ipyvasp 0.8.6__tar.gz → 0.8.8__tar.gz

{ipyvasp-0.8.6 → ipyvasp-0.8.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.6
+Version: 0.8.8
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -68,7 +68,7 @@ Interactively select bandstructure path by clicking on high symmetry points on p
 
 ![KP](KP.png)
 
-Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` or `WeasWidget` in Jupyterlab side by side.
+Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` in Jupyterlab side by side.
 
 ![snip](op.png)
 

{ipyvasp-0.8.6 → ipyvasp-0.8.8}/README.md

@@ -36,7 +36,7 @@ Interactively select bandstructure path by clicking on high symmetry points on p
 
 ![KP](KP.png)
 
-Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` or `WeasWidget` in Jupyterlab side by side.
+Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` in Jupyterlab side by side.
 
 ![snip](op.png)
 

{ipyvasp-0.8.6 → ipyvasp-0.8.8}/ipyvasp/_lattice.py

@@ -15,7 +15,7 @@ from matplotlib.collections import LineCollection
 from mpl_toolkits.mplot3d.art3d import Poly3DCollection, Line3DCollection
 import matplotlib.colors as mplc
 
-from ipywidgets import interactive
+from ipywidgets import interactive, IntSlider
 
 # Inside packages import
 from .core import plot_toolkit as ptk
@@ -1635,13 +1635,13 @@ def filter_sites(poscar_data, func, tol = 0.01):
         pos = data['positions'][indices]
         qos = data['positions'][others] # need edge items to include
 
-        if qos.shape:
+        if qos.size:
             qos = np.concatenate([[[i] for i in others], qos], axis=1) # need to keep index
             qos = np.array([qos + [0, *p] for p in product([-1,0,1],[-1,0,1],[-1,0,1])]).reshape((-1,4)) # all possible translations
             qos = qos[(qos[:,1:] < 1 + tol).all(axis=1) & (qos[:,1:] > -tol).all(axis=1)]# only in cell range
             qos = qos[[func(*q) for q in qos]] # masked only those are true
         
-        if qos.shape:
+        if qos.size:
             pos = np.concatenate([pos, qos[:,1:]],axis=0)
 
         all_pos.append(pos)
@@ -1681,10 +1681,10 @@ def iplot_lattice(
 
     Parameters
     ----------
-    sizes : float or tuple
-        Size of sites. Either one int/float or list equal to type of ions.
-    colors : tuple
-        Sequence of colors for each type. Automatically generated if not provided.
+    sizes : float or dict of type -> float
+        Size of sites. Either one int/float or a mapping like {'Ga': 2, ...}.
+    colors : color or dict of type -> color
+        Mapping of colors like {'Ga': 'red, ...} or a single color. Automatically generated color for missing types.
     bond_length : float or dict
         Length of bond in Angstrom. Auto calculated if not provides. Can be a dict like {'Fe-O':3.2,...} to specify bond length between specific types.
     bond_kws : dict
@@ -1717,17 +1717,9 @@ def iplot_lattice(
         fig = go.Figure()
 
     uelems = poscar_data.types.to_dict()
-    if not isinstance(sizes, (list, tuple, np.ndarray)):
-        sizes = [sizes for elem in uelems.keys()]
-
-    if colors and len(colors) != len(uelems.keys()):
-        print(
-            "Warning: Number of colors does not match number of atom types. Using default colors."
-        )
-
-    if (colors is None) or len(colors) != len(uelems.keys()):
-        colors = [_atom_colors[elem] for elem in uelems.keys()]
-        colors = ["rgb({},{},{})".format(*[int(_c * 255) for _c in c]) for c in colors]
+    _fcs = _fix_color_size(uelems, colors, sizes, 10, backend = 'plotly')
+    sizes  = [v['size'] for v in _fcs.values()]
+    colors = [v['color'] for v in _fcs.values()]
 
     _colors = np.array([colors[i] for i, vs in enumerate(uelems.values()) for v in vs],dtype=object) # could be mixed color types
 
@@ -1854,6 +1846,33 @@ def _validate_label_func(fmt_label, parameter):
     elif not isinstance(test_out, str):
         raise ValueError("fmt_label must return a string or a list/tuple of length 2.")
 
