TB2J 0.9.9rc14__py3-none-any.whl → 0.9.9rc16__py3-none-any.whl

TB2J/exchange.py

@@ -1,6 +1,6 @@
 import os
 import pickle
-from collections import OrderedDict, defaultdict
+from collections import defaultdict
 
 import numpy as np
 from tqdm import tqdm
@@ -96,78 +96,96 @@ 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.
 
-        # 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)
+        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()
 
-        # 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 _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)
+
+    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 = {}

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():
@@ -229,10 +232,30 @@ 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
 
 
 def parser_argument_to_dict(args) -> dict:
+    ind_mag_atoms = args.index_magnetic_atoms
+    if ind_mag_atoms is not None:
+        ind_mag_atoms = [int(i) - 1 for i in ind_mag_atoms]
+    else:
+        ind_mag_atoms = None
     return {
         "efermi": args.efermi,
         "magnetic_elements": args.elements,
@@ -250,4 +273,5 @@ def parser_argument_to_dict(args) -> dict:
         "orb_decomposition": args.orb_decomposition,
         "output_path": args.output_path,
         "orth": args.orth,
+        "index_magnetic_atoms": ind_mag_atoms,
     }

TB2J/rotate_siestaDM.py

@@ -1,28 +1,28 @@
 import sisl
 
+
 def rotate_siesta_DM(DM, noncollinear=False):
-    
-    angles_list = [ [0.0, 90.0, 0.0], [0.0, 90.0, 90.0] ]
+    angles_list = [[0.0, 90.0, 0.0], [0.0, 90.0, 90.0]]
     if noncollinear:
         angles_list += [[0.0, 45.0, 0.0], [0.0, 90.0, 45.0], [0.0, 45.0, 90.0]]
 
     for angles in angles_list:
         yield DM.spin_rotate(angles)
 
-def read_label(fdf_fname):
 
-    label = 'siesta'
-    with open(fdf_fname, 'r') as File:
+def read_label(fdf_fname):
+    label = "siesta"
+    with open(fdf_fname, "r") as File:
         for line in File:
-            corrected_line = line.lower().replace('.', '').replace('-', '')
-            if 'systemlabel' in corrected_line:
+            corrected_line = line.lower().replace(".", "").replace("-", "")
+            if "systemlabel" in corrected_line:
                 label = line.split()[1]
                 break
 
     return label
 
-def rotate_DM(fdf_fname, noncollinear=False):
 
+def rotate_DM(fdf_fname, noncollinear=False):
     fdf = sisl.get_sile(fdf_fname)
     DM = fdf.read_density_matrix()
     label = read_label(fdf_fname)
@@ -33,4 +33,6 @@ def rotate_DM(fdf_fname, noncollinear=False):
         rotated_DM.write(f"{label}_{i+1}.DM")
     DM.write(f"{label}_0.DM")
 
-    print(f"The output has been written to the {label}_i.DM files. {label}_0.DM contains the reference density matrix.")
+    print(
+        f"The output has been written to the {label}_i.DM files. {label}_0.DM contains the reference density matrix."
+    )

tb2j-0.9.9rc16.data/scripts/abacus2J.py

@@ -0,0 +1,62 @@
+#!python
+import argparse
+import sys
+
+from TB2J.exchange_params import add_exchange_args_to_parser
+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"
+    )
+    # 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()
+
+    index_magnetic_atoms = args.index_magnetic_atoms
+    if not index_magnetic_atoms is None:
+        index_magnetic_atoms = [i-1 for i in index_magnetic_atoms]
+
+    if args.elements is None and index_magnetic_atoms 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=index_magnetic_atoms,
+        cutoff=args.cutoff,
+    )
+
+
+if __name__ == "__main__":
+    run_abacus2J()

tb2j-0.9.9rc16.data/scripts/siesta2J.py

@@ -0,0 +1,78 @@
+#!python
+import argparse
+import sys
+
+from TB2J.exchange_params import add_exchange_args_to_parser
+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"
+    )
+    # 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
+
+    index_magnetic_atoms = args.index_magnetic_atoms
+    if index_magnetic_atoms is not None:
+        index_magnetic_atoms = [i - 1 for i in index_magnetic_atoms]
+
+    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=index_magnetic_atoms,
+    )
+
+
+if __name__ == "__main__":
+    run_siesta2J()

