TB2J 0.9.7rc0__py3-none-any.whl → 0.9.9rc0__py3-none-any.whl

TB2J/MAEGreen.py

@@ -2,8 +2,9 @@ from pathlib import Path
 
 import numpy as np
 import tqdm
+from typing_extensions import DefaultDict
 
-# from TB2J.abacus.abacus_wrapper import AbacusSplitSOCParser
+from HamiltonIO.abacus.abacus_wrapper import AbacusSplitSOCParser
 from TB2J.exchange import ExchangeNCL
 
 # from HamiltonIO.model.rotate_spin import rotate_Matrix_from_z_to_axis, rotate_Matrix_from_z_to_sperical
@@ -14,14 +15,20 @@ from TB2J.mathutils.rotate_spin import (
 
 
 class MAEGreen(ExchangeNCL):
-    def __init__(self, angles=None, **kwargs):
+    def __init__(self, angles=[], **kwargs):
         super().__init__(**kwargs)
-        self.es = None
         self.natoms = len(self.atoms)
+        nangles = len(angles[0])
+        self.es = np.zeros(nangles, dtype=complex)
+        self.es_atom = np.zeros((nangles, self.natoms), dtype=complex)
+        self.es_atom_orb = DefaultDict(lambda: 0)
         if angles is None or angles == "axis":
             self.set_angles_axis()
         elif angles == "scan":
             self.set_angles_scan()
+        else:
+            self.thetas = angles[0]
+            self.phis = angles[1]
 
     def set_angles_axis(self):
         """theta and phi are defined as the x, y, z, axis."""
@@ -42,43 +49,149 @@ class MAEGreen(ExchangeNCL):
         Hsoc_k = self.tbmodel.get_Hk_soc(self.G.kpts)
         na = len(thetas)
         dE_angle = np.zeros(na, dtype=complex)
-        dE_angle_atoms = np.zeros((na, self.natoms), dtype=complex)
+        dE_angle_atom = np.zeros((na, self.natoms), dtype=complex)
+        # dE_angle_orbitals = np.zeros((na, self.natoms, self.norb, self.norb), dtype=complex)
+        # dE_angle_orbitals = DefaultDict(lambda: 0)
+        dE_angle_atom_orb = DefaultDict(lambda: 0)
         for iangle, (theta, phi) in enumerate(zip(thetas, phis)):
             for ik, dHk in enumerate(Hsoc_k):
                 dHi = rotate_spinor_matrix(dHk, theta, phi)
                 GdH = G0K[ik] @ dHi
                 # dE += np.trace(GdH @ G0K[i].T.conj() @ dHi) * self.kweights[i]
                 # diagonal of second order perturbation.
-                dG2diag = np.diag(GdH @ GdH)
+                # dG2diag = np.diag(GdH @ GdH)
+                #dG2 = np.einsum("ij,ji->ij", GdH,   GdH)
+                dG2 = GdH * GdH.T
+                dG2sum = np.sum(dG2)
+
                 # dG2diag = np.diag(GdH @G0K[i].T.conj() @ dHi)
-                dE_angle[iangle] += np.sum(dG2diag) * self.G.kweights[ik]
+                #dE_angle[iangle] += np.trace(GdH@GdH) * self.G.kweights[ik]
+                #dE_angle[iangle] += np.trace(GdH@G0K[ik].T.conj()@dHi ) * self.G.kweights[ik]
+                dE_angle[iangle] += dG2sum * self.G.kweights[ik]
                 for iatom in range(self.natoms):
-                    dE_atom = np.sum(dG2diag[self.iorb(iatom)]) * self.G.kweights[ik]
-                    dE_angle_atoms[iangle, iatom] += dE_atom
-        return dE_angle, dE_angle_atoms
+                    iorb = self.iorb(iatom)
+                    #dG2= dG2[::2, ::2] + dG2[1::2, 1::2] + dG2[1::2, ::2] + dG2[::2, 1::2]
+                    dE_atom_orb = dG2[np.ix_(iorb, iorb)] * self.G.kweights[ik]
+                    dE_atom_orb = dE_atom_orb[::2, ::2] + dE_atom_orb[1::2, 1::2] + dE_atom_orb[1::2, ::2] + dE_atom_orb[::2, 1::2]
+                    mmat = self.mmats[iatom]
+                    dE_atom_orb =  mmat.T @ dE_atom_orb @ mmat
+
+                    dE_angle_atom_orb[(iangle, iatom)] += dE_atom_orb
+
+                    dE_atom = np.sum(dE_atom_orb)
+                    dE_angle_atom[iangle, iatom] += dE_atom
+        return dE_angle, dE_angle_atom, dE_angle_atom_orb
+
+    def get_perturbed_R(self, e, thetas, phis):
+        self.tbmodel.set_so_strength(0.0)
+        # Here only the first R vector is considered.
+        # TODO: consider all R vectors.
+        # Rlist = np.zeros((1, 3), dtype=float)
+        # G0K = self.G.get_Gk_all(e)
+        # G0R = k_to_R(self.G.kpts, Rlist, G0K, self.G.kweights)
+        # dE_angle = np.zeros(len(thetas), dtype=complex)
+        # dE_angle_atoms = np.zeros((len(thetas), self.natoms), dtype=complex)
+        pass
 
