ipyvasp 0.9.1__py2.py3-none-any.whl → 0.9.2__py2.py3-none-any.whl

ipyvasp/_lattice.py

@@ -1640,6 +1640,7 @@ def iplot_lattice(
     bond_kws=dict(line_width=4),
     site_kws=dict(line_color="rgba(1,1,1,0)", line_width=0.001, opacity=1),
     plot_cell=True,
+    label_sites = False,
     **kwargs,
 ):
     """Plotly's interactive plot of lattice.
@@ -1728,6 +1729,7 @@ def iplot_lattice(
                 line_color=unqc[i],
                 legendgroup="Bonds",
                 showlegend=showlegend,
+                hoverinfo='skip',
                 name="Bonds",
                 **bond_kws,
             ))
@@ -1736,18 +1738,24 @@ def iplot_lattice(
         **dict(line_color="rgba(1,1,1,0)", line_width=0.001, opacity=1),
         **site_kws,
     }
+
+    eqv_idxs = getattr(poscar_data.metadata, 'eqv_indices',np.array(range(poscar_data.positions.shape[0])))
+
     for (k, v), c, s in zip(uelems.items(), colors, sizes):
         coords = poscar_data.coords[v]
         labs = poscar_data.labels[v]
+        idxs = eqv_idxs[v]
+        hovertext = [f"<br>{x:7.3f} {y:7.3f} {z:7.3f}<br>Index: {idx}  Label: {lab}" for lab,idx, (x,y,z) in zip(labs,idxs, poscar_data.positions[idxs])]
 
         fig.add_trace(
             go.Scatter3d(
                 x=coords[:, 0].T,
                 y=coords[:, 1].T,
                 z=coords[:, 2].T,
-                mode="markers",
+                mode="markers+text" if label_sites else "markers",
                 marker_color=c,
-                hovertext=labs,
+                hovertext=hovertext,
+                text=["{}<sub>{}</sub>".format(*l.split()) for l in labs] if label_sites else None,
                 marker_size=s,
                 name=k,
                 **site_kws,

ipyvasp/_version.py

@@ -1 +1 @@
-__version__ = "0.9.1"
+__version__ = "0.9.2"

ipyvasp/core/serializer.py

@@ -338,7 +338,7 @@ class PoscarData(Dict2Data):
             raise TypeError("type_or_indices should be a species type like 'Ga' or list-like of indices to pick positions.")
         return points[type_or_indices]
 
-    def get_neighbors(self, k=5):
+    def get_neighbors(self, k=5, as_symbols=False):
         """Get the k nearest neighbors of each atom (including itself) in the lattice.
         Returns array (N, k) of indices of atoms. The first index is the atom itself.
 
@@ -362,7 +362,7 @@ class PoscarData(Dict2Data):
         tree = KDTree(cs)
         _, inn = tree.query(cs, k=k)
         output = (inn % N)[:N]  # to get the index of the atom in the original list
-        return output
+        return self.symbols[output] if as_symbols else output
 
     get_knn = get_neighbors  # important alias
 
@@ -445,7 +445,7 @@ class PoscarData(Dict2Data):
             for j in js:
                 bs = np.array([self.to_cartesian(self.positions[j] + p) for p in product([-1,0,1],[-1,0,1],[-1,0,1])])
                 ds = np.array([np.linalg.norm(a-b) for b in bs])
-                b = bs[ds.argsort()][0]
+                b = bs[ds.argsort()][0] # closest
                 t = tuple((self.to_fractional(b) - self.positions[j]).astype(int)) # keep track of translation vector
                 nears.append((j, b, t))
             

{ipyvasp-0.9.1.dist-info → ipyvasp-0.9.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.1
+Version: 0.9.2
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.9.1.dist-info → ipyvasp-0.9.2.dist-info}/RECORD

@@ -1,8 +1,8 @@
 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=BqlDmokeYgdnWGw8YPGPRm3-wrgteUJg1R3YK9suMLY,102554
-ipyvasp/_version.py,sha256=nowX8dTYmAqqc8x180AcV7Ru6brVwGyJwg9GfVedBCE,23
+ipyvasp/_lattice.py,sha256=DN3VZVjQ5fbzUrbpft75ieaP5ddyr6mIuZRHOwrFrK8,103052
+ipyvasp/_version.py,sha256=I3ASgj0LYAmGGQhqxkAYEEiiLOpQ1UAZGOd0bJAXSRw,23
 ipyvasp/bsdos.py,sha256=ZtQji-W11UdFFicAoWZjlqVhI5tqYu_jpKyPPWKkeeo,30634
 ipyvasp/cli.py,sha256=aWFEVhNmnW8eSOp5uh95JaDwLQ9K9nlCQcbnOSuhWgw,6844
 ipyvasp/evals_dataframe.py,sha256=-sqxK7LPV6sYDO_XXmZ80FznOaXTkVdbqJKKvTUtMak,20637
@@ -15,11 +15,11 @@ ipyvasp/widgets.py,sha256=fZ2b7EYYxuaAVfklnLa0VJ00U9Uyd7SqXrzt0hbLOvI,45400
 ipyvasp/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ipyvasp/core/parser.py,sha256=C3CaZsJbPME_ttYlYy4DXeOdL7dnkXs-cHRwFZL6bio,38058
 ipyvasp/core/plot_toolkit.py,sha256=8t5svyWbOm-PS7ZvIptnK6F46kp6uwoGNdohPv5dQKA,35962
-ipyvasp/core/serializer.py,sha256=_Ck51U_N6m4pTOkr3VxPtZumi8znrhneHjHuVtA7qDU,36661
+ipyvasp/core/serializer.py,sha256=XpqnfVGsUXiN2CuVRPyqsSVouxRBO-UH6AnsHnPYvZY,36729
 ipyvasp/core/spatial_toolkit.py,sha256=8DBYTiBFWJ7OBKuvOPw7UoEVCyNjJhSW0OcudjYZvAw,14748
-ipyvasp-0.9.1.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
-ipyvasp-0.9.1.dist-info/METADATA,sha256=1DwFCWMbumZTzK_LrDuuCTvlwinFEewM9RWGm-fa1oU,2420
-ipyvasp-0.9.1.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-ipyvasp-0.9.1.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
-ipyvasp-0.9.1.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
-ipyvasp-0.9.1.dist-info/RECORD,,
+ipyvasp-0.9.2.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
+ipyvasp-0.9.2.dist-info/METADATA,sha256=rbDpOJNtuinZ9AJi0pBcBTAYHLuoC_IbBvQagjXSHG4,2420
+ipyvasp-0.9.2.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+ipyvasp-0.9.2.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
+ipyvasp-0.9.2.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
+ipyvasp-0.9.2.dist-info/RECORD,,