ipyvasp 0.9.91__py2.py3-none-any.whl → 0.9.94__py2.py3-none-any.whl

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/_enplots.py

@@ -716,8 +716,9 @@ def splot_dos_lines(
             **legend_kws,
         }
         add_legend(ax, **kwargs)  # Labels are picked from plot
-
-    kws = dict(ylim=elim or []) if vertical else dict(xlim=elim or [])
+    
+    elim = elim if elim is not None else []
+    kws = dict(ylim=elim) if vertical else dict(xlim=elim)
     xlabel, ylabel = "Energy (eV)", "DOS"
     if vertical:
         xlabel, ylabel = ylabel, xlabel
@@ -754,7 +755,7 @@ def _format_rgb_data(
     if data["pros"].shape[2] == 2:
         data["norms"][:, :, 2] = np.nan  # Avoid wrong info here
     elif data["pros"].shape[2] == 1:
-        data["pros"][:, :, 1:] = np.nan
+        data["norms"][:, :, 1:] = np.nan
 
     lws = np.sum(rgb, axis=2)  # Sum of all colors
     lws = maxwidth * lws / (float(np.max(lws)) or 1)  # Normalize to maxwidth
@@ -773,8 +774,7 @@ def _format_rgb_data(
         indices = range(np.shape(data["evals"])[1])
 
     # 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, CDATA = [], [], [], [], []
     for i, b in enumerate(indices):
         K = [*K, *data["kpath"], np.nan]
         E = [*E, *data["evals"][:, i], np.nan]
@@ -784,32 +784,26 @@ def _format_rgb_data(
             "rgb(0,0,0)",
         ]
         S = [*S, *data["widths"][:, i], data["widths"][-1, i]]
-        PT = [*PT, *[f"{txt} [{s}, {p}, {d}]" for (s, p, d) in data["norms"][:, i]], ""]
-        OT = [*OT, *[f"Occ: {t:>7.4f}" for t in data["occs"][:, i]], ""]
-        KT = [
-            *KT,
-            *[
-                f"K<sub>{j+1}</sub>: {x:>7.3f}{y:>7.3f}{z:>7.3f}"
-                for j, (x, y, z) in enumerate(data["kpoints"])
-            ],
-            "",
-        ]
-        ET = [
-            *ET,
-            *["{}".format(b + 1) for _ in data["kpath"]],
-            "",
-        ]  # Add bands subscripts to labels.
-
-    T = [
-        f"</br>{p} </br></br>Band: {e}  {o}</br>{k}"
-        for (p, e, o, k) in zip(PT, ET, OT, KT)
-    ]
+
+        CDATA  = [*CDATA , *[
+            {
+                "nk":j+1,
+                **{f"k{u}":v for u,v in zip("xyz",xyz)},
+                "nb":b+1,
+                "occ":occ,
+                **{c:"" if np.isnan(v) else 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")}]
+
     return {
         "K": K,
         "E": E,
         "C": C,
         "S": S,
-        "T": T,
+        "CDATA": CDATA,
         "labels": labels,
     }  # K, energy, marker color, marker size, text, labels that get changed
 
@@ -830,10 +824,15 @@ def _fmt_labels(ticklabels):
         ]
     return ticklabels
 
+_hover_temp = { # keep order same
+    "xy":"(%{x}, %{y})",
+    "k": "<br>K<sub>%{customdata.nk}</sub>: %{customdata.kx:.3f} %{customdata.ky:.3f} %{customdata.kz:.3f}",
+    "b":"Band: %{customdata.nb}, Occ: %{customdata.occ:.4f}"
+}
 
 @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}
@@ -854,18 +853,15 @@ 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,
     )  # moking other arrays, we need only
-    K, E, T = data["K"], data["E"], data["T"]  # Fixed K and E as single line data
-    T = [
-        "Band" + t.split("Band")[1].split("Occ")[0] for t in T
-    ]  # Just Band number here
+    K, E = data["K"], data["E"]
 
     if fig is None:
         fig = go.Figure()
@@ -873,10 +869,12 @@ def iplot_bands(
     kwargs = {
         "mode": "markers + lines",
         "marker": dict(size=0.1),
+        "hovertemplate": "<br>".join(_hover_temp.values()),
+        "customdata": [{k:v for k,v in d.items() if not k in 'rgb'} for d in data["CDATA"]], # 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))
-
+    fig.add_trace(go.Scatter(x=K, y=E, **kwargs))
+    
     fig.update_layout(
         template="plotly_white",
         title=(
@@ -932,14 +930,7 @@ def iplot_rgb_lines(
     data = _format_rgb_data(
         K, E, pros, labels, interp, occs, kpoints, maxwidth=maxwidth, indices=indices
     )
-    K, E, C, S, T, labels = (
-        data["K"],
-        data["E"],
-        data["C"],
-        data["S"],
-        data["T"],
-        data["labels"],
-    )
+    K, E, C, S, labels = [data[key] for key in "K E C S labels".split()]
 
     if fig is None:
         fig = go.Figure()
@@ -948,13 +939,18 @@ def iplot_rgb_lines(
     kwargs.pop("marker_size", None)  # Provided by S
     kwargs.update(
         {
-            "hovertext": T,
             "marker": {
                 "line_color": "rgba(0,0,0,0)",
                 **kwargs.get("marker", {}),
                 "color": C,
                 "size": S,
             },
+            "hovertemplate": "<br>".join([_hover_temp["xy"],
+                "<br>Projection: [{}, {}, {}]".format(*labels), # clean labels instead of ''
+                "Value: [%{customdata.r}, %{customdata.g}, %{customdata.b}]",
+                _hover_temp["k"], _hover_temp["b"],
+            ]),
+            "customdata": data["CDATA"], # need for selection and hover template
         }
     )  # marker edge should be free
 
@@ -967,7 +963,7 @@ def iplot_rgb_lines(
         + ", ".join(labels)
         + "]",  # Do not set autosize = False, need to be responsive in widgets boxes
         margin=go.layout.Margin(l=60, r=50, b=40, t=75, pad=0),
-        yaxis=go.layout.YAxis(title_text="Energy (eV)", range=elim or [min(E), max(E)]),
+        yaxis=go.layout.YAxis(title_text="Energy (eV)",range=elim or [min(E), max(E)]),
         xaxis=go.layout.XAxis(
             ticktext=_fmt_labels(xticklabels),
             tickvals=xticks,

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/_version.py

@@ -1 +1 @@
-__version__ = "0.9.91"
+__version__ = "0.9.94"

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/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/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",))