ipyvasp 0.9.81__py2.py3-none-any.whl → 0.9.82__py2.py3-none-any.whl

ipyvasp/_version.py

@@ -1 +1 @@
-__version__ = "0.9.81"
+__version__ = "0.9.82"

ipyvasp/core/spatial_toolkit.py

@@ -315,6 +315,9 @@ def get_bz(basis, loop=True, primitive=False):
         "vertices": verts,
         "faces": idx_faces,
         "primitive": primitive,
+        "edges": np.unique(
+            np.sort([[i,j] for f in idx_faces for i,j in zip(f[:-1],f[1:])], axis=1),
+            axis=0)
     }
     from .serializer import BrZoneData  # to avoid circular import
 

ipyvasp/lattice.py

@@ -18,11 +18,13 @@ from contextlib import suppress
 import numpy as np
 from pandas.io.clipboard import clipboard_get, clipboard_set
 import matplotlib.colors as mcolors
+from mpl_toolkits.mplot3d.art3d import Poly3DCollection
+import plotly.graph_objects as go 
 
 
 from .core import serializer
 from .core import spatial_toolkit as stk
-from .core.plot_toolkit import iplot2widget
+from .core.plot_toolkit import get_axes, iplot2widget
 from .utils import _sig_kwargs, _sub_doc
 from . import _lattice as plat
 from ._lattice import (
@@ -354,11 +356,11 @@ class POSCAR:
     
     @property
     def last(self):
-        """Points to last created POSCAR instance during chained operations! You don't need to store results
+        """Points to last created POSCAR instance during chained operations! You don't need to store results.
         
         ```python
         pc = POSCAR()
-        pc.filter_atoms(lambda a: a.index in pc.data.types.Ga) # FINE
+        pc.filter_atoms(lambda a: a.index in pc.data.types.Ga) # FINE, can use a.symbol == 'Ga' too, but we need to show a point below
         pc.set_boundary([-2,2]).filter_atoms(lambda a: a.index in pc.data.types.Ga) # INCORRECT sites picked
         pc.set_boundary([-2,2]).filter_atoms(lambda a: a.index in pc.last.data.types.Ga) # PERFECT, pc.last is output of set_boundary
         ```
@@ -626,6 +628,57 @@ class POSCAR:
         if not hasattr(self, "_cell"):
             self._cell = self.get_cell()
         return self._cell
+    
+    def get_plane(self, hkl, d=1/2,tol=1e-2):
+        """Returns Nx3 vertices of a plane bound inside cell. .
+        hkl should be list of three miller indices. d is fractional distance in range 0,1 in direction of hkl. 
+        e.g. if there are 8 planes of atoms in a cubic cell, d = 0, 1/8,...7/8, 1 match position of those planes.
+        """
+        from sympy import Point3D, Line3D, Plane
+        V = self.data.rec_basis.dot(hkl)
+        normal = V/np.linalg.norm(V)
+        point = d*normal*np.linalg.norm(self.data.basis.dot(hkl)) # to make d 0-1
+        P = Plane(Point3D(*point),normal_vector=normal)
+
+        pts = []
+        for e in self.cell.vertices[self.cell.edges]:
+            L = Line3D(Point3D(*e[0]),Point3D(*e[1]))
+            if (isc := P.intersection(L)) and isinstance(isc[0],Point3D):
+                pts.append(isc[0])
+
+        pts = np.unique(np.array(pts,dtype=float),axis=0)
+        pts = pts[stk.order(pts,)]
+        qts = self.cell.to_fractional(pts)
+        qts = qts[(qts >= -tol).all(axis=1) & (qts <= 1 + tol).all(axis=1)]
+        pts = self.cell.to_cartesian(qts)
+        return pts
+    
+    def splot_plane(self, hkl, d=1/2,tol=1e-2,ax=None, **kwargs):
+        """Provide hkl and a 3D axes to plot plane. kwargs are passed to `mpl_toolkits.mplot3d.art3d.Poly3DCollection`
+        Note: You may get wrong plane if your basis are not aligned to axes. So you can use `transpose` or `set_zdir` methods before plottling cell.
+        """
+        P = self.get_plane(hkl,d=d,tol=tol)
+        if ax is None:
+            ax = get_axes(axes_3d=True)
+            ax.set( # it does not show otherwise
+                xlim=[P[:,0].min(),P[:,0].max()],
+                ylim=[P[:,1].min(),P[:,1].max()],
+                zlim=[P[:,2].min(),P[:,2].max()]
+            )
+        kwargs = {'alpha':0.5,'color':'#898','shade': False, **kwargs}
+        ax.add_collection(Poly3DCollection([P],**kwargs))
+        ax.autoscale_view()
+        return ax
+
+    def iplot_plane(self, hkl, d = 1/2, tol=1e-3, fig=None,**kwargs):
+        "Plot plane on a plotly Figure. kwargs are passed to `plotly.graph_objects.Mesh3d`."
+        if fig is None:
+            fig = go.Figure()
+
+        P = self.get_plane(hkl,d=d,tol=tol)
+        kwargs = {**dict(color='#8a8',opacity=0.7,alphahull=0, showlegend=True,name=str(hkl)),**kwargs}
+        fig.add_trace(go.Mesh3d({k:v for v,k in zip(P.T, 'xyz')},**kwargs))
+        return fig
 
