ipyvasp 0.8.8__py2.py3-none-any.whl → 0.8.9__py2.py3-none-any.whl

ipyvasp/_version.py

@@ -1 +1 @@
-__version__ = "0.8.8"
+__version__ = "0.8.9"

ipyvasp/core/serializer.py

@@ -422,7 +422,9 @@ class PoscarData(Dict2Data):
     
 
     def get_bond_data(self, site_indices, k = 5):
-        "Returns a DataFrame with bonds angle, bond length, vector positions etc. that can be used for plotting."
+        """Returns a DataFrame with bonds angle, bond length, vector positions etc. that can be used for plotting.
+        t_a and t_b are translation vectors to get them near selected sites. You can use `POSCAR.translate` if somehow need nearest coordinates.
+        """
         if k < 3:
             raise ValueError("k >= 3 is required!")
     
@@ -434,16 +436,18 @@ 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])
-                nears.append((j, bs[ds.argsort()][0]))
+                b = bs[ds.argsort()][0]
+                t = tuple((self.to_fractional(b) - self.positions[j]).astype(int)) # keep track of translation vector
+                nears.append((j, b, t))
             
-            for (m,b),(n, c) in combinations(nears,2):
-                v1, v2 = b-a, c-a
+            for (m,b,t1),(n, c,t2) in combinations(nears,2):
+                v1, v2 = b - a, c - a
                 n1, n2 = np.linalg.norm(v1), np.linalg.norm(v2)
                 name = '-'.join(self.symbols[[m,i,n]])
                 angle = np.degrees(np.arccos(v1.dot(v2)/(n1*n2)))
-                out.append([name, m,i,n, angle, n1, n2, *b, *a,  *c])
+                out.append([name, m,i,n, angle, n1, n2, t1,t2])
                 
-        columns = 'bond a o b angle d_ao d_bo ax ay az ox oy oz bx by bz'.split()
+        columns = 'bond a o b angle d_ao d_bo t_a t_b'.split()
         return DataFrame(out, columns=columns)
     
     def to_fractional(self, coords):

ipyvasp/lattice.py

@@ -293,7 +293,7 @@ class _AutoRenderer:
         return self._kws.copy() # avoid messing original
     
     def __repr__(self):
-        return f"AutoRenderer({self._kws})"
+        return f"AutoRenderer(params = {self._kws})"
 
 class POSCAR:
     _cb_instance = {}  # Loads last clipboard data if not changed

{ipyvasp-0.8.8.dist-info → ipyvasp-0.8.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.8
+Version: 0.8.9
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.8.8.dist-info → ipyvasp-0.8.9.dist-info}/RECORD

@@ -2,11 +2,11 @@ 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=TaiPj_cbBkmuCd40hM01_grNVLcn2hK70fTCN98GNgU,104018
-ipyvasp/_version.py,sha256=res1ssOJOgo4kIcsmM7GoDSrzysf0WOto1Y4Ht13EkE,23
+ipyvasp/_version.py,sha256=Fj0n620aEHCHlsmEXmEGKx9B0YdzMeN3Yc9ZouxRIBU,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=BaaIbf4c2tGv-FnucYfi_-oz_Ftk2UF5zWY2uwRM3yk,29633
+ipyvasp/lattice.py,sha256=Ow9BJa8ceasquLPOqsnpj2ysf45IHta1wLtEXoDHtTw,29642
 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
@@ -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=OsnYhlwt8O6UeJQMKmjp1-hwRjhxiqobV6bybfDECUY,35777
+ipyvasp/core/serializer.py,sha256=57e2ypF18tJI1zZi9kJiHGMBYgXvYEZpLmgnaaDdSk0,36067
 ipyvasp/core/spatial_toolkit.py,sha256=8DBYTiBFWJ7OBKuvOPw7UoEVCyNjJhSW0OcudjYZvAw,14748
-ipyvasp-0.8.8.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
-ipyvasp-0.8.8.dist-info/METADATA,sha256=H5l59fHjtTm__MaJClOvImDd75wAGaaNsPkdEEMkXBs,2420
-ipyvasp-0.8.8.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-ipyvasp-0.8.8.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
-ipyvasp-0.8.8.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
-ipyvasp-0.8.8.dist-info/RECORD,,
+ipyvasp-0.8.9.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
+ipyvasp-0.8.9.dist-info/METADATA,sha256=GcN76IweS9RJKKCj7fxtZwyap1w97BO1_hSDHnEk3Q8,2420
+ipyvasp-0.8.9.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+ipyvasp-0.8.9.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
+ipyvasp-0.8.9.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
+ipyvasp-0.8.9.dist-info/RECORD,,