TB2J 0.9.9rc7__py3-none-any.whl → 0.9.9rc9__py3-none-any.whl

TB2J/exchange.py

@@ -96,78 +96,93 @@ class Exchange(ExchangeParams):
 
     def _prepare_orb_dict(self):
         """
-        generate self.ind_mag_atoms and self.orb_dict
-        """
-        # adict: dictionary of {'Fe': ['dxy', 'dyz', ...], ...}
-        adict = OrderedDict()
-        # orb_dict: {ind_atom:[ind_orb,1,2], ...}
-        self.orb_dict = {}
-        # labels: {0:{dxy, ...}}
-        self.labels = {}
-        # magnetic atoms index
-        self.ind_mag_atoms = []
-
-        sdict = symbol_number(self.atoms)
-
-        for i, base in enumerate(self.basis):
-            if i not in self.exclude_orbs:
-                # e.g. Fe2, dxy, _, _
-                if isinstance(base, str):
-                    atom_sym, orb_sym = base.split("|")[:2]
-                    iatom = sdict[atom_sym]
-                else:
-                    try:
-                        atom_sym, orb_sym = base[:2]
-                        iatom = sdict[atom_sym]
-                    except Exception:
-                        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]
-                if iatom not in self.orb_dict:
-                    self.orb_dict[iatom] = [i]
-                    self.labels[iatom] = [orb_sym]
-                else:
-                    self.orb_dict[iatom] += [i]
-                    self.labels[iatom] += [orb_sym]
+        Generate orbital and magnetic atom mappings needed for exchange calculations.
+        
+        Creates:
+        - self.orb_dict: Maps atom indices to their orbital indices
+        - self.labels: Maps atom indices to their orbital labels
+        - self.ind_mag_atoms: List of indices of magnetic atoms
+        - self._spin_dict: Maps atom indices to spin indices
+        - self._atom_dict: Maps spin indices back to atom indices
+        """
+        self._create_orbital_mappings()
+        self._identify_magnetic_atoms()
+        self._validate_orbital_assignments()
+        self._create_spin_mappings()
+        self._prepare_orb_mmat()
 
-        # index of magnetic atoms
-        symbols = self.atoms.get_chemical_symbols()
-        tags = self.atoms.get_tags()
-        for i, (sym, tag) in enumerate(zip(symbols, tags)):
-            if sym in self.magnetic_elements or f"{sym}{tag}" in self.magnetic_elements:
-                self.ind_mag_atoms.append(i)
+    def _create_orbital_mappings(self):
+        """Create mappings between atoms and their orbitals."""
+        self.orb_dict = {}  # {atom_index: [orbital_indices]}
+        self.labels = {}     # {atom_index: [orbital_labels]}
+        atom_symbols = symbol_number(self.atoms)
+
+        for orb_idx, base in enumerate(self.basis):
+            if orb_idx in self.exclude_orbs:
+                continue
+                
+            # Extract atom and orbital info
+            if isinstance(base, str):
+                atom_sym, orb_sym = base.split("|")[:2]
+                atom_idx = atom_symbols[atom_sym]
+            else:
+                try:
+                    atom_sym, orb_sym = base[:2]
+                    atom_idx = atom_symbols[atom_sym]
+                except Exception:
+                    atom_idx = base.iatom
+                    atom_sym = base.iatom
+                    orb_sym = base.sym
+
+            # Update orbital mappings
+            if atom_idx not in self.orb_dict:
+                self.orb_dict[atom_idx] = [orb_idx]
+                self.labels[atom_idx] = [orb_sym]
+            else:
+                self.orb_dict[atom_idx].append(orb_idx)
+                self.labels[atom_idx].append(orb_sym)
 
-        # sanity check to see if some magnetic atom has no orbital.
-        for iatom in self.ind_mag_atoms:
-            if iatom not in self.orb_dict:
+    def _identify_magnetic_atoms(self):
+        """Identify which atoms are magnetic based on elements/tags."""
+        if self.index_magnetic_atoms is not None:
+            self.ind_mag_atoms = self.index_magnetic_atoms
+        else:
+            self.ind_mag_atoms = []
+            symbols = self.atoms.get_chemical_symbols()
+            tags = self.atoms.get_tags()
+
+            for atom_idx, (sym, tag) in enumerate(zip(symbols, tags)):
+                if sym in self.magnetic_elements or f"{sym}{tag}" in self.magnetic_elements:
+                    self.ind_mag_atoms.append(atom_idx)
+        print(f"Magnetic atoms: {self.ind_mag_atoms}")
+
+    def _validate_orbital_assignments(self):
+        """Validate that magnetic atoms have proper orbital assignments."""
+        # Check all magnetic atoms have orbitals
+        for atom_idx in self.ind_mag_atoms:
+            if atom_idx not in self.orb_dict:
                 raise ValueError(
-                    f"""Cannot find any orbital for atom {iatom}, which is supposed to be magnetic. Please check the Wannier functions."""
+                    f"Atom {atom_idx} is magnetic but has no orbitals assigned. "
+                    "Check Wannier function definitions."
                 )
+
+        # For non-collinear case, check spin-orbital pairing
         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 and False:
+            for atom_idx, orbitals in self.orb_dict.items():
+                if len(orbitals) % 2 != 0:
                     raise ValueError(
-                        f"""The number of spin-orbitals for atom {iatom} is not even,
-{nsorb} spin-orbitals are found near this atom.
-which means the spin up/down does not have same number of orbitals.
-This is often because the Wannier functions are wrongly defined,
-or badly localized. Please check the Wannier centers in the Wannier90 output file.
-"""
+                        f"Atom {atom_idx} has {len(orbitals)} spin-orbitals "
+                        "(should be even). Check Wannier function localization."
                     )
-        self._spin_dict = {}
-        self._atom_dict = {}
-        for ispin, iatom in enumerate(self.ind_mag_atoms):
-            self._spin_dict[iatom] = ispin
-            self._atom_dict[ispin] = iatom
 
