ipyvasp 0.8.9__py2.py3-none-any.whl → 0.9.0__py2.py3-none-any.whl

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/_version.py

@@ -1 +1 @@
-__version__ = "0.8.9"
+__version__ = "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())
@@ -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-0.8.9.dist-info → ipyvasp-0.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.9
+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-0.8.9.dist-info → ipyvasp-0.9.0.dist-info}/RECORD

@@ -1,12 +1,12 @@
 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=Fj0n620aEHCHlsmEXmEGKx9B0YdzMeN3Yc9ZouxRIBU,23
+ipyvasp/_lattice.py,sha256=ASHTQV3QK4mhx7eO3ISLvzm4fTg5KGiQ3iI0BqfmEac,102978
+ipyvasp/_version.py,sha256=Rqk_eJf2ntSg0XlEKqShPvNr_E2rQ3wfdU2Xyp-R4ls,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=Ow9BJa8ceasquLPOqsnpj2ysf45IHta1wLtEXoDHtTw,29642
+ipyvasp/lattice.py,sha256=t7lkewCbN8IFUIKia9Xkc8p0pTDBc_34NIrlWsXENGA,29800
 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
@@ -17,9 +17,9 @@ ipyvasp/core/parser.py,sha256=C3CaZsJbPME_ttYlYy4DXeOdL7dnkXs-cHRwFZL6bio,38058
 ipyvasp/core/plot_toolkit.py,sha256=8t5svyWbOm-PS7ZvIptnK6F46kp6uwoGNdohPv5dQKA,35962
 ipyvasp/core/serializer.py,sha256=57e2ypF18tJI1zZi9kJiHGMBYgXvYEZpLmgnaaDdSk0,36067
 ipyvasp/core/spatial_toolkit.py,sha256=8DBYTiBFWJ7OBKuvOPw7UoEVCyNjJhSW0OcudjYZvAw,14748
-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,,
+ipyvasp-0.9.0.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
+ipyvasp-0.9.0.dist-info/METADATA,sha256=q73Rkc1Kx_HfNBgB0LT-4Ca8EFz7wXr_9mgquNeGC9I,2420
+ipyvasp-0.9.0.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+ipyvasp-0.9.0.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
+ipyvasp-0.9.0.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
+ipyvasp-0.9.0.dist-info/RECORD,,