TB2J 0.7.7.1__py3-none-any.whl → 0.8.0__py3-none-any.whl

TB2J/abacus/test_read_HRSR.py

@@ -0,0 +1,44 @@
+from abacus_api import read_HR_SR
+import numpy as np
+
+
+def main():
+    # nspin = 2 case
+    nspin = 2
+    binary = False
+    file_path = "../abacus_example/case_Sr2Mn2O6/1_no_soc/OUT.Sr2Mn2O6/"
+    HR_file = [
+        file_path + "data-HR-sparse_SPIN0.csr",
+        file_path + "data-HR-sparse_SPIN1.csr",
+    ]
+    SR_file = file_path + "data-SR-sparse_SPIN0.csr"
+
+    basis_num, R_direct_coor, HR_up, HR_dn, SR = read_HR_SR(
+        nspin, binary, HR_file, SR_file
+    )
+
+    print("basis_num =", basis_num)
+    print("R_direct_coor =", R_direct_coor)
+    print("HR_up[1, 0, 15:22] =", HR_up[1, 0, 15:22])
+    print("HR_dn[1, 0, 15:22] =", HR_dn[1, 0, 15:22])
+    print("SR[1, 0, 15:22] =", SR[1, 0, 15:22])
+
+    # nspin = 4 case
+    nspin = 4
+    binary = False
+    file_path = "../abacus_example/case_Sr2Mn2O6/2_soc/OUT.Sr2Mn2O6/"
+    HR_file = file_path + "data-HR-sparse_SPIN0.csr"
+    SR_file = file_path + "data-SR-sparse_SPIN0.csr"
+
+    basis_num, R_direct_coor, HR, SR = read_HR_SR(nspin, binary, HR_file, SR_file)
+
+    print("basis_num =", basis_num)
+    print("R_direct_coor =", R_direct_coor)
+    print("HR[1, 0, 30:37] =", HR[1, 0, 30:37])
+    print("SR[1, 0, 30:37] =", SR[1, 0, 30:37])
+
+    return
+
+
+if __name__ == "__main__":
+    main()

TB2J/abacus/test_read_stru.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+@File    :   test_read_stru.py
+@Time    :   2024/02/02 09:52:23
+@Author  :   Shen Zhen-Xiong 
+@Email   :   shenzx@iai.ustc.edu.cn
+"""
+import os
+from stru_api import read_abacus, write_abacus, read_input
+
+
+def main():
+    stru_fe = read_abacus(os.path.join(os.getcwd(), "input/Fe.STRU"))
+    stru_sr2mn2o6 = read_abacus(
+        os.path.join(os.getcwd(), "input/Sr2Mn2O6.STRU"), verbose=True
+    )
+    write_abacus(
+        file=os.path.join(os.getcwd(), "STRU"),
+        atoms=stru_sr2mn2o6,
+        pp=stru_sr2mn2o6.info["pp"],
+        basis=stru_sr2mn2o6.info["basis"],
+    )
+    input_file = read_input(os.path.join(os.getcwd(), "input/INPUT"))
+    print(input_file["pseudo_dir"])
+    return
+
+
+if __name__ == "__main__":
+    main()