     def get_band_energy_vs_angles(self, thetas, phis):
-        nangles = len(thetas)
-        self.es = np.zeros(nangles, dtype=float)
-        self.es_atoms = np.zeros((nangles, self.natoms), dtype=float)
         for ie, e in enumerate(tqdm.tqdm(self.contour.path)):
-            dE_angle, dE_angle_atoms = self.get_perturbed(e, thetas, phis)
-            self.es -= np.imag(dE_angle * self.contour.weights[ie]) / np.pi
-            self.es_atoms -= np.imag(dE_angle_atoms * self.contour.weights[ie]) / np.pi
+            dE_angle, dE_angle_atom, dE_angle_atom_orb = self.get_perturbed(
+                e, thetas, phis
+            )
+            self.es += dE_angle * self.contour.weights[ie]
+            self.es_atom += dE_angle_atom * self.contour.weights[ie]
+            for key, value in dE_angle_atom_orb.items():
+                self.es_atom_orb[key] += dE_angle_atom_orb[key] * self.contour.weights[ie]
+
+        self.es = -np.imag(self.es) / np.pi
+        self.es_atom = -np.imag(self.es_atom) / np.pi
+        for key, value in self.es_atom_orb.items():
+            self.es_atom_orb[key] = -np.imag(value) / np.pi
 
     def output(self, output_path="TB2J_anisotropy"):
         Path(output_path).mkdir(exist_ok=True)
         fname = f"{output_path}/MAE.dat"
+        fname_orb = f"{output_path}/MAE_orb.dat"
         with open(fname, "w") as f:
-            f.write("# theta phi MAE, MAEatom1, atom2, ...\n")
+            f.write("# theta, phi, MAE(total), MAE(atom-wise) Unit: meV\n")
             for i, (theta, phi, e, es) in enumerate(
-                zip(self.thetas, self.phis, self.es, self.es_atoms)
+                zip(self.thetas, self.phis, self.es, self.es_atom)
             ):
-                f.write(f"{theta:.5f} {phi:.5f} {e:.8f} ")
+                f.write(f"{theta:.5f} {phi:.5f} {e*1e3:.8f} ")
                 for ea in es:
-                    f.write(f"{ea:.8f} ")
+                    f.write(f"{ea*1e3:.8f} ")
+                f.write("\n")
+
+        with open(fname_orb, "w") as f:
+            f.write("=" * 80 + "\n")
+            f.write("Orbitals for each atom: \n")
+            f.write("=" * 80 + "\n")
+            f.write("Note: the energies are in meV\n")
+            for iatom in range(self.natoms):
+                f.write(f"Atom {iatom:03d}: ")
+                for orb in self.orbital_names[iatom]:
+                    f.write(f"{orb} ")
+                f.write("\n")
+            for i, (theta, phi, e, eatom) in enumerate(
+                zip(self.thetas, self.phis, self.es, self.es_atom)
+            ):
+                f.write("-" * 60 + "\n")
+                f.write(f"Angle {i:03d}:   theta={theta:.5f} phi={phi:.5f} \n ")
+                f.write(f"E: {e*1e3:.8f} \n")
+                for iatom, ea in enumerate(eatom):
+                    f.write(f"Atom {iatom:03d}: {ea*1e3:.8f} \n")
+                    f.write("Orbital: ")
+                    eorb = self.es_atom_orb[(i, iatom)] 
+
+                    # write numpy matrix to file
+                    f.write(
+                        np.array2string(
+                            eorb*1e3, precision=4, separator=",", suppress_small=True
+                        )
+                    )
+
+                    eorb_diff = eorb -  self.es_atom_orb[(0, iatom)]
+                    f.write("Diference to the first angle: ")
+                    f.write(
+                        np.array2string(
+                            eorb_diff*1e3, precision=4, separator=",", suppress_small=True
+                        )
+                    )
                 f.write("\n")
 
