TB2J 0.9.10.1__py3-none-any.whl → 0.9.12.17__py3-none-any.whl

TB2J/scripts/TB2J_eigen.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+import argparse
+
+from TB2J.plot import write_eigen
+from TB2J.versioninfo import print_license
+
+"""
+The script to plot the magnon band structure.
+"""
+
+
+def write_eigen_info():
+    print_license()
+    parser = argparse.ArgumentParser(
+        description="TB2J_eigen.py: Write the eigen values and eigen vectors to file."
+    )
+    parser.add_argument(
+        "--path", default="./", type=str, help="The path of the TB2J_results file"
+    )
+
+    parser.add_argument(
+        "--qmesh",
+        help="qmesh in the format of kx ky kz. Monkhorst pack or Gamma-centered.",
+        type=int,
+        nargs="*",
+        default=[8, 8, 8],
+    )
+
+    parser.add_argument(
+        "--gamma",
+        help="whether shift the qpoint grid to  Gamma-centered. Default: False",
+        action="store_true",
+        default=True,
+    )
+
+    parser.add_argument(
+        "--output_fname",
+        type=str,
+        help="The file name of the output. Default: eigenJq.txt",
+        default="eigenJq.txt",
+    )
+
+    args = parser.parse_args()
+
+    write_eigen(args.qmesh, args.gamma, output_fname=args.output_fname)
+
+
+if __name__ == "__main__":
+    write_eigen_info()

TB2J/scripts/TB2J_magnon.py

@@ -0,0 +1,117 @@
+#!/usr/bin/env python3
+import argparse
+
+from TB2J.plot import plot_magnon_band, write_eigen
+from TB2J.versioninfo import print_license
+
+"""
+The script to plot the magnon band structure.
+"""
+
+
+def plot_magnon():
+    print_license()
+    parser = argparse.ArgumentParser(
+        description="TB2J_magnon: Plot magnon band structure from the TB2J magnetic interaction parameters"
+    )
+    parser.add_argument(
+        "--fname",
+        default="exchange.xml",
+        type=str,
+        help="exchange xml file name. default: exchange.xml",
+    )
+
+    parser.add_argument(
+        "--qpath",
+        default=None,
+        type=str,
+        help="The names of special q-points. If not given, the path will be automatically choosen. See https://wiki.fysik.dtu.dk/ase/ase/dft/kpoints.html for the table of special kpoints and the default path.",
+    )
+
+    parser.add_argument(
+        "--figfname",
+        default=None,
+        type=str,
+        help="The file name of the figure. It should be e.g. png, pdf or other types of files which could be generated by matplotlib.",
+    )
+
+    parser.add_argument(
+        "--Jq",
+        action="store_true",
+        help="To plot the eigenvalues of -J(q) instead of the magnon band",
+        default=False,
+    )
+
+    parser.add_argument(
+        "--no_Jiso",
+        action="store_true",
+        help="switch off isotropic exchange",
+        default=None,
+    )
+
+    parser.add_argument(
+        "--no_dmi", action="store_true", help="switch off dmi", default=None
+    )
+
+    parser.add_argument(
+        "--no_Jani",
+        action="store_true",
+        help="switch off anisotropic exchange",
+        default=None,
+    )
+
+    parser.add_argument(
+        "--write_emin", action="store_true", help="switch to write emin", default=False
+    )
+
+    parser.add_argument(
+        "--show",
+        action="store_true",
+        help="whether to show magnon band structure.",
+        default=False,
+    )
+
+    args = parser.parse_args()
+    if args.Jq:
+        if args.figfname is None:
+            args.figfname = "Eigen_Jq.pdf"
+        print(
+            "Plotting the eigenvalues of -J(q). The figure is written to %s"
+            % (args.figfname)
+        )
+    else:
+        if args.figfname is None:
+            args.figfname = "magnon_band.pdf"
+        print(
+            "Plotting the magnon band structure. The figure is written to %s"
+            % (args.figfname)
+        )
+
+    def nonone(x):
+        if x is None:
+            return x
+        else:
+            return not x
+
+    if args.write_emin:
+        write_eigen(
+            has_exchange=nonone(args.no_Jiso),
+            has_dmi=nonone(args.no_dmi),
+            has_bilinear=nonone(args.no_Jani),
+        )
+    else:
+        plot_magnon_band(
+            fname=args.fname,
+            knames=args.qpath,
+            npoints=300,
+            Jq=args.Jq,
+            figfname=args.figfname,
+            show=args.show,
+            has_exchange=nonone(args.no_Jiso),
+            has_dmi=nonone(args.no_dmi),
+            has_bilinear=nonone(args.no_Jani),
+        )
+
+
+if __name__ == "__main__":
+    plot_magnon()