TB2J/basis.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+class for basis set
+"""
+from typing import Any
+import numpy as np
+import dataclasses
+from TB2J.utils import symbol_number
+
+
+@dataclasses.dataclass
+class Basis:
+    iatom: int = 0
+    symbol: str = "unamed"
+    spin: int = 0
+
+    def __str__(self):
+        return f"{self.iatom}|{self.symbol}|{self.spin}"
+
+    def to_symnum_type(self, atoms=None, symbol_number=None):
+        if symbol_number is None:
+            symbol_number = symbol_number(atoms)
+        return f"{self.iatom}|{self.symbol}|{self.spin}"
+
+
+@dataclasses.dataclass
+class NAOBasis(Basis):
+    n: int = 0
+    l: int = 0
+    m: int = 0
+    zeta: int = 0
+    element: str = "unknown"
+
+    def __str__(self) -> str:
+        return super().__str__()
+
+
+# @dataclasses.dataclass
+#  inherit from tuple, the elements are basis.
+
+
+class BasisSet(list):
+    def set_atoms(self, atoms):
+        self._atoms = atoms
+
+    def get_iorbs_of_atom(self, iatom: int):
+        """
+        get the index of orbitals of an atom
+        """
+        return [i for i, basis in enumerate(self) if basis.iatom == iatom]
+
+    def get_iorbs_of_atom_spin(self, iatom: int, spin: int):
+        """
+        get the index of orbitals of an atom
+        """
+        return [
+            i
+            for i, basis in enumerate(self)
+            if basis.iatom == iatom and basis.spin == spin
+        ]
+
+    def find_iorbs(self, key=None):
+        """
+        find the index of orbitals of an atom
+        """
+        return [i for i, basis in enumerate(self) if key(basis)]

TB2J/exchange.py

@@ -220,20 +220,6 @@ class Exchange(ExchangeParams):
                     self.orb_dict[iatom] += [i]
                     self.labels[iatom] += [orb_sym]
 
-        # self.orb_slice = []
-
-        # for iatom in range(len(self.atoms)):
-        #    if iatom in self.orb_dict:
-        #        self.orb_slice.append(
-        #            slice(
-        #                self.orb_dict[iatom][0],
-        #                self.orb_dict[iatom][-1] + 1,
-        #            ))
-        #    else:
-        #        self.orb_slice.append(slice(0, 0))
-
-        # self.orb_slice = np.array(self.orb_slice)
-
         # index of magnetic atoms
         for i, sym in enumerate(self.atoms.get_chemical_symbols()):
             if sym in self.magnetic_elements:
@@ -302,6 +288,9 @@ or badly localized. Please check the Wannier centers in the Wannier90 output fil
         return self._atom_dict[ispin]
 
     def _prepare_distance(self):
+        """
+        prepare the distance between atoms.
+        """
         self.distance_dict = {}
         self.short_Rlist = []
         self.R_ijatom_dict = defaultdict(lambda: [])

TB2J/rotate_atoms.py

@@ -2,7 +2,7 @@
 import copy
 from ase.io import read, write
 import numpy as np
-from TB2J.io_merge import Rxx, Rxy, Rxz, Ryx, Ryy, Ryz, Rzx, Rzy, Rzz
+from TB2J.tensor_rotate import Rxx, Rxy, Rxz, Ryx, Ryy, Ryz, Rzx, Rzy, Rzz
 
 
 def rotate_atom_xyz(atoms):

TB2J/utils.py

@@ -24,6 +24,11 @@ def symbol_number(symbols):
     return result
 
 
+def symbol_number_list(symbols):
+    sdict = symbol_number(symbols)
+    return tuple(sdict.keys())
+
+
 def read_basis(fname):
     """
     return basis names from file (often named as basis.txt). Return a dict. key: basis name. value: basis index, from 0