+def _fix_color_size(types, colors, sizes, default_size, backend=None):
+    cs = {key: {'color': _atom_colors.get(key, 'blue'), 'size': default_size} for key in types}
+    for k in cs:
+        if len(cs[k]['color']) == 3: # otherwise its blue
+            if backend == 'plotly':
+                cs[k]['color'] = "rgb({},{},{})".format(*[int(255*c) for c in cs[k]['color']])
+            elif backend == 'ngl':
+                cs[k]['color'] = mplc.to_hex(cs[k]['color'])
+    
+    if isinstance(sizes,(int,float,np.integer)):
+        for k in cs:
+            cs[k]['size'] = sizes 
+    elif isinstance(sizes, dict):
+        for k,v in sizes.items():
+            cs[k]['size'] = v 
+    else:
+        raise TypeError("sizes should be a single int/float or dict as {'Ga':10,'As':15,...}")
+    
+    if isinstance(colors,dict):
+        for k,v in colors.items():
+            cs[k]['color'] = v 
+    elif isinstance(colors,(str,list,tuple,np.ndarray)):
+        for k in cs:
+            cs[k]['color'] = colors
+    elif colors is not None:
+        raise TypeError("colors should be a single valid color or dict as {'Ga':'red','As':'blue',...}")
+    return cs
 
 # Cell
 def splot_lattice(
@@ -1880,10 +1899,10 @@ def splot_lattice(
     ----------
     plane : str
         Plane to plot. Either 'xy','xz','yz' or None for 3D plot.
-    sizes : float or tuple
-        Size of sites. Either one int/float or list equal to type of ions.
-    colors : tuple
-        Sequence of colors for each ion type. If None, automatically generated.
+    sizes : float or dict of type -> float
+        Size of sites. Either one int/float or a mapping like {'Ga': 2, ...}.
+    colors : color or dict of type -> color
+        Mapping of colors like {'Ga': 'red, ...} or a single color. Automatically generated color for missing types.
     bond_length : float or dict
         Length of bond in Angstrom. Auto calculated if not provides. Can be a dict like {'Fe-O':3.2,...} to specify bond length between specific types.
     alpha : float
@@ -1941,23 +1960,10 @@ def splot_lattice(
             print(f"Warning: Parameters {list(kwargs.keys())} are not used when `plot_cell = False`.")
 
     uelems = poscar_data.types.to_dict()
-    if not isinstance(sizes, (list, tuple, np.ndarray)):
-        if not isinstance(sizes, (int, float, np.integer)):
-            raise ValueError("sizes must be a number or a list/tuple of numbers.")
-        sizes = [sizes for _ in uelems]
-    
-    if len(sizes) != len(uelems):
-        raise ValueError(
-            f"Length of `sizes` must be equal to number of elements in POSCAR. Got {len(sizes)} sizes for {len(uelems)} elements."
-        )
-        
-    if colors and len(colors) != len(uelems.keys()):
-        print(
-            "Warning: Number of colors does not match number of atom types. Using default colors."
-        )
 
-    if (colors is None) or len(colors) != len(uelems.keys()):
-        colors = [_atom_colors[elem] for elem in uelems.keys()]
+    _fcs = _fix_color_size(uelems, colors, sizes, 50)
+    sizes  = [v['size'] for v in _fcs.values()]
+    colors = [v['color'] for v in _fcs.values()]
 
     # Before doing other stuff, create something for legend.
     if showlegend:    
@@ -2691,8 +2697,12 @@ def deform_poscar(poscar_data, deformation):
 def view_poscar(poscar_data, **kwargs):
     "View a POSCAR in a jupyter notebook. kwargs are passed to splot_lattice. After setting a view, you can do view.f(**view.kwargs) to get same plot in a cell."
 
-    def view(elev=30, azim=30, roll=0):
+    def view(elev, azim, roll):
         ax = splot_lattice(poscar_data, **kwargs)
         ax.view_init(elev=elev, azim=azim, roll=roll)
+    
+    elev = IntSlider(description='elev', min=0,max=180,value=30, continuous_update=False)
+    azim = IntSlider(description='azim', min=0,max=360,value=30, continuous_update=False)
+    roll = IntSlider(description='roll', min=0,max=360,value=0, continuous_update=False)
 
-    return interactive(view, elev=(0, 180), azim=(0, 360), roll=(0, 360))
+    return interactive(view, elev=elev, azim=azim, roll=roll)

ipyvasp-0.8.8/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.8.8"

