Merge pull request #253 from SMTG-Bham/fix-bandstats

Fix band stats k-point labels

Author: utf

sumo/cli/bandplot.py

@@ -295,7 +295,7 @@ def bandplot(
     if code == "vasp":
         for vr_file in filenames:
             vr = BSVasprun(vr_file, parse_projected_eigen=parse_projected)
-            bs = vr.get_band_structure(line_mode=True)
+            bs = vr.get_band_structure(line_mode=True, efermi="smart")
             bandstructures.append(bs)
         bs = get_reconstructed_band_structure(bandstructures)
     elif code == "castep":

sumo/cli/bandstats.py

@@ -94,24 +94,26 @@ def bandstats(
     bandstructures = []
     for vr_file in filenames:
         vr = BSVasprun(vr_file, parse_projected_eigen=False)
-        bs = vr.get_band_structure(line_mode=True)
+        bs = vr.get_band_structure(line_mode=True, efermi="smart")
         bandstructures.append(bs)
-    bs = get_reconstructed_band_structure(bandstructures, force_kpath_branches=False)
+    bs, kpt_mapping = get_reconstructed_band_structure(
+        bandstructures, force_kpath_branches=True, return_forced_branch_kpt_map=True
+    )
 
     if bs.is_metal():
         logging.error("ERROR: System is metallic!")
         sys.exit()
 
-    _log_band_gap_information(bs)
+    _log_band_gap_information(bs, kpt_mapping=kpt_mapping)
 
     vbm_data = bs.get_vbm()
     cbm_data = bs.get_cbm()
 
     logging.info("\nValence band maximum:")
-    _log_band_edge_information(bs, vbm_data)
+    _log_band_edge_information(bs, vbm_data, kpt_mapping=kpt_mapping)
 
     logging.info("\nConduction band minimum:")
-    _log_band_edge_information(bs, cbm_data)
+    _log_band_edge_information(bs, cbm_data, kpt_mapping=kpt_mapping)
 
     if parabolic:
         logging.info("\nUsing parabolic fitting of the band edges")
@@ -179,11 +181,14 @@ def bandstats(
     return {"hole_data": hole_data, "electron_data": elec_data}
 
 
-def _log_band_gap_information(bs):
+def _log_band_gap_information(bs, kpt_mapping=None):
     """Log data about the direct and indirect band gaps.
 
     Args:
         bs (:obj:`~pymatgen.electronic_structure.bandstructure.BandStructureSymmLine`):
+        kpt_mapping (:obj:`dict`, optional): A mapping of k-point indicies from the
+            band structure with forced branches to the original band structure.
+
     """
     bg_data = bs.get_band_gap()
     if not bg_data["direct"]:
@@ -199,6 +204,7 @@ def _log_band_gap_information(bs):
             direct_kpoint = bs.kpoints[direct_kindex].frac_coords
             direct_kpoint = kpt_str.format(k=direct_kpoint)
             eq_kpoints = bs.get_equivalent_kpoints(direct_kindex)
+            eq_kpoints = _map_kpoints(eq_kpoints, kpt_mapping)
             k_indices = ", ".join(map(str, eq_kpoints))
 
             # add 1 to band indices to be consistent with VASP band numbers.
@@ -215,7 +221,9 @@ def _log_band_gap_information(bs):
 
         direct_kindex = direct_data[Spin.up]["kpoint_index"]
         direct_kpoint = kpt_str.format(k=bs.kpoints[direct_kindex].frac_coords)
-        k_indices = ", ".join(map(str, bs.get_equivalent_kpoints(direct_kindex)))
+        eq_kpoints = bs.get_equivalent_kpoints(direct_kindex)
+        eq_kpoints = _map_kpoints(eq_kpoints, kpt_mapping)
+        k_indices = ", ".join(map(str, eq_kpoints))
         b_indices = ", ".join(
             [str(i + 1) for i in direct_data[Spin.up]["band_indices"]]
         )
@@ -225,14 +233,16 @@ def _log_band_gap_information(bs):
         logging.info(f"  Band indices: {b_indices}")
 
 
-def _log_band_edge_information(bs, edge_data):
+def _log_band_edge_information(bs, edge_data, kpt_mapping=None):
     """Log data about the valence band maximum or conduction band minimum.
 
     Args:
         bs (:obj:`~pymatgen.electronic_structure.bandstructure.BandStructureSymmLine`):
             The band structure.
         edge_data (dict): The :obj:`dict` from ``bs.get_vbm()`` or
             ``bs.get_cbm()``
+        kpt_mapping (:obj:`dict`, optional): A mapping of k-point indicies from the
+            band structure with forced branches to the original band structure.
     """
     if bs.is_spin_polarized:
         spins = edge_data["band_index"].keys()
@@ -247,7 +257,9 @@ def _log_band_edge_information(bs, edge_data):
 
     kpoint = edge_data["kpoint"]
     kpoint_str = kpt_str.format(k=kpoint.frac_coords)
-    k_indices = ", ".join(map(str, edge_data["kpoint_index"]))
+    k_indices = ", ".join(
+        map(str, _map_kpoints(edge_data["kpoint_index"], kpt_mapping))
+    )
     k_degen = bs.get_kpoint_degeneracy(kpoint=kpoint.frac_coords)
 
     if kpoint.label:
@@ -311,6 +323,13 @@ def _log_effective_mass_data(data, is_spin_polarized, mass_type="m_e"):
     logging.info(f"  {mass_type}: {eff_mass:.3f} | {band_str} | {kpoint_str}")
 