-        self._prepare_orb_mmat()
+    def _create_spin_mappings(self):
+        """Create mappings between atom indices and spin indices."""
+        self._spin_dict = {}  # {atom_index: spin_index}
+        self._atom_dict = {}  # {spin_index: atom_index}
+
+        for spin_idx, atom_idx in enumerate(self.ind_mag_atoms):
+            self._spin_dict[atom_idx] = spin_idx
+            self._atom_dict[spin_idx] = atom_idx
 
     def _prepare_orb_mmat(self):
         self.mmats = {}
@@ -566,12 +581,23 @@ class ExchangeNCL(Exchange):
         AijRs: a list of AijR,
         wherer AijR: array of ((nR, n, n, 4,4), dtype=complex)
         """
+        # if method == "trapezoidal":
+        #    integrate = trapezoidal_nonuniform
+        # elif method == "simpson":
+        #    integrate = simpson_nonuniform
+        #
+
+        # self.rho = integrate(self.contour.path, rhoRs)
         for iR, R in enumerate(self.R_ijatom_dict):
             for iatom, jatom in self.R_ijatom_dict[R]:
                 f = AijRs[(R, iatom, jatom)]
+                # self.A_ijR[(R, iatom, jatom)] = integrate(self.contour.path, f)
                 self.A_ijR[(R, iatom, jatom)] = self.contour.integrate_values(f)
 
                 if self.orb_decomposition:
+                    # self.A_ijR_orb[(R, iatom, jatom)] = integrate(
+                    #    self.contour.path, AijRs_orb[(R, iatom, jatom)]
+                    # )
                     self.contour.integrate_values(AijRs_orb[(R, iatom, jatom)])
 
     def get_quantities_per_e(self, e):

TB2J/exchange_params.py

@@ -15,6 +15,7 @@ class ExchangeParams:
     efermi: float
     basis = []
     magnetic_elements = []
+    index_magnetic_atoms = None 
     include_orbs = {}
     _kmesh = [4, 4, 4]
     emin: float = -15
@@ -55,6 +56,7 @@ class ExchangeParams:
         mae_angles=None,
         orth=False,
         ibz=False,
+        index_magnetic_atoms=None,
     ):
         self.efermi = efermi
         self.basis = basis
@@ -79,6 +81,7 @@ class ExchangeParams:
         self.mae_angles = mae_angles
         self.orth = orth
         self.ibz = ibz
+        self.index_magnetic_atoms = index_magnetic_atoms
 
     def set_params(self, **kwargs):
         for key, val in kwargs.items():
@@ -229,6 +232,21 @@ def add_exchange_args_to_parser(parser: argparse.ArgumentParser):
         default=False,
     )
 
+    parser.add_argument(
+        "--mae_angles",
+        help="angles for computing MAE, default is 0 0 0",
+        type=float,
+        nargs="*",
+        default=[0.0, 0.0, 0.0],
+    )
+    parser.add_argument(
+        "--index_magnetic_atoms",
+        help="index of magnetic atoms in the unit cell, default is None. If specified, this will be used to determine the atoms to be considered as magnetic atoms, instead of determined from magnetic elements. Note that the index starts from 1 ",
+        type=int,
+        nargs="*",
+        default=None,
+    )
+
     return parser
 
 
@@ -250,4 +268,5 @@ def parser_argument_to_dict(args) -> dict:
         "orb_decomposition": args.orb_decomposition,
         "output_path": args.output_path,
         "orth": args.orth,
+        "index_magnetic_atoms": args.index_magnetic_atoms,
     }

TB2J/io_exchange/io_exchange.py

@@ -338,12 +338,6 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
             )
         return Jtensor
 
