ipyvasp 1.0.1__py2.py3-none-any.whl → 1.0.3__py2.py3-none-any.whl

ipyvasp/_lattice.py

@@ -232,7 +232,7 @@ def periodic_table(selection=None):
     return ax
 
 
-def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=False, comment="", scale=None):
+def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=False, comment="", scale=None, system=None):
     """Writes POSCAR data to a file or returns string
 
     Parameters
@@ -248,13 +248,15 @@ def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=F
         Add comment, previous comment will be there too.
     scale: float
         Scale factor for the basis vectors. Default is provided by loaded data.
+    system: str
+        System name to be used in POSCAR file instead of the one in `poscar_data.SYSTEM`.
 
 
     .. note::
         POSCAR is only written in direct format even if it was loaded from cartesian format.
     """
     _comment = poscar_data.metadata.comment + comment
-    out_str = f"{poscar_data.SYSTEM}  # " + (_comment or "Created by ipyvasp")
+    out_str = f"{system or poscar_data.SYSTEM}  # " + (_comment or "Created by ipyvasp")
 
     if scale is None:
         scale = poscar_data.metadata.scale
@@ -2296,10 +2298,6 @@ def set_boundary(poscar_data, a = [0,1], b = [0,1], c = [0,1]):
     del upos
     return serializer.PoscarData(data)
 
-    
-
-
-
 
 def rotate_poscar(poscar_data, angle_deg, axis_vec):
     """Rotate a given POSCAR.
@@ -2380,7 +2378,7 @@ def convert_poscar(poscar_data, atoms_mapping, basis_factor):
 
 
     .. note::
-        This can be used to strain basis vectors uniformly only. For non-uniform strain, use :func:`ipyvasp.POSCAR.strain`.
+        This can be used to strain basis vectors uniformly only. For non-uniform strain, use :func:`ipyvasp.POSCAR.deform`.
     """
     poscar_data = poscar_data.to_dict()  # Avoid modifying original
     poscar_data["types"] = {
@@ -2412,7 +2410,7 @@ def convert_poscar(poscar_data, atoms_mapping, basis_factor):
                 type(basis_factor)
             )
         )
-
+    poscar_data["SYSTEM"] = "".join(poscar_data["types"].keys())  # Update system name
     return serializer.PoscarData(poscar_data)  # Return new POSCAR
 
 
@@ -2431,7 +2429,7 @@ def transform_poscar(poscar_data, transformation, fill_factor=2, tol=1e-2):
 
 
     .. note::
-        This function keeps underlying lattice same.
+        This function keeps underlying lattice same. To apply strain, use `deform` function instead.
     """
     if callable(transformation):
         new_basis = np.array(transformation(*poscar_data.basis))  # mostly a tuple
@@ -2546,11 +2544,11 @@ def add_atoms(poscar_data, name, positions):
     data = poscar_data.to_dict()  # Copy data to avoid modifying original
     data["types"] = unique  # Update unique dictionary
     data["positions"] = new_pos  # Update positions
-    data["SYSTEM"] = f'{data["SYSTEM"]}+{name}'  # Update SYSTEM
     data["metadata"][
         "comment"
     ] = f'{data["metadata"]["comment"]} + Added {name!r}'  # Update comment
 
+    data["SYSTEM"] = "".join(data["types"].keys())  # Update system name
     return serializer.PoscarData(data)  # Return new POSCAR
 
 
@@ -2574,6 +2572,7 @@ def replace_atoms(poscar_data, func, name):
         for i, k in enumerate(new_types.keys())
         if len(new_types[k]) != 0
     }
+    data["SYSTEM"] = "".join(data["types"].keys())  # Update system name
     return serializer.PoscarData(data)  # Return new POSCAR
 
 def sort_poscar(poscar_data, new_order):
@@ -2593,7 +2592,7 @@ def sort_poscar(poscar_data, new_order):
         for i, k in enumerate(data["types"].keys())
         if len(data["types"][k]) != 0
     }
-
+    data["SYSTEM"] = "".join(data["types"].keys())  # Update system name
     return serializer.PoscarData(data)
 
 def remove_atoms(poscar_data, func, fillby=None):
@@ -2650,7 +2649,7 @@ def remove_atoms(poscar_data, func, fillby=None):
         for i, k in enumerate(new_types.keys())
         if len(new_types[k]) != 0
     }
-
+    data["SYSTEM"] = "".join(data["types"].keys())  # Update system name
     return serializer.PoscarData(data)  # Return new POSCAR
 
