/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.9.93"

{ipyvasp-0.9.91 → ipyvasp-0.9.93}/ipyvasp/bsdos.py

@@ -605,6 +605,7 @@ class Bands(_BandsDosBase):
         return iplot_bands(
             {"K": data.kpath, "indices": data.bands},
             data.evals[spin] - data.ezero,
+            occs = data.occs[spin],
             **kwargs,
         )
 

{ipyvasp-0.9.91 → ipyvasp-0.9.93}/ipyvasp/core/plot_toolkit.py

@@ -20,6 +20,7 @@ import PIL  # For text image.
 
 import plotly.graph_objects as go
 from plotly.io._base_renderers import open_html_in_browser
+from einteract import patched_plotly
 
 from .spatial_toolkit import to_R3, rotation
 from ..utils import _sig_kwargs
@@ -1011,7 +1012,7 @@ def iplot2html(fig, outfile=None, modebar=True):
 def iplot2widget(fig, fig_widget=None, template=None):
     "Converts plotly's figure to FigureWidget by copying attributes and data. If fig_widget is provided, it will update it. Adds template if provided. If fig is FigureWidget, it is just returned"
     if isinstance(fig, go.FigureWidget):
-        return fig
+        return patched_plotly(fig) # add attributes selected and clicked
     
     if not isinstance(fig, go.Figure):
         raise ValueError("fig must be instance of plotly.graph_objects.Figure")
@@ -1035,7 +1036,7 @@ def iplot2widget(fig, fig_widget=None, template=None):
         for data in fig.data:
             fig_widget.add_trace(data)
 
-    return fig_widget
+    return patched_plotly(fig_widget) # add attributes selected and clicked
 
 @_sig_kwargs(plt.imshow, ('ax','X'))
 def image2plt(image_or_fname, ax = None, crop = None, **kwargs):

{ipyvasp-0.9.91 → ipyvasp-0.9.93}/ipyvasp/lattice.py

@@ -342,7 +342,7 @@ class POSCAR:
             [
                 f"{k}={v}"
                 for k, v in zip(
-                    "abcαβγ", (*self.data.norms.round(3), *self.data.angles.round(3))
+                    ['a','b','c','alpha','beta','gamma'], (*self.data.norms.round(3), *self.data.angles.round(3))
                 )
             ]
         )
@@ -436,10 +436,10 @@ class POSCAR:
         return weas_viewer(self, **kwargs)
 
     def view_kpath(self, height='400px'):
-        "Initialize a KpathWidget instance to view kpath for current POSCAR, and you can select others too."
-        from .widgets import KpathWidget
+        "Initialize a KPathWidget instance to view kpath for current POSCAR, and you can select others too."
+        from .widgets import KPathWidget
 
-        return KpathWidget([self.path,],height=height)
+        return KPathWidget([self.path,],height=height)
 
     @_sub_doc(plat.iplot_lattice)
     @_sig_kwargs(plat.iplot_lattice, ("poscar_data",))