TB2J 0.9.9rc8__tar.gz → 0.9.9rc9__tar.gz

{tb2j-0.9.9rc8 → tb2j-0.9.9rc9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc8
+Version: 0.9.9rc9
 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>=0.1.9
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
+Requires-Dist: sisl>=0.9.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{tb2j-0.9.9rc8 → tb2j-0.9.9rc9}/TB2J/exchange.py

@@ -96,78 +96,93 @@ 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.
+        
+        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()
 
-        # 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)
+    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)
 
-        # 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 _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-0.9.9rc8 → tb2j-0.9.9rc9}/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():
@@ -229,6 +232,21 @@ 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
 
 
@@ -250,4 +268,5 @@ def parser_argument_to_dict(args) -> dict:
         "orb_decomposition": args.orb_decomposition,
         "output_path": args.output_path,
         "orth": args.orth,
+        "index_magnetic_atoms": args.index_magnetic_atoms,
     }

{tb2j-0.9.9rc8 → tb2j-0.9.9rc9}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc8
+Version: 0.9.9rc9
 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>=0.1.9
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
+Requires-Dist: sisl>=0.9.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

tb2j-0.9.9rc9/TB2J.egg-info/SOURCES.txt

@@ -0,0 +1,101 @@
+LICENSE
+README.md
+setup.py
+TB2J/Jdownfolder.py
+TB2J/Jtensor.py
+TB2J/MAE.py
+TB2J/MAEGreen.py
+TB2J/Oiju.py
+TB2J/Oiju_epc.py
+TB2J/__init__.py
+TB2J/anisotropy.py
+TB2J/basis.py
+TB2J/citation.py
+TB2J/contour.py
+TB2J/density_matrix.py
+TB2J/epc.py
+TB2J/exchange.py
+TB2J/exchangeCL2.py
+TB2J/exchange_params.py
+TB2J/exchange_pert.py
+TB2J/exchange_qspace.py
+TB2J/gpaw_wrapper.py
+TB2J/green.py
+TB2J/greentest.py
+TB2J/io_merge.py
+TB2J/kpoints.py
+TB2J/myTB.py
+TB2J/mycfr.py
+TB2J/orbital_magmom.py
+TB2J/orbmap.py
+TB2J/pauli.py
+TB2J/pert.py
+TB2J/plot.py
+TB2J/rotate_atoms.py
+TB2J/rotate_siestaDM.py
+TB2J/sisl_wrapper.py
+TB2J/symmetrize_J.py
+TB2J/tensor_rotate.py
+TB2J/thetaphi.py
+TB2J/utest.py
+TB2J/utils.py
+TB2J/versioninfo.py
+TB2J.egg-info/PKG-INFO
+TB2J.egg-info/SOURCES.txt
+TB2J.egg-info/dependency_links.txt
+TB2J.egg-info/entry_points.txt
+TB2J.egg-info/requires.txt
+TB2J.egg-info/top_level.txt
+TB2J/external/__init__.py
+TB2J/external/p_tqdm.py
+TB2J/interfaces/__init__.py
+TB2J/interfaces/gpaw_interface.py
+TB2J/interfaces/lawaf_interface.py
+TB2J/interfaces/manager.py
+TB2J/interfaces/siesta_interface.py
+TB2J/interfaces/wannier90_interface.py
+TB2J/interfaces/abacus/__init__.py
+TB2J/interfaces/abacus/abacus_api.py
+TB2J/interfaces/abacus/abacus_wrapper.py
+TB2J/interfaces/abacus/gen_exchange_abacus.py
+TB2J/interfaces/abacus/orbital_api.py
+TB2J/interfaces/abacus/stru_api.py
+TB2J/interfaces/abacus/test_density_matrix.py
+TB2J/interfaces/abacus/test_read_HRSR.py
+TB2J/interfaces/abacus/test_read_stru.py
+TB2J/io_exchange/__init__.py
+TB2J/io_exchange/io_exchange.py
+TB2J/io_exchange/io_multibinit.py
+TB2J/io_exchange/io_tomsasd.py
+TB2J/io_exchange/io_txt.py
+TB2J/io_exchange/io_uppasd.py
+TB2J/io_exchange/io_vampire.py
+TB2J/mathutils/__init__.py
+TB2J/mathutils/fermi.py
+TB2J/mathutils/fibonacci_sphere.py
+TB2J/mathutils/kR_convert.py
+TB2J/mathutils/lowdin.py
+TB2J/mathutils/rotate_spin.py
+TB2J/spinham/__init__.py
+TB2J/spinham/base_parser.py
+TB2J/spinham/constants.py
+TB2J/spinham/hamiltonian.py
+TB2J/spinham/hamiltonian_terms.py
+TB2J/spinham/plot.py
+TB2J/spinham/qsolver.py
+TB2J/spinham/spin_api.py
+TB2J/spinham/spin_xml.py
+TB2J/spinham/supercell.py
+TB2J/wannier/__init__.py
+TB2J/wannier/w90_parser.py
+TB2J/wannier/w90_tb_parser.py
+scripts/TB2J_downfold.py
+scripts/TB2J_eigen.py
+scripts/TB2J_magnon.py
+scripts/TB2J_magnon_dos.py
+scripts/TB2J_merge.py
+scripts/TB2J_rotate.py
+scripts/TB2J_rotateDM.py
+scripts/abacus2J.py
+scripts/siesta2J.py
+scripts/wann2J.py