 

ipyvasp/_version.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.3"

ipyvasp/cli.py

@@ -74,7 +74,7 @@ def get_gap(files: List[Path]):
     from .widgets import summarize
 
     def gap_summary(path):
-        gap = Vasprun(path).bands.gap
+        gap = Vasprun(path, skipk=0).bands.gap # don't skip k-points here
         delattr(gap, "coords")  # remove coords info
         d = gap.to_dict()
         d["kvbm"] = "(" + ",".join(str(round(k, 4)) for k in d["kvbm"]) + ")"

ipyvasp/core/plot_toolkit.py

@@ -15,7 +15,7 @@ from matplotlib.patches import FancyArrowPatch
 from cycler import cycler
 
 from IPython import get_ipython
-from IPython.display import HTML, set_matplotlib_formats
+from IPython.display import HTML
 import PIL  # For text image.
 
 import plotly.graph_objects as go
@@ -26,14 +26,11 @@ from .spatial_toolkit import to_R3, rotation
 from ..utils import _sig_kwargs
 
 
-def global_matplotlib_settings(rcParams={}, display_format="svg"):
+def global_matplotlib_settings(rcParams={}, display_format="svg"): 
     "Set global matplotlib settings for notebook."
-    # show SVG in notebook
-    if shell := get_ipython():
-        shell_name = shell.__class__.__name__
-        if shell_name in ("ZMQInteractiveShell", "Shell"):  # Shell for colab.
-            set_matplotlib_formats(display_format)
-
+    if ip := get_ipython():
+        ip.run_line_magic("config", f"InlineBackend.figure_formats = ['{display_format}', 'svg', 'retina','png','jpeg']")
+        
     # Gloabal settings matplotlib with some defaults
     rcParams = {
         "axes.linewidth": 0.4,
@@ -230,7 +227,6 @@ def get_axes(
         pass
 
     plt.subplots_adjust(**subplots_adjust_kwargs)
-
     return axs
 
 
@@ -891,7 +887,7 @@ def plt2text(
     if plt_fig == None:
         plt_fig = plt.gcf()
     plot_bytes = BytesIO()
-    plt.savefig(plot_bytes, format="png", dpi=600)
+    plt_fig.savefig(plot_bytes, format="png", dpi=600)
     img = PIL.Image.open(plot_bytes)
     # crop
     if crop:
@@ -952,9 +948,9 @@ def plt2html(plt_fig=None, transparent=True):
     if plt_fig is None:
         plt_fig = plt.gcf()
     plot_bytes = BytesIO()
-    plt.savefig(plot_bytes, format="svg", transparent=transparent)
+    plt_fig.savefig(plot_bytes, format="svg", transparent=transparent)
 
-    _ = plt.clf()  # Clear other display
+    plt.close(plt_fig)  # Close to avoid auto display in notebook
     return HTML("<svg" + plot_bytes.getvalue().decode("utf-8").split("<svg")[1])
 
 

{ipyvasp-1.0.1.dist-info → ipyvasp-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 1.0.1
+Version: 1.0.3
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -28,7 +28,7 @@ Requires-Dist: einteract
 Requires-Dist: sympy
 Provides-Extra: extra
 Requires-Dist: jupyterlab>=3.5.2; extra == "extra"
-Requires-Dist: ipython>=8.7; extra == "extra"
+Requires-Dist: ipython>=9.0; extra == "extra"
 Requires-Dist: ase>=3.22.1; extra == "extra"
 Requires-Dist: nglview>=3.0.4; extra == "extra"
 