TB2J/scripts/TB2J_magnon2.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+from TB2J.magnon import plot_tb2j_magnon_bands
+
+
+def plot_tb2j_magnon_bands_cli():
+    """Command line interface for plotting magnon band structures from TB2J data."""
+    import argparse
+
+    parser = argparse.ArgumentParser(
+        description="Plot magnon band structure from TB2J data",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+
+    parser.add_argument(
+        "-f", "--file", default="TB2J.pickle", help="Path to TB2J pickle file"
+    )
+
+    parser.add_argument(
+        "-p",
+        "--path",
+        help="High-symmetry k-point path (e.g., 'GXMG' for square lattice)",
+    )
+
+    parser.add_argument(
+        "-n",
+        "--npoints",
+        type=int,
+        default=300,
+        help="Number of k-points for band structure calculation",
+    )
+
+    parser.add_argument(
+        "-a",
+        "--anisotropic",
+        action="store_true",
+        help="Include anisotropic interactions",
+    )
+
+    parser.add_argument(
+        "-q",
+        "--quadratic",
+        action="store_true",
+        help="Include biquadratic interactions",
+    )
+
+    parser.add_argument("-o", "--output", help="Output filename for the plot")
+
+    parser.add_argument(
+        "--no-pbc",
+        nargs="+",
+        type=int,
+        choices=[0, 1, 2],
+        help="Disable periodic boundary conditions in specified directions (0=x, 1=y, 2=z)",
+    )
+
+    args = parser.parse_args()
+
+    # Set up periodic boundary conditions
+    pbc = [True, True, True]
+    if args.no_pbc:
+        for direction in args.no_pbc:
+            pbc[direction] = False
+    pbc = tuple(pbc)
+
+    # Plot the bands
+    plot_tb2j_magnon_bands(
+        pickle_file=args.file,
+        path=args.path,
+        npoints=args.npoints,
+        anisotropic=args.anisotropic,
+        quadratic=args.quadratic,
+        pbc=pbc,
+        filename=args.output,
+    )
+
+
+if __name__ == "__main__":
+    plot_tb2j_magnon_bands_cli()

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/scripts/TB2J_merge.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+import argparse
+
+from TB2J.io_merge import merge
+from TB2J.versioninfo import print_license
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="TB2J_merge: merge the exchange parameters calculated from different directions. It can accept two types of calculations, first, the lattice structures are rotated from the original structure, from z to x, y, and z, respectively. The structures could be generated using the TB2J_rotate.py command. The second type is the three calculations have the spins along the x, y, and z axis, respectively."
+    )
+    parser.add_argument(
+        "directories",
+        type=str,
+        nargs="+",
+        help="The three directories the TB2J calculations are done. Inside each of them, there should be a TB2J_results directory which contains the magnetic interaction parameter files. e.g. Fe_x Fe_y Fe_z. Alternatively, it could  be the TB2J results directories.",
+    )
+
+    parser.add_argument(
+        "--type",
+        "-T",
+        type=str,
+        help="The type of calculations, either structure of spin, meaning that the three calculations are done by rotating the structure/spin. ",
+    )
+    parser.add_argument(
+        "--output_path",
+        help="The path of the output directory, default is TB2J_results",
+        type=str,
+        default="TB2J_results",
+    )
+    parser.add_argument(
+        "--main_path",
+        help="The path containning the reference structure.",
+        type=str,
+        default=None,
+    )
+
+    args = parser.parse_args()
+    # merge(*(args.directories), args.type.strip().lower(), path=args.output_path)
+    # merge(*(args.directories), method=args.type.strip().lower(), path=args.output_path)
+    # merge2(args.directories, args.type.strip().lower(), path=args.output_path)
+    print_license()
+    print("Merging the TB2J results from the following directories: ", args.directories)
+    merge(*args.directories, main_path=args.main_path, write_path=args.output_path)
+    print("Merging completed. The results are saved in:", args.output_path)
+
+
+if __name__ == "__main__":
+    main()

