ipyvasp 0.8.8__tar.gz → 0.9.0__tar.gz

{ipyvasp-0.8.8 → ipyvasp-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.8
+Version: 0.9.0
 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 → ipyvasp-0.9.0}/ipyvasp/_lattice.py

@@ -1447,9 +1447,9 @@ def _fix_sites(
         pos = pos + (txyz - txyz.astype(int))
 
     # Fix coordinates of sites distributed on edges and faces
-    pos -= (pos > (1 - tol)).astype(
-        int
-    )  # Move towards orign for common fixing like in joining POSCARs
+    if not hasattr(poscar_data.metadata, 'source_indices'): # no more fixing over there
+        pos -= (pos > (1 - tol)).astype(int)  # Move towards orign for common fixing like in joining POSCARs
+    
     out_dict["positions"] = pos
     out_dict["metadata"]["comment"] = "Modified by ipyvasp"
 
@@ -1460,45 +1460,14 @@ def _fix_sites(
             vpos = pos[v]
             vlabs = labels[v]
             inds = np.array(v)
-            cond_ops = [
-                (
-                    ((vpos[:, 0] + 1) < (tol + 1)),
-                    [[1, 0, 0]],
-                ),  # Add 1 to x if within tol
-                (
-                    ((vpos[:, 1] + 1) < (tol + 1)),
-                    [[0, 1, 0]],
-                ),  # Add 1 to y on modified and if within tol
-                (
-                    ((vpos[:, 2] + 1) < (tol + 1)),
-                    [[0, 0, 1]],
-                ),  # Add 1 to z and if within tol
-                (
-                    ((vpos[:, 0:2] + 1) < (tol + 1)).all(axis=1),
-                    [[1, 1, 0]],
-                ),  # Add 1 to x and y if within tol
-                (
-                    ((vpos[:, 1:3] + 1) < (tol + 1)).all(axis=1),
-                    [[0, 1, 1]],
-                ),  # Add 1 to y and z if within tol
-                (
-                    ((vpos[:, [0, 2]] + 1) < (tol + 1)).all(axis=1),
-                    [[1, 0, 1]],
-                ),  # Add 1 to x and z if within tol
-                (
-                    ((vpos + 1) < (tol + 1)).all(axis=1),
-                    [[1, 1, 1]],
-                ),  # Add 1 to all if within tol
-            ]
-            spos = [vpos[c] + op for c, op in cond_ops]
-            slab = [vlabs[c] for c, op in cond_ops]
-            sinds = [inds[c] for c, op in cond_ops]
-
-            new_dict[k] = {
-                "pos": np.vstack([vpos, *spos]),
-                "lab": np.hstack([vlabs, *slab]),
-                "inds": np.hstack([inds, *sinds]),
-            }
+
+            ivpos = np.concatenate([np.indices((len(vpos),)).reshape((-1,1)),vpos],axis=1) # track of indices
+            ivpos = np.array([ivpos + [0, *p] for p in set(product([-1,0,1],[-1,0,1],[-1,0,1]))]).reshape((-1,4))
+            ivpos = ivpos[(ivpos[:,1:] > -tol).all(axis=1) & (ivpos[:,1:] < 1 + tol).all(axis=1)]
+            ivpos = ivpos[ivpos[:,0].argsort()]
+            idxs = ivpos[:,0].ravel().astype(int).tolist()
+
+            new_dict[k] = {"pos": ivpos[:,1:], "lab": vlabs[idxs], "inds": inds[idxs]}
             new_dict[k]["range"] = range(start, start + len(new_dict[k]["pos"]))
             start += len(new_dict[k]["pos"])
 
@@ -1622,41 +1591,35 @@ def _filter_pairs(labels, pairs, dist, bond_length):
     # Return all pairs otherwise
     return pairs  # None -> auto calculate bond_length, number -> use that number
 
