ipyvasp 0.8.0__tar.gz → 0.8.1__tar.gz

{ipyvasp-0.8.0 → ipyvasp-0.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.0
+Version: 0.8.1
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -32,7 +32,7 @@ Requires-Dist: nglview>=3.0.4; extra == "extra"
 
 # ipyvasp
 
-An successor of [pivotpy](https://github.com/massgh/pivotpy) for VASP-based DFT pre and post processing tool.
+An VASP-based DFT pre and post processing tool.
 
 ## Install
 Currently the package is being built and not stable. If you want to use development version, install this way:(recommended to install in a virtual environment)
@@ -68,6 +68,9 @@ Interactively select bandstructure path by clicking on high symmetry points on p
 
 ![KP](KP.png)
 
-More coming soon!
+Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` or `WeasWidget` in Jupyterlab side by side.
+
+![snip](op.png)
 
 
+More coming soon!

{ipyvasp-0.8.0 → ipyvasp-0.8.1}/README.md

@@ -1,6 +1,6 @@
 # ipyvasp
 
-An successor of [pivotpy](https://github.com/massgh/pivotpy) for VASP-based DFT pre and post processing tool.
+An VASP-based DFT pre and post processing tool.
 
 ## Install
 Currently the package is being built and not stable. If you want to use development version, install this way:(recommended to install in a virtual environment)
@@ -36,6 +36,9 @@ Interactively select bandstructure path by clicking on high symmetry points on p
 
 ![KP](KP.png)
 
-More coming soon!
+Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` or `WeasWidget` in Jupyterlab side by side.
 
+![snip](op.png)
 
+
+More coming soon!

{ipyvasp-0.8.0 → ipyvasp-0.8.1}/ipyvasp/_lattice.py

@@ -4,7 +4,7 @@ import numpy as np
 from pathlib import Path
 import requests as req
 import inspect
-from itertools import combinations
+from itertools import combinations, product
 from functools import lru_cache
 
 from scipy.spatial import ConvexHull, KDTree
@@ -215,7 +215,7 @@ def periodic_table():
     return ax
 
 
-def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=False):
+def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=False, comment=""):
     """Writes POSCAR data to a file or returns string
 
     Parameters
@@ -227,13 +227,15 @@ def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=F
         See `ipyvasp.POSCAR.data.get_selective_dynamics` for more info.
     overwrite: bool
         If file already exists, overwrite=True changes it.
+    comment: str
+        Add comment, previous comment will be there too.
 
 
     .. note::
         POSCAR is only written in direct format even if it was loaded from cartesian format.
     """
-    _comment = poscar_data.metadata.comment
-    out_str = f"{poscar_data.SYSTEM}  # " + (_comment or "Created by Pivopty")
+    _comment = poscar_data.metadata.comment + comment
+    out_str = f"{poscar_data.SYSTEM}  # " + (_comment or "Created by ipyvasp")
     scale = poscar_data.metadata.scale
     out_str += "\n  {:<20.14f}\n".format(scale)
     out_str += "\n".join(
@@ -531,9 +533,9 @@ class InvokeMaterialsProject:
                 else:
                     print(self._cif)
 
-            def write_poscar(self, outfile=None, overwrite=False):
+            def write_poscar(self, outfile=None, overwrite=False, comment=""):
                 "Use `ipyvasp.lattice.POSCAR.write` if you need extra options."
-                write_poscar(self.export_poscar(), outfile=outfile, overwrite=overwrite)
+                write_poscar(self.export_poscar(), outfile=outfile, overwrite=overwrite, comment=comment)
 
             def export_poscar(self):
                 "Export poscar data form cif content."
@@ -1578,18 +1580,18 @@ def _get_bond_length(poscar_data, bond_length=None):
         )  # Add 5% margin over mean distance, this covers same species too, and in multiple species, this will stop bonding between same species.
 
 
-def _masked_data(poscar_data, mask_sites):
-    "Returns indices of sites which satisfy the mask_sites function."
-    if not callable(mask_sites):
-        raise TypeError("`mask_sites` should be a callable function.")
+def _masked_data(poscar_data, func):
+    "Returns indices of sites which satisfy the func."
+    if not callable(func):
+        raise TypeError("`func` should be a callable function.")
 
