TB2J 0.8.0__py3-none-any.whl → 0.8.2.1__py3-none-any.whl

TB2J/__init__.py

@@ -1 +1 @@
-__version__ = "0.8.0"
+__version__ = "0.8.2.1"

TB2J/abacus/abacus_wrapper.py

@@ -4,6 +4,7 @@
 The abacus wrapper
 """
 from pathlib import Path
+import os
 import numpy as np
 from scipy.linalg import eigh
 from TB2J.utils import symbol_number_list
@@ -117,13 +118,20 @@ class AbacusParser:
                         return "non-polarized"
                     elif nspin == 2:
                         return "collinear"
-                    elif nspin == 2:
+                    elif nspin == 4:
                         return "noncollinear"
                     else:
                         raise ValueError("nspin should be either 1 or 4.")
 
     def read_atoms(self):
-        self.atoms = read_abacus(str(Path(self.outpath) / "../Stru"))
+        path1=str(Path(self.outpath) / "../STRU")
+        path2=str(Path(self.outpath) / "../Stru")
+        if os.path.exists(path1):
+            self.atoms = read_abacus(path1)
+        elif os.path.exists(path2):
+            self.atoms = read_abacus(path2)
+        else:
+            raise Exception("The STRU or Stru file cannot be found.")
         return self.atoms
 
     def read_basis(self):
@@ -145,14 +153,15 @@ class AbacusParser:
 
     def Read_HSR_noncollinear(self, binary=None):
         p = Path(self.outpath)
-        SR_filename = (p / "data-SR-sparse_SPIN0.csr").as_posix()
-        HR_filename = p / "data-HR-sparse_SPIN0.csr".as_posix()
-        self.nbasis, self.Rlist, self.HR, self.SR = read_HR_SR(
+        SR_filename = str(p / "data-SR-sparse_SPIN0.csr")
+        HR_filename = str(p / "data-HR-sparse_SPIN0.csr")
+        nbasis, Rlist, HR, SR = read_HR_SR(
             nspin=4,
             binary=self.binary,
             HR_fileName=HR_filename,
             SR_fileName=SR_filename,
         )
+        return nbasis, Rlist, HR, SR
 
     def get_models(self):
         if self.spin == "collinear":
@@ -205,7 +214,7 @@ class AbacusParser:
             return basis
 
 
-def test_abacus_wrapper():
+def test_abacus_wrapper_collinear():
     outpath = "/Users/hexu/projects/TB2J_abacus/abacus-tb2j-master/abacus_example/case_Fe/1_no_soc/OUT.Fe"
     parser = AbacusParser(outpath=outpath, spin=None, binary=False)
     atoms = parser.read_atoms()
@@ -216,8 +225,19 @@ def test_abacus_wrapper():
     # print(H.shape)
     # print(H.diagonal().real)
     # print(model_up.get_HR0().diagonal().real)
-    print(parser.get_efermi())
+    print(parser.efermi)
+
+
+def test_abacus_wrapper_ncl():
+    outpath = "/Users/hexu/projects/TB2J_abacus/abacus-tb2j-master/abacus_example/case_Fe/2_soc/OUT.Fe"
+
+    parser = AbacusParser(outpath=outpath, spin=None, binary=False)
+    atoms = parser.read_atoms()
+    model = parser.get_models()
+    H, S, E, V = model.HSE_k([0, 0, 0])
+    print(parser.efermi)
 
 
 if __name__ == "__main__":
-    test_abacus_wrapper()
+    # test_abacus_wrapper()
+    test_abacus_wrapper_ncl()