     def run(self, output_path="TB2J_anisotropy"):
         self.get_band_energy_vs_angles(self.thetas, self.phis)
-        self.output()
+        self.output(output_path=output_path)
+
+
+def abacus_get_MAE(
+    path_nosoc,
+    path_soc,
+    kmesh,
+    thetas,
+    phis,
+    gamma=True,
+    output_path="TB2J_anisotropy",
+    magnetic_elements=None,
+    nel=None,
+    width=0.1,
+    **kwargs
+):
+    """Get MAE from Abacus with magnetic force theorem. Two calculations are needed. First we do an calculation with SOC but the soc_lambda is set to 0. Save the density. The next calculatin we start with the density from the first calculation and set the SOC prefactor to 1. With the information from the two calcualtions, we can get the band energy with magnetic moments in the direction, specified in two list, thetas, and phis."""
+    parser = AbacusSplitSOCParser(
+        outpath_nosoc=path_nosoc, outpath_soc=path_soc, binary=False
+    )
+    model = parser.parse()
+    if nel is not None:
+        model.nel = nel
+    mae = MAEGreen(tbmodels=model, atoms = model.atoms, kmesh=kmesh, efermi=None,  basis=model.basis, angles=[thetas, phis], magnetic_elements=magnetic_elements, **kwargs)
+    mae.run(output_path=output_path)
+    #es = mae.get_band_energy_vs_angles(thetas, phis)
+    #if outfile:
+    #    with open(outfile, "w") as f:
+    #        f.write("#theta, phi, energy\n")
+    #        for theta, phi, e in zip(thetas, phis, es):
+    #            f.write(f"{theta:5.3f}, {phi:5.3f}, {e:10.9f}\n")
+    #return es
+
+

TB2J/exchange.py

@@ -50,7 +50,8 @@ class Exchange(ExchangeParams):
         os.makedirs(self.orbpath, exist_ok=True)
 
     def _adjust_emin(self):
-        self.emin = self.G.find_energy_ingap(rbound=self.efermi - 5.0) - self.efermi
+        #self.emin = self.G.find_energy_ingap(rbound=self.efermi - 10.0) - self.efermi
+        self.emin = -12.0
         print(f"A gap is found at {self.emin}, set emin to it.")
 
     def set_tbmodels(self, tbmodels):
@@ -114,14 +115,19 @@ class Exchange(ExchangeParams):
                 # e.g. Fe2, dxy, _, _
                 if isinstance(base, str):
                     atom_sym, orb_sym = base.split("|")[:2]
+                    iatom = sdict[atom_sym]
                 else:
-                    atom_sym, orb_sym = base[:2]
+                    try:
+                        atom_sym, orb_sym = base[:2]
+                    except Exception as e:
+                        iatom = base.iatom
+                        atom_sym = base.iatom
+                        orb_sym = base.sym
 
                 if atom_sym in adict:
                     adict[atom_sym].append(orb_sym)
                 else:
                     adict[atom_sym] = [orb_sym]
-                iatom = sdict[atom_sym]
                 if iatom not in self.orb_dict:
                     self.orb_dict[iatom] = [i]
                     self.labels[iatom] = [orb_sym]
@@ -144,8 +150,9 @@ class Exchange(ExchangeParams):
                 )
         if not self._is_collinear:
             for iatom, orb in self.orb_dict.items():
+                print(f"iatom: {iatom}, orb: {orb}")
                 nsorb = len(self.orb_dict[iatom])
-                if nsorb % 2 != 0:
+                if nsorb % 2 != 0 and False:
                     raise ValueError(
                         f"""The number of spin-orbitals for atom {iatom} is not even,
 {nsorb} spin-orbitals are found near this atom.
@@ -166,7 +173,10 @@ or badly localized. Please check the Wannier centers in the Wannier90 output fil
         self.mmats = {}
         self.orbital_names = {}
         self.norb_reduced = {}
-        if self.backend_name.upper() == "SIESTA":
+        print(f"self.backend_name: {self.backend_name}")
+        if self.backend_name.upper() in ["SIESTA", "ABACUS", "LCAOHAMILTONIAN"]:
+            print(f"magntic_elements: {self.magnetic_elements}")
+            print(f"include_orbs: {self.include_orbs}")
             syms = self.atoms.get_chemical_symbols()
             for iatom, orbs in self.labels.items():
                 if (self.include_orbs is not None) and syms[iatom] in self.include_orbs:
@@ -176,6 +186,7 @@ or badly localized. Please check the Wannier centers in the Wannier90 output fil
                         include_only=self.include_orbs[syms[iatom]],
                     )
                 else:
+                    print(f"orbs: {orbs}")
                     mmat, reduced_orbs = map_orbs_matrix(
                         orbs, spinor=not (self._is_collinear), include_only=None
                     )
@@ -231,7 +242,7 @@ or badly localized. Please check the Wannier centers in the Wannier90 output fil
         """
         sum up the contribution of all the orbitals with same (n,l,m)
         """
-        if self.backend_name.upper() == "SIESTA":
+        if self.backend_name.upper() in ["SIESTA", "ABACUS", "LCAOHAMILTONIAN"]:
             mmat_i = self.mmats[iatom]
             mmat_j = self.mmats[jatom]
             Jorbij = mmat_i.T @ Jorbij @ mmat_j

