ipyvasp 0.8.9__py2.py3-none-any.whl → 0.9.1__py2.py3-none-any.whl

ipyvasp/_lattice.py

@@ -1440,65 +1440,34 @@ def _fix_sites(
     labels = np.array(poscar_data.labels)  # We need to store equivalent labels as well
     out_dict = poscar_data.to_dict()  # For output
 
-    if translate and isinstance(translate, (int, np.integer, float)):
+    if isinstance(translate, (int, np.integer, float)):
         pos = pos + (translate - int(translate))  # Only translate in 0 - 1
-    elif translate and len(translate) == 3:
+    elif isinstance(translate,(tuple, list, np.ndarray)) and len(translate) == 3:
         txyz = np.array([translate])
         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 getattr(poscar_data.metadata, 'eqv_fix', True): # 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"
 
     # Add equivalent sites on edges and faces if given,handle each sepecies separately
-    if eqv_sites:
+    if eqv_sites and getattr(poscar_data.metadata, 'eqv_fix', True): 
         new_dict, start = {}, 0
         for k, v in out_dict["types"].items():
             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 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"])
 
@@ -1594,9 +1563,7 @@ def _masked_data(poscar_data, func):
     if not isinstance(func(0, 0, 0, 0), bool):
         raise TypeError("`func` should return a boolean value.")
 
-    eqv_inds = None
-    if hasattr(poscar_data.metadata, "eqv_indices"):
-        eqv_inds = tuple(poscar_data.metadata.eqv_indices)
+    eqv_inds  = tuple(getattr(poscar_data.metadata, "eqv_indices",[]))
 
     pick = []
     for i, pos in enumerate(poscar_data.positions):
@@ -1622,41 +1589,39 @@ 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]`. 
+
+    Note: If you are filtering a plane with more than one non-zero hkl like 110, you may first need to translate or set boundary on POSCAR to bring desired plane in full view to include all atoms.
+    """
+    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 = [], []
+    eqvi = data['metadata'].pop('eqv_indices', []) # no need of this
+    
+    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(eqvi[indices] if len(eqvi) else 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_fix'] = False
+    data['metadata']['eqv_labels']  = np.array(eqv_labs) # need these for compare to previous
 
-    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)
 
@@ -2241,7 +2206,7 @@ def scale_poscar(poscar_data, scale=(1, 1, 1), tol=1e-2):
     return serializer.PoscarData(new_poscar)
 
 def set_boundary(poscar_data, a = [0,1], b = [0,1], c = [0,1]):
-    "View atoms outside cell boundary along a,b,c directions."
+    "View atoms in a given boundary along a,b,c directions."
     for d, name in zip([a,b,c],'abc'):
         if not isinstance(d,(list,tuple)) or len(d) != 2:
             raise ValueError(f"{name} should be a list/tuple of type [min, max]")
@@ -2253,17 +2218,13 @@ def set_boundary(poscar_data, a = [0,1], b = [0,1], c = [0,1]):
     for key, value in poscar_data.types.items():
         pos = data['positions'][value]
         for i, (l,h), shift in zip(range(3), [a,b,c],np.eye(3)):
-            while pos[:,i].min() > np.floor(l):
-                pos = np.concatenate([pos, pos - shift],axis=0)
-            
-            while pos[:,i].max() < np.ceil(h):
-                pos = np.concatenate([pos, pos + shift],axis=0)
-
+            pos = np.concatenate([pos + shift*k for k in np.arange(np.floor(l), np.ceil(h))],axis=0)
             pos = pos[(pos[:,i] >= l) & (pos[:,i] <= h)]
         
         upos[key] = pos
     
     data['positions'] = np.concatenate(list(upos.values()), axis = 0)
+    data['metadata']['eqv_fix'] = False
 
     ranges = np.cumsum([0, *[len(v) for v in upos.values()]])
     data['types'] = {key: range(i,j) for key, i,j in zip(upos,ranges[:-1],ranges[1:])}
@@ -2293,20 +2254,6 @@ def rotate_poscar(poscar_data, angle_deg, axis_vec):
     p_dict["metadata"]["comment"] = f"Modified by ipyvasp"
     return serializer.PoscarData(p_dict)
 