TB2J/abacus/gen_exchange_abacus.py

@@ -68,7 +68,7 @@ data directory: {outpath}
     else:
         tbmodel = parser.get_models()
         print("Starting to calculate exchange.")
-        description = f""" Input from collinear Abacus data.
+        description = f""" Input from non-collinear Abacus data.
 data directory: {outpath}
 \n"""
         exchange = ExchangeNCL(
@@ -83,6 +83,7 @@ data directory: {outpath}
             nz=nz,
             exclude_orbs=exclude_orbs,
             Rcut=Rcut,
+            np=np,
             use_cache=use_cache,
             description=description,
         )
@@ -93,8 +94,8 @@ data directory: {outpath}
 
 if __name__ == "__main__":
     gen_exchange_abacus(
-        path="/Users/hexu/projects/TB2J_abacus/abacus-tb2j-master/abacus_example/case_Fe/1_no_soc",
-        label="Fe",
+        path="/Users/hexu/projects/TB2J_abacus/abacus-tb2j-master/abacus_example/case_Fe/2_soc",
+        suffix="Fe",
         magnetic_elements=["Fe"],
         nz=50,
         Rcut=8,

TB2J/abacus/stru_api.py

@@ -1,7 +1,8 @@
 # -*- coding: utf-8 -*-
 """
-Created on Wed Jun 13 10:31:30 2018
-@author: shenzx
+@author: Zhen-Xiong Shen
+@email: shenzx@iai.ustc.edu.cn
+@workplace: Institute of Artificial Intelligence, Hefei Comprehensive National Science Center
 
 Modified on Wed Aug 01 11:44:51 2022
 @author: Ji Yu-yang

TB2J/io_exchange/io_exchange.py

@@ -19,6 +19,7 @@ from datetime import datetime
 import matplotlib.pyplot as plt
 from TB2J.spinham.spin_api import SpinModel
 from TB2J.io_exchange.io_txt import write_Jq_info
+from TB2J.utils import symbol_number
 
 
 class SpinIO(object):
@@ -212,7 +213,23 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
     def get_spin_ispin(self, i):
         return self.spinat[self.iatom(i)]
 
+    def get_symbol_number_ispin(self, symnum):
+        """
+        Return the spin index for a given symbol number.
+        """
+        symdict = symbol_number(self.atoms)
+        return self.index_spin[symdict[symnum]]
+
+    def i_spin(self, i):
+        if isinstance(i, int):
+            return i
+        elif isinstance(i, str):
+            return self.get_symbol_number_ispin(i)
+        else:
+            raise ValueError("i must be either an integer or a string.")
+
     def get_charge_ispin(self, i):
+        i = self.i_spin(i)
         return self.charges[self.iatom(i)]
 
     def get_spin_iatom(self, iatom):
@@ -222,6 +239,8 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
         return self.charges[iatom]
 
     def get_J(self, i, j, R, default=None):
+        i = self.i_spin(i)
+        j = self.i_spin(j)
         key = (
             tuple(R),
             i,
@@ -233,6 +252,8 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
             return default
 
     def get_Jiso(self, i, j, R, default=None):
+        i = self.i_spin(i)
+        j = self.i_spin(j)
         key = (
             tuple(R),
             i,
@@ -244,6 +265,8 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
             return default
 
     def get_DMI(self, i, j, R, default=None):
+        i = self.i_spin(i)
+        j = self.i_spin(j)
         key = (
             tuple(R),
             i,
@@ -261,6 +284,8 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
         param j: spin index j
         param R (tuple of integers): cell index R
         """
+        i = self.i_spin(i)
+        j = self.i_spin(j)
         key = (
             tuple(R),
             i,
@@ -278,6 +303,8 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
         param j: spin index j
         param R (tuple of integers): cell index R
         """
+        i = self.i_spin(i)
+        j = self.i_spin(j)
         if iso_only:
             Jtensor = np.eye(3) * self.get_J(i, j, R)
         else:
@@ -295,6 +322,8 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
         returns:
             Jmat: (3*nspin,3*nspin) matrix.
         """
+        i = self.i_spin(i)
+        j = self.i_spin(j)
         n3 = self.nspin * 3
         Jmat = np.zeros((n3, n3), dtype=float)
         for i in range(self.nspin):

TB2J/io_merge.py

@@ -215,9 +215,9 @@ class Merger2:
                 )
                 w = Jani_removed / Jani
                 Jani_sum += Jani * w  # Jani_removed
-                print(f"{Jani* w=}")
+                #print(f"{Jani* w=}")
                 weights += w
-            print(f"{weights=}")
+            #print(f"{weights=}")
             if np.any(weights == 0):
                 raise RuntimeError(
                     "The data set to be merged does not give a complete anisotropic J tensor, please add more data"