TB2J/exchange_params.py

@@ -56,8 +56,11 @@ class ExchangeParams:
     ):
         self.efermi = efermi
         self.basis = basis
-        self.magnetic_elements = magnetic_elements
-        self.include_orbs = include_orbs
+        # self.magnetic_elements = magnetic_elements
+        # self.include_orbs = include_orbs
+        self.magnetic_elements, self.include_orbs = self.set_magnetic_elements(
+            magnetic_elements, include_orbs
+        )
         self._kmesh = kmesh
         self.emin = emin
         self.emax = emax
@@ -82,6 +85,28 @@ class ExchangeParams:
         with open(fname, "w") as myfile:
             yaml.dump(self.__dict__, myfile)
 
+    def set_magnetic_elements(self, magnetic_elements, include_orbs):
+        # magnetic_elements = exargs.pop("magnetic_elements")
+        # include_orbs = exargs.pop("include_orbs")
+        if include_orbs is None:
+            include_orbs = {}
+        if isinstance(magnetic_elements, str):
+            magnetic_elements = [magnetic_elements]
+        print(f"magnetic_elements: {magnetic_elements}")
+        print(f"include_orbs: {include_orbs}")
+        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
+
+        print(f"magnetic_elements: {magnetic_elements}")
+        print(f"include_orbs: {include_orbs}")
+        magnetic_elements = list(include_orbs.keys())
+        return magnetic_elements, include_orbs
+
 
 def add_exchange_args_to_parser(parser: argparse.ArgumentParser):
     parser.add_argument(

TB2J/interfaces/abacus/abacus_wrapper.py

@@ -192,6 +192,7 @@ class AbacusParser:
     def read_basis(self):
         fname = str(Path(self.outpath) / "Orbital")
         self.basis = parse_abacus_orbital(fname)
+        print(self.basis)
         return self.basis
 
     def read_HSR_collinear(self, binary=None):

TB2J/interfaces/abacus/gen_exchange_abacus.py

@@ -27,7 +27,7 @@ def gen_exchange_abacus(
     exclude_orbs=[],
     Rcut=None,
     use_cache=False,
-    np=1,
+    nproc=1,
     output_path="TB2J_results",
     orb_decomposition=False,
     description=None,
@@ -60,9 +60,10 @@ data directory: {outpath}
             nz=nz,
             exclude_orbs=exclude_orbs,
             Rcut=Rcut,
-            np=np,
+            nproc=nproc,
             use_cache=use_cache,
             output_path=output_path,
+            orb_decomposition=orb_decomposition,
             description=description,
         )
         exchange.run(path=output_path)
@@ -86,8 +87,9 @@ data directory: {outpath}
             nz=nz,
             exclude_orbs=exclude_orbs,
             Rcut=Rcut,
-            np=np,
+            nproc=nproc,
             use_cache=use_cache,
+            orb_decomposition=orb_decomposition,
             description=description,
         )
         exchange.run()

TB2J/interfaces/abacus/orbital_api.py

@@ -16,13 +16,14 @@ class AbacusOrbital:
     Orbital class
     """
 