-    def get_J_tensor_dict(self):
-        Jdict = {}
-        for i, j, R in self.ijR_list():
-            Jdict[(i, j, R)] = self.get_J_tensor(i, j, R)
-        return Jdict
-
     def get_full_Jtensor_for_one_R(self, R, iso_only=False):
         """
         Return the full exchange tensor of all i and j for cell R.
@@ -411,7 +405,6 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
         self.write_multibinit(path=os.path.join(path, "Multibinit"))
         self.write_tom_format(path=os.path.join(path, "TomASD"))
         self.write_vampire(path=os.path.join(path, "Vampire"))
-        self.write_matjes(path=os.path.join(path, "Matjes"))
 
         self.plot_all(savefile=os.path.join(path, "JvsR.pdf"))
         # self.write_Jq(kmesh=[9, 9, 9], path=path)
@@ -580,11 +573,6 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
 
         write_uppasd(self, path=path)
 
-    def write_matjes(self, path):
-        from TB2J.io_exchange.io_matjes import write_matjes
-
-        write_matjes(self, path=path)
-
 
 def gen_distance_dict(ind_mag_atoms, atoms, Rlist):
     distance_dict = {}
@@ -600,21 +588,6 @@ def gen_distance_dict(ind_mag_atoms, atoms, Rlist):
     return distance_dict
 
 
-def get_ind_shell(distance_dict, symprec=1e-5):
-    """
-    return a dictionary of shell index for each pair of atoms.
-    The index of shell is the ith shortest distances between all magnetic atom pairs.
-    """
-    shell_dict = {}
-    distances = np.array([x[1] for x in distance_dict.values()])
-    distances_int = np.round(distances / symprec).astype(int)
-    dint = sorted(np.unique(distances_int))
-    dintdict = dict(zip(dint, range(len(dint))))
-    for key, val in enumerate(distances_int):
-        shell_dict[key] = dintdict[val]
-    return shell_dict
-
-
 def test_spin_io():
     import numpy as np
     from ase import Atoms

TB2J/mycfr.py

@@ -64,6 +64,10 @@ class CFR:
         # zp = 1j / eigp * kb * self.T
         # Rp = 0.25 * np.diag(eigv)**2 * zp **2
 
+        # print the poles and the weights
+        for i in range(len(self.poles)):
+            print("Pole: ", self.poles[i], "Weight: ", self.weights[i])
+
         # add a point to the poles: 1e10j
         self.path = np.concatenate((self.path, [self.Rinf * 1j]))
         # self.path = np.concatenate((self.path, [0.0]))

TB2J/symmetrize_J.py

@@ -9,7 +9,7 @@ from TB2J.versioninfo import print_license
 
 
 class TB2JSymmetrizer:
-    def __init__(self, exc, symprec=1e-8, verbose=True, Jonly=True):
+    def __init__(self, exc, symprec=1e-8, verbose=True, Jonly=False):
         # list of pairs with the index of atoms
         ijRs = exc.ijR_list_index_atom()
         finder = SymmetryPairFinder(atoms=exc.atoms, pairs=ijRs, symprec=symprec)
@@ -25,12 +25,6 @@ class TB2JSymmetrizer:
             )
             print("-" * 30)
             if exc.has_dmi:
-                # raise NotImplementedError(
-                #    "Symmetrization of DMI is not yet implemented."
-                #    )
-                # raise Warning(
-                #        "WARNING: Symmetrization of DMI is not yet implemented."
-                #        )
                 print(
                     "WARNING: Currently only the isotropic exchange is symmetrized. Symmetrization of DMI and anisotropic exchange are not yet implemented."
                 )
@@ -39,7 +33,7 @@ class TB2JSymmetrizer:
             print("Symmetry found:")
             print(finder.spacegroup)
             print("-" * 30)
-        self.pldict = finder.get_symmetry_pair_list_dict()
+        self.pgdict = finder.get_symmetry_pair_group_dict()
         self.exc = exc
         self.new_exc = copy.deepcopy(exc)
         self.Jonly = Jonly
@@ -52,25 +46,21 @@ class TB2JSymmetrizer:
         Symmetrize the exchange parameters J.
         """
         symJdict = {}
-        reduced_symJdict = {}
         # Jdict = self.exc.exchange_Jdict
-        for ishell, pairlist in enumerate(self.pldict.pairlists):
-            ijRs = pairlist.get_all_ijR()
+        # ngroup = self.pgdict
+        for pairgroup in self.pgdict.groups:
+            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]
             Javg = np.average(Js)
             for i, j, R in ijRs_spin:
                 symJdict[(R, i, j)] = Javg
-            ijRs_ref = ijRs_spin[0]
-            i, j, R = ijRs_ref
-            reduced_symJdict[(R, i, j)] = Javg
         self.new_exc.exchange_Jdict = symJdict
         if self.Jonly:
             self.new_exc.has_dmi = False
             self.new_exc.dmi_ddict = None
             self.new_exc.has_bilinear = False
             self.new_exc.Jani_dict = None
-            self.new_exc.reduced_exchange_Jdict = reduced_symJdict
             self.has_uniaxial_anisotropy = False
             self.k1 = None
             self.k1dir = None
@@ -134,12 +124,12 @@ def symmetrize_J_cli():
         help="precision for symmetry detection. default is 1e-5 Angstrom",
     )
 
