TB2J 0.9.5rc0__py3-none-any.whl → 0.9.6rc0__py3-none-any.whl

TB2J-0.9.5rc0.data/scripts/wann2J.py

@@ -1,194 +0,0 @@
-#!python
-import argparse
-import sys
-from TB2J.manager 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(
-        "--elements",
-        help="elements to be considered in Heisenberg model",
-        default=None,
-        type=str,
-        nargs="*",
-    )
-    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(
-        "--write_dm",
-        help="whether to write density matrix",
-        action="store_true",
-        default=False,
-    )
-
-    parser.add_argument(
-        "--rcut",
-        help="cutoff of spin pair distance. The default is to calculate all commensurate R point to the k mesh.",
-        default=None,
-        type=float,
-    )
-    parser.add_argument("--efermi", help="Fermi energy in eV", default=None, type=float)
-    parser.add_argument(
-        "--kmesh",
-        help="kmesh in the format of kx ky kz",
-        type=int,
-        nargs="*",
-        default=[5, 5, 5],
-    )
-    parser.add_argument(
-        "--emin",
-        help="energy minimum below efermi, default -14 eV",
-        type=float,
-        default=-14.0,
-    )
-    parser.add_argument(
-        "--emax",
-        help="energy maximum above efermi, default 0.0 eV",
-        type=float,
-        default=0.0,
-    )
-    parser.add_argument(
-        "--nz",
-        help="number of steps for semicircle contour, default: 100",
-        default=100,
-        type=int,
-    )
-    parser.add_argument(
-        "--cutoff",
-        help="The minimum of J amplitude to write, (in eV), default is 1e-5 eV",
-        default=1e-5,
-        type=float,
-    )
-    parser.add_argument(
-        "--exclude_orbs",
-        help="the indices of wannier functions to be excluded from magnetic site. counting start from 0",
-        default=[],
-        type=int,
-        nargs="+",
-    )
-
-    parser.add_argument(
-        "--np",
-        help="number of cpu cores to use in parallel, default: 1",
-        default=1,
-        type=int,
-    )
-
-    parser.add_argument(
-        "--use_cache",
-        help="whether to use disk file for temporary storing wavefunctions and hamiltonian to reduce memory usage. Default: False",
-        action="store_true",
-        default=False,
-    )
-
-    parser.add_argument(
-        "--description",
-        help="add description of the calculatiion to the xml file. Essential information, like the xc functional, U values, magnetic state should be given.",
-        type=str,
-        default="Calculated with TB2J.",
-    )
-
-    parser.add_argument(
-        "--spinor",
-        action="store_true",
-        help="Whether to use spinor wannier function.",
-        default=False,
-    )
-
-    parser.add_argument(
-        "--orb_decomposition",
-        default=False,
-        action="store_true",
-        help="whether to do orbital decomposition in the non-collinear mode.",
-    )
-
-    parser.add_argument(
-        "--output_path",
-        help="The path of the output directory, default is TB2J_results",
-        type=str,
-        default="TB2J_results",
-    )
-
-    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)
-
-    args = parser.parse_args()
-
-    if args.efermi is None:
-        print("Please input fermi energy using --efermi ")
-        sys.exit()
-    if args.elements is None:
-        print("Please input the magnetic elements, e.g. --elements Fe Ni")
-        sys.exit()
-
-    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,
-        np=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,
-    )
-
-
-if __name__ == "__main__":
-    run_wann2J()

TB2J/{abacus → interfaces/abacus}/test_density_matrix.py

@@ -1,5 +1,5 @@
-from scipy.linalg import eigh
 import numpy as np
+from scipy.linalg import eigh
 
 
 def gen_random_hermitean_matrix(n):