{tb2j-0.9.9rc8 → tb2j-0.9.9rc9}/TB2J.egg-info/requires.txt

@@ -8,3 +8,4 @@ packaging>=20.0
 HamiltonIO>=0.1.9
 pre-commit
 sympair>0.1.0
+sisl>=0.9.0

tb2j-0.9.9rc9/scripts/abacus2J.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+import argparse
+import sys
+
+from TB2J.interfaces import gen_exchange_abacus
+from TB2J.versioninfo import print_license
+from TB2J.exchange_params import add_exchange_args_to_parser
+
+
+def run_abacus2J():
+    print_license()
+    parser = argparse.ArgumentParser(
+        description="abacus2J: Using magnetic force theorem to calculate exchange parameter J from abacus Hamiltonian in the LCAO mode"
+    )
+    # Add ABACUS specific arguments
+    parser.add_argument(
+        "--path", help="the path of the abacus calculation", default="./", type=str
+    )
+    parser.add_argument(
+        "--suffix",
+        help="the label of the abacus calculation. There should be an output directory called OUT.suffix",
+        default="abacus",
+        type=str,
+    )
+
+    # Add common exchange arguments
+    parser = add_exchange_args_to_parser(parser)
+
+
+    args = parser.parse_args()
+
+    if args.elements is None:
+        print("Please input the magnetic elements, e.g. --elements Fe Ni")
+        sys.exit()
+
+    # include_orbs = {}
+
+    gen_exchange_abacus(
+        path=args.path,
+        suffix=args.suffix,
+        kmesh=args.kmesh,
+        magnetic_elements=args.elements,
+        include_orbs={},
+        Rcut=args.rcut,
+        emin=args.emin,
+        nz=args.nz,
+        description=args.description,
+        output_path=args.output_path,
+        use_cache=args.use_cache,
+        nproc=args.nproc,
+        exclude_orbs=args.exclude_orbs,
+        orb_decomposition=args.orb_decomposition,
+        index_magnetic_atoms=args.index_magnetic_atoms,
+        cutoff=args.cutoff,
+    )
+
+
+if __name__ == "__main__":
+    run_abacus2J()