-    if len(inspect.signature(mask_sites).parameters) != 4:
+    if len(inspect.signature(func).parameters) != 4:
         raise ValueError(
-            "`mask_sites` takes exactly 4 arguments: (index,x,y,z) in fractional coordinates"
+            "`func` takes exactly 4 arguments: (index,x,y,z) in fractional coordinates"
         )
 
-    if not isinstance(mask_sites(0, 0, 0, 0), bool):
-        raise TypeError("`mask_sites` should return a boolean value.")
+    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"):
@@ -1598,7 +1600,7 @@ def _masked_data(poscar_data, mask_sites):
     pick = []
     for i, pos in enumerate(poscar_data.positions):
         idx = eqv_inds[i] if eqv_inds else i  # map to original index
-        if mask_sites(idx, *pos):
+        if func(idx, *pos):
             pick.append(i)
     return pick  # could be duplicate indices
 
@@ -1620,6 +1622,43 @@ def _filter_pairs(labels, pairs, dist, bond_length):
     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."""
+    idxs = _masked_data(poscar_data, func)
+    data = poscar_data.to_dict() 
+    all_pos, npos = [], []
+    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)]
+        pos = data['positions'][indices]
+        qos = data['positions'][others] # need edge items to include
+
+        if qos.shape:
+            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.shape:
+            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)
+
+    ranges = np.cumsum([0, *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)
+
 # Cell
 def iplot_lattice(
     poscar_data,
@@ -1632,7 +1671,6 @@ def iplot_lattice(
     origin=(0, 0, 0),
     fig=None,
     ortho3d=True,
-    mask_sites=None,
     bond_kws=dict(line_width=4),
     site_kws=dict(line_color="rgba(1,1,1,0)", line_width=0.001, opacity=1),
     plot_cell=True,
@@ -1648,9 +1686,6 @@ def iplot_lattice(
         Sequence of colors for each type. Automatically generated if not provided.
     bond_length : float or dict
         Length of bond in Angstrom. Auto calculated if not provides. Can be a dict like {'Fe-O':3.2,...} to specify bond length between specific types.
-    mask_sites : callable
-        Provide a mask function `f(index, x,y,z) -> bool` to show only selected sites.
-        For example, to show only sites with z > 0.5, use `mask_sites = lambda i, x,y,z: x > 0.5`.
     bond_kws : dict
         Keyword arguments passed to `plotly.graph_objects.Scatter3d` for bonds.
         Default is jus hint, you can use any keyword argument that is accepted by `plotly.graph_objects.Scatter3d`.
@@ -1664,23 +1699,17 @@ def iplot_lattice(
 
     kwargs are passed to `iplot_bz`.
     """
+    if len(poscar_data.positions) < 1:
+        raise ValueError("Need at least 1 atom!")
+    
     poscar_data = _fix_sites(
         poscar_data, tol=tol, eqv_sites=eqv_sites, translate=translate, origin=origin
     )
+    
     blen = _get_bond_length(poscar_data, bond_length)
 
-    sites = None
-    coords = poscar_data.coords
-    if (
-        mask_sites is not None
-    ):  # not None is important, as it can be False given by user
-        sites = _masked_data(poscar_data, mask_sites)
-        coords = poscar_data.coords[sites]
-        if not sites:
-            raise ValueError("No sites found with given mask_sites function.")
-
-    coords, pairs, dist = get_pairs(coords, r=blen)
-    _labels = poscar_data.labels[sites] if sites else poscar_data.labels
+    coords, pairs, dist = get_pairs(poscar_data.coords, r=blen)
+    _labels = poscar_data.labels
     pairs = _filter_pairs(_labels, pairs, dist, bond_length)
 
     if not fig:
@@ -1738,13 +1767,8 @@ def iplot_lattice(
         **site_kws,
     }
     for (k, v), c, s in zip(uelems.items(), colors, sizes):
-        if sites:
-            v = [i for i in v if i in sites]  # Only show selected sites.
-            coords = poscar_data.coords[v]
-            labs = poscar_data.labels[v]
-        else:
-            coords = poscar_data.coords[v]
-            labs = poscar_data.labels[v]
+        coords = poscar_data.coords[v]
+        labs = poscar_data.labels[v]
 