TB2J-0.8.0.data/scripts/abacus2J.py

@@ -0,0 +1,151 @@
+#!python
+from TB2J.abacus.gen_exchange_abacus import gen_exchange_abacus
+from TB2J.versioninfo import print_license
+import sys
+import argparse
+
+
+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"
+    )
+
+    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,
+    )
+
+    parser.add_argument(
+        "--elements",
+        help="list of elements to be considered in Heisenberg model.",
+        # ,  For each element, a postfixes can be used to specify the orbitals(Only with Siesta backend), eg. Fe_3d, or Fe_3d_4s ",
+        default=None,
+        type=str,
+        nargs="*",
+    )
+    parser.add_argument(
+        "--rcut",
+        help="range of R. The default is all the commesurate R to the kmesh",
+        default=None,
+        type=float,
+    )
+    parser.add_argument(
+        "--efermi", help="Fermi energy in eV. For test only. ", default=None, type=float
+    )
+    parser.add_argument(
+        "--kmesh",
+        help="kmesh in the format of kx ky kz. Monkhorst pack. If all the numbers are odd, it is Gamma cenetered. (strongly recommended), Default: 5 5 5",
+        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(
+        "--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(
+        "--nz", help="number of integration steps. Default: 50", default=50, type=int
+    )
+
+    parser.add_argument(
+        "--cutoff",
+        help="The minimum of J amplitude to write, (in eV). Default: 1e-7 eV",
+        default=1e-7,
+        type=float,
+    )
+
+    parser.add_argument(
+        "--exclude_orbs",
+        help="the indices of wannier functions to be excluded from magnetic site. counting start from 0. Default is none.",
+        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(
+        "--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(
+        "--orb_decomposition",
+        default=False,
+        action="store_true",
+        help="whether to do orbital decomposition in the non-collinear mode. Default: False.",
+    )
+
+    parser.add_argument(
+        "--fname",
+        default="exchange.xml",
+        type=str,
+        help="exchange xml file name. default: exchange.xml",
+    )
+
+    parser.add_argument(
+        "--output_path",
+        help="The path of the output directory, default is TB2J_results",
+        type=str,
+        default="TB2J_results",
+    )
+
+    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_abacus(
+        path=args.path,
+        suffix=args.suffix,
+        kmesh=args.kmesh,
+        magnetic_elements=list(include_orbs.keys()),
+        include_orbs=include_orbs,
+        Rcut=args.rcut,
+        emin=args.emin,
+        nz=args.nz,
+        description=args.description,
+        output_path=args.output_path,
+        use_cache=args.use_cache,
+        np=args.np,
+        exclude_orbs=args.exclude_orbs,
+        orb_decomposition=args.orb_decomposition,
+    )
+
+
+if __name__ == "__main__":
+    run_abacus2J()

{TB2J-0.7.7.1.dist-info → TB2J-0.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: TB2J
-Version: 0.7.7.1
+Version: 0.8.0
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Home-page: UNKNOWN
 Author: Xu He

