TB2J 0.9.9rc14__tar.gz → 0.9.9rc17__tar.gz

{tb2j-0.9.9rc14 → tb2j-0.9.9rc17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc14
+Version: 0.9.9rc17
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -24,6 +24,7 @@ Requires-Dist: packaging>=20.0
 Requires-Dist: HamiltonIO>=0.2.1
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
+Requires-Dist: sisl>=0.9.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{tb2j-0.9.9rc14 → tb2j-0.9.9rc17}/TB2J/exchange.py

@@ -1,6 +1,6 @@
 import os
 import pickle
-from collections import OrderedDict, defaultdict
+from collections import defaultdict
 
 import numpy as np
 from tqdm import tqdm
@@ -96,78 +96,96 @@ class Exchange(ExchangeParams):
 
     def _prepare_orb_dict(self):
         """
-        generate self.ind_mag_atoms and self.orb_dict
-        """
-        # adict: dictionary of {'Fe': ['dxy', 'dyz', ...], ...}
-        adict = OrderedDict()
-        # orb_dict: {ind_atom:[ind_orb,1,2], ...}
-        self.orb_dict = {}
-        # labels: {0:{dxy, ...}}
-        self.labels = {}
-        # magnetic atoms index
-        self.ind_mag_atoms = []
-
-        sdict = symbol_number(self.atoms)
-
-        for i, base in enumerate(self.basis):
-            if i not in self.exclude_orbs:
-                # e.g. Fe2, dxy, _, _
-                if isinstance(base, str):
-                    atom_sym, orb_sym = base.split("|")[:2]
-                    iatom = sdict[atom_sym]
-                else:
-                    try:
-                        atom_sym, orb_sym = base[:2]
-                        iatom = sdict[atom_sym]
-                    except Exception:
-                        iatom = base.iatom
-                        atom_sym = base.iatom
-                        orb_sym = base.sym
-
-                if atom_sym in adict:
-                    adict[atom_sym].append(orb_sym)
-                else:
-                    adict[atom_sym] = [orb_sym]
-                if iatom not in self.orb_dict:
-                    self.orb_dict[iatom] = [i]
-                    self.labels[iatom] = [orb_sym]
-                else:
-                    self.orb_dict[iatom] += [i]
-                    self.labels[iatom] += [orb_sym]
+        Generate orbital and magnetic atom mappings needed for exchange calculations.
 
-        # index of magnetic atoms
-        symbols = self.atoms.get_chemical_symbols()
-        tags = self.atoms.get_tags()
-        for i, (sym, tag) in enumerate(zip(symbols, tags)):
-            if sym in self.magnetic_elements or f"{sym}{tag}" in self.magnetic_elements:
-                self.ind_mag_atoms.append(i)
+        Creates:
+        - self.orb_dict: Maps atom indices to their orbital indices
+        - self.labels: Maps atom indices to their orbital labels
+        - self.ind_mag_atoms: List of indices of magnetic atoms
+        - self._spin_dict: Maps atom indices to spin indices
+        - self._atom_dict: Maps spin indices back to atom indices
+        """
+        self._create_orbital_mappings()
+        self._identify_magnetic_atoms()
+        self._validate_orbital_assignments()
+        self._create_spin_mappings()
+        self._prepare_orb_mmat()
 
-        # sanity check to see if some magnetic atom has no orbital.
-        for iatom in self.ind_mag_atoms:
-            if iatom not in self.orb_dict:
+    def _create_orbital_mappings(self):
+        """Create mappings between atoms and their orbitals."""
+        self.orb_dict = {}  # {atom_index: [orbital_indices]}
+        self.labels = {}  # {atom_index: [orbital_labels]}
+        atom_symbols = symbol_number(self.atoms)
+
+        for orb_idx, base in enumerate(self.basis):
+            if orb_idx in self.exclude_orbs:
+                continue
+
+            # Extract atom and orbital info
+            if isinstance(base, str):
+                atom_sym, orb_sym = base.split("|")[:2]
+                atom_idx = atom_symbols[atom_sym]
+            else:
+                try:
+                    atom_sym, orb_sym = base[:2]
+                    atom_idx = atom_symbols[atom_sym]
+                except Exception:
+                    atom_idx = base.iatom
+                    atom_sym = base.iatom
+                    orb_sym = base.sym
+
+            # Update orbital mappings
+            if atom_idx not in self.orb_dict:
+                self.orb_dict[atom_idx] = [orb_idx]
+                self.labels[atom_idx] = [orb_sym]
+            else:
+                self.orb_dict[atom_idx].append(orb_idx)
+                self.labels[atom_idx].append(orb_sym)
+
+    def _identify_magnetic_atoms(self):
+        """Identify which atoms are magnetic based on elements/tags."""
+        if self.index_magnetic_atoms is not None:
+            self.ind_mag_atoms = self.index_magnetic_atoms
+        else:
+            self.ind_mag_atoms = []
+            symbols = self.atoms.get_chemical_symbols()
+            tags = self.atoms.get_tags()
+
+            for atom_idx, (sym, tag) in enumerate(zip(symbols, tags)):
+                if (
+                    sym in self.magnetic_elements
+                    or f"{sym}{tag}" in self.magnetic_elements
+                ):
+                    self.ind_mag_atoms.append(atom_idx)
+        print(f"Magnetic atoms: {self.ind_mag_atoms}")
+
+    def _validate_orbital_assignments(self):
+        """Validate that magnetic atoms have proper orbital assignments."""
+        # Check all magnetic atoms have orbitals
+        for atom_idx in self.ind_mag_atoms:
+            if atom_idx not in self.orb_dict:
                 raise ValueError(
-                    f"""Cannot find any orbital for atom {iatom}, which is supposed to be magnetic. Please check the Wannier functions."""
+                    f"Atom {atom_idx} is magnetic but has no orbitals assigned. "
+                    "Check Wannier function definitions."
                 )
+
+        # For non-collinear case, check spin-orbital pairing
         if not self._is_collinear:
-            for iatom, orb in self.orb_dict.items():
-                # print(f"iatom: {iatom}, orb: {orb}")
-                nsorb = len(self.orb_dict[iatom])
-                if nsorb % 2 != 0 and False:
+            for atom_idx, orbitals in self.orb_dict.items():
+                if len(orbitals) % 2 != 0:
                     raise ValueError(
-                        f"""The number of spin-orbitals for atom {iatom} is not even,
-{nsorb} spin-orbitals are found near this atom.
-which means the spin up/down does not have same number of orbitals.
-This is often because the Wannier functions are wrongly defined,
-or badly localized. Please check the Wannier centers in the Wannier90 output file.
-"""
+                        f"Atom {atom_idx} has {len(orbitals)} spin-orbitals "
+                        "(should be even). Check Wannier function localization."
                     )
-        self._spin_dict = {}
-        self._atom_dict = {}
-        for ispin, iatom in enumerate(self.ind_mag_atoms):
-            self._spin_dict[iatom] = ispin
-            self._atom_dict[ispin] = iatom
 