         fig.add_trace(
             go.Scatter3d(
@@ -1830,7 +1854,6 @@ def splot_lattice(
     translate=None,
     origin=(0, 0, 0),
     ax=None,
-    mask_sites=None,
     showlegend=True,
     fmt_label=None,
     site_kws=dict(alpha=0.7),
@@ -1852,9 +1875,6 @@ def splot_lattice(
         Length of bond in Angstrom. Auto calculated if not provides. Can be a dict like {'Fe-O':3.2,...} to specify bond length between specific types.
     alpha : float
         Opacity of points and bonds.
-    mask_sites : callable
-        Provide a mask function `f(index, x,y,z) -> bool` to show only selected sites.
-        For example, to show only sites with z > 0.5, use `mask_sites = lambda i,x,y,z: x > 0.5`.
     showlegend : bool
         Default is True, show legend for each ion type.
     site_kws : dict
@@ -1875,6 +1895,9 @@ def splot_lattice(
     .. tip::
         Use `plt.style.use('ggplot')` for better 3D perception.
     """
+    if len(poscar_data.positions) < 1:
+        raise ValueError("Need at least 1 atom!")
+    
     # Plane fix
     if plane and plane not in "xyzxzyx":
         raise ValueError("plane expects in 'xyzxzyx' or None.")
@@ -1887,21 +1910,8 @@ def splot_lattice(
         poscar_data, tol=tol, eqv_sites=eqv_sites, translate=translate, origin=origin
     )
     blen = _get_bond_length(poscar_data, bond_length)
-
-    sites = None
-    coords = poscar_data.coords  # take all sites
-    filtered_elems = list(poscar_data.types.keys())
-    if mask_sites is not None:  # not None is important, user can give anything
-        sites = _masked_data(poscar_data, mask_sites)
-        if not sites:
-            raise ValueError("No sites found with given mask_sites function.")
-        
-        coords = poscar_data.coords[sites]
-        filtered_elems = np.unique(poscar_data.symbols[sites]).tolist()
-
-    labels = [poscar_data.labels[i] for i in sites] if sites else poscar_data.labels
-
-    coords, pairs, dist = get_pairs(coords, r=blen)
+    labels = poscar_data.labels
+    coords, pairs, dist = get_pairs(poscar_data.coords, r=blen)
     pairs = _filter_pairs(labels, pairs, dist, bond_length)
 
     if fmt_label is not None:
@@ -1939,10 +1949,7 @@ def splot_lattice(
     # Before doing other stuff, create something for legend.
     if showlegend:    
         for key, c, s in zip(uelems.keys(), colors, sizes):
-            if key in filtered_elems:
-                ax.scatter(
-                    [], [], s=s, color=c, label=key, **site_kws
-                )  # Works both for 3D and 2D.
+            ax.scatter([], [], s=s, color=c, label=key, **site_kws)  # Works both for 3D and 2D.
         ptk.add_legend(ax)
 
     # Now change colors and sizes to whole array size
@@ -1951,10 +1958,6 @@ def splot_lattice(
     )
     sizes = np.array([sizes[i] for i, vs in enumerate(uelems.values()) for v in vs])
 
-    if sites:
-        colors = colors[sites]
-        sizes = sizes[sites]
-
     if np.any(pairs):
         coords_p = coords[pairs]  # paired points
         _colors = colors[pairs]  # Colors at pairs
@@ -2218,6 +2221,40 @@ def scale_poscar(poscar_data, scale=(1, 1, 1), tol=1e-2):
     new_poscar["positions"] = np.array(positions)
     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."
+    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]")
+        if d[1] < d[0]:
+            raise ValueError(f"{name} should be in increasing order as [min, max]")
+        
+    data = poscar_data.to_dict()
+    upos = {}
+    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 = pos[(pos[:,i] >= l) & (pos[:,i] <= h)]
+        
+        upos[key] = pos
+    
+    data['positions'] = np.concatenate(list(upos.values()), axis = 0)
+
+    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:])}
+    del upos
+    return serializer.PoscarData(data)
+
+    
+
+
+
 
 def rotate_poscar(poscar_data, angle_deg, axis_vec):
     """Rotate a given POSCAR.
@@ -2560,6 +2597,26 @@ def replace_atoms(poscar_data, func, name):
     }
     return serializer.PoscarData(data)  # Return new POSCAR
 