-    # parser.add_argument(
-    #    "--Jonly",
-    #    action="store_true",
-    #    help="symmetrize only the exchange parameters and discard the DMI and anisotropic exchange",
-    #    default=True,
-    # )
+    parser.add_argument(
+        "--Jonly",
+        action="store_true",
+        help="symmetrize only the exchange parameters and discard the DMI and anisotropic exchange",
+        default=False,
+    )
 
     args = parser.parse_args()
     if args.inpath is None:
@@ -149,8 +139,7 @@ def symmetrize_J_cli():
         path=args.inpath,
         output_path=args.outpath,
         symprec=args.symprec,
-        # Jonly=args.Jonly,
-        Jonly=True,
+        Jonly=args.Jonly,
     )
 
 

TB2J/thetaphi.py

@@ -0,0 +1,16 @@
+import numpy as np
+
+
+def theta_phi_even_spaced(n):
+    """
+    Return n evenly spaced theta and phi values in the ranges [0, pi] and [0, 2*pi] respectively.
+    """
+    phis = []
+    thetas = []
+    for i in range(n):
+        phi = 2 * np.pi * i / n
+        phis.append(phi)
+        r = np.sin(np.pi * i / n)
+        theta = np.arccos(1 - 2 * r)
+        thetas.append(theta)
+    return thetas, phis

tb2j-0.9.9rc9.data/scripts/abacus2J.py

@@ -0,0 +1,59 @@
+#!python
+import argparse
+import sys
+
+from TB2J.interfaces import gen_exchange_abacus
+from TB2J.versioninfo import print_license
+from TB2J.exchange_params import add_exchange_args_to_parser
+
+
+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()
+
+    if args.elements 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.nproc,
+        exclude_orbs=args.exclude_orbs,
+        orb_decomposition=args.orb_decomposition,
+        index_magnetic_atoms=args.index_magnetic_atoms,
+        cutoff=args.cutoff,
+    )
+
+
+if __name__ == "__main__":
+    run_abacus2J()

tb2j-0.9.9rc9.data/scripts/siesta2J.py

@@ -0,0 +1,75 @@
+#!python
+import argparse
+import sys
+
+from TB2J.interfaces import gen_exchange_siesta
+from TB2J.versioninfo import print_license
+from TB2J.exchange_params import add_exchange_args_to_parser
+
+
+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
+
+    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=args.index_magnetic_atoms,
+    )
+
+
+if __name__ == "__main__":
+    run_siesta2J()

{tb2j-0.9.9rc7.data → tb2j-0.9.9rc9.data}/scripts/wann2J.py

@@ -89,6 +89,7 @@ def run_wann2J():
         # qspace=args.qspace,
         write_density_matrix=args.write_dm,
         orb_decomposition=args.orb_decomposition,
+        index_magnetic_atoms=args.index_magnetic_atoms,
     )
 
 

{tb2j-0.9.9rc7.dist-info → tb2j-0.9.9rc9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc7
+Version: 0.9.9rc9
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -24,6 +24,7 @@ Requires-Dist: packaging>=20.0
 Requires-Dist: HamiltonIO>=0.1.9
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
+Requires-Dist: sisl>=0.9.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{tb2j-0.9.9rc7.dist-info → tb2j-0.9.9rc9.dist-info}/RECORD

