TB2J 0.9.11.1__tar.gz → 0.9.11.3__tar.gz

{tb2j-0.9.11.1 → tb2j-0.9.11.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.11.1
+Version: 0.9.11.3
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author-email: Xu He <mailhexu@gmail.com>
 Maintainer-email: Xu He <mailhexu@gmail.com>

{tb2j-0.9.11.1 → tb2j-0.9.11.3}/TB2J/magnon/magnon3.py

@@ -31,6 +31,7 @@ class MagnonParameters:
     Q: Optional[List[float]] = None
     uz_file: Optional[str] = None
     n: Optional[List[float]] = None
+    spin_conf_file: Optional[str] = None
     show: bool = False
 
     @classmethod
@@ -57,6 +58,8 @@ class MagnonParameters:
         # Convert path to absolute path if uz_file is relative to it
         if self.uz_file and not Path(self.uz_file).is_absolute():
             self.uz_file = str(Path(self.path) / self.uz_file)
+        if self.spin_conf_file and not Path(self.spin_conf_file).is_absolute():
+            self.spin_conf_file = str(Path(self.path) / self.spin_conf_file)
 
 
 @dataclass
@@ -76,7 +79,7 @@ class Magnon:
     _n: np.ndarray
     pbc: tuple = (True, True, True)
 
-    def set_reference(self, Q, uz, n):
+    def set_reference(self, Q, uz, n, magmoms=None):
         """
         Set reference propagation vector and quantization axis
 
@@ -92,6 +95,8 @@ class Magnon:
         self.set_propagation_vector(Q)
         self._uz = np.array(uz, dtype=float)
         self._n = np.array(n, dtype=float)
+        if magmoms is not None:
+            self.magmom = np.array(magmoms, dtype=float)
 
     def set_propagation_vector(self, Q):
         """Set propagation vector"""
@@ -653,26 +658,40 @@ def plot_magnon_bands_from_TB2J(
     )
 
     # Set reference vectors if provided
-    if any(x is not None for x in [params.Q, params.uz_file, params.n]):
-        Q = [0, 0, 0] if params.Q is None else params.Q
-        n = [0, 0, 1] if params.n is None else params.n
-
-        # Handle quantization axes
-        if params.uz_file is not None:
-            uz = np.loadtxt(params.uz_file)
-            if uz.shape[1] != 3:
-                raise ValueError(
-                    f"Quantization axes file should contain a natom×3 array. Got shape {uz.shape}"
-                )
-            if uz.shape[0] != magnon.nspin:
-                raise ValueError(
-                    f"Number of spins in uz file ({uz.shape[0]}) does not match the system ({magnon.nspin})"
-                )
-        else:
-            # Default: [0, 0, 1] for all spins
-            uz = np.array([[0.0, 0.0, 1.0] for _ in range(magnon.nspin)])
+    Q = [0, 0, 0] if params.Q is None else params.Q
+    n = [0, 0, 1] if params.n is None else params.n
+
+    # Handle quantization axes
+    if params.uz_file is not None:
+        uz = np.loadtxt(params.uz_file)
+        if uz.shape[1] != 3:
+            raise ValueError(
+                f"Quantization axes file should contain a natom×3 array. Got shape {uz.shape}"
+            )
+        if uz.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in uz file ({uz.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        # Default: [0, 0, 1] for all spins
+        # uz = np.array([[0.0, 0.0, 1.0] for _ in range(magnon.nspin)])
+        uz = np.array([[0, 0, 1]], dtype=float)
+
+    print(params)
+    if params.spin_conf_file is not None:
+        magmoms = np.loadtxt(params.spin_conf_file)
+        if magmoms.shape[1] != 3:
+            raise ValueError(
+                f"Spin configuration file should contain a nspin×3 array. Got shape {magmoms.shape}"
+            )
+        if magmoms.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in spin configuration file ({magmoms.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        magmoms = None
 
-        magnon.set_reference(Q, uz, n)
+    magnon.set_reference(Q, uz, n, magmoms)
 
     # Get band structure data
     print(f"\nCalculating bands along path {params.kpath}...")
@@ -737,27 +756,32 @@ def main():
 