-
-def set_origin(poscar_data, origin):
-    """Set origin of POSCAR sites to a given position in fractional coordinates.
-    The following example demonstrates the use of this function.
-
-    >>> import ipyvasp as ipv
-    >>> poscar = ipv.POSCAR("POSCAR")
-    >>> ax = poscar.splot_cell() # plot original cell
-    >>> poscar_shifted = poscar.scale((3,3,3)).set_origin((1/3,1/3,1/3))
-    >>> poscar_shifted.splot_lattice(ax=ax, plot_cell=False) # displays sites around original cell
-    """
-    return _fix_sites(poscar_data, eqv_sites=False, origin=origin)
-
-
 def set_zdir(poscar_data, hkl, phi=0):
     """Set z-direction of POSCAR along a given hkl direction and returns new data.
 
@@ -2438,7 +2385,7 @@ def transform_poscar(poscar_data, transformation, fill_factor=2, tol=1e-2):
 
     _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 = np.concatenate([pos + [*p,0] for p in 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

ipyvasp/_version.py

@@ -1 +1 @@
-__version__ = "0.8.9"
+__version__ = "0.9.1"

ipyvasp/core/serializer.py

@@ -328,6 +328,15 @@ class PoscarData(Dict2Data):
     def symbols(self):
         "Returns the symbols of the atoms in the poscar data without numbers"
         return np.array([lab.split()[0] for lab in self.labels])
+    
+    def get_sites(self, type_or_indices, as_coords=False):
+        "Shortcut method for `POSCAR.data.positions[POSCAR.data.types['name']]` or with regular indexing."
+        points = self.coords if as_coords else self.positions
+        if isinstance(type_or_indices,str) and type_or_indices in self.types:
+            return points[self.types[type_or_indices]]
+        elif not isinstance(type_or_indices,(list,range,tuple)):
+            raise TypeError("type_or_indices should be a species type like 'Ga' or list-like of indices to pick positions.")
+        return points[type_or_indices]
 
     def get_neighbors(self, k=5):
         """Get the k nearest neighbors of each atom (including itself) in the lattice.
@@ -390,7 +399,7 @@ class PoscarData(Dict2Data):
 
         dists = []
         for idx in idx1:
-            for trans in set(product([-1,0,1],[-1,0,1],[-1,0,1])):
+            for trans in product([-1,0,1],[-1,0,1],[-1,0,1]):
                 C = self.to_cartesian(self.positions[idx] + trans) # translate around to get lowest distance
 
                 dists = [
@@ -412,7 +421,7 @@ class PoscarData(Dict2Data):
         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]))]
+                bs = [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])
                 d = ds[ds > 0].min() # no same site distance
                 if min < d < max:

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())
@@ -254,18 +256,18 @@ class _AutoRenderer:
     _figw = None
     _kws = {} 
 
-    def __init__(self, pc_instance):
-        self._pc = pc_instance
+    def __init__(self, pc_cls):
+        self._pc = pc_cls
 
     def on(self, template=None):
         "Enable auto rendering. In Jupyterlab, you can use `Create New View for Output` to drag a view on side."
         self.off()
-        type(self)._figw = iplot2widget(self._pc.iplot_lattice(**self._kws), fig_widget=self._figw,template=template)
+        type(self)._figw = iplot2widget(self._pc._last.iplot_lattice(**self._kws), fig_widget=self._figw,template=template)
         
         def ip_display(that):
             iplot2widget(that.iplot_lattice(**self._kws), fig_widget=self._figw, template=template)
         
-        type(self._pc)._ipython_display_ = ip_display
+        self._pc._ipython_display_ = ip_display
         
         from ipywidgets import Button, VBox
         btn = Button(description='Disable Auto Rendering',icon='close',layout={'width': 'max-content'})
@@ -279,14 +281,14 @@ class _AutoRenderer:
             self._box.close()
             type(self)._figw = None # no need to close figw, it raise warning, but now garbage collected
         
-        if hasattr(type(self._pc), '_ipython_display_'):
-            del type(self._pc)._ipython_display_
+        if hasattr(self._pc, '_ipython_display_'):
+            del self._pc._ipython_display_
 
     @_sig_kwargs(plat.iplot_lattice,('poscar_data',))
     def update_params(self, **kwargs):
         type(self)._kws = kwargs
-        if hasattr(type(self._pc), '_ipython_display_'):
-            self._pc._ipython_display_()
+        if hasattr(self._pc, '_ipython_display_'):
+            self._pc._last._ipython_display_()
     
     @property
     def params(self):
@@ -302,7 +304,6 @@ class POSCAR:
     def __init__(self, path=None, content=None, data=None):
         """
         POSCAR class to contain data and related methods, data is PoscarData, json/tuple file/string.
-        Do not use `data` yourself, it's for operations on poscar.
 