TB2J/scripts/TB2J_plot_magnon_bands.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+import warnings
+
+from TB2J.magnon.magnon3 import main
+
+warnings.warn(
+    """ 
+        # !!!!!!!!!!!!!!!!!! WARNING: =============================
+        # 
+        # This functionality is under development and should not be used in production.
+        # It is provided for testing and development purposes only.
+        # Please use with caution and report any issues to the developers.
+        #
+        # This warning will be removed in future releases.
+        # =====================================
+
+        """,
+    UserWarning,
+    stacklevel=2,
+)
+# Call the main function from the magnons module
+main()

TB2J/scripts/TB2J_rotate.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+import argparse
+
+from TB2J.rotate_atoms import rotate_xyz
+
+
+def main():
+    parser = argparse.ArgumentParser(description="")
+    parser.add_argument(
+        "fname", help="name of the file containing the atomic structure", type=str
+    )
+    parser.add_argument(
+        "--ftype",
+        help="type of the output files, e.g.  xyz. Please use the format which contains the full cell matrix. (e.g. .cif file should not be used) ",
+        default="xyz",
+        type=str,
+    )
+    parser.add_argument(
+        "--noncollinear",
+        action="store_true",
+        help="If present, six different configurations will be generated. These are required for non-collinear systems.",
+    )
+
+    args = parser.parse_args()
+    rotate_xyz(args.fname, ftype=args.ftype, noncollinear=args.noncollinear)
+
+
+if __name__ == "__main__":
+    main()

TB2J/scripts/TB2J_rotateDM.py

@@ -0,0 +1,21 @@
+#!/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(
+        "--noncollinear",
+        action="store_true",
+        help="If present, six different configurations will be generated. These are required for non-collinear systems.",
+    )
+
+    args = parser.parse_args()
+    rotate_DM(args.fdf_fname, noncollinear=args.noncollinear)
+
+
+if __name__ == "__main__":
+    main()

TB2J/scripts/abacus2J.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python3
+import argparse
+import sys
+
+from TB2J.exchange_params import add_exchange_args_to_parser
+from TB2J.interfaces import gen_exchange_abacus
+from TB2J.versioninfo import print_license
+
+
+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()
+
+    index_magnetic_atoms = args.index_magnetic_atoms
+    if index_magnetic_atoms is not None:
+        index_magnetic_atoms = [i - 1 for i in index_magnetic_atoms]
+
+    if args.elements is None and index_magnetic_atoms 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.np,
+        exclude_orbs=args.exclude_orbs,
+        orb_decomposition=args.orb_decomposition,
+        index_magnetic_atoms=index_magnetic_atoms,
+    )
+
+
+if __name__ == "__main__":
+    run_abacus2J()

TB2J/scripts/siesta2J.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+import argparse
+import sys
+
+from TB2J.exchange_params import add_exchange_args_to_parser
+from TB2J.interfaces import gen_exchange_siesta
+from TB2J.versioninfo import print_license
+
+
+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
+
+    index_magnetic_atoms = args.index_magnetic_atoms
+    if index_magnetic_atoms is not None:
+        index_magnetic_atoms = [i - 1 for i in index_magnetic_atoms]
+
+    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=index_magnetic_atoms,
+    )
+
+
+if __name__ == "__main__":
+    run_siesta2J()