-
 def filter_sites(poscar_data, func, tol = 0.01):
     """Filter sites based on a function that acts on index and fractional positions such as `lambda i,x,y,z: condition`. 
-    This may include equivalent sites, so it should be used for plotting purpose only, e.g. showing atoms on a plane."""
+    This may include equivalent sites, so it should be used for plotting purpose only, e.g. showing atoms on a plane.
+    An attribute `source_indices` is added to metadata which is useful to pick other things such as `OUTCAR.ion_pot[POSCAR.filter(...).data.metadata.source_indices]`. 
+    """
+    if hasattr(poscar_data.metadata, 'source_indices'):
+        raise ValueError("Cannot filter an already filtered POSCAR data.")
+    
+    poscar_data = _fix_sites(poscar_data, tol = tol, eqv_sites=True)
     idxs = _masked_data(poscar_data, func)
     data = poscar_data.to_dict() 
-    all_pos, npos = [], []
+    all_pos, npos, eqv_labs, finds = [], [0,],[],[]
     for value in poscar_data.types.values():
-        indices = [i for i in value if i in idxs]
-        others = [j for j in value if not (j in indices)]
+        indices = [i for i in value if i in idxs] # search from value make sure only non-equivalent sites added
+        finds.extend(poscar_data.metadata.eqv_indices[indices])
+        eqv_labs.extend(poscar_data.labels[indices])
         pos = data['positions'][indices]
-        qos = data['positions'][others] # need edge items to include
-
-        if qos.size:
-            qos = np.concatenate([[[i] for i in others], qos], axis=1) # need to keep index
-            qos = np.array([qos + [0, *p] for p in product([-1,0,1],[-1,0,1],[-1,0,1])]).reshape((-1,4)) # all possible translations
-            qos = qos[(qos[:,1:] < 1 + tol).all(axis=1) & (qos[:,1:] > -tol).all(axis=1)]# only in cell range
-            qos = qos[[func(*q) for q in qos]] # masked only those are true
-        
-        if qos.size:
-            pos = np.concatenate([pos, qos[:,1:]],axis=0)
-
         all_pos.append(pos)
         npos.append(len(pos))
     
     if not np.sum(npos):
         raise ValueError("No sites found with given filter func!")
     
-    if not 'prev_positions' in data['metadata']: # keep always the starting one
-        data['metadata']['prev_positions'] = poscar_data.positions 
-        data['metadata']['prev_types'] = poscar_data.types
-    
     data['positions'] = np.concatenate(all_pos, axis = 0)
+    data['metadata']['source_indices'] = np.array(finds)
+    data['metadata']['eqv_labels']  = np.array(eqv_labs) # need these for compare to previous
+    data['metadata'].pop('eqv_indices', None) # no need of this
 
-    ranges = np.cumsum([0, *npos])
+    ranges = np.cumsum(npos)
     data['types'] = {key: range(i,j) for key, i,j in zip(data['types'],ranges[:-1],ranges[1:]) if range(i,j)} # avoid empty
     return serializer.PoscarData(data)
 

ipyvasp-0.9.0/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.9.0"

{ipyvasp-0.8.8 → ipyvasp-0.9.0}/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-0.8.8 → ipyvasp-0.9.0}/ipyvasp/lattice.py

@@ -85,6 +85,7 @@ def ngl_viewer(
     plot_vectors=True,
     dashboard=False,
     origin=(0, 0, 0),
+    eqv_sites = True,
 ):
     """Display structure in Jupyter notebook using nglview.
 
@@ -135,7 +136,7 @@ def ngl_viewer(
 
     # Only show equivalent sites if plotting cell, only shift origin otherwise
     poscar = POSCAR(  # don't change instance itself, make new one
-        data=plat._fix_sites(poscar.data, eqv_sites=True if plot_cell else False, origin=origin)
+        data=plat._fix_sites(poscar.data, eqv_sites=eqv_sites, origin=origin)
     )
 
     _types = poscar.data.types.to_dict()
@@ -187,7 +188,8 @@ def weas_viewer(poscar,
     bond_length=None,
     model_style = 1,
     plot_cell=True,
-    origin = (0,0,0)
+    origin = (0,0,0),
+    eqv_sites = True,
     ):
     """
     sizes : float or dict of type -> float
@@ -215,7 +217,7 @@ def weas_viewer(poscar,
     
     # Only show equivalent sites if plotting cell, only shift origin otherwise
     poscar = POSCAR(  # don't change instance itself, make new one
-        data=plat._fix_sites(poscar.data, eqv_sites=True if plot_cell else False, origin=origin)
+        data=plat._fix_sites(poscar.data, eqv_sites=eqv_sites, origin=origin)
     )
 
     w = WeasWidget(from_ase=poscar.to_ase())
@@ -293,7 +295,7 @@ 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
@@ -565,6 +567,11 @@ class POSCAR:
     def data(self):
         "Data object in POSCAR."
         return self._data
+    
+    @property
+    def metadata(self):
+        "Metadata associated with this POSCAR."
+        return self._data.metadata
 
     def copy(self):
         "Copy POSCAR object. It avoids accidental changes to numpy arrays in original object."
@@ -674,8 +681,8 @@ class POSCAR:
     
     @_sub_doc(plat.filter_sites)
     @_sig_kwargs(plat.filter_sites,("poscar_data",))
-    def filter_sites(self, func):
-        return self.__class__(data = plat.filter_sites(self.data, func))
+    def filter_sites(self, func, tol=0.01):
+        return self.__class__(data = plat.filter_sites(self.data, func,tol=tol))
 
     @_sub_doc(plat.set_origin)
     def set_origin(self, origin):

{ipyvasp-0.8.8 → ipyvasp-0.9.0}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.8
+Version: 0.9.0
 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/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.8.8"