@@ -11,9 +11,9 @@ TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=zLHQZZ3hhgLkLFPATCraLOJyLJKLC0fba_L_5sRz23o,3246
 TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
-TB2J/exchange.py,sha256=742vEE8DQJuWBTlq45RQoPy0-_n_TT6BZOb_DoTpDKI,25739
+TB2J/exchange.py,sha256=eVZ2Prm9faSPZNUJELTsGbfOPCw3QqUKIy5E_7tL03s,27015
 TB2J/exchangeCL2.py,sha256=P7bklMXVYX_tn9DbjEPqeTir1SeZyfPBIP1fhWUzLmY,11419
-TB2J/exchange_params.py,sha256=AcGYYky27DXSF3yDZWVjksr_3rt6im6qeIzpOwvqssk,7141
+TB2J/exchange_params.py,sha256=xw3STJlumf5tNhnfzICzWzAl7srOy-wnyLsi-rImdSQ,7883
 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=9L7tBarFBHoIhpuc9zuwA6HdnlgH834SQrPek4yRoWk,3191
 TB2J/myTB.py,sha256=ok_B4my29bOIghMSZfx0Es6G8FaXaIiLP4gPxTdSj00,17659
-TB2J/mycfr.py,sha256=Wgj6PpA-oVuxm8Hh32FVw_vthozVBrDJhRV1hA1ku44,3752
+TB2J/mycfr.py,sha256=ZF1PEE2khlKd_4gPyMkoNXepX3XqwWAL2kDbRJNVX-Y,3908
 TB2J/orbital_magmom.py,sha256=JTwO9ZDgRRQndqR9aFIua4eTvwLMoGsTiY_HaIPMZ2I,889
 TB2J/orbmap.py,sha256=XLQjKMxCy2eADaM5eb2F_zG08V7lzpXJxp5uEtTeVYI,7194
 TB2J/pauli.py,sha256=ESpAhk6LG5ugzuW1YFUTqiDxcg-pQ7wNnzR2FtUnvKM,5295
@@ -31,8 +31,9 @@ TB2J/plot.py,sha256=AnFIFWE2vlmj7Z6f_7-dX_O1stJN-qbuiurPj43dUCM,4104
 TB2J/rotate_atoms.py,sha256=Dwptn-wdDW4zYzjYb95yxTzuZOe9WPuLjh3d3-YcSs0,3277
 TB2J/rotate_siestaDM.py,sha256=eR97rspdrRaK9YTwQwUKfobI0S9UnEcbEZ2f5IgR7Tk,1070
 TB2J/sisl_wrapper.py,sha256=A5x1-tt8efUSPeGY5wM5m6-pJYQFXTCzQHVqD6RBa2g,14792
-TB2J/symmetrize_J.py,sha256=gN6Y8zV4IrO5rPh0SG8KHkekrJjMQzNY4GGe2ZBtwbc,4993
+TB2J/symmetrize_J.py,sha256=IypvLL0JxExq-cmqc4o0nLL8psE7OC9ijj9YMcsqJeA,4487
 TB2J/tensor_rotate.py,sha256=4-DfT_Mg5e40fbd74M5W0D5DqmUq-kVOOLDkkkI834A,8083
+TB2J/thetaphi.py,sha256=Z7N3EOSM7rjHd7b9HxMYLPQO__uR0VwEiV9b471Yudc,399
 TB2J/utest.py,sha256=z_ahi7tpHQF9WlHNQihcQ7qzfezRJQXQt28eB1X_z64,3897
 TB2J/utils.py,sha256=DHkc7BK0KUGesfoAv1OxMgIw_iZzcFXh--3ybsFSd_c,12535
 TB2J/versioninfo.py,sha256=atoCpy6lEcGTCC3xahrxEJjoHgoYVtL41Q_3Ryvp76I,338
@@ -54,8 +55,7 @@ TB2J/interfaces/abacus/test_density_matrix.py,sha256=bMWWJYtDS57SpPZ-eZXZ9Hr_UK4
 TB2J/interfaces/abacus/test_read_HRSR.py,sha256=W1oO_yigT50Yb5_u-KB_IfTpM7kArGkBuMSMs0H4CTs,1235
 TB2J/interfaces/abacus/test_read_stru.py,sha256=hoKPHVco8vwzC7Gao4bOPCdAPhh29x-9DTJJqRr7AYM,788
 TB2J/io_exchange/__init__.py,sha256=KfGHum7B8E4G_KKfillqw0lErtoyKEuFUUttHLs-mg4,32
-TB2J/io_exchange/io_exchange.py,sha256=7-Xt7_K5FKVrFkFvBrHhJGCRrL2Sw7zY-93GRBBv2GM,21050
-TB2J/io_exchange/io_matjes.py,sha256=klM5Z_t2kk0y_1IoqIILLnhUgjHQmXXmsXiono2LeMU,8594
+TB2J/io_exchange/io_exchange.py,sha256=gaT0fXD3EzPsMgE_VX9gvcf7nEGY3KVYN8xxTAPzxc0,20120
 TB2J/io_exchange/io_multibinit.py,sha256=8PDmWxzGuv-GwJosj2ZTmiyNY_duFVWJ4ekCuSqGdd8,6739
