TB2J 0.9.9rc14__py3-none-any.whl → 0.9.9rc17__py3-none-any.whl

tb2j-0.9.9rc17.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-0.9.9rc17.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-0.9.9rc17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc14
+Version: 0.9.9rc17
 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-0.9.9rc17.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
@@ -54,18 +54,23 @@ TB2J/interfaces/abacus/stru_api.py,sha256=Ac03ikHRsZRXqTul4IUge7D2iG_xLh4_oyYfeP
 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
 TB2J/interfaces/abacus/test_read_stru.py,sha256=hoKPHVco8vwzC7Gao4bOPCdAPhh29x-9DTJJqRr7AYM,788
-TB2J/io_exchange/__init__.py,sha256=KfGHum7B8E4G_KKfillqw0lErtoyKEuFUUttHLs-mg4,32
+TB2J/io_exchange/__init__.py,sha256=LqEnG67qDVKt4hCUywDEQvUIJ7jsQjmtueOW_J16NOE,54
 TB2J/io_exchange/io_exchange.py,sha256=6fefcfYAyRojkCJA5bFwAa2Hjwx6epysfyX8Snj9DWc,20102
 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
 TB2J/io_exchange/io_uppasd.py,sha256=bI4iPEgnK4TvCZNvb6x2xYXgjW7pEehCqmcizy2pqFU,3301
 TB2J/io_exchange/io_vampire.py,sha256=UllC4twf06_q2vBCnAYFzEDGvS8mSefwQXDquBuyc0M,5583
-TB2J/mathutils/__init__.py,sha256=tQLBfHkZqdVfVxPOahy42qMUkFYnFFFhM-uc4QsYFxI,27
+TB2J/magnon/__init__.py,sha256=jdUFkOlhrpHRmKavAXVcFdZgtY7lKZVzMPFlLmmCErM,113
+TB2J/magnon/io_exchange2.py,sha256=vKKQXhPSvoeKNIc0Kh0GaTFph36jSW0Z46nAAbSEcAg,22993
+TB2J/magnon/plot.py,sha256=kwq9LL0FRVo-SLYNkE-ghlyjz8DZD-c4LAWg8si5GJo,1674
+TB2J/magnon/structure.py,sha256=rKefzXgQlEjVvV-A7E2IogVDWwf5egZr3Wxxu6HuJU4,7685
+TB2J/mathutils/__init__.py,sha256=u3QCXBUmKOtJc5PWMFS65e1WhP43UpSf48S7aJZCohc,50
 TB2J/mathutils/fermi.py,sha256=72tZ5CptGmYaBUD0xLWltuH7LBXcrMUwODyW6-WqlzI,638
 TB2J/mathutils/fibonacci_sphere.py,sha256=l0USn25ZCAWF6l4UleyWaeLthsj9TThV9iWmfi6DbaM,2344
 TB2J/mathutils/kR_convert.py,sha256=p_9XWJVNanTzTK2rI6KRjTkbSq42la6N448-zJOsMwY,2671
 TB2J/mathutils/lowdin.py,sha256=RYbm9OcnFnjcZFdC5YcNUsI9cOJmoDLsWSSCaP0GqKQ,499
+TB2J/mathutils/magnons.py,sha256=o9O7OR39RK1cl46MtiUO9Kd1IZYDOR3ANe82FZ7laY8,1085
 TB2J/mathutils/rotate_spin.py,sha256=lbGzve_36FyNjanXqdxYDb102kA4_5OycRlBcm-tH-g,8360
 TB2J/spinham/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 TB2J/spinham/base_parser.py,sha256=oQRHvFE_BlUtTaTZykKgvicu40oXcbICB-D1aAt-qlA,2196
@@ -80,19 +85,20 @@ 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
-tb2j-0.9.9rc14.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
-tb2j-0.9.9rc14.dist-info/RECORD,,
+tb2j-0.9.9rc17.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
+tb2j-0.9.9rc17.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
+tb2j-0.9.9rc17.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
+tb2j-0.9.9rc17.data/scripts/TB2J_magnon2.py,sha256=9HKNXwPlwaEnAlJXVLrbQFhWj3fGLlBAp-nMXWDTbE0,1911
+tb2j-0.9.9rc17.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
+tb2j-0.9.9rc17.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
+tb2j-0.9.9rc17.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
+tb2j-0.9.9rc17.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
+tb2j-0.9.9rc17.data/scripts/abacus2J.py,sha256=VD1ldQP-PIMyxo3Rzzwk_06fJEbbU7oiU3aRXNHK0a0,1826
+tb2j-0.9.9rc17.data/scripts/siesta2J.py,sha256=QJ6c0DbqxaqYEesxiL5R9nK9-flNLrr7hajKfCwirYc,2318
+tb2j-0.9.9rc17.data/scripts/wann2J.py,sha256=OA31VHEXbQMD-JozoLUHDF6vB9Sr62d804OApSKtSnU,3240
+tb2j-0.9.9rc17.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
+tb2j-0.9.9rc17.dist-info/METADATA,sha256=r-lDBhH1xqc2V1ekn53vtmh6yUSfXzjEW0vJ8B7BDGA,1688
+tb2j-0.9.9rc17.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+tb2j-0.9.9rc17.dist-info/entry_points.txt,sha256=Hdz1WC9waUzyFVmowKnbbZ6j-J4adHh_Ko6JpxGYAtE,131
+tb2j-0.9.9rc17.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
+tb2j-0.9.9rc17.dist-info/RECORD,,

{tb2j-0.9.9rc14.dist-info → tb2j-0.9.9rc17.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

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()