TB2J/manager.py

@@ -284,6 +284,21 @@ def gen_exchange_siesta(
         raise ImportError(
             f"sisl version is {sisl.__version__}, but should be larger than 0.10.0."
         )
+
+    include_orbs = {}
+    if isinstance(magnetic_elements, str):
+        magnetic_elements = [magnetic_elements]
+    for element in magnetic_elements:
+        if "_" in element:
+            elem = element.split("_")[0]
+            orb = element.split("_")[1:]
+            include_orbs[elem] = orb
+        else:
+            include_orbs[element] = None
+    magnetic_elements = list(include_orbs.keys())
+    print(magnetic_elements)
+    print(include_orbs)
+
     fdf = sisl.get_sile(fdf_fname)
     geom = fdf.read_geometry()
     H = fdf.read_hamiltonian()

TB2J/myTB.py

@@ -9,7 +9,7 @@ from collections import defaultdict
 # from tbmodels import Model
 from ase.atoms import Atoms
 from TB2J.utils import auto_assign_basis_name
-from TB2J.wannier import parse_ham, parse_xyz, parse_atoms
+from TB2J.wannier import parse_ham, parse_xyz, parse_atoms, parse_tb
 
 
 class AbstractTB:
@@ -84,6 +84,7 @@ class MyTB(AbstractTB):
         self,
         nbasis,
         data=None,
+        R_degens=None,
         positions=None,
         sparse=False,
         ndim=3,
@@ -93,6 +94,7 @@ class MyTB(AbstractTB):
         """
         :param nbasis: number of basis.
         :param data: a dictionary of {R: matrix}. R is a tuple, matrix is a nbasis*nbasis matrix.
+        :param R_degens: degeneracy of R.
         :param positions: reduced positions.
         :param sparse: Bool, whether to use a sparse matrix.
         :param ndim: number of dimensions.
@@ -107,6 +109,10 @@ class MyTB(AbstractTB):
         self._nspin = nspin
         self._norb = nbasis // nspin
         self._ndim = ndim
+        if R_degens is not None:
+            self.R_degens = R_degens
+        else:
+            self.R_degens = np.ones(len(self.data.keys()), dtype=int)
         if positions is None:
             self._positions = np.zeros((nbasis, self.ndim))
         else:
@@ -121,7 +127,6 @@ class MyTB(AbstractTB):
         self.k2Rfactor = -2.0j * np.pi
         self.is_siesta = False
         self.is_orthogonal = True
-
         self._name = "Wannier"
 
     def set_atoms(self, atoms):
@@ -178,12 +183,17 @@ class MyTB(AbstractTB):
         :param path: path
         :param prefix: prefix to the wannier files, often wannier90, or wannier90_up, or wannier90_dn for vasp.
         """
-        # tbmodel = Model.from_wannier_folder(
-        #    folder=path, prefix=prefix)
-        # m = MyTB.from_tbmodel(tbmodel)
 