+def sort_poscar(poscar_data, new_order):
+    "sort poscar with new_order list/tuple of species."
+    if not isinstance(new_order, (list, tuple)):
+        raise TypeError(f"new_order should be a list/tuple of types, got {type(new_order)}")
+    
+    data = poscar_data.to_dict() 
+    if not all([set(new_order).issubset(data["types"]), set(data["types"]).issubset(new_order)]):
+        raise ValueError(f"new_order should contain all existings types {list(data['types'])}")
+    
+    data["types"] = {key:data["types"][key] for key in new_order}
+    data["positions"] = data["positions"][[i for tp in data["types"].values() for i in tp]]
+    idxs = np.cumsum([0, *map(len, data["types"].values())])
+    data["types"] = {
+        k: range(idxs[i], idxs[i + 1])
+        for i, k in enumerate(data["types"].keys())
+        if len(data["types"][k]) != 0
+    }
+
+    return serializer.PoscarData(data)
+
 
 def remove_atoms(poscar_data, func, fillby=None):
     """Remove atoms that satisfy `func(x,y,z) -> bool` on their fractional coordinates x,y,z.

ipyvasp-0.8.1/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.8.1"

{ipyvasp-0.8.0 → ipyvasp-0.8.1}/ipyvasp/bsdos.py

@@ -149,7 +149,9 @@ _spin_doc = """spin : int
     plotting other with same parameters will use the same data."""
 _kind_doc = """kpairs : list/tuple
     List of pair of indices to rearrange a computed path. For example, if you computed
-    0:L, 15:G, 25:X, 34:M path and want to plot it as X-G|M-X, use [(25,15), (34,25)] as kpairs."""
+    0:L, 15:G, 25:X, 34:M path and want to plot it as X-G|M-X, use [(25,15), (34,25)] as kpairs.  
+bands : list/tuple
+    List of indices of bands. If given, this ovverides elim."""
 _proj_doc = """projections : dict
     Mapping from str -> [atoms, orbs]. Use dict to select specific projections, 
     e.g. {'Ga-s': (0,[0]), 'Ga1-p': ([0],[1,2,3])} in case of GaAs. If values of the dict 
@@ -335,7 +337,7 @@ class Bands(_BandsDosBase):
 
         return serializer.Dict2Data(out)
 
-    def get_data(self, elim=None, ezero=None, projections: dict = None, kpairs=None):
+    def get_data(self, elim=None, ezero=None, projections: dict = None, kpairs=None, bands=None):
         """
         Selects bands and projections to use in plotting functions. If input arguments are same as previous call, returns cached data.
 
@@ -345,12 +347,13 @@ class Bands(_BandsDosBase):
         ezero : float, None by default. If not None, elim is applied around this energy.
         projections : dict, str -> [atoms, orbs]. Use dict to select specific projections, e.g. {'Ga-s': (0,[0]), 'Ga1-p': ([0],[1,2,3])} in case of GaAs. If values of the dict are callable, they must accept two arguments evals, occs of shape (spin,kpoints, bands) and return array of shape (kpoints, bands).
         kpairs : list, tuple of integers, None by default to select all kpoints in given order. Use this to select specific kpoints intervals in specific order.
+        bands : list,tuple of integers, this ovverides elim if given.
 
         Returns
         -------
         data : Selected bands and projections data to be used in bandstructure plotting functions under this class as `data` argument.
         """
-        if self.data and self._data_args == (elim, ezero, projections, kpairs):
+        if self.data and self._data_args == (elim, ezero, projections, kpairs, bands):
             return self.data
 
         if kpairs and not isinstance(kpairs, (list, tuple)):
@@ -377,7 +380,7 @@ class Bands(_BandsDosBase):
                 kpairs[-1][-1],
             ]  # flatten and add last index
 
-        self._data_args = (elim, ezero, projections)
+        self._data_args = (elim, ezero, projections, bands)
 
         (
             (spins, uspins),
@@ -393,7 +396,7 @@ class Bands(_BandsDosBase):
             atoms=uatoms,
             orbs=uorbs,
             spins=uspins or None,
-            bands=None,
+            bands=bands,
         )  # picks available spins if uspins is None
 
         if not spins:
@@ -508,9 +511,9 @@ class Bands(_BandsDosBase):
         {"K :.*ax :": f"{_spin_doc}\n{_kind_doc}\nax :"},
     )
     @_sig_kwargs(splot_bands, ("K", "E"))
-    def splot_bands(self, spin=0, kpairs=None, ezero=None, **kwargs):
+    def splot_bands(self, spin=0, kpairs=None, ezero=None, bands=None, **kwargs):
         kwargs, elim = self._handle_kwargs(spin=spin, **kwargs)
-        data = self.get_data(elim=elim, ezero=ezero, kpairs=kpairs)
+        data = self.get_data(elim=elim, ezero=ezero, kpairs=kpairs, bands=bands)
         return splot_bands(data.kpath, data.evals[spin] - data.ezero, **kwargs)
 