     @_sub_doc(stk.get_bz, {"basis :.*loop :": "loop :"})
     @_sig_kwargs(stk.get_bz, ("basis",))

{ipyvasp-0.9.81.dist-info → ipyvasp-0.9.82.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.81
+Version: 0.9.82
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.9.81.dist-info → ipyvasp-0.9.82.dist-info}/RECORD

@@ -2,11 +2,11 @@ ipyvasp/__init__.py,sha256=rlorju9arMtHw1QRYPljday-PyZWJdSCxg4lw3g6t0Q,1409
 ipyvasp/__main__.py,sha256=eJV1TZSiT8mC_VqAeksNnBI2I8mKMiPkEIlwikbtOjI,216
 ipyvasp/_enplots.py,sha256=D38paN8zqZgluNAwmCwcocd7-_h_T0HTGolI1eBkDes,37484
 ipyvasp/_lattice.py,sha256=8jaiSBz0cKfAwzkLQTCOvPNOBVeWtL5tahgp-LIoDdk,105571
-ipyvasp/_version.py,sha256=CTUf1M5sj6XFicmUC1ATWl8zxY86WlKZLcC7FUJ7tEs,24
+ipyvasp/_version.py,sha256=Oukmd6D0UJTqAdg4-8VB8ZHKeAiTHoyIqdUQToKmrkg,24
 ipyvasp/bsdos.py,sha256=JvYvHLqMp3eVaJ0amD-9kxp7FehQIFq3WFUxsO5dj0Q,31794
 ipyvasp/cli.py,sha256=aWFEVhNmnW8eSOp5uh95JaDwLQ9K9nlCQcbnOSuhWgw,6844
 ipyvasp/evals_dataframe.py,sha256=-sqxK7LPV6sYDO_XXmZ80FznOaXTkVdbqJKKvTUtMak,20637
-ipyvasp/lattice.py,sha256=r53Vpa4jmP3zyu4LDR7uSYtYN27nbbtbtqG1235xw74,30735
+ipyvasp/lattice.py,sha256=sibDi_3rzMRVzwRNmF0rE1qLFWZdMKs9VCu66NLOmQM,33389
 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
@@ -16,10 +16,10 @@ ipyvasp/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ipyvasp/core/parser.py,sha256=TmRoIhyIGJ4nr32tb1MAAy5clUZh0CQh-2hP8mnTaVc,38221
 ipyvasp/core/plot_toolkit.py,sha256=3RoPsND5gPssBSfS5H4TjoZ2Qz7B97vpxeKadc2cRRs,36046
 ipyvasp/core/serializer.py,sha256=-PvCDXZqaCTnwBY5CS_B7_cmnbKy3g6cfEOr_Nrbde8,38415
-ipyvasp/core/spatial_toolkit.py,sha256=8DBYTiBFWJ7OBKuvOPw7UoEVCyNjJhSW0OcudjYZvAw,14748
-ipyvasp-0.9.81.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
-ipyvasp-0.9.81.dist-info/METADATA,sha256=ki2crXrujbpJ8e7hkfA6AJOFq4BxV-6S1dNozy45nA0,2421
-ipyvasp-0.9.81.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-ipyvasp-0.9.81.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
-ipyvasp-0.9.81.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
-ipyvasp-0.9.81.dist-info/RECORD,,
+ipyvasp/core/spatial_toolkit.py,sha256=dXowREhiFzBvvr5f_bApzFhf8IzjH2E2Ix90oCBUetY,14885
+ipyvasp-0.9.82.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
+ipyvasp-0.9.82.dist-info/METADATA,sha256=QoQeGuDqagJcuMNorpZL9w8qW2IivoxL-5I_JvdOHWs,2421
+ipyvasp-0.9.82.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+ipyvasp-0.9.82.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
+ipyvasp-0.9.82.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
+ipyvasp-0.9.82.dist-info/RECORD,,