{TB2J-0.7.7.1.dist-info → TB2J-0.8.0.dist-info}/RECORD

@@ -2,13 +2,14 @@ TB2J/Jdownfolder.py,sha256=Nw2ixvn2Uq-o1wficz6rdaYHjfRN3U_kQCvrNJGNb68,6980
 TB2J/Jtensor.py,sha256=0fhfOcfVQGu75gytEnApKWTJZfg9ksKJ0anJgco5wRQ,3179
 TB2J/Oiju.py,sha256=yQMfxQGnOSLbuTS22upkEFsJ9UAZk7wFaWynvg1NVdA,3595
 TB2J/Oiju_epc.py,sha256=sqjLIuWWT-d0uH2O7-6mobsUYQjHP5GyGlmdYqvkXFk,7332
-TB2J/__init__.py,sha256=ktDriQEDrUb4TztGOpVXCVG2-0_SL1KalaY0XS35y7o,24
+TB2J/__init__.py,sha256=iPlYCcIzuzW7T2HKDkmYlMkRI51dBLfNRxPPiWrfw9U,22
+TB2J/basis.py,sha256=DFo6_QUwjBwisP6zGxvoO0lpGTMDPAOkiL9giNCjOjA,1558
 TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=aw8LX6wVFCRPhcpkzuI0jGnHisvk4cezvUhkF_6Yx94,2633
 TB2J/cut_cell.py,sha256=kr9WeQhBQLm8QXL2B3NcsSYmSw-OAtJk3f9wksAOZbs,2952
 TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
-TB2J/exchange.py,sha256=9iSbQCBKvfQ_wOmRx-nHTImsNnBiFqhEyCbmh2cDN1Q,30418
+TB2J/exchange.py,sha256=AMR4fOS1OHD3Qh1AKt0RMDDUDSfCvr_zPPL39qMgHrk,30046
 TB2J/exchangeCL2.py,sha256=mODZU5KKWb2q5KzZAXoAt90vNjjFeLc8L_LySicWV3w,11350
 TB2J/exchange_pert.py,sha256=52XWeVW7JZ_JRUXEfqRfgia8NE_K1R9a0IrJZoLh8gY,8521
 TB2J/exchange_qspace.py,sha256=ZL68qBGFUaQ9BsSPsJaaoWOr9RssPiqX34R_9I3nk_8,8436
@@ -24,13 +25,21 @@ TB2J/orbmap.py,sha256=RCMJkOPGbfPrcZzcc5ia1ZMKBQWxGcyj8W1ve8BJaEw,6669
 TB2J/pauli.py,sha256=_FIF62jq2CkQdWC473a3S2F6NmzCdeCnglO9PjNVmMI,4120
 TB2J/pert.py,sha256=RaCJfewl0doht4cjAnzzGKe-uj2le4aqe0iPKFrq9fo,1192
 TB2J/plot.py,sha256=AnFIFWE2vlmj7Z6f_7-dX_O1stJN-qbuiurPj43dUCM,4104
-TB2J/rotate_atoms.py,sha256=xHjFMRTOgJfYtvKftJt4Lyft_O4HLkLlQNZ-Ysj4U3g,3026
+TB2J/rotate_atoms.py,sha256=-fxlQN7LbyQAbGUCUBqDJ5ENR0pT8MLBd-5sLxaX_vI,3031
 TB2J/sisl_wrapper.py,sha256=wk9tYfF9cPLYXAbs5Vs3Uf_wbPCtFSgH9CS0ClIhqvE,10580
 TB2J/supercell.py,sha256=4hgLGPBLRUDhtD-eF29v46ex7fHdkH-OENjS2wGLFww,19588
 TB2J/tensor_rotate.py,sha256=4-DfT_Mg5e40fbd74M5W0D5DqmUq-kVOOLDkkkI834A,8083
 TB2J/utest.py,sha256=z_ahi7tpHQF9WlHNQihcQ7qzfezRJQXQt28eB1X_z64,3897
-TB2J/utils.py,sha256=esEUiODLZPGDY7ego2z_1Yzp5M3Ew1TaFdm7yiK_j7U,9161
+TB2J/utils.py,sha256=xIKX6p6ULoESWngDLSJsfQQewxsvIWI5l7Uwj_Y5H7U,9262
 TB2J/versioninfo.py,sha256=wZwS9QDFRVDe7rf8JyPDDI8UGdTQiO6Pb_sWv8GAegA,337
+TB2J/abacus/__init__.py,sha256=5sHiDnF2L-Y80QeET9zOiS83a5T_TQAXvnIhcYB6wNU,56
+TB2J/abacus/abacus_api.py,sha256=D_NyXW-Pno92d3RVHByx0l1HDPHQAvXsmQVt8cfIGR8,7267
+TB2J/abacus/abacus_wrapper.py,sha256=-d0vYFi3IkTpSkiKyF_0_qkiYHIu2nqk46SWeNcmeTU,7832
+TB2J/abacus/gen_exchange_abacus.py,sha256=dRDZWELfD209uNEyr-QscgYm3ZvGW-Lb9LoJFIbobxQ,2952
+TB2J/abacus/orbital_api.py,sha256=l48Hn5z7TA0TH7Is4NDmz74b6B9L2ztYO4dRR37U4mQ,1562
+TB2J/abacus/stru_api.py,sha256=uB_SGqcmYaj4zPGD_2eqSymcXWpu8paxXprFuJsowIQ,67790