     @_sub_doc(
@@ -518,9 +521,9 @@ class Bands(_BandsDosBase):
         {"K :.*ax :": f"{_proj_doc}\n{_spin_doc}\n{_kind_doc}\nax :"},
     )
     @_sig_kwargs(splot_rgb_lines, ("K", "E", "pros", "labels"))
-    def splot_rgb_lines(self, projections, spin=0, kpairs=None, ezero=None, **kwargs):
+    def splot_rgb_lines(self, projections, spin=0, kpairs=None, ezero=None, bands=None, **kwargs):
         kwargs, elim = self._handle_kwargs(spin=spin, **kwargs)
-        data = self.get_data(elim, ezero, projections, kpairs=kpairs)
+        data = self.get_data(elim, ezero, projections, kpairs=kpairs, bands=bands)
         return splot_rgb_lines(
             data.kpath, data.evals[spin] - data.ezero, data.pros, data.labels, **kwargs
         )
@@ -530,10 +533,10 @@ class Bands(_BandsDosBase):
         {"K :.*axes :": f"{_proj_doc}\n{_spin_doc}\n{_kind_doc}\naxes :"},
     )
     @_sig_kwargs(splot_color_lines, ("K", "E", "pros", "labels"))
-    def splot_color_lines(self, projections, spin=0, kpairs=None, ezero=None, **kwargs):
+    def splot_color_lines(self, projections, spin=0, kpairs=None, ezero=None, bands=None, **kwargs):
         kwargs, elim = self._handle_kwargs(spin=spin, **kwargs)
         data = self.get_data(
-            elim, ezero, projections, kpairs=kpairs
+            elim, ezero, projections, kpairs=kpairs, bands=bands
         )  # picked relative limit
         return splot_color_lines(
             data.kpath, data.evals[spin] - data.ezero, data.pros, data.labels, **kwargs
@@ -544,9 +547,9 @@ class Bands(_BandsDosBase):
         {"K :.*fig :": f"{_proj_doc}\n{_spin_doc}\n{_kind_doc}\nfig :"},
     )
     @_sig_kwargs(iplot_rgb_lines, ("K", "E", "pros", "labels", "occs", "kpoints"))
-    def iplot_rgb_lines(self, projections, spin=0, kpairs=None, ezero=None, **kwargs):
+    def iplot_rgb_lines(self, projections, spin=0, kpairs=None, ezero=None, bands=None, **kwargs):
         kwargs, elim = self._handle_kwargs(spin=spin, **kwargs)
-        data = self.get_data(elim, ezero, projections, kpairs=kpairs)
+        data = self.get_data(elim, ezero, projections, kpairs=kpairs, bands=bands)
         # Send K and bands in place of K for use in iplot_rgb_lines to depict correct band number
         return iplot_rgb_lines(
             {"K": data.kpath, "indices": data.bands},
@@ -563,9 +566,9 @@ class Bands(_BandsDosBase):
         {"K :.*fig :": f"{_spin_doc}\n{_kind_doc}\nfig :"},
     )
     @_sig_kwargs(iplot_bands, ("K", "E"))
-    def iplot_bands(self, spin=0, kpairs=None, ezero=None, **kwargs):
+    def iplot_bands(self, spin=0, kpairs=None, ezero=None, bands=None, **kwargs):
         kwargs, elim = self._handle_kwargs(spin=spin, **kwargs)
-        data = self.get_data(elim, ezero, kpairs=kpairs)
+        data = self.get_data(elim, ezero, kpairs=kpairs, bands=bands)
         # Send K and bands in place of K for use in iplot_rgb_lines to depict correct band number
         return iplot_bands(
             {"K": data.kpath, "indices": data.bands},
@@ -573,13 +576,14 @@ class Bands(_BandsDosBase):
             **kwargs,
         )
 