-        self._prepare_orb_mmat()
+    def _create_spin_mappings(self):
+        """Create mappings between atom indices and spin indices."""
+        self._spin_dict = {}  # {atom_index: spin_index}
+        self._atom_dict = {}  # {spin_index: atom_index}
+
+        for spin_idx, atom_idx in enumerate(self.ind_mag_atoms):
+            self._spin_dict[atom_idx] = spin_idx
+            self._atom_dict[spin_idx] = atom_idx
 
     def _prepare_orb_mmat(self):
         self.mmats = {}

{tb2j-0.9.9rc14 → tb2j-0.9.9rc17}/TB2J/exchange_params.py

@@ -15,6 +15,7 @@ class ExchangeParams:
     efermi: float
     basis = []
     magnetic_elements = []
+    index_magnetic_atoms = None
     include_orbs = {}
     _kmesh = [4, 4, 4]
     emin: float = -15
@@ -55,6 +56,7 @@ class ExchangeParams:
         mae_angles=None,
         orth=False,
         ibz=False,
+        index_magnetic_atoms=None,
     ):
         self.efermi = efermi
         self.basis = basis
@@ -79,6 +81,7 @@ class ExchangeParams:
         self.mae_angles = mae_angles
         self.orth = orth
         self.ibz = ibz
+        self.index_magnetic_atoms = index_magnetic_atoms
 
     def set_params(self, **kwargs):
         for key, val in kwargs.items():
@@ -229,10 +232,30 @@ def add_exchange_args_to_parser(parser: argparse.ArgumentParser):
         default=False,
     )
 
+    parser.add_argument(
+        "--mae_angles",
+        help="angles for computing MAE, default is 0 0 0",
+        type=float,
+        nargs="*",
+        default=[0.0, 0.0, 0.0],
+    )
+    parser.add_argument(
+        "--index_magnetic_atoms",
+        help="index of magnetic atoms in the unit cell, default is None. If specified, this will be used to determine the atoms to be considered as magnetic atoms, instead of determined from magnetic elements. Note that the index starts from 1 ",
+        type=int,
+        nargs="*",
+        default=None,
+    )
+
     return parser
 
 
 def parser_argument_to_dict(args) -> dict:
+    ind_mag_atoms = args.index_magnetic_atoms
+    if ind_mag_atoms is not None:
+        ind_mag_atoms = [int(i) - 1 for i in ind_mag_atoms]
+    else:
+        ind_mag_atoms = None
     return {
         "efermi": args.efermi,
         "magnetic_elements": args.elements,
@@ -250,4 +273,5 @@ def parser_argument_to_dict(args) -> dict:
         "orb_decomposition": args.orb_decomposition,
         "output_path": args.output_path,
         "orth": args.orth,
+        "index_magnetic_atoms": ind_mag_atoms,
     }

{tb2j-0.9.9rc14 → tb2j-0.9.9rc17}/TB2J/io_exchange/__init__.py

@@ -1 +1,3 @@
 from .io_exchange import SpinIO
+
+__all__ = ["SpinIO"]

tb2j-0.9.9rc17/TB2J/magnon/__init__.py

@@ -0,0 +1,3 @@
+from .io_exchange2 import ExchangeIO, plot_tb2j_magnon_bands
+
+__all__ = ["ExchangeIO", "plot_tb2j_magnon_bands"]