 
+def _map_kpoints(kpt_idxs, kpt_mapping):
+    """Map k-point indices to the original band structure."""
+    if not kpt_mapping:
+        return kpt_idxs
+    return sorted(set([kpt_mapping.get(k, k) for k in kpt_idxs]))
+
+
 def _get_parser():
     parser = argparse.ArgumentParser(
         description="""

sumo/electronic_structure/bandstructure.py

@@ -190,7 +190,9 @@ def get_projections(bs, selection, normalise=None):
     return spec_proj
 
 
-def get_reconstructed_band_structure(list_bs, efermi=None, force_kpath_branches=True):
+def get_reconstructed_band_structure(
+    list_bs, efermi=None, force_kpath_branches=True, return_forced_branch_kpt_map=False
+):
     """Combine a list of band structures into a single band structure.
 
     This is typically very useful when you split non self consistent
@@ -210,12 +212,17 @@ def get_reconstructed_band_structure(list_bs, efermi=None, force_kpath_branches=
             across all band structures is used.
         force_kpath_branches (bool): Force a linemode band structure to contain
             branches by adding repeated high-symmetry k-points in the path.
+        return_forced_branch_kpt_map (bool): If True, return a mapping of the
+            the new k-points to the original k-points.
 
     Returns:
         :obj:`pymatgen.electronic_structure.bandstructure.BandStructure` or \
         :obj:`pymatgen.electronic_structure.bandstructureBandStructureSymmLine`:
         A band structure object. The type depends on the type of the band
         structures in ``list_bs``.
+        If return_forced_branch_kpt_map is True, then a tuple is returned
+        containing the band structure and the mapping from the new k-points
+        to the original k-points.
     """
     if efermi is None:
         efermi = sum(b.efermi for b in list_bs) / len(list_bs)
@@ -244,13 +251,17 @@ def get_reconstructed_band_structure(list_bs, efermi=None, force_kpath_branches=
         structure=list_bs[0].structure,
         projections=projections,
     )
-    if force_kpath_branches:
-        return force_branches(bs)
-    else:
-        return bs
+    branch_bs, mapping = force_branches(bs, return_mapping=True)
+    if force_kpath_branches and return_forced_branch_kpt_map:
+        return branch_bs, mapping
+    elif force_kpath_branches:
+        return branch_bs
+    elif return_forced_branch_kpt_map:
+        return bs, mapping
+    return bs
 
 
-def force_branches(bandstructure):
+def force_branches(bandstructure, return_mapping=False):
     """Force a linemode band structure to contain branches.
 
     Branches give a specific portion of the path from one high-symmetry point
@@ -262,9 +273,14 @@ def force_branches(bandstructure):
 
     Args:
         bandstructure: A band structure object.
+        return_mapping: If True, return a mapping of the new k-points (with branches)
+            to the original k-points.
 
     Returns:
-        A band structure with brnaches.
+        A band structure with branches.
+        If return_forced_branch_kpt_map is True, then a tuple is returned
+        containing the band structure and the mapping from the new k-points
+        to the original k-points.
     """
     kpoints = np.array([k.frac_coords for k in bandstructure.kpoints])
     labels_dict = {k: v.frac_coords for k, v in bandstructure.labels_dict.items()}
@@ -275,6 +291,7 @@ def force_branches(bandstructure):
     # already.
     dup_ids = []
     high_sym_kpoints = tuple(map(tuple, labels_dict.values()))
+    mapping = {}
     for i, k in enumerate(kpoints):
         dup_ids.append(i)
         if (
@@ -287,6 +304,7 @@ def force_branches(bandstructure):
             )
         ):
             dup_ids.append(i)
+        mapping[len(dup_ids) - 1] = i
 
     kpoints = kpoints[dup_ids]
 
@@ -297,7 +315,7 @@ def force_branches(bandstructure):
         if len(bandstructure.projections) != 0:
             projections[spin] = bandstructure.projections[spin][:, dup_ids]
 
-    return type(bandstructure)(
+    bs = type(bandstructure)(
         kpoints,
         eigenvals,
         bandstructure.lattice_rec,
@@ -306,6 +324,9 @@ def force_branches(bandstructure):
         structure=bandstructure.structure,
         projections=projections,
     )
+    if return_mapping:
+        return bs, mapping
+    return bs
 
 
 def string_to_spin(spin_string):

sumo/electronic_structure/dos.py

@@ -99,7 +99,7 @@ def load_dos(
     else:
         vr = vasprun
 
-    band = vr.get_band_structure()
+    band = vr.get_band_structure(efermi="smart")
     dos = vr.complete_dos
 
     dos, band = _scissor_dos(dos, band, scissor)