         Parameters
         ----------
@@ -312,14 +313,20 @@ class POSCAR:
 
         Prefrence order: data > content > path
 
+        Note: During chained operations where functions are acting on index of sites, use `self.last` instead of `self` to point to latest POSCAR in chain.
+        
+        ```python
+        pc = POSCAR()
+        pc.filter_sites(lambda i,x,y,z: i in pc.data.types.Ga) # FINE
+        pc.set_boundary([-2,2]).filter_sites(lambda i,x,y,z: i in pc.data.types.Ga) # INCORRECT sites may be picked
+        pc.set_boundary([-2,2]).filter_sites(lambda i,x,y,z: i in pc.last.data.types.Ga) # PERFECT, pc.last is output of set_boundary
+        ```
+
         Tip: You can use `self.auto_renderer.on()` to keep doing opertions and visualize while last line of any cell is a POSCAR object.
         """
         self._path = Path(path or "POSCAR")  # Path to file
         self._content = content
-
-        if not hasattr(self, '_renderer'): # Only once
-            type(self)._renderer = _AutoRenderer(self) # assign to class
-        self._renderer._pc = self # keep latest refrence there too, for update_params on right one
+        self.__class__._last = self # need this to access in lambda in chain operations
 
         if data:
             self._data = serializer.PoscarData.validated(data)
@@ -345,6 +352,19 @@ class POSCAR:
     def path(self):
         return self._path
     
+    @property
+    def last(self):
+        """Points to last created POSCAR instance during chained operations!
+        
+        ```python
+        pc = POSCAR()
+        pc.filter_sites(lambda i,x,y,z: i in pc.data.types.Ga) # FINE
+        pc.set_boundary([-2,2]).filter_sites(lambda i,x,y,z: i in pc.data.types.Ga) # INCORRECT sites may be picked
+        pc.set_boundary([-2,2]).filter_sites(lambda i,x,y,z: i in pc.last.data.types.Ga) # PERFECT, pc.last is output set_boundary
+        ```
+        """
+        return self._last
+    
     @property
     def auto_renderer(self):
         """A renderer for auto viewing POSCAR when at last line of cell.
@@ -356,6 +376,8 @@ class POSCAR:
         In Jupyterlab, you can use `Create New View for Output` to drag a view on side.
         In VS Code, you can open another view of Notebook to see it on side while doing operations.
         """
+        if not hasattr(self, '_renderer'):
+            self.__class__._renderer = _AutoRenderer(self.__class__) # assign to class
         return self._renderer
 
     def to_ase(self):
@@ -565,6 +587,11 @@ 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."
@@ -674,12 +701,8 @@ 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))
-
-    @_sub_doc(plat.set_origin)
-    def set_origin(self, origin):
-        return self.__class__(data=plat.set_origin(self.data, origin=origin))
+    def filter_sites(self, func, tol=0.01):
+        return self.__class__(data = plat.filter_sites(self.data, func,tol=tol))
 
     @_sub_doc(plat.rotate_poscar)
     def rotate(self, angle_deg, axis_vec):

{ipyvasp-0.8.9.dist-info → ipyvasp-0.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.9
+Version: 0.9.1
 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-0.9.1.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=BqlDmokeYgdnWGw8YPGPRm3-wrgteUJg1R3YK9suMLY,102554
+ipyvasp/_version.py,sha256=nowX8dTYmAqqc8x180AcV7Ru6brVwGyJwg9GfVedBCE,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=wz5CKv5YJbELvG2lbrYnXoT7u9R70Jkr_i3olE4Hx4I,30643
 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=57e2ypF18tJI1zZi9kJiHGMBYgXvYEZpLmgnaaDdSk0,36067
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 ipyvasp/core/spatial_toolkit.py,sha256=8DBYTiBFWJ7OBKuvOPw7UoEVCyNjJhSW0OcudjYZvAw,14748
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