TB2J/scripts/wann2J.py

@@ -0,0 +1,101 @@
+#!/usr/bin/env python3
+import argparse
+import sys
+
+from TB2J.exchange_params import add_exchange_args_to_parser
+from TB2J.interfaces import gen_exchange
+from TB2J.versioninfo import print_license
+
+
+def run_wann2J():
+    print_license()
+    parser = argparse.ArgumentParser(
+        description="wann2J: Using magnetic force theorem to calculate exchange parameter J from wannier functions"
+    )
+    parser.add_argument(
+        "--path", help="path to the wannier files", default="./", type=str
+    )
+    parser.add_argument(
+        "--posfile", help="name of the position file", default="POSCAR", type=str
+    )
+    parser.add_argument(
+        "--prefix_spinor",
+        help="prefix to the spinor wannier files",
+        default="wannier90",
+        type=str,
+    )
+    parser.add_argument(
+        "--prefix_up",
+        help="prefix to the spin up wannier files",
+        default="wannier90.up",
+        type=str,
+    )
+    parser.add_argument(
+        "--prefix_down",
+        help="prefix to the spin down wannier files",
+        default="wannier90.dn",
+        type=str,
+    )
+    parser.add_argument(
+        "--groupby",
+        help="In the spinor case, the order of the orbitals have two conventions: 1: group by spin (orb1_up, orb2_up,... orb1_down, ...), 2,group by orbital (orb1_up, orb1_down, orb2_up, ...,). Use 'spin' in the former case and 'orbital' in the latter case. The default is spin.",
+        default="spin",
+        type=str,
+    )
+    parser.add_argument(
+        "--wannier_type",
+        help="The type of Wannier function, either Wannier90 or banddownfolder",
+        type=str,
+        default="Wannier90",
+    )
+
+    # parser.add_argument("--qspace",
+    #                    action="store_true",
+    #                    help="Whether to calculate J in qspace first and transform to real space.",
+    #                    default=False)
+
+    add_exchange_args_to_parser(parser)
+
+    args = parser.parse_args()
+
+    if args.efermi is None:
+        print("Please input fermi energy using --efermi ")
+        sys.exit()
+    if args.elements is None and args.index_magnetic_atoms is None:
+        print("Please input the magnetic elements, e.g. --elements Fe Ni")
+        sys.exit()
+
+    index_magnetic_atoms = args.index_magnetic_atoms
+    if index_magnetic_atoms is not None:
+        index_magnetic_atoms = [i - 1 for i in index_magnetic_atoms]
+
+    gen_exchange(
+        path=args.path,
+        colinear=(not args.spinor),
+        groupby=args.groupby,
+        posfile=args.posfile,
+        efermi=args.efermi,
+        kmesh=args.kmesh,
+        magnetic_elements=args.elements,
+        Rcut=args.rcut,
+        prefix_SOC=args.prefix_spinor,
+        prefix_up=args.prefix_up,
+        prefix_dn=args.prefix_down,
+        emin=args.emin,
+        emax=args.emax,
+        nz=args.nz,
+        use_cache=args.use_cache,
+        nproc=args.np,
+        description=args.description,
+        output_path=args.output_path,
+        exclude_orbs=args.exclude_orbs,
+        wannier_type=args.wannier_type,
+        # qspace=args.qspace,
+        write_density_matrix=args.write_dm,
+        orb_decomposition=args.orb_decomposition,
+        index_magnetic_atoms=index_magnetic_atoms,
+    )
+
+
+if __name__ == "__main__":
+    run_wann2J()

TB2J/spinham/hamiltonian.py

@@ -19,7 +19,6 @@ from .plot import group_band_path
 from ase.cell import Cell
 from .qsolver import QSolver
 import json
-import os
 
 
 class NumpyEncoder(json.JSONEncoder):

TB2J/symmetrize_J.py

@@ -33,7 +33,7 @@ class TB2JSymmetrizer:
             print("Symmetry found:")
             print(finder.spacegroup)
             print("-" * 30)
-        self.pgdict = finder.get_symmetry_pair_group_dict()
+        self.pgdict = finder.get_symmetry_pair_list_dict()
         self.exc = exc
         self.new_exc = copy.deepcopy(exc)
         self.Jonly = Jonly
@@ -48,7 +48,7 @@ class TB2JSymmetrizer:
         symJdict = {}
         # Jdict = self.exc.exchange_Jdict
         # ngroup = self.pgdict
-        for pairgroup in self.pgdict.groups:
+        for pairgroup in self.pgdict.pairlists:
             ijRs = pairgroup.get_all_ijR()
             ijRs_spin = [self.exc.ijR_index_atom_to_spin(*ijR) for ijR in ijRs]
             Js = [self.exc.get_J(*ijR_spin) for ijR_spin in ijRs_spin]

TB2J/tensor_rotate.py

@@ -1,7 +1,6 @@
 import numpy as np
-import scipy as sp
 from scipy.spatial.transform import Rotation
-from numpy.linalg import norm, det
+from numpy.linalg import norm
 
 
 # Rotation from a to b

TB2J/versioninfo.py

@@ -1,7 +1,10 @@
+import importlib.metadata
 from datetime import datetime
 
 import TB2J
 
+__version__ = importlib.metadata.version("TB2J")
+
 
 def print_license():
     print(

TB2J/wannier/w90_tb_parser.py

@@ -2,10 +2,8 @@
 parse the tb files in Wannier90
 """
 
-import os
 import re
 import numpy as np
-from typing import List, Tuple, Dict
 
 
 def ssrline(file):