-        nbasis, data = parse_ham(fname=os.path.join(path, prefix + "_hr.dat"))
-        xcart, _, _ = parse_xyz(fname=os.path.join(path, prefix + "_centres.xyz"))
+        tb_fname = os.path.join(path, prefix + "_tb.dat")
+        hr_fname = os.path.join(path, prefix + "_hr.dat")
+        if os.path.exists(tb_fname):
+            xcart, nbasis, data, R_degens = parse_tb(fname=tb_fname)
+        else:
+            nbasis, data, R_degens = parse_ham(
+                fname=os.path.join(path, prefix + "_hr.dat")
+            )
+            xcart, _, _ = parse_xyz(fname=os.path.join(path, prefix + "_centres.xyz"))
+
         if atoms is None:
             atoms = parse_atoms(os.path.join(path, prefix + ".win"))
         cell = atoms.get_cell()
@@ -200,7 +210,7 @@ class MyTB(AbstractTB):
                 data[key][1::2, ::2] = dtmp[norb:, :norb]
                 data[key][1::2, 1::2] = dtmp[norb:, norb:]
         ind, positions = auto_assign_basis_name(xred, atoms)
-        m = MyTB(nbasis=nbasis, data=data, positions=xred)
+        m = MyTB(nbasis=nbasis, data=data, positions=xred, R_degens=R_degens)
         nm = m.shift_position(positions)
         nm.set_atoms(atoms)
         return nm
@@ -243,13 +253,16 @@ class MyTB(AbstractTB):
         """
         Hk = np.zeros((self.nbasis, self.nbasis), dtype="complex")
         if convention == 2:
-            for R, mat in self.data.items():
-                phase = np.exp(self.R2kfactor * np.dot(k, R))
+            for iR, (R, mat) in enumerate(self.data.items()):
+                phase = np.exp(self.R2kfactor * np.dot(k, R))  # /self.R_degens[iR]
                 H = mat * phase
                 Hk += H + H.conjugate().T
         elif convention == 1:
-            for R, mat in self.data.items():
-                phase = np.exp(self.R2kfactor * np.dot(k, R + self.rjminusri))
+            for iR, (R, mat) in enumerate(self.data.items()):
+                phase = (
+                    np.exp(self.R2kfactor * np.dot(k, R + self.rjminusri))
+                    / self.R_degens[iR]
+                )
                 H = mat * phase
                 Hk += H + H.conjugate().T
         else:
@@ -369,7 +382,7 @@ class MyTB(AbstractTB):
         newpos = copy.deepcopy(pos)
         for i in range(self.nbasis):
             newpos[i] = pos[i] - shift[i]
-        d = MyTB(self.nbasis, ndim=self.ndim, nspin=self.nspin)
+        d = MyTB(self.nbasis, ndim=self.ndim, nspin=self.nspin, R_degens=self.R_degens)
         d._positions = newpos
 
         for R, v in self.data.items():