{ipyvasp-1.0.1.dist-info → ipyvasp-1.0.3.dist-info}/RECORD

@@ -1,10 +1,10 @@
 ipyvasp/__init__.py,sha256=pzTqeKuf6sN2GQmaexmMgG677ggT3sxIFyQDXq_2whU,1422
 ipyvasp/__main__.py,sha256=eJV1TZSiT8mC_VqAeksNnBI2I8mKMiPkEIlwikbtOjI,216
 ipyvasp/_enplots.py,sha256=gJ7S9WBmrxvDEbmoccDRaJG01kpx9oNlRf7mozigbgY,37872
-ipyvasp/_lattice.py,sha256=YVUgI4ne0qAZCTwjFoITAv34KcRMoHotpAeNuAx-dW8,105935
-ipyvasp/_version.py,sha256=j9q3lYMZra0QrErNnn9E5GNXxWLOlDgeOkmX8oXa7ro,23
+ipyvasp/_lattice.py,sha256=4xI8LBypEhTLFxSSsUCGSJjKesxcymIyYBLeM21sO6Q,106414
+ipyvasp/_version.py,sha256=jESq7ftlDB8Kg0mmAcsPtQSIA_t3PZO7335uh0WruS4,23
 ipyvasp/bsdos.py,sha256=omEiQrdbyZDI0Vd39bktzEyw2Il_w9rFsmYR_jEF-Xk,32180
-ipyvasp/cli.py,sha256=aWFEVhNmnW8eSOp5uh95JaDwLQ9K9nlCQcbnOSuhWgw,6844
+ipyvasp/cli.py,sha256=-Lf-qdTvs7WyrA4ALNLaoqxMjLsZkXdPviyQps3ezqg,6880
 ipyvasp/evals_dataframe.py,sha256=KWbkvQJSyXeTSG6LJGcZKs0s5-tor5uPee2P8FJd7vs,20759
 ipyvasp/lattice.py,sha256=NAe4cmXwkd6V0pRDTw1g5_CoNMfqOIT-NpyOSlSfyv0,33710
 ipyvasp/misc.py,sha256=ItSsG_aWiQZNRXM2F23atmNVdedyXFYtoShflYRvzOU,2645
@@ -14,12 +14,12 @@ ipyvasp/utils.py,sha256=1eVDhYzK3dr0AC_CouWrU3xIhbVJu7AABscV-qi_vAA,18000
 ipyvasp/widgets.py,sha256=JcLKjn_Wbi5VXgNOB-SB30dD_-dPTslaKFpJwGgr0Mg,53319
 ipyvasp/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ipyvasp/core/parser.py,sha256=i1lMlfVPEA0-UFDz9lQnlVlMnVFBkEHBsqYPF3ez_2I,39805
-ipyvasp/core/plot_toolkit.py,sha256=XUB8VYBjv81WowafgLEyHELmzQn-PT36KwLJZKXIx_c,36304
+ipyvasp/core/plot_toolkit.py,sha256=459jw5WELvEYWgAvDNF5pxmgEUB6UJIdIJDbTgthWoo,36233
 ipyvasp/core/serializer.py,sha256=aEc7K5jVga8gxm9Tt2OgBw8wnsmWZGtODBnwRJ_5sf0,38423
 ipyvasp/core/spatial_toolkit.py,sha256=dXowREhiFzBvvr5f_bApzFhf8IzjH2E2Ix90oCBUetY,14885
-ipyvasp-1.0.1.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
-ipyvasp-1.0.1.dist-info/METADATA,sha256=n2ix06x91IihFM--xF5l9914VZIsbg_CO4PahbgVJlY,3220
-ipyvasp-1.0.1.dist-info/WHEEL,sha256=Kh9pAotZVRFj97E15yTA4iADqXdQfIVTHcNaZTjxeGM,110
-ipyvasp-1.0.1.dist-info/entry_points.txt,sha256=aU-gGjQG2Q8XfxDlNc_8__cwfp8WG2K5ZgFPInTm2jg,45
-ipyvasp-1.0.1.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
-ipyvasp-1.0.1.dist-info/RECORD,,
+ipyvasp-1.0.3.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
+ipyvasp-1.0.3.dist-info/METADATA,sha256=Owasm1AcDcwSx5cG2PJ_AfoIeBKLlcIhawG2AUeTDfE,3220
+ipyvasp-1.0.3.dist-info/WHEEL,sha256=Kh9pAotZVRFj97E15yTA4iADqXdQfIVTHcNaZTjxeGM,110
+ipyvasp-1.0.3.dist-info/entry_points.txt,sha256=aU-gGjQG2Q8XfxDlNc_8__cwfp8WG2K5ZgFPInTm2jg,45
+ipyvasp-1.0.3.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
+ipyvasp-1.0.3.dist-info/RECORD,,