{ipyvasp-0.8.6 → ipyvasp-0.8.8}/ipyvasp/core/plot_toolkit.py

@@ -1015,14 +1015,18 @@ def iplot2widget(fig, fig_widget=None, template=None):
 
     if fig_widget is None:
         fig_widget = go.FigureWidget()
+        scene = fig.layout.scene # need to copy scane form given fig
     elif not isinstance(fig_widget, go.FigureWidget):
         raise ValueError("fig_widget must be FigureWidget")
+    else:
+        scene = fig_widget.layout.scene # keep scene from widget
 
     fig_widget.data = []  # Clear previous data
     if template is not None:
-        fig.layout.template = template  # will make white flash if not done before
-
+        fig.layout.template = template  # will make white flash if not done before 
+    
     fig_widget.layout = fig.layout
+    fig_widget.layout.scene = scene # reset scene back
 
     with fig_widget.batch_update():
         for data in fig.data:

{ipyvasp-0.8.6 → ipyvasp-0.8.8}/ipyvasp/lattice.py

@@ -75,7 +75,7 @@ def download_structure(
 def ngl_viewer(
     poscar,
     colors=None,
-    sizes=None,
+    sizes=0.5,
     plot_cell=True,
     linewidth=0.05,
     color=[0, 0, 0.2],
@@ -91,13 +91,12 @@ def ngl_viewer(
     Parameters
     ----------
     poscar : ipyvasp.POSCAR
-    colors : list or str
-        List of colors for each atom type. If str, use sames colors for all.
+    sizes : float or dict of type -> float
+        Size of sites. Either one int/float or a mapping like {'Ga': 2, ...}.
+    colors : color or sheme name or dict of type -> color
+        Mapping of colors like {'Ga': 'red, ...} or a single color. Automatically generated color for missing types.
         If `colors = 'element'`, then element colors from `nglview` will be used.
         You can use `nglview.color.COLOR_SCHEME` to see available color schemes to use.
-        If colors is None, then default colors from ipyvasp will be used that are same in `[i,s]plot_lattice`.
-    sizes : list
-        List of sizes for each atom type.
     plot_cell : bool
         Plot unit cell. Default True.
     linewidth : float
@@ -139,26 +138,10 @@ def ngl_viewer(
         data=plat._fix_sites(poscar.data, eqv_sites=True if plot_cell else False, origin=origin)
     )
 
-    _types = list(poscar.data.types.keys())
-    _sizes = [0.5 for _ in _types]
-    _colors = [mcolors.to_hex(plat._atom_colors[e]) for e in _types]
-
-    if sizes:
-        if len(sizes) != len(_types):
-            raise ValueError(
-                "sizes must have the same length as the number of atom types."
-            )
-        _sizes = sizes
-
-    if colors:
-        if isinstance(colors, str):
-            _colors = [colors for _ in _types]  # All same color, may be 'element'
-        else:
-            if len(colors) != len(_types):
-                raise ValueError(
-                    "colors must have the same length as the number of atom types."
-                )
-            _colors = [mcolors.to_hex(c) for c in colors]
+    _types = poscar.data.types.to_dict()
+    _fcs = plat._fix_color_size(_types,colors,sizes,0.5, backend='ngl')
+    _sizes = [v['size'] for v in _fcs.values()]
+    _colors = [v['color'] for v in _fcs.values()]
 
     view = nv.NGLWidget(
         nv.ASEStructure(poscar.to_ase()),
@@ -199,7 +182,7 @@ def ngl_viewer(
 
 
 def weas_viewer(poscar,
-    sizes=None,
+    sizes=1,
     colors=None,
     bond_length=None,
     model_style = 1,
@@ -207,9 +190,11 @@ def weas_viewer(poscar,
     origin = (0,0,0)
     ):
     """
-    colors : list or str
-        List of colors for each atom type. If str, use 'VESTA','JMOL','CPK'.
-        By default, ipyvasp colors are used.
+    sizes : float or dict of type -> float
+        Size of sites. Either one int/float or a mapping like {'Ga': 2, ...}.
+    colors : color, color scheme or dict of type -> color
+        Mapping of colors like {'Ga': 'red, ...} or a single color. Automatically generated color for missing types.
+        You can use color schemes as 'VESTA','JMOL','CPK'.
     sizes : list
         List of sizes for each atom type.
     model_type: int
@@ -236,8 +221,7 @@ def weas_viewer(poscar,
     w = WeasWidget(from_ase=poscar.to_ase())
     w.avr.show_bonded_atoms = False if plot_cell else True # plot_cell fix atoms itself
     w.avr.model_style = model_style
-    w.avr.show_cell = plot_cell  
-              
+    w.avr.show_cell = plot_cell         
 