 TB2J/io_exchange/io_tomsasd.py,sha256=NqkAC1Fl-CUnFA21eBzSy_S5F_oeQFJysw4UukQbN8o,4173
 TB2J/io_exchange/io_txt.py,sha256=BMr1eSILlKpgtjvDx7uw2VMAkEKSvGEPNxpaT_zev0I,10547
@@ -80,19 +80,19 @@ 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-0.9.9rc7.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
-tb2j-0.9.9rc7.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-tb2j-0.9.9rc7.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-tb2j-0.9.9rc7.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-tb2j-0.9.9rc7.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
-tb2j-0.9.9rc7.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
-tb2j-0.9.9rc7.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
-tb2j-0.9.9rc7.data/scripts/abacus2J.py,sha256=0HLXoJhAkiZ-ZM1cs26lncccxE8-TzC8JiDTba1h1uM,4163
-tb2j-0.9.9rc7.data/scripts/siesta2J.py,sha256=gp31LioqpPkDmMY0y_5gXIjOBPNnf080P37pRo0yjw8,4886
-tb2j-0.9.9rc7.data/scripts/wann2J.py,sha256=pTFDf6h72I_LN_NX5UivyCoJPgwvyAyHW175nSAJvLo,2987
-tb2j-0.9.9rc7.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-tb2j-0.9.9rc7.dist-info/METADATA,sha256=H5g8ApE237zxKx8_mx0Fr1fUCz2m97VkgDY5LBFYzlg,1660
-tb2j-0.9.9rc7.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-tb2j-0.9.9rc7.dist-info/entry_points.txt,sha256=Hdz1WC9waUzyFVmowKnbbZ6j-J4adHh_Ko6JpxGYAtE,131
-tb2j-0.9.9rc7.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
-tb2j-0.9.9rc7.dist-info/RECORD,,
+tb2j-0.9.9rc9.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
+tb2j-0.9.9rc9.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
+tb2j-0.9.9rc9.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
+tb2j-0.9.9rc9.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
+tb2j-0.9.9rc9.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
+tb2j-0.9.9rc9.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
+tb2j-0.9.9rc9.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
+tb2j-0.9.9rc9.data/scripts/abacus2J.py,sha256=n9sOFZvPMPSzyBJjfpX4dnn7ek4bbOUBrhcEABdYUR8,1635
+tb2j-0.9.9rc9.data/scripts/siesta2J.py,sha256=yl43Hoz9XCmjiZ4P1w7UM1BtmJg-eSbMpAm-2_eEUlA,2160
+tb2j-0.9.9rc9.data/scripts/wann2J.py,sha256=Z5MSAtS5i5OrPlwDURnPr87dtYF4GbH_NixUi6WYsA8,3043
+tb2j-0.9.9rc9.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
+tb2j-0.9.9rc9.dist-info/METADATA,sha256=52dNL8vQEWQYUP7KsQfqUGLmaK-y4nSY6MhN9f2j_Sc,1687
+tb2j-0.9.9rc9.dist-info/WHEEL,sha256=ck4Vq1_RXyvS4Jt6SI0Vz6fyVs4GWg7AINwpsaGEgPE,91
+tb2j-0.9.9rc9.dist-info/entry_points.txt,sha256=Hdz1WC9waUzyFVmowKnbbZ6j-J4adHh_Ko6JpxGYAtE,131
+tb2j-0.9.9rc9.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
+tb2j-0.9.9rc9.dist-info/RECORD,,