-    def view_bands(self):
+    def view_bands(self, height="450px"):
         "Initialize and return `ipyvasp.widgets.BandsWidget` to view bandstructure interactively."
         use_vaspout = True if isinstance(self.source, vp.Vaspout) else False
         return wdg.BandsWidget(
             use_vaspout=use_vaspout,
-            path=self.source.path.parent,
+            path=str(self.source.path.parent),
             glob=self.source.path.name,
+            height=height,
         )
 
 
@@ -677,6 +681,7 @@ class DOS(_BandsDosBase):
             raise ValueError("spin must be 0,1,2,3 for dos")
 
         kwargs.pop("spin", None)  # remove from kwargs as plots don't need it
+        kwargs.pop("bands", None) # not required internally
         return kwargs, kwargs.get("elim", None)
 
     @_sub_doc(

{ipyvasp-0.8.0 → ipyvasp-0.8.1}/ipyvasp/core/serializer.py

@@ -211,11 +211,20 @@ class Dict2Data:
     def values(self):
         return self.__dict__.values()
 
-    def __getitem__(self, key):
-        return self.__dict__[key]
-
     def items(self):
         return self.__dict__.items()
+    
+    def __getitem__(self, key):
+        return self.__dict__[key]
+    
+    def __contains__(self, key):
+        return key in self.__dict__
+    
+    def __iter__(self):
+        return iter(self.__dict__)
+    
+    def __len__(self):
+        return len(self.__dict__)
 
 
 class SpinData(Dict2Data):
@@ -375,6 +384,9 @@ class PoscarData(Dict2Data):
             raise ValueError(
                 "atom2 must be a string such as 'As' or a dict with a single key as {'As':0}"
             )
+        
+        if len(set([*idx1, *idx2])) < 2: # itself or no atom exists
+            return np.nan # No mean of distnace in this case
 
         dists = []
         for idx in idx1:
@@ -388,7 +400,7 @@ class PoscarData(Dict2Data):
 
         dists = np.array(dists)
         dists = dists[dists > 0]  # Remove distance with itself
-        return np.min(dists)
+        return np.min(dists) if dists.size else np.nan
     
     def to_fractional(self, coords):
         "Converts cartesian coordinates to fractional coordinates in the basis of cell."

{ipyvasp-0.8.0 → ipyvasp-0.8.1}/ipyvasp/lattice.py

@@ -12,6 +12,8 @@ __all__ = [
 from pathlib import Path
 from contextlib import redirect_stdout
 from io import StringIO
+from itertools import permutations
+from contextlib import suppress
 
 import numpy as np
 from pandas.io.clipboard import clipboard_get, clipboard_set
@@ -198,6 +200,78 @@ def ngl_viewer(
     return view
 