{tb2j-0.9.9rc14.data → tb2j-0.9.9rc16.data}/scripts/wann2J.py

@@ -61,10 +61,14 @@ def run_wann2J():
     if args.efermi is None:
         print("Please input fermi energy using --efermi ")
         sys.exit()
-    if args.elements is None:
+    if args.elements is None and args.index_magnetic_atoms is None:
         print("Please input the magnetic elements, e.g. --elements Fe Ni")
         sys.exit()
 
+    index_magnetic_atoms = args.index_magnetic_atoms
+    if index_magnetic_atoms is not None:
+        index_magnetic_atoms = [i - 1 for i in index_magnetic_atoms]
+
     gen_exchange(
         path=args.path,
         colinear=(not args.spinor),
@@ -89,6 +93,7 @@ def run_wann2J():
         # qspace=args.qspace,
         write_density_matrix=args.write_dm,
         orb_decomposition=args.orb_decomposition,
+        index_magnetic_atoms=index_magnetic_atoms,
     )
 
 

{tb2j-0.9.9rc14.dist-info → tb2j-0.9.9rc16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc14
+Version: 0.9.9rc16
 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>=0.2.1
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
+Requires-Dist: sisl>=0.9.0
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{tb2j-0.9.9rc14.dist-info → tb2j-0.9.9rc16.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=1kkrrQvmoOaPgT_rKG7wgLy31rWpbFGNYXai1ysd58M,26221
+TB2J/exchange.py,sha256=HSvB_keITEeaoNG661feoEcCwjkQlavQQiIi1ONsI3Y,27035
 TB2J/exchangeCL2.py,sha256=P7bklMXVYX_tn9DbjEPqeTir1SeZyfPBIP1fhWUzLmY,11419
-TB2J/exchange_params.py,sha256=AcGYYky27DXSF3yDZWVjksr_3rt6im6qeIzpOwvqssk,7141
+TB2J/exchange_params.py,sha256=d1nFBFwut9SvxUmPRzPzRxD6y0KAP2IvGoEOQ2Jec9U,8049
 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
@@ -29,7 +29,7 @@ TB2J/pauli.py,sha256=ESpAhk6LG5ugzuW1YFUTqiDxcg-pQ7wNnzR2FtUnvKM,5295
 TB2J/pert.py,sha256=RaCJfewl0doht4cjAnzzGKe-uj2le4aqe0iPKFrq9fo,1192
 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/rotate_siestaDM.py,sha256=I4ytO8uFP8_GFyBs9-zMdiMSZS3Y3lj2dSLfNBNI2ZY,1078
 TB2J/sisl_wrapper.py,sha256=A5x1-tt8efUSPeGY5wM5m6-pJYQFXTCzQHVqD6RBa2g,14792
 TB2J/symmetrize_J.py,sha256=IypvLL0JxExq-cmqc4o0nLL8psE7OC9ijj9YMcsqJeA,4487
 TB2J/tensor_rotate.py,sha256=4-DfT_Mg5e40fbd74M5W0D5DqmUq-kVOOLDkkkI834A,8083
@@ -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-0.9.9rc14.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
-tb2j-0.9.9rc14.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-tb2j-0.9.9rc14.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-tb2j-0.9.9rc14.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-tb2j-0.9.9rc14.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
-tb2j-0.9.9rc14.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
-tb2j-0.9.9rc14.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
-tb2j-0.9.9rc14.data/scripts/abacus2J.py,sha256=0HLXoJhAkiZ-ZM1cs26lncccxE8-TzC8JiDTba1h1uM,4163
-tb2j-0.9.9rc14.data/scripts/siesta2J.py,sha256=gp31LioqpPkDmMY0y_5gXIjOBPNnf080P37pRo0yjw8,4886
-tb2j-0.9.9rc14.data/scripts/wann2J.py,sha256=pTFDf6h72I_LN_NX5UivyCoJPgwvyAyHW175nSAJvLo,2987
-tb2j-0.9.9rc14.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-tb2j-0.9.9rc14.dist-info/METADATA,sha256=EIyzpsZFIW8RLeCDLgJDZGnwwqmlFobdrx1kqvs9S_Y,1661
-tb2j-0.9.9rc14.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
-tb2j-0.9.9rc14.dist-info/entry_points.txt,sha256=Hdz1WC9waUzyFVmowKnbbZ6j-J4adHh_Ko6JpxGYAtE,131
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tb2j-0.9.9rc14.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-0.9.9rc14.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()