{tb2j-0.9.9rc7.dist-info → tb2j-0.9.9rc9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: setuptools (80.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

TB2J/io_exchange/io_matjes.py

@@ -1,225 +0,0 @@
-import os
-
-import numpy as np
-
-from TB2J.utils import symbol_number
-from ase.units import Bohr, nm
-
-
-def get_ind_shell(distance_dict, symprec=1e-5):
-    """
-    return a dictionary of shell index for each pair of atoms.
-    The index of shell is the ith shortest distances between all magnetic atom pairs.
-    """
-    shell_dict = {}
-    distances = np.array([x[1] for x in distance_dict.values()])
-    distances_int = np.round(distances / symprec).astype(int)
-    dint = sorted(np.unique(distances_int))
-    dintdict = dict(zip(dint, range(len(dint))))
-    for key, val in distance_dict.items():
-        di = np.round(val[1] / symprec).astype(int)
-        shell_dict[key] = dintdict[di]
-    return shell_dict
-
-
-def _write_symmetry(cls, path, fname="symmetry.in", symmetry=True):
-    fname = os.path.join(path, fname)
-    if not symmetry:
-        with open(fname, "w") as myfile:
-            myfile.write("1 \n")
-            myfile.write("\n")
-            myfile.write("! identity operation\n")
-            myfile.write("1.0000000000 0.0000000000 0.0000000000\n")
-            myfile.write("0.0000000000 1.0000000000 0.0000000000\n")
-            myfile.write("0.0000000000 0.0000000000 1.0000000000\n")
-            myfile.write("0.0000000000 0.0000000000 0.0000000000\n")
-    else:
-        raise NotImplementedError("Symmetry not implemented yet")
-
-
-def write_matjes(cls, path="TB2J_results/Matjes", symmetry=False):
-    if not os.path.exists(path):
-        os.makedirs(path)
-    inputfname = os.path.join(path, "input")
-    with open(inputfname, "w") as myfile:
-        _write_lattice_supercell(cls, myfile)
-        _write_atoms(cls, myfile)
-        _write_magnetic_interactions(cls, myfile)
-        #_write_isotropic_exchange(cls, myfile, symmetry=symmetry)
-        _write_magnetic_anisotropy(cls, myfile)
-        # _write_dmi(cls, myfile)
-        _write_exchange_tensor(cls, myfile, symmetry=symmetry)
-        _write_parameters(cls, myfile, symmetry=symmetry)
-    print(f"writting symmetries ")
-    _write_symmetry(cls, path,  fname="symmetries.in", symmetry=False)
-
-def _write_parameters(cls, myfile, symmetry=False):
-    if symmetry:
-        myfile.write("cal_sym T\n")
-        myfile.write("sym_mode 2\n")
-    else:
-        myfile.write("cal_sym F \n")
-        myfile.write("sym_mode 0\n")
-
-def _write_lattice_supercell(cls, myfile):
-    myfile.write("# Lattice and supercell\n")
-    myfile.write(
-        "Periodic_log .T. .T. .T.      # periodic boundary conditions along vector 1, 2 and 3\n"
-    )
-    myfile.write("Nsize 8 8 8                 # size of the supercell\n")
-    try:
-        unitcell = cls.atoms.get_cell().reshape((3, 3))
-    except Exception:
-        unitcell = cls.atoms.get_cell().array.reshape((3, 3))
-    uc_lengths = np.linalg.norm(unitcell, axis=1) 
-    unitcell /= uc_lengths[:, None]
-    myfile.write(f"alat {uc_lengths[0]/nm}  {uc_lengths[1]/nm} {uc_lengths[2]/nm}              #lattice constant lengths\n")
-    myfile.write(
-        "lattice                         #lattice vector should be orthogonal or expressed in cartesian\n")
-    myfile.write(
-        f"{unitcell[0][0]} {unitcell[0][1]} {unitcell[0][2]}     # a_11 a_12 a_1      first lattice vector in line (does not need to be normalize)\n"
-    )
-    myfile.write(
-        f"{unitcell[1][0]} {unitcell[1][1]} {unitcell[1][2]}      # a_21 a_22 a_23    second lattice vector in line (does not need to be normalize)\n"
-    )
-    myfile.write(
-        f"{unitcell[2][0]} {unitcell[2][1]} {unitcell[2][2]}     # a_31 a_32 a_33                     third lattice vector in line\n"
-    )
-
-
-def get_atoms_info(atoms, spinat, symmetry=False):
-    if symmetry:
-        raise NotImplementedError("Symmetry not implemented yet")
-    else:
-        symnum = symbol_number(atoms)
-        atom_types = list(symnum.keys())
-        magmoms = np.linalg.norm(spinat, axis=1)
-        masses = atoms.get_masses()
-        tags = [i for i in range(len(atom_types))]
-    return atom_types, magmoms, masses, tags
-
-
-def _write_atoms(cls, myfile, symmetry=False):
-    myfile.write("\n")
-    myfile.write("# Atoms\n")
-    atom_types, magmoms, masses, tags = get_atoms_info(
-        cls.atoms, cls.spinat, symmetry=symmetry
-    )
-
-    myfile.write(f"atomtypes  {len(atom_types)}       #Number of types atom\n")
-    for i, atom_type in enumerate(atom_types):
-        m = magmoms[i]
-        mass = masses[i]
-        charge = 0
-        myfile.write(
-            f"{atom_type} {m} {mass} 0.0  F 0 # atom type: (name, mag. moment, mass, charge, displacement, number TB-orb.)\n"
-        )
-
-    myfile.write(
-        f"\natoms {len(cls.atoms)}          positions of the atom in the unit cell\n"
-    )
-    for i, atom in enumerate(cls.atoms):
-        spos = cls.atoms.get_scaled_positions()[i]
-        myfile.write(f"{atom_types[tags[i]]} {spos[0]}, {spos[1]}, {spos[2]}  \n")
-
-
-def _write_magnetic_interactions(cls, myfile, symmetry=False):
-    myfile.write("\nThe Hamiltonian\n")
-    myfile.write("# Magnetic interactions\n")
-
-