     # Command line arguments (used if no config file is provided)
     parser.add_argument(
+        "-p",
         "--path",
         default="TB2J_results",
         help="Path to TB2J results directory (default: TB2J_results)",
     )
     parser.add_argument(
+        "-k",
         "--kpath",
         default=None,
         help="k-path specification (default: auto-detected from type of cell)",
     )
     parser.add_argument(
+        "-n",
         "--npoints",
         type=int,
         default=300,
         help="Number of k-points along the path (default: 300)",
     )
     parser.add_argument(
+        "-o",
         "--output",
         default="magnon_bands.png",
         help="Output file name (default: magnon_bands.png)",
     )
     parser.add_argument(
+        "-j",
         "--Jiso",
         action="store_true",
         default=True,
@@ -770,18 +794,21 @@ def main():
         help="Exclude isotropic exchange interactions",
     )
     parser.add_argument(
+        "-a",
         "--Jani",
         action="store_true",
         default=False,
         help="Include anisotropic exchange interactions (default: False)",
     )
     parser.add_argument(
+        "-d",
         "--DMI",
         action="store_true",
         default=False,
         help="Include Dzyaloshinskii-Moriya interactions (default: False)",
     )
     parser.add_argument(
+        "-q",
         "--Q",
         nargs=3,
         type=float,
@@ -789,11 +816,19 @@ def main():
         help="Propagation vector [Qx, Qy, Qz] (default: [0, 0, 0])",
     )
     parser.add_argument(
+        "-u",
         "--uz-file",
         type=str,
-        help="Path to file containing quantization axes for each spin (natom×3 array)",
+        help="Path to file containing quantization axes for each spin (nspin×3 array)",
+    )
+    parser.add_argument(
+        "-c",
+        "--spin-conf-file",
+        type=str,
+        help="Path to file containing magnetic moments for each spin (nspin×3 array)",
     )
     parser.add_argument(
+        "-v",
         "--n",
         nargs=3,
         type=float,
@@ -802,6 +837,7 @@ def main():
     )
 
     parser.add_argument(
+        "-s",
         "--show",
         action="store_true",
         default=False,
@@ -833,6 +869,7 @@ def main():
             DMI=args.DMI,
             Q=args.Q if args.Q is not None else None,
             uz_file=args.uz_file,
+            spin_conf_file=args.spin_conf_file,
             n=args.n if args.n is not None else None,
             show=args.show,
         )