     if bond_length:
         if isinstance(bond_length,(int,float)):
@@ -247,40 +231,73 @@ def weas_viewer(poscar,
         elif isinstance(bond_length, dict):
             for key, value in bond_length.items():
                 w.avr.bond.settings[key].update({'max': value})
-
-    if sizes is not None:
-        if not isinstance(sizes, (list,tuple)) or len(sizes) != len(poscar.data.types):
-            raise ValueError(f"sizes should be list/tuple of same sizes as atom types = {len(poscar.data.types)}.")
-        for key, value in zip(poscar.data.types,sizes):
-            w.avr.species.settings[key].update({"radius": value})
     
-    if colors is None:
-        colors = [plat._atom_colors[key] for key in poscar.data.types]
+    _fcs = plat._fix_color_size(poscar.data.types.to_dict(), colors, sizes, 1)
 
-    if isinstance(colors, str):
-        if not colors in ['VESTA','JMOL','CPK']:
-            raise ValueError("colors should be one of ['VESTA','JMOL','CPK'] if given as string!")
-        
-        w.avr.color_type = colors
-
-    if not isinstance(colors, str):
-        if not isinstance(colors, (list,tuple)) or len(colors) != len(poscar.data.types):
-            raise ValueError(f"colors should be list/tuple of same sizes as atom types = {len(poscar.data.types)}.")
+    for key, value in _fcs.items():
+        w.avr.species.settings[key].update({"radius": value["size"]})
 
-        colors = {key: value for key, value in zip(poscar.data.types,colors)}
+    if isinstance(colors, str) and colors in ['VESTA','JMOL','CPK']:
+        w.avr.color_type = colors
+    else:
+        colors = {key: value["color"] for key, value in _fcs.items()}
         for key,value in colors.items():
             w.avr.species.settings[key].update({"color": value})
         for (k1,c1), (k2,c2) in permutations(colors.items(),2):
             with suppress(KeyError):
                 w.avr.bond.settings[f'{k1}-{k2}'].update({'color1':c1,'color2':c2})
-                
+    
     return w
 
 
+class _AutoRenderer:
+    _figw = None
+    _kws = {} 
+
+    def __init__(self, pc_instance):
+        self._pc = pc_instance
+
+    def on(self, template=None):
+        "Enable auto rendering. In Jupyterlab, you can use `Create New View for Output` to drag a view on side."
+        self.off()
+        type(self)._figw = iplot2widget(self._pc.iplot_lattice(**self._kws), fig_widget=self._figw,template=template)
+        
+        def ip_display(that):
+            iplot2widget(that.iplot_lattice(**self._kws), fig_widget=self._figw, template=template)
+        
+        type(self._pc)._ipython_display_ = ip_display
+        
+        from ipywidgets import Button, VBox
+        btn = Button(description='Disable Auto Rendering',icon='close',layout={'width': 'max-content'})
+        btn.on_click(lambda btn: self.off())
+        type(self)._box = VBox([btn, self._figw])
+        return display(self._box)
+
+    def off(self):
+        "Disable auto rendering."
+        if hasattr(self, '_box'):
+            self._box.close()
+            type(self)._figw = None # no need to close figw, it raise warning, but now garbage collected
+        
+        if hasattr(type(self._pc), '_ipython_display_'):
+            del type(self._pc)._ipython_display_
+
+    @_sig_kwargs(plat.iplot_lattice,('poscar_data',))
+    def update_params(self, **kwargs):
+        type(self)._kws = kwargs
+        if hasattr(type(self._pc), '_ipython_display_'):
+            self._pc._ipython_display_()
+    
+    @property
+    def params(self):
+        return self._kws.copy() # avoid messing original
+    
+    def __repr__(self):
+        return f"AutoRenderer({self._kws})"
+
 class POSCAR:
     _cb_instance = {}  # Loads last clipboard data if not changed
     _mp_instance = {}  # Loads last mp data if not changed
-    _update_kws = {}  # kwargs to pass to auto update figurewidget
 
     def __init__(self, path=None, content=None, data=None):
         """
@@ -294,10 +311,16 @@ class POSCAR:
         data : PoscarData object. This assumes positions are in fractional coordinates.
 