-def _write_isotropic_exchange(cls, myfile, symmetry=False):
-    myfile.write("\nmagnetic_J\n")
-    shell_dict = get_ind_shell(cls.distance_dict)
-    if symmetry:
-        Jdict = cls.reduced_exchange_Jdict
-    else:
-        Jdict = cls.exchange_Jdict
-    for key, val in Jdict.items():
-        R, i, j = key
-        ishell = shell_dict[(R, i, j)]
-        myfile.write(
-            f"{i+1} {j+1} {ishell} {val}     # between atoms type {i+1} and {j+1}, shell {R}, amplitude in eV  \n"
-        )
-    myfile.write(
-        "\nc_H_J -1        apply 1/2 in front of the sum of the exchange energy - default is -1\n"
-    )
-
-
-def _write_magnetic_anisotropy(cls, myfile):
-    if cls.k1 is None:
-        return
-    else:
-        myfile.write("\nmagnetic_anisotropy \n")
-        for i, k1 in enumerate(cls.k1):
-            myfile.write(
-                f"{i+1} {cls.k1dir[i][0]} {cls.k1dir[i][1]} {cls.k1dir[i][2]} {k1}     anisotropy of atoms type {i+1}, direction {cls.k1dir[i][0]} {cls.k1dir[i][1]} {cls.k1dir[i][2]} and amplitude in eV\n"
-            )
-        myfile.write("\nc_H_ani 1.0\n")
-
-
-def _write_dmi(cls, myfile):
-    if cls.has_dmi:
-        myfile.write("\nmagnetic_D\n")
-        for key, val in cls.dmi_ddict.items():
-            R, i, j = key
-            myfile.write(
-                f"{i+1} {j+1} {R[0]} {R[1]} {R[2]} {val}         #between atoms type {i+1} and {j+1}, mediated by atom type {R}, shell {R}, amplitude in eV\n"
-            )
-        myfile.write(
-            "\nc_H_D   -1.0             # coefficients to put in from of the sum - default is -1\n"
-        )
-
-
-def _write_exchange_tensor(cls, myfile, symmetry=False):
-    myfile.write(
-        "\nmagnetic_r2_tensor #Exchange tensor elements, middle 9 entries: xx, xy, xz, yx, etc. (in units of eV) and direction in which it should be applied\n"
-    )
-
-    Jtensor = cls.get_J_tensor_dict()
-    shelldict = get_ind_shell(cls.distance_dict)
-    unitcell = cls.atoms.get_cell().array.reshape((3, 3))
-    uc_lengths = np.linalg.norm(unitcell, axis=1) 
-    if Jtensor is not None:
-        for key, val in Jtensor.items():
-            i, j, R = key
-            # distance vector
-            dvec = cls.distance_dict[(R, i, j)][0]/nm/uc_lengths
-            dscalar = np.linalg.norm(dvec)
-            val = np.real(val)
-            ishell = shelldict[(R, i, j)]
-            myfile.write(
-                f"{i+1} {j+1} {ishell} {' '.join([str(x) for x in val.flatten()])}  {dvec[0]} {dvec[1]} {dvec[2]} \n"
-                #f"{i+1} {j+1} {dscalar} {' '.join([str(x) for x in val.flatten()])}  {dvec[0]} {dvec[1]} {dvec[2]} \n"
-            )
-        myfile.write(
-            "\nc_H_Exchten -1         apply 1/2 in front of the sum of the exchange tensor energy - default is -1\n"
-        )
-
-def rattle_atoms_and_cell(atoms, stdev=0.001, cell_stdev=0.001):
-    """
-    Rattle both atomic positions and cell parameters.
-    
-    Parameters:
-    -----------
-    atoms: ASE atoms object
-        The atoms to be rattled
-    stdev: float
-        Standard deviation for atomic displacement in Angstrom
-    cell_stdev: float
-        Standard deviation for cell parameter variation (fractional)
-    
-    Returns:
-    --------
-    None
-        The atoms object is modified in-place
-    """
-    # Rattle atomic positions
-    positions = atoms.get_positions()
-    displacement = np.random.normal(0, stdev, positions.shape)
-    atoms.set_positions(positions + displacement)
-    
-    # Rattle cell parameters
-    cell = atoms.get_cell()
-    cell_noise = np.random.normal(0, cell_stdev, cell.shape)
-    atoms.set_cell(cell * (1 + cell_noise), scale_atoms=True)

tb2j-0.9.9rc7.data/scripts/abacus2J.py

@@ -1,146 +0,0 @@
-#!python
-import argparse
-import sys
-
-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"
-    )
-
-    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(
-        "--nproc",
-        "--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 = {}
-
-    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.nproc,
-        exclude_orbs=args.exclude_orbs,
-        orb_decomposition=args.orb_decomposition,
-    )
-
-
-if __name__ == "__main__":
-    run_abacus2J()

tb2j-0.9.9rc7.data/scripts/siesta2J.py

@@ -1,163 +0,0 @@
-#!python
-import argparse
-import sys
-
-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"
-    )
-    parser.add_argument(
-        "--fdf_fname", help="path of the input fdf file", default="./", 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(
-        "--emax",
-        help="energy maximum above efermi. Default 0.0 eV",
-        type=float,
-        default=0.05,
-    )
-    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-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 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",
-    )
-
-    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,
-    )
-
-    parser.add_argument(
-        "--orth",
-        help="whether to use orthogonalization before the diagonization of the electron Hamiltonian. Default: False",
-        action="store_true",
-        default=False,
-    )
-
-    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_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,
-    )
-
-
-if __name__ == "__main__":
-    run_siesta2J()