-    iatom: int
-    sym: str
-    spin: int
-    element: str
-    l: int
-    m: int
-    z: int
+    iatom: int = 0
+    sym: str = ""
+    spin: int = 0
+    element: str = ""
+    n: int = 0
+    l: int = 0
+    m: int = 0
+    z: int = 0
 
 
 def parse_abacus_orbital(fname):
@@ -38,10 +39,11 @@ def parse_abacus_orbital(fname):
             iatom, element, l, m, z, sym = seg
             iatom = int(iatom)
             ispin = 0
+            n = 0
             l = int(l)
             m = int(m)
             z = int(z)
-            orbs.append(AbacusOrbital(iatom, sym, ispin, element, l, m, z))
+            orbs.append(AbacusOrbital(iatom, sym, ispin, element, n, l, m, z))
             line = myfile.readline()
     return orbs
 

TB2J/interfaces/siesta_interface.py

@@ -89,18 +89,6 @@ def gen_exchange_siesta(fdf_fname, read_H_soc=False, **kwargs):
             f"sisl version is {sisl.__version__}, but should be larger than 0.10.0."
         )
 
-    magnetic_elements = exargs.pop("magnetic_elements")
-    include_orbs = exargs.pop("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())
     output_path = exargs.pop("output_path")
 
     parser = SislParser(
@@ -122,8 +110,8 @@ def gen_exchange_siesta(fdf_fname, read_H_soc=False, **kwargs):
             atoms=tbmodel_up.atoms,
             basis=basis,
             efermi=0.0,
-            magnetic_elements=magnetic_elements,
-            include_orbs=include_orbs,
+            # magnetic_elements=exargs['magnetic_elements'],
+            # include_orbs=ex
             **exargs,
         )
         exchange.run(path=output_path)
@@ -149,8 +137,8 @@ Warning: The DMI component parallel to the spin orientation, the Jani which has
                 atoms=model.atoms,
                 basis=basis,
                 efermi=0.0,
-                magnetic_elements=magnetic_elements,
-                include_orbs=include_orbs,
+                # magnetic_elements=magnetic_elements,
+                # include_orbs=include_orbs,
                 output_path=output_path,
                 **exargs,
             )
@@ -167,14 +155,14 @@ Warning: The DMI component parallel to the spin orientation, the Jani which has
                 atoms=model.atoms,
                 basis=basis,
                 efermi=None,
-                magnetic_elements=magnetic_elements,
-                include_orbs=include_orbs,
+                # magnetic_elements=magnetic_elements,
+                # include_orbs=include_orbs,
                 **exargs,
             )
             # thetas = [0, np.pi / 2, np.pi, 3 * np.pi / 2]
             # phis = [0, 0, 0, 0]
             # MAE.set_angles(thetas=thetas, phis=phis)
-            MAE.run(output_path=output_path)
+            MAE.run(output_path=f"{output_path}_anisotropy")
             print(
                 f"MAE calculation finished. The results are in {output_path} directory."
             )
@@ -191,8 +179,8 @@ Warning: The DMI component parallel to the spin orientation, the Jani which has
                     atoms=model.atoms,
                     basis=basis,
                     efermi=None,  # set to None, compute from efermi.
-                    magnetic_elements=magnetic_elements,
-                    include_orbs=include_orbs,
+                    # magnetic_elements=magnetic_elements,
+                    # include_orbs=include_orbs,
                     **exargs,
                 )
                 exchange.run(path=output_path_full)

TB2J/orbmap.py

@@ -1,5 +1,6 @@
 import re
 from collections import defaultdict
+
 import numpy as np
 
 
@@ -7,30 +8,45 @@ def split_orb_name(name):
     """
     split name to : n, l, label
     """
-    m = re.findall(r"(\d[a-z\d\-]*)(.*)", name)
+    m = re.findall(r"([a-z\d\-\^\*]*)(.*)", name)
     m = m[0]
     return m[0], m[1]
 
 
 def map_orbs_matrix(orblist, spinor=False, include_only=None):
+    """
+    map the orbitals to a matrix
+    Method:
+    1. split the orbital name to n, l, label
+    2. group the orbitals by n, l
+    3. create a matrix with 1 for each orbital in the group
+    4. return the matrix and the group names
+    """
+
     if spinor:
         orblist = orblist[::2]
 
     norb = len(orblist)
 
+    print("orblist: ", orblist)
     ss = [split_orb_name(orb) for orb in orblist]
     orbdict = dict(zip(ss, range(norb)))
 
     reduced_orbdict = defaultdict(lambda: [])
 