TB2J/sisl_wrapper.py

@@ -258,6 +258,110 @@ class SislWrapper(AbstractTB):
         return 0.0
 
 
+class SislWFSXWrapper(SislWrapper):
+    """Wrapper for retrieving eigenvalues and eigenvectors from siesta WFSX file
+
+    Parameters
+    ----------
+    geom : sisl.Geometry
+        the geometry containing information about atomic positions and orbitals
+    wfsx_sile: sisl.io.siesta.wfsxSileSiesta
+        file reader for WFSX file
+    spin : sisl.physics.Spin
+        spin object carrying information about spin configurations and spin component.
+    ispin : None or int
+        index of spin channel to be considered. Only takes effect for collinear spin calculations (UP: 0, DOWN: 1).
+        (default: None)
+    shift_fermi: None or float
+        energy shift to be applied to all energies. If `None` no shift is applied. (default: None)
+    """
+
+    def __init__(self, geom, wfsx_sile, spin, ispin=None, shift_fermi=None):
+        # super().__init__(geom, spin=spin, ispin=ispin, shift_fermi=shift_fermi)
+        super().__init__(sisl_hamiltonian, geom=None, spin=None)
+        self.geom = geom
+        self.wfsx_sile = wfsx_sile
+        self.read_all()
+
+    def read_all(self):
+        """Read all wavefunctions, eigenvalues, and k-points from WFSX file."""
+        evals = []
+        evecs = []
+        wfsx_kpts = []
+
+        def change_gauge(k, evec):
+            """Change the eigenvector gauge"""
+            phase = np.dot(
+                self.geom.xyz[self.geom.o2a(np.arange(self.geom.no)), :],
+                np.dot(k, self.geom.rcell),
+            )
+            if self.spin.has_noncolinear:
+                # for NC/SOC we have a 2x2 spin-box per orbital
+                phase = np.repeat(phase, 2)
+            # r -> R gauge tranformation.
+            return evec * np.exp(1j * phase).reshape(1, -1)
+
+        # Read wavefunctions and eigenvalues
+        for wfc in self.wfsx_sile.yield_eigenstate(parent=self.geom):
+            wfsx_kpts.append(wfc.info["k"])
+            evals.append(wfc.c)
+            # To get the same eigvecs as eigh returns we need to transpose the
+            # array and change the gauge from 'r' to 'R'
+            evecs.append(change_gauge(wfc.info["k"], wfc.state).T)
+
+        # If any k-point occurs more than once in the WaveFuncKPoints block,
+        # we discard the duplicates
+        is_duplicate = self._is_duplicate(wfsx_kpts)
+        self.wfsx_kpts = wfsx_kpts[~is_duplicate]
+        self.evals = np.array(evals, dtype=float)[~is_duplicate]
+        if self.shift_fermi is not None:
+            self.evals += self.shift_fermi
+        self.evecs = np.array(evecs, dtype=np.complex64, order="C")[~is_duplicate]
+
+    def _is_duplicate(self, array):
+        # TODO: Move into utils
+        # Find all matches (i,j): array[i] == array[j]
+        matches = np.all(np.isclose(array[None, :], array[:, None]), axis=-1)
+        # Remove double counting of matches: (i,j) and (j,i)
+        # Also, remove matches of elements with themselves: (i,i)