tb2j-0.9.11.3/TB2J/magnon/plot_magnon_dos_cli.py

@@ -0,0 +1,211 @@
+#!/usr/bin/env python3
+"""Command-line tool for plotting magnon DOS from TB2J results."""
+
+import argparse
+from pathlib import Path
+
+import numpy as np
+
+from TB2J.magnon.magnon3 import Magnon
+from TB2J.magnon.magnon_dos import plot_magnon_dos
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Calculate and plot magnon DOS from TB2J results"
+    )
+    parser.add_argument(
+        "-p",
+        "--path",
+        default="TB2J_results",
+        help="Path to TB2J results directory (default: TB2J_results)",
+    )
+    parser.add_argument(
+        "--kmesh",
+        type=int,
+        nargs=3,
+        default=[20, 20, 20],
+        metavar=("nx", "ny", "nz"),
+        help="k-point mesh dimensions (default: 20, 20, 20)",
+    )
+    parser.add_argument(
+        "--no-gamma",
+        action="store_false",
+        dest="gamma",
+        help="Exclude Gamma point from k-mesh",
+    )
+    parser.add_argument(
+        "--width",
+        type=float,
+        default=0.001,
+        help="Gaussian smearing width in eV (default: 0.001)",
+    )
+    parser.add_argument(
+        "--window",
+        type=float,
+        nargs=2,
+        metavar=("emin", "emax"),
+        help="Energy window in meV (optional)",
+    )
+    parser.add_argument(
+        "--npts",
+        type=int,
+        default=401,
+        help="Number of energy points (default: 401)",
+    )
+    parser.add_argument(
+        "-o",
+        "--output",
+        default="magnon_dos.png",
+        help="Output filename for plot (default: magnon_dos.png)",
+    )
+    parser.add_argument(
+        "-s",
+        "--show",
+        action="store_true",
+        dest="show",
+        help="Show plot window",
+    )
+
+    # Exchange interaction options (same as in magnon bands)
+    parser.add_argument(
+        "-j",
+        "--Jiso",
+        action="store_true",
+        default=True,
+        help="Include isotropic exchange interactions (default: True)",
+    )
+    parser.add_argument(
+        "--no-Jiso",
+        action="store_false",
+        dest="Jiso",
+        help="Exclude isotropic exchange interactions",
+    )
+    parser.add_argument(
+        "-a",
+        "--Jani",
+        action="store_true",
+        default=False,
+        help="Include anisotropic exchange interactions (default: False)",
+    )
+    parser.add_argument(
+        "-d",
+        "--DMI",
+        action="store_true",
+        default=False,
+        help="Include Dzyaloshinskii-Moriya interactions (default: False)",
+    )
+
+    # Reference vector options (same as in magnon bands)
+    parser.add_argument(
+        "-q",
+        "--Q",
+        nargs=3,
+        type=float,
+        metavar=("Qx", "Qy", "Qz"),
+        help="Propagation vector [Qx, Qy, Qz] (default: [0, 0, 0])",
+    )
+    parser.add_argument(
+        "-u",
+        "--uz-file",
+        type=str,
+        help="Path to file containing quantization axes for each spin (nspin×3 array)",
+    )
+    parser.add_argument(
+        "-c",
+        "--spin-conf-file",
+        type=str,
+        help="Path to file containing magnetic moments for each spin (nspin×3 array)",
+    )
+    parser.add_argument(
+        "-v",
+        "--n",
+        nargs=3,
+        type=float,
+        metavar=("nx", "ny", "nz"),
+        help="Normal vector for rotation [nx, ny, nz] (default: [0, 0, 1])",
+    )
+
+    args = parser.parse_args()
+
+    # Check if TB2J results exist
+    if not Path(args.path).exists():
+        raise FileNotFoundError(f"TB2J results not found at {args.path}")
+
+    # Load magnon calculator with exchange interaction options
+    print(f"Loading exchange parameters from {args.path}...")
+    magnon = Magnon.from_TB2J_results(
+        path=args.path, Jiso=args.Jiso, Jani=args.Jani, DMI=args.DMI
+    )
+
+    # Set reference vectors if provided (same logic as in magnon bands)
+    Q = [0, 0, 0] if args.Q is None else args.Q
+    n = [0, 0, 1] if args.n is None else args.n
+
+    # Handle quantization axes
+    if args.uz_file is not None:
+        # Make path relative to TB2J results if not absolute
+        uz_file = args.uz_file
+        if not Path(uz_file).is_absolute():
+            uz_file = str(Path(args.path) / uz_file)
+
+        uz = np.loadtxt(uz_file)
+        if uz.shape[1] != 3:
+            raise ValueError(
+                f"Quantization axes file should contain a nspin×3 array. Got shape {uz.shape}"
+            )
+        if uz.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in uz file ({uz.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        # Default: [0, 0, 1] for all spins
+        uz = np.array([[0, 0, 1]], dtype=float)
+
+    # Handle spin configuration
+    if args.spin_conf_file is not None:
+        # Make path relative to TB2J results if not absolute
+        spin_conf_file = args.spin_conf_file
+        if not Path(spin_conf_file).is_absolute():
+            spin_conf_file = str(Path(args.path) / spin_conf_file)
+
+        magmoms = np.loadtxt(spin_conf_file)
+        if magmoms.shape[1] != 3:
+            raise ValueError(
+                f"Spin configuration file should contain a nspin×3 array. Got shape {magmoms.shape}"
+            )
+        if magmoms.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in spin configuration file ({magmoms.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        magmoms = None
+
+    # Set reference configuration
+    magnon.set_reference(Q, uz, n, magmoms)
+
+    # Convert window from meV to eV if provided
+    window = None
+    if args.window is not None:
+        window = (args.window[0] / 1000, args.window[1] / 1000)
+
+    # Calculate and plot DOS
+    print("\nCalculating magnon DOS...")
+    _dos = plot_magnon_dos(
+        magnon,
+        kmesh=args.kmesh,
+        gamma=args.gamma,
+        width=args.width,
+        window=window,
+        npts=args.npts,
+        filename=args.output,
+        show=args.show,
+    )
+
+    print(f"\nPlot saved to {args.output}")
+    data_file = Path(args.output).with_suffix(".json")
+    print(f"DOS data saved to {data_file}")
+
+
+if __name__ == "__main__":
+    main()

{tb2j-0.9.11.1 → tb2j-0.9.11.3}/TB2J/scripts/TB2J_eigen.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
+import argparse
+
 from TB2J.plot import write_eigen
 from TB2J.versioninfo import print_license
-import argparse
 
 """
 The script to plot the magnon band structure.

