ipyvasp 0.8.1__py2.py3-none-any.whl → 0.8.3__py2.py3-none-any.whl

ipyvasp/_lattice.py

@@ -1728,7 +1728,7 @@ def iplot_lattice(
         colors = [_atom_colors[elem] for elem in uelems.keys()]
         colors = ["rgb({},{},{})".format(*[int(_c * 255) for _c in c]) for c in colors]
 
-    _colors = np.array([colors[i] for i, vs in enumerate(uelems.values()) for v in vs])
+    _colors = np.array([colors[i] for i, vs in enumerate(uelems.values()) for v in vs],dtype=object) # could be mixed color types
 
     if np.any(pairs):
         coords_p = coords[pairs]  # paired points
@@ -1742,25 +1742,37 @@ def iplot_lattice(
             colors_n = [*colors_n, *_c]  # same shape.
 
         coords_n = np.array(coords_n)
-        colors_n = np.array(colors_n)
+        colors_n = np.array(colors_n, dtype=object)
+
+        # Instead of plotting for each pair, we can make only as little lines as types of atoms to speec up
+        unqc = [] # mixed colors type can't be sorted otherwise
+        for c in colors_n:
+            if c not in unqc:
+                unqc.append(c)
+
+        clabs = [unqc.index(c) for c in colors_n] # few colors categories
+        corder = np.argsort(clabs) # coordinates order for those categories
+
+        groups = dict([(i,[]) for i in range(len(unqc))])
+        for co in corder:
+            groups[clabs[co]].append(coords_n[co])
+            groups[clabs[co]].append([[np.nan, np.nan, np.nan]]) # nan to break links outside bonds
+
+        for i in range(len(unqc)):
+            groups[i] = np.concatenate(groups[i], axis=0)
 
         bond_kws = {"line_width": 4, **bond_kws}
 
-        for (i, cp), c in zip(enumerate(coords_n), colors_n):
+        for i, cp in groups.items():
             showlegend = True if i == 0 else False
-            fig.add_trace(
-                go.Scatter3d(
-                    x=cp[:, 0].T,
-                    y=cp[:, 1].T,
-                    z=cp[:, 2].T,
-                    mode="lines",
-                    line_color=c,
-                    legendgroup="Bonds",
-                    showlegend=showlegend,
-                    name="Bonds",
-                    **bond_kws,
-                )
-            )
+            fig.add_trace(go.Scatter3d(x=cp[:, 0].T, y=cp[:, 1].T, z=cp[:, 2].T,
+                mode="lines",
+                line_color=unqc[i],
+                legendgroup="Bonds",
+                showlegend=showlegend,
+                name="Bonds",
+                **bond_kws,
+            ))
 
     site_kws = {
         **dict(line_color="rgba(1,1,1,0)", line_width=0.001, opacity=1),

ipyvasp/_version.py

@@ -1 +1 @@
-__version__ = "0.8.1"
+__version__ = "0.8.3"

ipyvasp/lattice.py

@@ -530,7 +530,7 @@ class POSCAR:
 
 
     def update_weas(self, handle):
-        """Send result of any options to view on opened weas widget handle with default parameters becuase any operations 
+        """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())

{ipyvasp-0.8.1.dist-info → ipyvasp-0.8.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.1
+Version: 0.8.3
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.8.1.dist-info → ipyvasp-0.8.3.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=w2TMjj_joyx9Hh6w7bDaadRZWAZtDVnhrVv1LBbMl14,103718
-ipyvasp/_version.py,sha256=0lm9BoMiB5E8MMchhjjo1ZNAXLprgR2dERt6EhxaImk,23
+ipyvasp/_lattice.py,sha256=GlSoBwS_LckiZIArtZ3CbFfktG29oBqEAZtLHwYtzak,104390
+ipyvasp/_version.py,sha256=AM0-MB9td9-Rmee_1ARKY1bWYwq-qbjwR15DCGe0x6o,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=YUe2NRx3TqkWMgQ67-aGyGVWt3y_mbaVtqO9uPFB4iU,28466
+ipyvasp/lattice.py,sha256=t_aIkfVtD9Thi0b3ACEtAYcTuzt0SGCtub7hKV-Q83c,28468
 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=cHGlaDEyhlfsNgy5SDMcZewc2DIy7uyMyCmsrvOAqlM,33539
 ipyvasp/core/spatial_toolkit.py,sha256=8DBYTiBFWJ7OBKuvOPw7UoEVCyNjJhSW0OcudjYZvAw,14748
-ipyvasp-0.8.1.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
-ipyvasp-0.8.1.dist-info/METADATA,sha256=vZ0lf1cYIRWSJ2jVaP74T2rkDUMfw8JtTpA4FRg-_bc,2436
-ipyvasp-0.8.1.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-ipyvasp-0.8.1.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
-ipyvasp-0.8.1.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
-ipyvasp-0.8.1.dist-info/RECORD,,
+ipyvasp-0.8.3.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
+ipyvasp-0.8.3.dist-info/METADATA,sha256=D-Nih1mFlk8fKFpiqyWI-BRn-WjTO71qajTgY0V_IRc,2436
+ipyvasp-0.8.3.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+ipyvasp-0.8.3.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
+ipyvasp-0.8.3.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
+ipyvasp-0.8.3.dist-info/RECORD,,