+    print(f"Orbital dictionary: {orbdict}")
+    print("include_only: ", include_only)
+
     if include_only is None:
         for key, val in orbdict.items():
             reduced_orbdict[key[0]].append(val)
     else:
         for key, val in orbdict.items():
-            if key[0][:2] in include_only:
+            if key[0][:2] in include_only or key[0][:1] in include_only:
+                # [:2] for 3d, 4d, 5d, etc. and [:1] for s, p, d, etc
                 reduced_orbdict[key[0]].append(val)
 
+    print(f"reduced_orbdict: {reduced_orbdict}")
     reduced_orbs = tuple(reduced_orbdict.keys())
     ngroup = len(reduced_orbdict)
     mmat = np.zeros((norb, ngroup), dtype=int)

{TB2J-0.9.7rc0.data → TB2J-0.9.9rc0.data}/scripts/abacus2J.py

@@ -81,6 +81,7 @@ def run_abacus2J():
     )
 
     parser.add_argument(
+        "--nproc",
         "--np",
         help="number of cpu cores to use in parallel, default: 1",
         default=1,
@@ -121,28 +122,21 @@ def run_abacus2J():
         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
+    # include_orbs = {}
 
     gen_exchange_abacus(
         path=args.path,
         suffix=args.suffix,
         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,
         nz=args.nz,
         description=args.description,
         output_path=args.output_path,
         use_cache=args.use_cache,
-        nproc=args.np,
+        nproc=args.nproc,
         exclude_orbs=args.exclude_orbs,
         orb_decomposition=args.orb_decomposition,
     )

{TB2J-0.9.7rc0.data → TB2J-0.9.9rc0.data}/scripts/siesta2J.py

@@ -128,20 +128,22 @@ def run_siesta2J():
         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
+    # 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_siesta(
         fdf_fname=args.fdf_fname,
         kmesh=args.kmesh,
-        magnetic_elements=list(include_orbs.keys()),
-        include_orbs=include_orbs,
+        # 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,

{TB2J-0.9.7rc0.dist-info → TB2J-0.9.9rc0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: TB2J
-Version: 0.9.7rc0
+Version: 0.9.9rc0
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com