+        matches = np.triu(matches, 1)
+
+        # Finally determine elements which are duplicates
+        return np.any(matches, axis=0)
+
+    def find_all(self, kpts):
+        """Find the correct eigenvectors and eigenvalues and sort them
+        to match the order in kpts.
+
+        Parameters
+        ----------
+        kpts : list of float (3,) or (nk, 3)
+            list of k points
+
+        Returns
+        -------
+        evals : list of float (nk, n)
+            list of eigenvalues for every requested k point
+        evecs :
+            list of eiegnvector for every requested k point
+        """
+        kpts = np.asarray(kpts)
+        sort_idx = np.where(
+            np.all(np.isclose(self.wfsx_kpts[None, :], kpts[:, None]), axis=-1)
+        )[1]
+        if len(sort_idx) < len(kpts):
+            # k-point not found
+            raise ValueError(
+                f"{self.__class__.__name__}._read_all unable to find at least one "
+                "required k point in '{self.wfsx_sile.file}'. Please, ensure that "
+                "all k points listed below are included:\n"
+                + "\n".join([str(k) for k in kpts])
+            )
+        if not np.all(np.isclose(self.wfsx_kpts[sort_idx], kpts)):
+            # raise ValueError(       wfsx_kpts = np.asarray(wfsx_kpts)
+            pass
+
+
 # def test():
 #    fdf = sisl.get_sile('/home/hexu/projects/learn_siesta/SMO_Wannier/siesta.fdf')
 #    H = fdf.read_hamiltonian(order='nc',dim=2)

TB2J/wannier/__init__.py

@@ -1 +1 @@
-from TB2J.wannier.w90_parser import parse_xyz, parse_ham, parse_atoms
+from TB2J.wannier.w90_parser import parse_xyz, parse_ham, parse_atoms, parse_tb

TB2J/wannier/w90_parser.py

@@ -5,6 +5,7 @@ import numpy as np
 from ase.io import read
 from ase.atoms import Atoms
 from ase.units import Angstrom, Bohr
+from .w90_tb_parser import parse_tb_file
 
 unit_dict = {"ANG": Angstrom, "BOHR": Bohr}
 
@@ -49,6 +50,7 @@ def parse_ham(fname="wannier90_hr.dat", cutoff=None):
     for i in range(3, 3 + nline):
         d = map(float, lines[i].strip().split())
         dlist += d
+    R_degens = np.array(dlist, dtype=int)
     H_mnR = defaultdict(lambda: np.zeros((n_wann, n_wann), dtype=complex))
     for i in range(3 + nline, 3 + nline + n_wann**2 * n_R):
         t = lines[i].strip().split()
@@ -65,7 +67,7 @@ def parse_ham(fname="wannier90_hr.dat", cutoff=None):
                 H_mnR[R][m, n] = val / 2.0
         else:
             H_mnR[R][m, n] = val / 2.0
-    return n_wann, H_mnR
+    return n_wann, H_mnR, R_degens
 
 
 def parse_cell(fname, unit=Angstrom):
@@ -138,3 +140,11 @@ def parse_atoms(fname):
         taus = taus * factor
         atoms = Atoms(symbols=symbols, cell=cell, positions=taus)
     return atoms
+
+
+def parse_tb(fname):
+    """
+    return the wannier center, number of wannier functions and the Hamiltonian from the wannier90 _tb.dat file.
+    """
+    result = parse_tb_file(fname)
+    return result["centers"], result["n_wann"], result["H"], result["Rdegens"]