 
+def weas_viewer(poscar,
+    sizes=None,
+    colors=None,
+    bond_length=None,
+    model_style = 1,
+    plot_cell=True
+    ):
+    """
+    colors : list or str
+        List of colors for each atom type. If str, use 'VESTA','JMOL','CPK'.
+        By default, ipyvasp colors are used.
+    sizes : list
+        List of sizes for each atom type.
+    model_type: int
+        whether to show Balls (0), Ball + Stick (1), Polyheda (2) or Sticks (3).
+    plot_cell : bool
+        Plot unit cell. Default True.
+    bond_length : float or dict
+        Length of bond in Angstrom. Auto calculated if not provides. Can be a dict like {'Fe-O':3.2,...} to specify bond length between specific types.
+    
+    Returns a WeasWidget instance. You can use `.export_image`, `save_image` and other operations on it.
+    """
+    
+    from weas_widget import WeasWidget
+
+    if len(poscar.data.positions) < 1:
+        raise ValueError("Need at least 1 atom!")
+
+    w = WeasWidget(from_ase=poscar.to_ase())
+    w.avr.show_bonded_atoms = True
+    w.avr.model_style = model_style
+    w.avr.show_cell = plot_cell  
+              
+
+    if bond_length:
+        if isinstance(bond_length,(int,float)):
+            for a,b in permutations(list(poscar.data.types.keys()),2):
+                with suppress(KeyError):
+                    w.avr.bond.settings[f'{a}-{b}'].update({'max': bond_length})
+        elif isinstance(bond_length, dict):
+            for key, value in bond_length.items():
+                w.avr.bond.settings[key].update({'max': value})
+
+    if sizes is not None:
+        if not isinstance(sizes, (list,tuple)) or len(sizes) != len(poscar.data.types):
+            raise ValueError(f"sizes should be list/tuple of same sizes as atom types = {len(poscar.data.types)}.")
+        for key, value in zip(poscar.data.types,sizes):
+            w.avr.species.settings[key].update({"radius": value})
+    
+    if colors is None:
+        colors = [plat._atom_colors[key] for key in poscar.data.types]
+
+    if isinstance(colors, str):
+        if not colors in ['VESTA','JMOL','CPK']:
+            raise ValueError("colors should be one of ['VESTA','JMOL','CPK'] if given as string!")
+        
+        w.avr.color_type = colors
+
+    if not isinstance(colors, str):
+        if not isinstance(colors, (list,tuple)) or len(colors) != len(poscar.data.types):
+            raise ValueError(f"colors should be list/tuple of same sizes as atom types = {len(poscar.data.types)}.")
+
+        colors = {key: value for key, value in zip(poscar.data.types,colors)}
+        for key,value in colors.items():
+            w.avr.species.settings[key].update({"color": value})
+        for (k1,c1), (k2,c2) in permutations(colors.items(),2):
+            with suppress(KeyError):
+                w.avr.bond.settings[f'{k1}-{k2}'].update({'color1':c1,'color2':c2})
+                
+    return w
+
+
 class POSCAR:
     _cb_instance = {}  # Loads last clipboard data if not changed
     _mp_instance = {}  # Loads last mp data if not changed
@@ -272,6 +346,8 @@ class POSCAR:
         """
         if viewer is None:
             return plat.view_poscar(self.data, **kwargs)
+        elif viewer in "weas":
+            return weas_viewer(self, **kwargs)
         elif viewer in "nglview":
             return print(
                 f"Use `self.view_ngl()` for better customization in case of viewer={viewer!r}"
@@ -285,6 +361,12 @@ class POSCAR:
     @_sig_kwargs(ngl_viewer, ("poscar",))
     def view_ngl(self, **kwargs):
         return ngl_viewer(self, **kwargs)
+    
+    @_sub_doc(weas_viewer)
+    @_sig_kwargs(weas_viewer, ("poscar",))
+    def view_weas(self, **kwargs):
+        return weas_viewer(self, **kwargs)
+    
 
     def view_kpath(self):
         "Initialize a KpathWidget instance to view kpath for current POSCAR, and you can select others too."
@@ -446,6 +528,14 @@ class POSCAR:
         "Writes POSCAR to clipboard (as implemented by pandas library) for copy in other programs such as vim."
         clipboard_set(self.content)  # write to clipboard
 
+
+    def update_weas(self, handle):
+        """Send result of any options to view on opened weas widget handle with default parameters becuase any operations 
+        can be incompatible with presious state of POSCAR. VESTA color scheme is used here.
+        Useful in Jupyterlab side panel to look operations results on POSCAR."""
+        handle.from_ase(self.to_ase())
+        handle.avr.color_type = 'VESTA'
+
     @property
     def data(self):
         "Data object in POSCAR."
@@ -454,6 +544,11 @@ class POSCAR:
     def copy(self):
         "Copy POSCAR object. It avoids accidental changes to numpy arrays in original object."
         return self.__class__(data=self.data.copy())
+    
+    @_sub_doc(plat.sort_poscar)
+    def sort(self, new_order):
+        return self.__class__(data=plat.sort_poscar(self.data, new_order))
+
 
     @property
     def content(self):
@@ -546,6 +641,16 @@ class POSCAR:
     @_sig_kwargs(plat.scale_poscar, ("poscar_data",))
     def scale(self, scale=(1, 1, 1), **kwargs):
         return self.__class__(data=plat.scale_poscar(self.data, scale, **kwargs))
+    
+    @_sub_doc(plat.set_boundary)
+    @_sig_kwargs(plat.set_boundary,("poscar_data",))
+    def set_boundary(self, a = [0,1], b=[0,1],c=[0,1]):
+        return self.__class__(data = plat.set_boundary(self.data, a=a,b=b,c=c))
+    
+    @_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):

{ipyvasp-0.8.0 → ipyvasp-0.8.1}/ipyvasp/widgets.py

@@ -252,7 +252,7 @@ class FilesWidget(VBox):
         other_widgets=None,
         other_controls=None,
         options={"manual": False},
-        height="90vh",
+        height="400px",
         **kwargs,
     ):
         """
@@ -384,7 +384,7 @@ class FilesWidget(VBox):
         other_widgets=None,
         other_controls=None,
         options={"manual": False},
-        height="90vh",
+        height="400px",
         **kwargs,
     ):
         """Interact with a function that takes a selected Path as first argument.
@@ -649,7 +649,7 @@ class BandsWidget(VBox):
     self.selected_data returns the last selection of points within a box or lasso. You can plot that output separately as plt.plot(data.xs, data.ys) after a selection.
     """
 