{TB2J-0.9.7rc0.dist-info → TB2J-0.9.9rc0.dist-info}/RECORD

@@ -1,7 +1,7 @@
 TB2J/Jdownfolder.py,sha256=Rmg6KfQ-Lkhei5daTJ2POzr0XL-R1WM-rzUnDcfoDhc,9595
 TB2J/Jtensor.py,sha256=t6OsqrSlYW6Im4H7ykVAW8Al_pFXN4C5yj2UEsV6r7g,3181
 TB2J/MAE.py,sha256=9VwwLpUALaaVwn4LTnhSISJMT7MDym247sSKT5Rum0o,10989
-TB2J/MAEGreen.py,sha256=SkDct7cD5hDAAYW9Y3oYQZVt1AyLA53xDqLL1mT5Nq0,3461
+TB2J/MAEGreen.py,sha256=piat8q_df9rVezExlSEPlAhmld-GDQNRp23vNhZ6kOg,8488
 TB2J/Oiju.py,sha256=cNGv8N5uH_swGq7cnAt2OyiDfqtjLlLrwseGu0E4iaM,3383
 TB2J/Oiju_epc.py,sha256=oytM3NYW7nWmklrGgNlqwIpI_JYv_hb7ZnR4o9nYNog,6809
 TB2J/__init__.py,sha256=hcEWkag_UvLm1ZSbjsgcTWkGVlR3Bwmzg1QYAwsvf-g,24
@@ -11,9 +11,9 @@ TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=4wFZSPV81WwuUrvn1MENMnP-cW5ICDy8azOdTO8HJdw,2877
 TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
-TB2J/exchange.py,sha256=2uTz88pZf3NuKLLiFTHyXf5URhCZkzUlxkVJdtzZPHk,25252
+TB2J/exchange.py,sha256=qVIlbTeEMtPPG4yDJlJoy5OCUAkZFrAR2zyK_et9Mno,25834
 TB2J/exchangeCL2.py,sha256=vJgVBpvtTE2K7Xf7hGQNc3C87VvVXTa689Qd5827ItE,11165
-TB2J/exchange_params.py,sha256=zhOPyvgngPXlYbZ8TUEFXIpYak3MPh3Lh24m8WWWgnU,5846
+TB2J/exchange_params.py,sha256=BgWbdX-PYwLlrOeBX0Xg2jvMBk3axR9zzlE-3PoKV1I,6908
 TB2J/exchange_pert.py,sha256=jmFMtQbYa_uczM4VAeS6TijkIHRFIqEzZJswzE9Wfuo,8523
 TB2J/exchange_qspace.py,sha256=ZL68qBGFUaQ9BsSPsJaaoWOr9RssPiqX34R_9I3nk_8,8436
 TB2J/gpaw_wrapper.py,sha256=aJ--9Dtyq7jOP1Hkh-Sh1nWcfXm6zKcljOCO0DNCAr0,6890
@@ -22,7 +22,7 @@ TB2J/greentest.py,sha256=2ISSfhor9ecSEOi_E6b4Cv26wEIQlwlzca0ru8z44_E,1603
 TB2J/io_merge.py,sha256=E1_GfAB2HGpW-ipaO2lqU9SvaslwkiLxssn4DqJpMT8,6899
 TB2J/kpoints.py,sha256=6XK2KqTncidEq3o9GuO6VEZRPNTRtWeXg9QfcV-9smI,532
 TB2J/myTB.py,sha256=ok_B4my29bOIghMSZfx0Es6G8FaXaIiLP4gPxTdSj00,17659
-TB2J/orbmap.py,sha256=RCMJkOPGbfPrcZzcc5ia1ZMKBQWxGcyj8W1ve8BJaEw,6669
+TB2J/orbmap.py,sha256=g5Lhp6UkDZ7-1T9k0oO43gb2O7j2aGVKMdUeM3QdNAY,7186
 TB2J/pauli.py,sha256=ESpAhk6LG5ugzuW1YFUTqiDxcg-pQ7wNnzR2FtUnvKM,5295
 TB2J/pert.py,sha256=RaCJfewl0doht4cjAnzzGKe-uj2le4aqe0iPKFrq9fo,1192
 TB2J/plot.py,sha256=AnFIFWE2vlmj7Z6f_7-dX_O1stJN-qbuiurPj43dUCM,4104
@@ -40,13 +40,13 @@ TB2J/interfaces/__init__.py,sha256=4tiLoXQ73Nlyi9L4j8jJXOYzXluVNPxQZkwfkQZEGHg,3
 TB2J/interfaces/gpaw_interface.py,sha256=GCDlJ-hRWfChvWwsgBDYSmVqO4sH9HAuGZTV9GqgN6c,1504
 TB2J/interfaces/lawaf_interface.py,sha256=PieLnmppdafOYsgeHznqOou1g9L1sam5jOm3KaObdqo,4408
 TB2J/interfaces/manager.py,sha256=PQMLEfMCT5GnDWSl2nI4JOgRPm_fysyR-6Y6l97xWcw,860
-TB2J/interfaces/siesta_interface.py,sha256=1XOTZYM0uRBqdsTbDo86PZOM0J_uaiDZ9-gPW2PXooE,7704
+TB2J/interfaces/siesta_interface.py,sha256=1kiEUedsXYLajRypHhwi6tV3LioeiBi65zhgtidwmY4,7253
 TB2J/interfaces/wannier90_interface.py,sha256=qzRgXUBb7t1Aiegrl_RV51BB8csdtVM0EP0Z4pjmTcs,4467
 TB2J/interfaces/abacus/__init__.py,sha256=leas71oCvM_HxrF4gnO5A_VKcJmDAgsI1BUctLU3OBw,177
 TB2J/interfaces/abacus/abacus_api.py,sha256=lNV4LNkLcKw7Zux4MQYM9wnh3eFTlcSqbf4Pb7pqhrk,7243
-TB2J/interfaces/abacus/abacus_wrapper.py,sha256=LyfbiuzsE4NiPIw3GOuZDezxi7CSmLvaYWyn3doV8jQ,12015
-TB2J/interfaces/abacus/gen_exchange_abacus.py,sha256=U4s1wC_M2h0MJxlCbs92Ue8AHdMXfc6AK9BB5FjdIwU,3008
-TB2J/interfaces/abacus/orbital_api.py,sha256=9_t89bWptSw0mI9IvmYXODerj0s5e9eiKMAp74YE0Sk,1495
+TB2J/interfaces/abacus/abacus_wrapper.py,sha256=8ZA8oA_YWvRF0Uj_SX1q1vl8ZyEVhHC_tu37JhV02gg,12041