TB2J/wannier/w90_tb_parser.py

@@ -0,0 +1,129 @@
+"""
+parse the tb files in Wannier90
+"""
+
+import os
+import re
+import numpy as np
+from typing import List, Tuple, Dict
+
+
+def ssrline(file):
+    """
+    Read a line and split it into a list of strings"""
+    line = file.readline().strip()
+    return re.split(r"\s+", line)
+
+
+def parse_vector(file, vector_type, size):
+    result = np.zeros((size,), dtype=vector_type)
+    for i in range(size):
+        result[i] = np.fromstring(file.readline().strip(), sep=" ")
+        result[i] = result[i].astype(vector_type)
+    return result
+
+
+def find_Rvectors(Rvectors, R):
+    for i, Rvec in enumerate(Rvectors):
+        if np.all(Rvec == R):
+            return i
+    return -1
+
+
+def parse_tb_file(filename):
+    with open(filename, "r") as io:
+        header = io.readline().strip()
+        a1 = np.fromstring(io.readline().strip(), sep=" ")
+        a2 = np.fromstring(io.readline().strip(), sep=" ")
+        a3 = np.fromstring(io.readline().strip(), sep=" ")
+        # a1, a2, a3 = np.array(list(map(float, [a1, a2, a3])), dtype=np.float64)
+        # lattice = np.vstack((a1.reshape(-1, 1), a2.reshape(-1, 1), a3.reshape(-1, 1))).T
+        lattice = np.vstack((a1, a2, a3))
+
+        n_wann = int(ssrline(io)[0])
+        n_Rvecs = int(ssrline(io)[0])
+
+        Rdegens = []
+        line = io.readline().strip()
+        while line != "":
+            Rdegens += [int(x) for x in line.split()]
+            line = io.readline().strip()
+        assert len(Rdegens) == n_Rvecs, "Rdegens length does not match n_Rvecs"
+
+        Rvectors = np.zeros((n_Rvecs, 3), dtype=np.int32)
+        # H = np.zeros((n_Rvecs,n_wann, n_wann), dtype=np.complex128)
+        H = {}
+        r_x = np.zeros((n_Rvecs, n_wann, n_wann), dtype=np.complex128)
+        r_y = np.zeros((n_Rvecs, n_wann, n_wann), dtype=np.complex128)
+        r_z = np.zeros((n_Rvecs, n_wann, n_wann), dtype=np.complex128)
+        pos_operator = np.zeros((n_Rvecs, n_wann, n_wann, 3), dtype=np.complex128)
+
+        for iR in range(n_Rvecs):
+            # read Rvectors
+            Rvectors[iR] = np.fromstring(io.readline().strip(), sep=" ")
+            Rvectors[iR] = Rvectors[iR].astype(np.int32)
+            R = tuple(Rvectors[iR])
+            H[R] = np.zeros((n_wann, n_wann), dtype=np.complex128)
+            # read H
+            for n in range(n_wann):
+                for m in range(n_wann):
+                    line = ssrline(io)
+                    assert (
+                        m == int(line[0]) - 1 and n == int(line[1]) - 1
+                    ), "Unexpected indices"
+                    reH, imH = float(line[2]), float(line[3])
+                    # H[iR][m, n] = reH + 1j * imH
+                    H[R][m, n] = (reH + 1j * imH) / 2.0
+            io.readline()  # empty line
+        # set the onsite term to half
+        # np.fill_diagonal(H[(0, 0, 0)], H[(0, 0, 0)].diagonal() / 2.0)
+        # print("onsite H from TB: ", H[(0, 0, 0)].diagonal())
+
+        iR0 = find_Rvectors(Rvectors, [0, 0, 0])
+        for iR in range(n_Rvecs):
+            # read Rvectors
+            line = io.readline().strip()
+            Rvectors[iR] = np.fromstring(line, sep=" ")
+            Rvectors[iR] = Rvectors[iR].astype(np.int32)
+            # read r_x, r_y, r_z
+            for n in range(n_wann):
+                for m in range(n_wann):
+                    line = ssrline(io)
+                    assert (
+                        m == int(line[0]) - 1 and n == int(line[1]) - 1
+                    ), f"Unexpected indices in line {line}"
+                    pos_operator[iR, m, n, 0] = complex(float(line[2]), float(line[3]))
+                    pos_operator[iR, m, n, 1] = complex(float(line[4]), float(line[5]))
+                    pos_operator[iR, m, n, 2] = complex(float(line[6]), float(line[7]))
+            io.readline()
+
+        # print(
+        #    f"Reading tb.dat file: {filename} | Header: {header} | n_wann: {n_wann} | n_Rvecs: {n_Rvecs}"
+        # )
+
+        centers = pos_operator[iR0, :, :, :].diagonal(offset=0, axis1=0, axis2=1).T.real
+
+        return {
+            "n_wann": n_wann,
+            "lattice": lattice,
+            "Rvectors": Rvectors,
+            "Rdegens": Rdegens,
+            "H": H,
+            "pos_operator": pos_operator,
+            "centers": centers,
+            "header": header,
+        }
+
+
+def test_parse_tb_file():
+    filename = "cri3_up_tb.dat"
+    result = parse_tb_file(filename)
+    # rvecs=result["Rvectors"]
+    # iR=find_Rvectors(rvecs, [0, 0, 0])
+    # for i in range(30):
+    #    print(np.real(result["pos_operator"][iR, i, i, :]))
+    print(result["centers"])
+
+
+if __name__ == "__main__":
+    test_parse_tb_file()

