ipyvasp 0.8.2__py2.py3-none-any.whl → 0.8.4__py2.py3-none-any.whl

ipyvasp/_lattice.py

@@ -1753,12 +1753,12 @@ def iplot_lattice(
         clabs = [unqc.index(c) for c in colors_n] # few colors categories
         corder = np.argsort(clabs) # coordinates order for those categories
 
-        groups = {0:[],1:[],2:[]}
+        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]])
+            groups[clabs[co]].append([[np.nan, np.nan, np.nan]]) # nan to break links outside bonds
 
-        for i in range(3):
+        for i in range(len(unqc)):
             groups[i] = np.concatenate(groups[i], axis=0)
 
         bond_kws = {"line_width": 4, **bond_kws}

ipyvasp/_version.py

@@ -1 +1 @@
-__version__ = "0.8.2"
+__version__ = "0.8.4"

ipyvasp/core/serializer.py

@@ -12,11 +12,12 @@ import json, re
 import pickle
 import inspect
 from collections import namedtuple
-from itertools import product
+from itertools import product,combinations
 from copy import deepcopy
 from pathlib import Path
 
 import numpy as np
+from pandas import DataFrame
 from scipy.spatial import KDTree
 
 from .spatial_toolkit import (
@@ -352,7 +353,6 @@ 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
-        output[:,1:] = np.sort(output[:,1:], axis=1)  # sort the indices of neighbors
         return output
 
     get_knn = get_neighbors  # important alias
@@ -402,6 +402,50 @@ class PoscarData(Dict2Data):
         dists = dists[dists > 0]  # Remove distance with itself
         return np.min(dists) if dists.size else np.nan
     
+    
+    def get_distances(self, type1, type2, min=-np.infty, max=np.infty):
+        """Get an array of all distnaces in a range set by min and max between type 1 and type2.
+        For example `get_distances('Ga','As',2,3)[:,-1].mean()` can be used to get average bond length between Ga and As in GaAs. 
+        Returned array is of shape (N,3) where first two entries in columns are indices of pairs between which distance was calculated.
+        """
+        out = []
+        for i in self.types[type1]:
+            for j in [k for k in self.types[type2] if k != i]:
+                a = self.coords[i]
+                bs = [self.to_cartesian(self.positions[j] + p) for p in set(product([-1,0,1],[-1,0,1],[-1,0,1]))]
+                ds = np.array([np.linalg.norm(a-b) for b in bs])
+                d = ds[ds > 0].min() # no same site distance
+                if min < d < max:
+                    out.append([i, j, d])
+        out = np.array(out,dtype=object)
+        return out[out[:,-1].argsort()] if out.size else out
+    
+
+    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."
+        if k < 3:
+            raise ValueError("k >= 3 is required!")
+    
+        idxs = self.get_knn(k)[list(site_indices)]
+        out = []
+        for i, *js in idxs:
+            a = self.coords[i]
+            nears = []  # neaigbors could be on other side, bring close
+            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]))
+            
+            for (m,b),(n, c) 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])
+                
+        columns = 'bond a o b angle d_ao d_bo ax ay az ox oy oz bx by bz'.split()
+        return DataFrame(out, columns=columns)
+    
     def to_fractional(self, coords):
         "Converts cartesian coordinates to fractional coordinates in the basis of cell."
         return to_basis(self.basis, coords)

{ipyvasp-0.8.2.dist-info → ipyvasp-0.8.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.2
+Version: 0.8.4
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.8.2.dist-info → ipyvasp-0.8.4.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=c7IXlc9wgkXQhRMUASx6AYelvOUgY_kdC9UgCYWcqrY,104323
-ipyvasp/_version.py,sha256=UcaL9hG0xAfKWNMY82a1It6J8RjG16fehQmQxqtxSuk,23
+ipyvasp/_lattice.py,sha256=GlSoBwS_LckiZIArtZ3CbFfktG29oBqEAZtLHwYtzak,104390
+ipyvasp/_version.py,sha256=xN6PfPY25p649J9o3dNFb_Eo4-lIyF4ED9Z8avJ_oLw,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=cktbPZTJ4K0_6-vKYqtQ1xIIPZg-gHJY5793M9XoYQ0,35754
-ipyvasp/core/serializer.py,sha256=cHGlaDEyhlfsNgy5SDMcZewc2DIy7uyMyCmsrvOAqlM,33539
+ipyvasp/core/serializer.py,sha256=OsnYhlwt8O6UeJQMKmjp1-hwRjhxiqobV6bybfDECUY,35777
 ipyvasp/core/spatial_toolkit.py,sha256=8DBYTiBFWJ7OBKuvOPw7UoEVCyNjJhSW0OcudjYZvAw,14748
-ipyvasp-0.8.2.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
-ipyvasp-0.8.2.dist-info/METADATA,sha256=I8LjhKFTv6dbwOC6p0Sq8StMK_yZ4-29CXPFE1B09cE,2436
-ipyvasp-0.8.2.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-ipyvasp-0.8.2.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
-ipyvasp-0.8.2.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
-ipyvasp-0.8.2.dist-info/RECORD,,
+ipyvasp-0.8.4.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
+ipyvasp-0.8.4.dist-info/METADATA,sha256=kqxdZoEwpufVzOboGCLzNj_Q9y0I8cjcbWLz-FtSl-Q,2436
+ipyvasp-0.8.4.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+ipyvasp-0.8.4.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
+ipyvasp-0.8.4.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
+ipyvasp-0.8.4.dist-info/RECORD,,