ipyvasp 0.8.3__tar.gz → 0.8.5__tar.gz

{ipyvasp-0.8.3 → ipyvasp-0.8.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.3
+Version: 0.8.5
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.8.3 → ipyvasp-0.8.5}/ipyvasp/_lattice.py

@@ -23,7 +23,7 @@ from .core import parser as vp, serializer
 from .core.spatial_toolkit import (
     to_plane,
     rotation,
-    inside_convexhull,
+    inside_convexhull, # be there for export
     to_basis,
     to_R3,
     get_TM,
@@ -31,6 +31,7 @@ from .core.spatial_toolkit import (
     coplanar,
 )
 from .core.plot_toolkit import quiver3d
+from .utils import color as tcolor
 
 
 # These colors are taken from Mathematica's ColorData["Atoms"]
@@ -2397,12 +2398,12 @@ def convert_poscar(poscar_data, atoms_mapping, basis_factor):
     return serializer.PoscarData(poscar_data)  # Return new POSCAR
 
 
-def transform_poscar(poscar_data, transformation, zoom=2, tol=1e-2):
+def transform_poscar(poscar_data, transformation, fill_factor=2, tol=1e-2):
     """Transform a POSCAR with a given transformation matrix or function that takes old basis and return target basis.
     Use `get_TM(basis1, basis2)` to get transformation matrix from one basis to another or function to return new basis of your choice.
     An example of transformation function is `lambda a,b,c: a + b, a-b, c` which will give a new basis with a+b, a-b, c as basis vectors.
 
-    You may find errors due to missing atoms in the new basis, use `zoom` to increase the size of given cell to include any possible site in new cell.
+    You may find errors due to missing atoms in the new basis, use `fill_factor` and `tol` to include any possible site in new cell.
 
     Examples
     --------
@@ -2426,74 +2427,38 @@ def transform_poscar(poscar_data, transformation, zoom=2, tol=1e-2):
         raise Exception(
             "transformation should be a function that accept 3 arguemnts or 3x3 matrix"
         )
+    if not isinstance(fill_factor,int):
+        raise TypeError(f'fill_factor should be int, got {type(fill_factor)}')
 
-    def get_cell_vertices(basis):
-        verts = get_bz(basis, primitive=True).vertices
-        return verts - np.mean(
-            verts, axis=0
-        )  # Center around origin, otherwise it never going to be inside convex hull
-
-    TM = get_TM(
-        poscar_data.basis, new_basis
-    )  # Transformation matrix to save before scaling
-    old_numbers = [len(v) for v in poscar_data.types.to_dict().values()]
-    chull = ConvexHull(
-        np.max([zoom, 2]) * get_cell_vertices(new_basis)
-    )  # Convex hull of new cell, make it at least two times to avoid losing sites because of translation
-
-    while any(
-        inside_convexhull(chull, get_cell_vertices(poscar_data.basis))
-    ):  # Check if all vertices of old cell are inside new cell
-        poscar_data = scale_poscar(
-            poscar_data, [2, 2, 2], tol=tol
-        )  # Repeat in all directions
-
-    points = to_basis(
-        new_basis, poscar_data.coords
-    )  # Transform coordinates to new basis around origin
-
-    # Let's bring the most central point to origin
-    close_to_origin = np.linalg.norm(points - np.mean(points, axis=0), axis=1)
-    nearest_idx = np.argsort(close_to_origin)[0]
-    points = points - points[nearest_idx]  # one point is at origin now
+    _p = range(-fill_factor, fill_factor + 1)
+    pos = np.concatenate([poscar_data.positions,[[i] for i,_ in enumerate(poscar_data.positions)]], axis=1) # keep track of index
+    pos = np.concatenate([pos + [*p,0] for p in set(product(_p,_p,_p))],axis=0) # increaser by fill_factor^3
+    pos[:,:3] = to_basis(new_basis, poscar_data.to_cartesian(pos[:,:3])) # convert to coords in this and to points in new
+    pos = pos[(pos[:,:3] <= 1 - tol).all(axis=1) & (pos[:,:3] >= -tol).all(axis=1)]
+    pos = pos[pos[:,-1].argsort()] # sort for species
 