{tb2j-0.9.11.1 → tb2j-0.9.11.3}/TB2J/scripts/TB2J_magnon.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
+import argparse
+
 from TB2J.plot import plot_magnon_band, write_eigen
 from TB2J.versioninfo import print_license
-import argparse
 
 """
 The script to plot the magnon band structure.

tb2j-0.9.11.3/TB2J/scripts/TB2J_magnon_dos.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python3
+
+from TB2J.plot import command_line_plot_magnon_dos
+
+command_line_plot_magnon_dos()

{tb2j-0.9.11.1 → tb2j-0.9.11.3}/TB2J/scripts/TB2J_rotate.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 import argparse
-from TB2J.rotate_atoms import rotate_atom_xyz, rotate_xyz, check_ftype
+
+from TB2J.rotate_atoms import rotate_xyz
 
 
 def main():
@@ -17,7 +18,7 @@ def main():
     parser.add_argument(
         "--noncollinear",
         action="store_true",
-        help="If present, six different configurations will be generated. These are required for non-collinear systems."
+        help="If present, six different configurations will be generated. These are required for non-collinear systems.",
     )
 
     args = parser.parse_args()

{tb2j-0.9.11.1 → tb2j-0.9.11.3}/TB2J/scripts/TB2J_rotateDM.py

@@ -1,16 +1,16 @@
 #!/usr/bin/env python3
 import argparse
+
 from TB2J.rotate_siestaDM import rotate_DM
 
+
 def main():
     parser = argparse.ArgumentParser(description="")
-    parser.add_argument(
-        "--fdf_fname", help="Name of the *.fdf siesta file."
-    )
+    parser.add_argument("--fdf_fname", help="Name of the *.fdf siesta file.")
     parser.add_argument(
         "--noncollinear",
         action="store_true",
-        help="If present, six different configurations will be generated. These are required for non-collinear systems."
+        help="If present, six different configurations will be generated. These are required for non-collinear systems.",
     )
 
     args = parser.parse_args()

{tb2j-0.9.11.1 → tb2j-0.9.11.3}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.11.1
+Version: 0.9.11.3
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author-email: Xu He <mailhexu@gmail.com>
 Maintainer-email: Xu He <mailhexu@gmail.com>

tb2j-0.9.11.3/TB2J.egg-info/SOURCES.txt

@@ -0,0 +1,116 @@
+LICENSE
+README.md
+pyproject.toml
+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/downfold/Hdownfolder.py
+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/magnon/__init__.py
+TB2J/magnon/io_exchange2.py
+TB2J/magnon/magnon3.py
+TB2J/magnon/magnon_band.py
+TB2J/magnon/magnon_dos.py
+TB2J/magnon/magnon_io.py
+TB2J/magnon/magnon_math.py
+TB2J/magnon/plot.py
+TB2J/magnon/plot_magnon_dos_cli.py
+TB2J/magnon/structure.py
+TB2J/mathutils/__init__.py
+TB2J/mathutils/auto_kpath.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/scripts/TB2J_downfold.py
+TB2J/scripts/TB2J_eigen.py
+TB2J/scripts/TB2J_magnon.py
+TB2J/scripts/TB2J_magnon2.py
+TB2J/scripts/TB2J_magnon_dos.py
+TB2J/scripts/TB2J_merge.py
+TB2J/scripts/TB2J_plot_magnon_bands.py
+TB2J/scripts/TB2J_rotate.py
+TB2J/scripts/TB2J_rotateDM.py
+TB2J/scripts/__init__.py
+TB2J/scripts/abacus2J.py
+TB2J/scripts/siesta2J.py
+TB2J/scripts/wann2J.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

{tb2j-0.9.11.1 → tb2j-0.9.11.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "TB2J"
-version = "0.9.11.1"
+version = "0.9.11.3"
 description = "TB2J: First principle to Heisenberg exchange J using tight-binding Green function method"
 readme = "README.md"
 license = { text = "BSD-2-Clause" }

tb2j-0.9.11.1/.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-0.9.11.1/.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