ipyvasp 0.7.9__tar.gz → 0.8.1__tar.gz

{ipyvasp-0.7.9 → ipyvasp-0.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.7.9
+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-0.7.9 → 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-0.7.9 → 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-0.7.9 → 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-0.7.9 → ipyvasp-0.8.1}/ipyvasp/cli.py

@@ -112,14 +112,16 @@ def _get_E0(files: List[Path]):
 def _set_dir(
     paths: List[Path], command: Annotated[str, typer.Option("-c", "--command")] = "",
     ignore_error: Annotated[bool, typer.Option("-i", "--ignore-error")] = False,
-    time_interval: Annotated[int, typer.Option("-t",'--time-interval')] = 0
+    time_interval: Annotated[int, typer.Option("-t",'--time-interval')] = 0,
+    extra_command: Annotated[str, typer.Option("-e", "--extra-command")] = "",
 ):
     """Set multiple directories like a for loop to execute a shell command within each of them.
     It will raise an error if the command fails in any of the directories. 
     To ignore the error and keep running in other directiories in sequence, use -i/--ignore-error. 
     It will raise the shell errors but python will go through all the directories.
 
-    To keep repeating a command after some time interval, use -t/--time-interval (seconds). Only works for a command
+    To keep repeating a command after some time interval, use -t/--time-interval (seconds). Only works for a command.
+    Use -e/--extra-command to run (in pwd) before looping over directories. This can be used to cleanup (previous results etc.) with each time recursion.
     
     Examples:
     
@@ -143,30 +145,43 @@ def _set_dir(
     
     abs_paths = [f.absolute() for f in dirs] # absolute path is must but after filtering
     
-    def run(abs_paths, dirs, command, ignore_error):
+    def exec_cmd(command, path, ignore_error=ignore_error):
+        if command:
+            if os == "Windows":
+                try:
+                    p = Popen("pwsh.exe -NoProfile -c " + command, shell=False)
+                except:
+                    p = Popen("powershell.exe -NoProfile -c " + command, shell=False)
+
+            else:
+                p = Popen(command, shell=True)  # Linux, MacOS, shell to get args
+
+            p.wait()
+            if not ignore_error and p.returncode != 0:
+                raise RuntimeError(f"Command {command} failed in {path}. Exiting...\n" +
+                "Use -i or --ignore-error switch to suppress error and continue in other directories silently."
+                )
+
+    def run(abs_paths, dirs, command, ec=extra_command):
+        if ec:
+            exec_cmd(ec, Path('.').absolute())
+            print(color.bb("\n"+f" {command} ".center(80,"-")))
+
         for path, d in zip(abs_paths,dirs):
             with set_dir(path):
                 print(color.gb(f"📁  {str(d)!r}"))
-
-                if command:
-                    if os == "Windows":
-                        try:
-                            p = Popen("pwsh.exe -NoProfile -c " + command, shell=False)
-                        except:
-                            p = Popen("powershell.exe -NoProfile -c " + command, shell=False)
-
-                    else:
-                        p = Popen(command, shell=True)  # Linux, MacOS, shell to get args
-
-                    p.wait()
-                    if not ignore_error and p.returncode != 0:
-                        raise RuntimeError(f"Command {command} failed in {path}. Exiting...\n" +
-                        "Use -i or --ignore-error switch to suppress error and continue in other directories silently."
-                        )
-    
+                exec_cmd(command, path)
+                
     if time_interval > 0 and command: # repeat only if command given
         while True: # keep going until interrupted
-            run(abs_paths, dirs, command, ignore_error)
+            run(abs_paths, dirs, command)
             sleep(time_interval)
     else:
-        run(abs_paths, dirs, command, ignore_error)
+        run(abs_paths, dirs, command)
+
+@app.command('get-bib')
+def _get_bib(doi: List[str]):
+    "Get bibliography entries from doi. Can provide many DOIs."
+    from .misc import get_bib
+    for d in doi: # all of them
+        print(get_bib(d))

{ipyvasp-0.7.9 → 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-0.7.9 → 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-0.7.9 → ipyvasp-0.8.1}/ipyvasp/misc.py

@@ -1,5 +1,6 @@
-__all__ = ["parse_text", "get_E0", "OUTCAR"]
+__all__ = ["parse_text", "get_bib", "get_E0", "OUTCAR"]
 
+import requests
 from pathlib import Path
 from itertools import islice
 
@@ -24,6 +25,16 @@ def parse_text(path, shape, slice, **kwargs):
         )  # should be under open file context
     return data
 
+def get_bib(DOI):
+    "Get bibligraphy entry from DOI"
+    response = requests.get(
+        f'http://dx.doi.org/{DOI}', 
+        headers={'Accept':'text/bibliography;style=bibtex'})
+    if response.status_code == 200:
+        return response.content.decode('utf-8')
+    
+    return response.status_code
+
 def get_E0(path: Path = 'OSZICAR'):
     "Get the E0 from the last line of OSZICAR."
     fh = Path(path)

{ipyvasp-0.7.9 → 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-0.7.9 → ipyvasp-0.8.1}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.7.9
+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-0.7.9/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.7.9"