         Prefrence order: data > content > path
+
+        Tip: You can use `self.auto_renderer.on()` to keep doing opertions and visualize while last line of any cell is a POSCAR object.
         """
         self._path = Path(path or "POSCAR")  # Path to file
         self._content = content
 
+        if not hasattr(self, '_renderer'): # Only once
+            type(self)._renderer = _AutoRenderer(self) # assign to class
+        self._renderer._pc = self # keep latest refrence there too, for update_params on right one
+
         if data:
             self._data = serializer.PoscarData.validated(data)
         else:
@@ -321,6 +344,19 @@ class POSCAR:
     @property
     def path(self):
         return self._path
+    
+    @property
+    def auto_renderer(self):
+        """A renderer for auto viewing POSCAR when at last line of cell.
+
+        Use `auto_renderer.on()` to enable it.
+        Use `auto_renderer.off()` to disable it.
+        Use `auto_renderer.[params, update_params()]` to view and update parameters.
+        
+        In Jupyterlab, you can use `Create New View for Output` to drag a view on side.
+        In VS Code, you can open another view of Notebook to see it on side while doing operations.
+        """
+        return self._renderer
 
     def to_ase(self):
         """Convert to ase.Atoms format. You need to have ase installed.
@@ -353,6 +389,8 @@ class POSCAR:
             return plat.view_poscar(self.data, **kwargs)
         elif viewer in "weas":
             return weas_viewer(self, **kwargs)
+        elif viewer in "plotly":
+            return self.view_plotly(**kwargs)
         elif viewer in "nglview":
             return print(
                 f"Use `self.view_ngl()` for better customization in case of viewer={viewer!r}"
@@ -371,7 +409,6 @@ class POSCAR:
     @_sig_kwargs(weas_viewer, ("poscar",))
     def view_weas(self, **kwargs):
         return weas_viewer(self, **kwargs)
-    
 
     def view_kpath(self):
         "Initialize a KpathWidget instance to view kpath for current POSCAR, and you can select others too."
@@ -381,18 +418,9 @@ class POSCAR:
 
     @_sub_doc(plat.iplot_lattice)
     @_sig_kwargs(plat.iplot_lattice, ("poscar_data",))
-    def view_widget(self, **kwargs):
-        self.__class__._update_kws = kwargs  # attach to class, not self
+    def view_plotly(self, **kwargs):
         return iplot2widget(self.iplot_lattice(**kwargs))
 
-    @_sig_kwargs(plat.iplot_lattice, ("poscar_data",))
-    def update_widget(self, handle, **kwargs):
-        """Update widget (if shown in notebook) after some operation on POSCAR with `handle` returned by `view_widget`
-        kwargs are passed to `self.iplot_lattice` method.
-        """
-        kwargs = {**self.__class__._update_kws, **kwargs}
-        iplot2widget(self.iplot_lattice(**kwargs), fig_widget=handle)
-
     @classmethod
     def from_file(cls, path):
         "Load data from POSCAR file"
@@ -533,14 +561,6 @@ class POSCAR:
         "Writes POSCAR to clipboard (as implemented by pandas library) for copy in other programs such as vim."
         clipboard_set(self.content)  # write to clipboard
 
-
-    def update_weas(self, handle):
-        """Send result of any operation to view on opened weas widget handle with default parameters becuase any operations 
-        can be incompatible with presious state of POSCAR. VESTA color scheme is used here.
-        Useful in Jupyterlab side panel to look operations results on POSCAR."""
-        handle.from_ase(self.to_ase())
-        handle.avr.color_type = 'VESTA'
-
     @property
     def data(self):
         "Data object in POSCAR."

{ipyvasp-0.8.6 → ipyvasp-0.8.8}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.6
+Version: 0.8.8
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -68,7 +68,7 @@ Interactively select bandstructure path by clicking on high symmetry points on p
 
 ![KP](KP.png)
 
-Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` or `WeasWidget` in Jupyterlab side by side.
+Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` in Jupyterlab side by side.
 
 ![snip](op.png)
 

ipyvasp-0.8.6/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.8.6"