+TB2J/interfaces/abacus/gen_exchange_abacus.py,sha256=N8H-iwyOmOJIo2ZC_owmyrXLhcr_QmZzTI4yxhxYZns,3121
+TB2J/interfaces/abacus/orbital_api.py,sha256=SpSm5fhyqLYbprNd6Lxx0oR1Fw5TUJHfNc-0x_4FW1U,1561
 TB2J/interfaces/abacus/stru_api.py,sha256=Ac03ikHRsZRXqTul4IUge7D2iG_xLh4_oyYfeP9tzGE,67881
 TB2J/interfaces/abacus/test_density_matrix.py,sha256=bMWWJYtDS57SpPZ-eZXZ9Hr_UK4mv8ZHM7SzItG3IVA,774
 TB2J/interfaces/abacus/test_read_HRSR.py,sha256=W1oO_yigT50Yb5_u-KB_IfTpM7kArGkBuMSMs0H4CTs,1235
@@ -76,19 +76,19 @@ TB2J/spinham/supercell.py,sha256=y17uUC6r3gQb278FhxIW4CABihfLTvKFj6flyXrCPR8,122
 TB2J/wannier/__init__.py,sha256=7ojCbM84PYv1X1Tbo4NHI-d3gWmQsZB_xiYqbfxVV1E,80
 TB2J/wannier/w90_parser.py,sha256=dbd63LuKyv2DVUzqRINGsbDzEsOxsQyE8_Ear_LQIRg,4620
 TB2J/wannier/w90_tb_parser.py,sha256=qt8pnuprmPp9iIAYwPkPbmEzk6ZPgMq2xognoQp7vwc,4610
-TB2J-0.9.7rc0.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
-TB2J-0.9.7rc0.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-TB2J-0.9.7rc0.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-TB2J-0.9.7rc0.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-TB2J-0.9.7rc0.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
-TB2J-0.9.7rc0.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
-TB2J-0.9.7rc0.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
-TB2J-0.9.7rc0.data/scripts/abacus2J.py,sha256=_Wiu0NekWKNZ1XVAEBNQOWTi8hE_KXg6iGxfHgcdKqI,4396
-TB2J-0.9.7rc0.data/scripts/siesta2J.py,sha256=wQ9fbyiVyau7WwfusNvHxqBGfD_9_7GZmYZ6pqe6RaM,4806
-TB2J-0.9.7rc0.data/scripts/wann2J.py,sha256=pTFDf6h72I_LN_NX5UivyCoJPgwvyAyHW175nSAJvLo,2987
-TB2J-0.9.7rc0.dist-info/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-TB2J-0.9.7rc0.dist-info/METADATA,sha256=kFTVwu8e7Fcb9srTmKweSf8AmnGq636h4Fu3Ix-e5Tk,1482
-TB2J-0.9.7rc0.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
-TB2J-0.9.7rc0.dist-info/entry_points.txt,sha256=Hdz1WC9waUzyFVmowKnbbZ6j-J4adHh_Ko6JpxGYAtE,131
-TB2J-0.9.7rc0.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
-TB2J-0.9.7rc0.dist-info/RECORD,,
+TB2J-0.9.9rc0.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
+TB2J-0.9.9rc0.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
+TB2J-0.9.9rc0.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
+TB2J-0.9.9rc0.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
+TB2J-0.9.9rc0.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
+TB2J-0.9.9rc0.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
+TB2J-0.9.9rc0.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
+TB2J-0.9.9rc0.data/scripts/abacus2J.py,sha256=0HLXoJhAkiZ-ZM1cs26lncccxE8-TzC8JiDTba1h1uM,4163
+TB2J-0.9.9rc0.data/scripts/siesta2J.py,sha256=gp31LioqpPkDmMY0y_5gXIjOBPNnf080P37pRo0yjw8,4886
+TB2J-0.9.9rc0.data/scripts/wann2J.py,sha256=pTFDf6h72I_LN_NX5UivyCoJPgwvyAyHW175nSAJvLo,2987
+TB2J-0.9.9rc0.dist-info/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
+TB2J-0.9.9rc0.dist-info/METADATA,sha256=vpJtzOgP1WB0OQ3OWBOdNHus5aTxbosw7em62Q_lgl8,1482
+TB2J-0.9.9rc0.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+TB2J-0.9.9rc0.dist-info/entry_points.txt,sha256=Hdz1WC9waUzyFVmowKnbbZ6j-J4adHh_Ko6JpxGYAtE,131
+TB2J-0.9.9rc0.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
+TB2J-0.9.9rc0.dist-info/RECORD,,

{TB2J-0.9.7rc0.dist-info → TB2J-0.9.9rc0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.1.0)
+Generator: setuptools (72.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any