tb2j-0.9.9rc9/scripts/siesta2J.py

@@ -0,0 +1,75 @@
+#!/usr/bin/env python3
+import argparse
+import sys
+
+from TB2J.interfaces import gen_exchange_siesta
+from TB2J.versioninfo import print_license
+from TB2J.exchange_params import add_exchange_args_to_parser
+
+
+def run_siesta2J():
+    print_license()
+    parser = argparse.ArgumentParser(
+        description="siesta2J: Using magnetic force theorem to calculate exchange parameter J from siesta Hamiltonian"
+    )
+    # Add siesta specific arguments
+    parser.add_argument(
+        "--fdf_fname", help="path of the input fdf file", default="./", type=str
+    )
+    parser.add_argument(
+        "--fname",
+        default="exchange.xml",
+        type=str,
+        help="exchange xml file name. default: exchange.xml",
+    )
+    parser.add_argument(
+        "--split_soc",
+        help="whether the SOC part of the Hamiltonian can be read from the output of siesta. Default: False",
+        action="store_true",
+        default=False,
+    )
+
+    # Add common exchange arguments
+    parser = add_exchange_args_to_parser(parser)
+
+
+    args = parser.parse_args()
+
+    if args.elements is None:
+        print("Please input the magnetic elements, e.g. --elements Fe Ni")
+        sys.exit()
+
+    # include_orbs = {}
+    # for element in args.elements:
+    #    if "_" in element:
+    #        elem = element.split("_")[0]
+    #        orb = element.split("_")[1:]
+    #        include_orbs[elem] = orb
+    #    else:
+    #        include_orbs[element] = None
+
+    gen_exchange_siesta(
+        fdf_fname=args.fdf_fname,
+        kmesh=args.kmesh,
+        # magnetic_elements=list(include_orbs.keys()),
+        # include_orbs=include_orbs,
+        magnetic_elements=args.elements,
+        include_orbs={},
+        Rcut=args.rcut,
+        emin=args.emin,
+        emax=args.emax,
+        nz=args.nz,
+        description=args.description,
+        output_path=args.output_path,
+        use_cache=args.use_cache,
+        nproc=args.np,
+        exclude_orbs=args.exclude_orbs,
+        orb_decomposition=args.orb_decomposition,
+        read_H_soc=args.split_soc,
+        orth=args.orth,
+        index_magnetic_atoms=args.index_magnetic_atoms,
+    )
+
+
+if __name__ == "__main__":
+    run_siesta2J()

{tb2j-0.9.9rc8 → tb2j-0.9.9rc9}/scripts/wann2J.py

@@ -89,6 +89,7 @@ def run_wann2J():
         # qspace=args.qspace,
         write_density_matrix=args.write_dm,
         orb_decomposition=args.orb_decomposition,
+        index_magnetic_atoms=args.index_magnetic_atoms,
     )
 
 

{tb2j-0.9.9rc8 → tb2j-0.9.9rc9}/setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from setuptools import find_packages, setup
 
-__version__ = "0.9.9_rc8"
+__version__ = "0.9.9rc9"
 
 long_description = """TB2J is a Python package aimed to compute automatically the magnetic interactions (superexchange  and Dzyaloshinskii-Moriya) between atoms of magnetic crystals from DFT Hamiltonian based on Wannier functions or Linear combination of atomic orbitals. It uses the Green's function method and take the local rigid spin rotation as a perturbation. The package can take the output from Wannier90, which is interfaced with many density functional theory codes or from codes based on localised orbitals. A minimal user input is needed, which allows for an easily integration into a high-throughput workflows. """
 
@@ -43,6 +43,7 @@ setup(
         "HamiltonIO>=0.1.9",
         "pre-commit",
         "sympair>0.1.0",
+        "sisl>=0.9.0",
     ],
     classifiers=[
         "Development Status :: 3 - Alpha",

tb2j-0.9.9rc8/.github/workflows/pylint.yml.bak

@@ -1,23 +0,0 @@
-name: Pylint
-
-on: [push]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.8", "3.9", "3.10"]
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install pylint
-    - name: Analysing the code with pylint
-      run: |
-        pylint $(git ls-files '*.py')

tb2j-0.9.9rc8/.github/workflows/python-app.yml

@@ -1,44 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python application
-
-on:
-  push:
-    branches: [ "master" ]
-  pull_request:
-    branches: [ "master" ]
-
-permissions:
-  contents: read
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.10"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        #pytest
-        #  - pwd
-        python -m pip install . 
-        cd examples/abinit-w90/SrMnO3
-        ls -lah
-        sh get_J.sh
-        cd TB2J_results/Multibinit
-        TB2J_magnon.py --figfname magnon.png