ipyvasp 0.8.5__py2.py3-none-any.whl → 0.8.7__py2.py3-none-any.whl

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 colors is not None and isinstance(colors,(str,list,tuple,np.ndarray)):
+        for k in cs:
+            cs[k]['color'] = colors
+    else:
+        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/_version.py

@@ -1 +1 @@
-__version__ = "0.8.5"
+__version__ = "0.8.7"

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
@@ -136,31 +135,13 @@ def ngl_viewer(
 
     # Only show equivalent sites if plotting cell, only shift origin otherwise
     poscar = POSCAR(  # don't change instance itself, make new one
-        data=plat._fix_sites(
-            poscar.data, eqv_sites=True if plot_cell else False, origin=origin
-        )
+        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()),
@@ -201,16 +182,19 @@ def ngl_viewer(
 
 
 def weas_viewer(poscar,
-    sizes=None,
+    sizes=1,
     colors=None,
     bond_length=None,
     model_style = 1,
-    plot_cell=True
+    plot_cell=True,
+    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
@@ -221,18 +205,23 @@ def weas_viewer(poscar,
         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.
     
     Returns a WeasWidget instance. You can use `.export_image`, `save_image` and other operations on it.
+    Read what you can do more with `WeasWidget` [here](https://weas-widget.readthedocs.io/en/latest/index.html).
     """
     
     from weas_widget import WeasWidget
 
     if len(poscar.data.positions) < 1:
         raise ValueError("Need at least 1 atom!")
+    
+    # Only show equivalent sites if plotting cell, only shift origin otherwise
+    poscar = POSCAR(  # don't change instance itself, make new one
+        data=plat._fix_sites(poscar.data, eqv_sites=True if plot_cell else False, origin=origin)
+    )
 
     w = WeasWidget(from_ase=poscar.to_ase())
-    w.avr.show_bonded_atoms = True
+    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)):
@@ -242,40 +231,30 @@ 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]
-
-    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
+    _fcs = plat._fix_color_size(poscar.data.types.to_dict(), colors, sizes, 1)
 
-    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 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
+    _plotly_kws = {}  # kwargs to pass to auto update figurewidget
+    _weas_kws = {}
 
     def __init__(self, path=None, content=None, data=None):
         """
@@ -365,6 +344,7 @@ class POSCAR:
     @_sub_doc(weas_viewer)
     @_sig_kwargs(weas_viewer, ("poscar",))
     def view_weas(self, **kwargs):
+        self.__class__._weas_kws = kwargs  # attach to class, not self
         return weas_viewer(self, **kwargs)
     
 
@@ -376,17 +356,13 @@ 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):
+        self.__class__._plotly_kws = kwargs  # attach to class, not self
         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)
+    def update_plotly(self, handle):
+        "Update plotly widget (already shown in notebook) after some operation on POSCAR with `handle` returned by `view_plotly`."
+        iplot2widget(self.iplot_lattice(**self._plotly_kws), fig_widget=handle)
 
     @classmethod
     def from_file(cls, path):
@@ -530,11 +506,9 @@ class POSCAR:
 
 
     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.
+        """Send result of any operation to view on opened weas widget handle.
         Useful in Jupyterlab side panel to look operations results on POSCAR."""
-        handle.from_ase(self.to_ase())
-        handle.avr.color_type = 'VESTA'
+        handle.children = weas_viewer(self, **self._weas_kws).children # does not work properly otherwise
 
     @property
     def data(self):

{ipyvasp-0.8.5.dist-info → ipyvasp-0.8.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.5
+Version: 0.8.7
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.8.5.dist-info → ipyvasp-0.8.7.dist-info}/RECORD

@@ -1,12 +1,12 @@
 ipyvasp/__init__.py,sha256=7o41i5eYlNKg1Hsv0DLNFZ81GilxB02IXAJN-QiJQi0,1420
 ipyvasp/__main__.py,sha256=eJV1TZSiT8mC_VqAeksNnBI2I8mKMiPkEIlwikbtOjI,216
 ipyvasp/_enplots.py,sha256=D38paN8zqZgluNAwmCwcocd7-_h_T0HTGolI1eBkDes,37484
-ipyvasp/_lattice.py,sha256=-0Zo12xSPgwWy1TEPtrsX6iEBah6VhpH4GuZ7f98K8g,103373
-ipyvasp/_version.py,sha256=80NvSNse6emwcC7J2uzxIjsOMz3EsAiMsuAyJRp8sE0,23
+ipyvasp/_lattice.py,sha256=AU_iQ4ZdJ0fEb8FxiADexOsVMp_zWJ11HLxBg_u9q7M,104022
+ipyvasp/_version.py,sha256=ggGr8Eeuw9YZ1g40gSyKadNe96lor0upJSmlkeVHJlg,23
 ipyvasp/bsdos.py,sha256=ZtQji-W11UdFFicAoWZjlqVhI5tqYu_jpKyPPWKkeeo,30634
 ipyvasp/cli.py,sha256=aWFEVhNmnW8eSOp5uh95JaDwLQ9K9nlCQcbnOSuhWgw,6844
 ipyvasp/evals_dataframe.py,sha256=-sqxK7LPV6sYDO_XXmZ80FznOaXTkVdbqJKKvTUtMak,20637
-ipyvasp/lattice.py,sha256=ElvILd6TbIGvbH3jj5537EhHl6T5gx6rYhejNMGzyNs,28489
+ipyvasp/lattice.py,sha256=HUMh1GYS8CbY7D4VssRQbOV-klm7pK6gnfUU_evwC0k,27752
 ipyvasp/misc.py,sha256=SZJ_ePUR2-HEKYTEpDHVRVE7zpIQVTCjiuw0BCC9UTU,2349
 ipyvasp/potential.py,sha256=tzA73c5lkp6ahLSJchMrU043-QWaOV0nIOUA7VMmfKQ,11408
 ipyvasp/surface.py,sha256=MjE5oB0wW6Pca_C-xu8rN6OMH7lUEeNPNyM7Kz_Im-8,23766
@@ -17,9 +17,9 @@ ipyvasp/core/parser.py,sha256=C3CaZsJbPME_ttYlYy4DXeOdL7dnkXs-cHRwFZL6bio,38058
 ipyvasp/core/plot_toolkit.py,sha256=cktbPZTJ4K0_6-vKYqtQ1xIIPZg-gHJY5793M9XoYQ0,35754
 ipyvasp/core/serializer.py,sha256=OsnYhlwt8O6UeJQMKmjp1-hwRjhxiqobV6bybfDECUY,35777
 ipyvasp/core/spatial_toolkit.py,sha256=8DBYTiBFWJ7OBKuvOPw7UoEVCyNjJhSW0OcudjYZvAw,14748
-ipyvasp-0.8.5.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
-ipyvasp-0.8.5.dist-info/METADATA,sha256=zDQVItXjnjkNp9_9hmGBltvvx1m85_5NHlGKjmzvNms,2436
-ipyvasp-0.8.5.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-ipyvasp-0.8.5.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
-ipyvasp-0.8.5.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
-ipyvasp-0.8.5.dist-info/RECORD,,
+ipyvasp-0.8.7.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
+ipyvasp-0.8.7.dist-info/METADATA,sha256=xAr8HFygxeP0mLIRR5Pqbb04UuUOoXGwr7rUq4uDy2I,2436
+ipyvasp-0.8.7.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+ipyvasp-0.8.7.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
+ipyvasp-0.8.7.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
+ipyvasp-0.8.7.dist-info/RECORD,,