-    def __init__(self, use_vaspout=False, height="90vh", **file_widget_kwargs):
+    def __init__(self, use_vaspout=False, height="450px", **file_widget_kwargs):
         super().__init__(_dom_classes=["BandsWidget"])
         self._bands = None
         self._use_vaspout = use_vaspout
@@ -659,7 +659,7 @@ class BandsWidget(VBox):
         )
         self._click = Dropdown(description="Click", options=["None", "VBM", "CBM"])
         self._ktcicks = Text(description="kticks")
-        self._elim = Text(description="elim", value="-10, 10")
+        self._brange = ipw.IntRangeSlider(description="bands",min=1, max=1) # number, not index
         self._ppicks = PropsPicker(
             on_button_click=self._update_graph, on_selection_changed=self._warn_update
         )
@@ -677,7 +677,7 @@ class BandsWidget(VBox):
             other_widgets=[self._fig],
             other_controls=[
                 self._tsd,
-                self._elim,
+                self._brange,
                 self._ktcicks,
                 ipw.HTML("<hr/>"),
                 self._ppicks,
@@ -691,7 +691,7 @@ class BandsWidget(VBox):
         self._tsd.observe(self._change_theme, "value")
         self._click.observe(self._click_save_data, "value")
         self._ktcicks.observe(self._warn_update, "value")
-        self._elim.observe(self._warn_update, "value")
+        self._brange.observe(self._warn_update, "value")
 
     @property
     def path(self):
@@ -708,6 +708,7 @@ class BandsWidget(VBox):
             self._ktcicks.value = ", ".join(
                 f"{k}:{v}" for k, v in self.bands.get_kticks()
             )
+            self._brange.max = self.bands.source.summary.NBANDS
             if self.bands.source.summary.LSORBIT:
                 self._click.options = ["None", "VBM", "CBM", "so_max", "so_min"]
             else:
@@ -762,8 +763,8 @@ class BandsWidget(VBox):
                 for vs in self._ktcicks.value.split(",")
             ]
             kticks = [(int(vs[0]), vs[1]) for vs in hsk if len(vs) == 2] or None
-            elim = [float(v) for v in self._elim.value.split(",") if v.strip()] or None
-            self._kwargs = {"elim": elim, "kticks": kticks}
+            self._kwargs = {"kticks": kticks, # below numbers instead of index and full shown range
+                "bands": range(self._brange.value[0] - 1, self._brange.value[1]) if self._brange.value else None}
 
             if self._ppicks.projections:
                 self._kwargs = {"projections": self._ppicks.projections, **self._kwargs}
@@ -871,7 +872,7 @@ class KpathWidget(VBox):
     - To break the path between two points "Γ" and "X" type "Γ 0,X" in the "Labels" box, zero means no points in interval.
     """
 
-    def __init__(self, height="90vh", **files_widget_kwargs):
+    def __init__(self, height="400px", **files_widget_kwargs):
         super().__init__(_dom_classes=["KpathWidget"])
         self._fig = go.FigureWidget()
         self._sm = SelectMultiple(options=[], layout=Layout(width="auto"))

{ipyvasp-0.8.0 → ipyvasp-0.8.1}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.0
+Version: 0.8.1
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -32,7 +32,7 @@ Requires-Dist: nglview>=3.0.4; extra == "extra"
 
 # ipyvasp
 
-An successor of [pivotpy](https://github.com/massgh/pivotpy) for VASP-based DFT pre and post processing tool.
+An VASP-based DFT pre and post processing tool.
 
 ## Install
 Currently the package is being built and not stable. If you want to use development version, install this way:(recommended to install in a virtual environment)
@@ -68,6 +68,9 @@ Interactively select bandstructure path by clicking on high symmetry points on p
 
 ![KP](KP.png)
 
-More coming soon!
+Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` or `WeasWidget` in Jupyterlab side by side.
+
+![snip](op.png)
 
 
+More coming soon!

ipyvasp-0.8.0/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.8.0"