{TB2J-0.8.0.dist-info → TB2J-0.8.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: TB2J
-Version: 0.8.0
+Version: 0.8.2.1
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Home-page: UNKNOWN
 Author: Xu He

{TB2J-0.8.0.dist-info → TB2J-0.8.2.1.dist-info}/RECORD

@@ -2,7 +2,7 @@ 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=iPlYCcIzuzW7T2HKDkmYlMkRI51dBLfNRxPPiWrfw9U,22
+TB2J/__init__.py,sha256=Gz3blTF1z7t2vohcgNvCiRBFGzinOatDXOyHy8k81ow,24
 TB2J/basis.py,sha256=DFo6_QUwjBwisP6zGxvoO0lpGTMDPAOkiL9giNCjOjA,1558
 TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=aw8LX6wVFCRPhcpkzuI0jGnHisvk4cezvUhkF_6Yx94,2633
@@ -16,17 +16,17 @@ TB2J/exchange_qspace.py,sha256=ZL68qBGFUaQ9BsSPsJaaoWOr9RssPiqX34R_9I3nk_8,8436
 TB2J/gpaw_wrapper.py,sha256=aJ--9Dtyq7jOP1Hkh-Sh1nWcfXm6zKcljOCO0DNCAr0,6890
 TB2J/green.py,sha256=aaXFZn8B60kjsvThoBk0fVi5jm5RJBb-LT4E9XCFo2w,13169
 TB2J/greentest.py,sha256=2ISSfhor9ecSEOi_E6b4Cv26wEIQlwlzca0ru8z44_E,1603
-TB2J/io_merge.py,sha256=p9ylwsWRN3YgUgj0GH0J9-GlTUUfuyIMJYxDhYxhV7g,15261
+TB2J/io_merge.py,sha256=H1jovWIvYRw4KABS6mEL5OwGZHm9emJ-QJjQpeJHwRU,15263
 TB2J/kpoints.py,sha256=6XK2KqTncidEq3o9GuO6VEZRPNTRtWeXg9QfcV-9smI,532
-TB2J/manager.py,sha256=IqZ0cpGz6pBFA7uf9Jc1GzSDCxdIDnTlS1BWqq2mkzw,15389
+TB2J/manager.py,sha256=hiryBJ5b2LMmZ34GXc-gbk3WhWHh6Tjy5OXD-lposVo,15846
 TB2J/mathutils.py,sha256=tHA6q3KPDpXLIbZHdDZ2NU5s886VVM_oEG490zQ6Ris,300
-TB2J/myTB.py,sha256=WAGXqJ4SHSUQhHLN8ODTYXoExw9oEDK2eNY0YS-RAy0,17158
+TB2J/myTB.py,sha256=cm9Kkyzi686QyoxrR3lm4rsSnE6Imee3-j2xM78XnGI,17721
 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=-fxlQN7LbyQAbGUCUBqDJ5ENR0pT8MLBd-5sLxaX_vI,3031
-TB2J/sisl_wrapper.py,sha256=wk9tYfF9cPLYXAbs5Vs3Uf_wbPCtFSgH9CS0ClIhqvE,10580
+TB2J/sisl_wrapper.py,sha256=szeNB_VrRklcMCfWrwnI1Vsv5wqJ92EwwlrWNrIPHM0,14785
 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
@@ -34,16 +34,16 @@ 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/abacus_wrapper.py,sha256=cvOem5WiWYcYqLRBopPACTMEFOvl2jFu2O9rlNbtoPI,8488
+TB2J/abacus/gen_exchange_abacus.py,sha256=lKZqkWMnLQtaSwgn8O5Fzr-pV6tzwoMqfZU_vbET6gU,2973
 TB2J/abacus/orbital_api.py,sha256=l48Hn5z7TA0TH7Is4NDmz74b6B9L2ztYO4dRR37U4mQ,1562
-TB2J/abacus/stru_api.py,sha256=uB_SGqcmYaj4zPGD_2eqSymcXWpu8paxXprFuJsowIQ,67790
+TB2J/abacus/stru_api.py,sha256=aBKKlZ2hvAZChVCfNxRdxH51rfHKqZn6kOlazY-yW8k,67888
 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
-TB2J/io_exchange/io_exchange.py,sha256=ucd5wtRrMfobpHmF45C-NSmJjuE9Ho8kBe3W6q8KqWw,18550
+TB2J/io_exchange/io_exchange.py,sha256=eJRQM1-ikuNJTfCAB0tgTFwvMA_TiWkGlevVu5CeeAk,19408
 TB2J/io_exchange/io_multibinit.py,sha256=8PDmWxzGuv-GwJosj2ZTmiyNY_duFVWJ4ekCuSqGdd8,6739
 TB2J/io_exchange/io_pickle.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 TB2J/io_exchange/io_tomsasd.py,sha256=NqkAC1Fl-CUnFA21eBzSy_S5F_oeQFJysw4UukQbN8o,4173
@@ -60,19 +60,20 @@ TB2J/spinham/qsolver.py,sha256=Sr9I3aGfVNYn5wzwPx1QonHe6ZZUXBAujWRa7nTA5u4,4986
 TB2J/spinham/spin_api.py,sha256=oN3AKg1WQl0YzR4f5ealcJOaVoAy8d7HodIwrbXvQeY,2219
 TB2J/spinham/spin_xml.py,sha256=mneeZzkCE5andvIlur_6VK3XzWvoL-PVqSoWKXtDYTM,11033
 TB2J/spinham/supercell.py,sha256=y17uUC6r3gQb278FhxIW4CABihfLTvKFj6flyXrCPR8,12217
-TB2J/wannier/__init__.py,sha256=XGE3zbL2zI4CK08oNDOhOiAfF6aGl0lj3wE2VxswpYE,70
-TB2J/wannier/w90_parser.py,sha256=1MtVqOmMKwz4_jrkxyju9WfEBqzTXdgxpF6f0IGnAKo,4102
-TB2J-0.8.0.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
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-TB2J-0.8.0.data/scripts/wann2J.py,sha256=0g8Y5RbsYgV7iuoRQEeOnpaBy3oNpRfiw1dy6lWD13E,6520
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+TB2J-0.8.2.1.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
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