TB2J 0.9.9rc12__py3-none-any.whl → 0.9.9rc16__py3-none-any.whl

TB2J/exchange_params.py

@@ -251,6 +251,11 @@ def add_exchange_args_to_parser(parser: argparse.ArgumentParser):
 
 
 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,
@@ -268,5 +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": args.index_magnetic_atoms,
+        "index_magnetic_atoms": ind_mag_atoms,
     }

TB2J/io_exchange/io_exchange.py

@@ -8,16 +8,13 @@ write not only xml output.
 - tom's asd inputs.
 """
 
+# matplotlib.use("Agg")
+import gc
 import os
 import pickle
 from collections.abc import Iterable
 from datetime import datetime
 
-import matplotlib
-
-matplotlib.use("Agg")
-import gc
-
 import matplotlib.pyplot as plt
 import numpy as np
 

TB2J/rotate_atoms.py

@@ -15,7 +15,6 @@ def rotate_atom_xyz(atoms, noncollinear=False):
     will be generated.
     """
 
-    yield atoms
     rotation_axes = [(1, 0, 0), (0, 1, 0)]
     if noncollinear:
         rotation_axes += [(1, 1, 0), (1, 0, 1), (0, 1, 1)]
@@ -24,7 +23,6 @@ def rotate_atom_xyz(atoms, noncollinear=False):
         rotated_atoms = copy.deepcopy(atoms)
         rotated_atoms.rotate(90, axis, rotate_cell=True)
         yield rotated_atoms
-    yield atoms 
 
 
 def rotate_atom_spin_one_rotation(atoms, Rotation):
@@ -111,5 +109,7 @@ def rotate_xyz(fname, ftype="xyz", noncollinear=False):
     rotated = rotate_atom_xyz(atoms, noncollinear=noncollinear)
 
     for i, rotated_atoms in enumerate(rotated):
-        write(f"atoms_{i}.{ftype}", rotated_atoms)
+        write(f"atoms_{i+1}.{ftype}", rotated_atoms)
+    write(f"atoms_0.{ftype}", atoms)
+
     print(f"The output has been written to the atoms_i.{ftype} files. atoms_0.{ftype} contains the reference structure.")

{tb2j-0.9.9rc12.data → tb2j-0.9.9rc16.data}/scripts/abacus2J.py

@@ -28,7 +28,11 @@ def run_abacus2J():
 
     args = parser.parse_args()
 
-    if args.elements is None:
+    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()
 
@@ -49,7 +53,7 @@ def run_abacus2J():
         nproc=args.nproc,
         exclude_orbs=args.exclude_orbs,
         orb_decomposition=args.orb_decomposition,
-        index_magnetic_atoms=args.index_magnetic_atoms,
+        index_magnetic_atoms=index_magnetic_atoms,
         cutoff=args.cutoff,
     )
 

{tb2j-0.9.9rc12.data → tb2j-0.9.9rc16.data}/scripts/siesta2J.py

@@ -47,6 +47,10 @@ def run_siesta2J():
     #    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,
@@ -66,7 +70,7 @@ def run_siesta2J():
         orb_decomposition=args.orb_decomposition,
         read_H_soc=args.split_soc,
         orth=args.orth,
-        index_magnetic_atoms=args.index_magnetic_atoms,
+        index_magnetic_atoms=index_magnetic_atoms,
     )
 
 

{tb2j-0.9.9rc12.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),
@@ -89,7 +93,7 @@ def run_wann2J():
         # qspace=args.qspace,
         write_density_matrix=args.write_dm,
         orb_decomposition=args.orb_decomposition,
-        index_magnetic_atoms=args.index_magnetic_atoms,
+        index_magnetic_atoms=index_magnetic_atoms,
     )
 
 

{tb2j-0.9.9rc12.dist-info → tb2j-0.9.9rc16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc12
+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
@@ -21,7 +21,7 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: HamiltonIO>=0.1.10
+Requires-Dist: HamiltonIO>=0.2.1
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
 Requires-Dist: sisl>=0.9.0

{tb2j-0.9.9rc12.dist-info → tb2j-0.9.9rc16.dist-info}/RECORD

@@ -13,7 +13,7 @@ TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
 TB2J/exchange.py,sha256=HSvB_keITEeaoNG661feoEcCwjkQlavQQiIi1ONsI3Y,27035
 TB2J/exchangeCL2.py,sha256=P7bklMXVYX_tn9DbjEPqeTir1SeZyfPBIP1fhWUzLmY,11419
-TB2J/exchange_params.py,sha256=eEO7DX9Hy9HiQ_ZyAvsBcc7KhB6jeKJKZzrhf74YKMk,7882
+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
@@ -28,7 +28,7 @@ TB2J/orbmap.py,sha256=XLQjKMxCy2eADaM5eb2F_zG08V7lzpXJxp5uEtTeVYI,7194
 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=53UuQr5IoQu5g4klQb_aP4WrDykGkBZTkGgdS-O-Q80,3270
+TB2J/rotate_atoms.py,sha256=Dwptn-wdDW4zYzjYb95yxTzuZOe9WPuLjh3d3-YcSs0,3277
 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
@@ -55,7 +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=gaT0fXD3EzPsMgE_VX9gvcf7nEGY3KVYN8xxTAPzxc0,20120
+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
@@ -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-0.9.9rc12.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
-tb2j-0.9.9rc12.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-tb2j-0.9.9rc12.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-tb2j-0.9.9rc12.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-tb2j-0.9.9rc12.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
-tb2j-0.9.9rc12.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
-tb2j-0.9.9rc12.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
-tb2j-0.9.9rc12.data/scripts/abacus2J.py,sha256=r6P9upWah9Dpeqli-oLD7a1wnQc8rvHT6ed0qw4lUYE,1634
-tb2j-0.9.9rc12.data/scripts/siesta2J.py,sha256=Px6eB4OOa00hoCzCoXcuNGiH025udgxudkDfuzGYMRE,2159
-tb2j-0.9.9rc12.data/scripts/wann2J.py,sha256=Z5MSAtS5i5OrPlwDURnPr87dtYF4GbH_NixUi6WYsA8,3043
-tb2j-0.9.9rc12.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
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-tb2j-0.9.9rc12.dist-info/RECORD,,
+tb2j-0.9.9rc16.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
+tb2j-0.9.9rc16.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
+tb2j-0.9.9rc16.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
+tb2j-0.9.9rc16.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
+tb2j-0.9.9rc16.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
+tb2j-0.9.9rc16.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
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+tb2j-0.9.9rc16.data/scripts/siesta2J.py,sha256=QJ6c0DbqxaqYEesxiL5R9nK9-flNLrr7hajKfCwirYc,2318
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+tb2j-0.9.9rc16.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
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+tb2j-0.9.9rc16.dist-info/RECORD,,

{tb2j-0.9.9rc12.dist-info → tb2j-0.9.9rc16.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.4.0)
+Generator: setuptools (80.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any