+TB2J/abacus/test_read_HRSR.py,sha256=cAT-e79jGjCBXLTJ9UYX0WvalG_yD4Awl79tTOUcwaQ,1254
+TB2J/abacus/test_read_stru.py,sha256=CpK4zWhlCVAMCmYQmp9Hy-A40OblZQLFpo5JokpNcWQ,785
 TB2J/external/__init__.py,sha256=yD_ZIMi76H49rj6GAQpiB7UlKa3TgSaMkkLHT6M-8w8,137
 TB2J/external/p_tqdm.py,sha256=ug1jy3-43r8iW7bC37xzPSIe0EjYKH_GUluGzMiQiDw,5831
 TB2J/io_exchange/__init__.py,sha256=KfGHum7B8E4G_KKfillqw0lErtoyKEuFUUttHLs-mg4,32
@@ -53,16 +62,17 @@ TB2J/spinham/spin_xml.py,sha256=mneeZzkCE5andvIlur_6VK3XzWvoL-PVqSoWKXtDYTM,1103
 TB2J/spinham/supercell.py,sha256=y17uUC6r3gQb278FhxIW4CABihfLTvKFj6flyXrCPR8,12217
 TB2J/wannier/__init__.py,sha256=XGE3zbL2zI4CK08oNDOhOiAfF6aGl0lj3wE2VxswpYE,70
 TB2J/wannier/w90_parser.py,sha256=1MtVqOmMKwz4_jrkxyju9WfEBqzTXdgxpF6f0IGnAKo,4102
-TB2J-0.7.7.1.data/scripts/TB2J_downfold.py,sha256=F9oImXFysejCMP7eIBjbCX2jdHFOCvDW5beF1sG-UM8,1854
-TB2J-0.7.7.1.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-TB2J-0.7.7.1.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-TB2J-0.7.7.1.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-TB2J-0.7.7.1.data/scripts/TB2J_merge.py,sha256=uZKLM__EyCHwxrQvx3Wd73dOEADp_SqfYC8KQvA-N9g,1622
-TB2J-0.7.7.1.data/scripts/TB2J_rotate.py,sha256=XPacPb7-DaFafBXFdWuNW_eNbjd5XPdNhBRNYhge_cg,634
-TB2J-0.7.7.1.data/scripts/siesta2J.py,sha256=Q_kvdgE34JJKVUMgBCSe07kARge0XULJ9B6z8hQFu6M,4706
-TB2J-0.7.7.1.data/scripts/wann2J.py,sha256=0g8Y5RbsYgV7iuoRQEeOnpaBy3oNpRfiw1dy6lWD13E,6520
-TB2J-0.7.7.1.dist-info/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-TB2J-0.7.7.1.dist-info/METADATA,sha256=xt1oF6lHnUCU_prKTcgg0q_unLRqZ4eBDnkwDWjPfrY,1464
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-TB2J-0.7.7.1.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
-TB2J-0.7.7.1.dist-info/RECORD,,
+TB2J-0.8.0.data/scripts/TB2J_downfold.py,sha256=F9oImXFysejCMP7eIBjbCX2jdHFOCvDW5beF1sG-UM8,1854
+TB2J-0.8.0.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
+TB2J-0.8.0.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
+TB2J-0.8.0.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
+TB2J-0.8.0.data/scripts/TB2J_merge.py,sha256=uZKLM__EyCHwxrQvx3Wd73dOEADp_SqfYC8KQvA-N9g,1622
+TB2J-0.8.0.data/scripts/TB2J_rotate.py,sha256=XPacPb7-DaFafBXFdWuNW_eNbjd5XPdNhBRNYhge_cg,634
+TB2J-0.8.0.data/scripts/abacus2J.py,sha256=M4B07lvTCDczTPTqvnDh_PERzCARAd09TLKv4aIdSQM,4408
+TB2J-0.8.0.data/scripts/siesta2J.py,sha256=Q_kvdgE34JJKVUMgBCSe07kARge0XULJ9B6z8hQFu6M,4706
+TB2J-0.8.0.data/scripts/wann2J.py,sha256=0g8Y5RbsYgV7iuoRQEeOnpaBy3oNpRfiw1dy6lWD13E,6520
+TB2J-0.8.0.dist-info/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
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