     new_poscar = poscar_data.to_dict()  # Update in it
     new_poscar["basis"] = new_basis
     new_poscar["metadata"]["scale"] = np.linalg.norm(new_basis[0])
     new_poscar["metadata"]["comment"] = f"Transformed by ipyvasp"
-    new_poscar["metadata"][
-        "TM"
-    ] = TM  # Save transformation matrix in both function and matrix given
+    new_poscar["metadata"]["TM"] = get_TM(poscar_data.basis, new_basis)  # save Transformation matrix
+    old_numbers = [len(v) for v in poscar_data.types.values()]
 
-    uelems = poscar_data.types.to_dict()
-    positions, shift, unique_dict = [], 0, {}
-    for key, value in uelems.items():
-        s_p = points[value]
-        s_p = s_p[
-            ((s_p > -tol) & (s_p < 1 - tol)).all(axis=1)
-        ]  # Get sites within tolerance, for very far sites
 
-        if s_p.size == 0:
-            raise Exception(
-                f"No sites found for {key!r}, transformation stopped! You may need to modify `transformation` or increase `zoom` value."
-            )
+    uelems, start = {}, 0
+    for k, v in poscar_data.types.items():
+        uelems[k] = range(start, start + len(pos[(pos[:,-1] >= v.start) & (pos[:,-1] < v.stop)]))
+        start = uelems[k].stop
 
-        unique_dict[key] = range(shift, shift + len(s_p))
-        positions = [*positions, *s_p]  # Pick sites
-        shift += len(s_p)  # Update for next element
-
-    # Final check if crystal is still same
-    new_numbers = [len(v) for v in unique_dict.values()]
-    ratio = [
-        round(new / old, 4) for new, old in zip(new_numbers, old_numbers)
-    ]  # Round to avoid floating point errors,can cover 1 to 10000 atoms transformation
+    # warn if crystal formula changes
+    new_numbers = [len(v) for v in uelems.values()]
+    ratio = (np.array(new_numbers)/old_numbers).round(4) # Round to avoid floating point errors,can cover 1 to 10000 atoms transformation
     if len(np.unique(ratio)) != 1:
-        raise Exception(
-            f"Transformation failed, atoms proportion changed: {old_numbers} -> {new_numbers}, if your transformation is an allowed one for this structure, increase `zoom` value."
-        )
+        print(tcolor.rb(f"WARNING: Transformation failed, atoms proportion changed: {old_numbers} -> {new_numbers}." 
+              " If your transformation is an allowed one for this structure, increase `fill_factor` or `tol`."))
 
-    new_poscar["types"] = unique_dict
-    new_poscar["positions"] = np.array(positions)
+    new_poscar["types"] = uelems
+    new_poscar["positions"] = np.array(pos[:,:3])
     return serializer.PoscarData(new_poscar)
 
 

ipyvasp-0.8.5/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.8.5"

{ipyvasp-0.8.3 → ipyvasp-0.8.5}/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-0.8.3 → ipyvasp-0.8.5}/ipyvasp/lattice.py

@@ -685,9 +685,9 @@ class POSCAR:
         return stk.get_TM(self.data.basis, target_basis)
 
     @_sub_doc(plat.transform_poscar)
-    def transform(self, transformation, zoom=2, tol=1e-2):
+    def transform(self, transformation, fill_factor=2, tol=1e-2):
         return self.__class__(
-            data=plat.transform_poscar(self.data, transformation, zoom=zoom, tol=tol)
+            data=plat.transform_poscar(self.data, transformation, fill_factor=fill_factor, tol=tol)
         )
 
     @_sub_doc(plat.transpose_poscar)

{ipyvasp-0.8.3 → ipyvasp-0.8.5}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.3
+Version: 0.8.5
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

ipyvasp-0.8.3/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.8.3"