TB2J 0.8.2.2__py3-none-any.whl → 0.8.2.4__py3-none-any.whl

TB2J/__init__.py

@@ -1 +1 @@
-__version__ = "0.8.2.2"
+__version__ = "0.8.2.4"

TB2J/io_exchange/io_exchange.py

@@ -322,8 +322,6 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
         returns:
             Jmat: (3*nspin,3*nspin) matrix.
         """
-        i = self.i_spin(i)
-        j = self.i_spin(j)
         n3 = self.nspin * 3
         Jmat = np.zeros((n3, n3), dtype=float)
         for i in range(self.nspin):

TB2J/manager.py

@@ -296,12 +296,11 @@ def gen_exchange_siesta(
         else:
             include_orbs[element] = None
     magnetic_elements = list(include_orbs.keys())
-    print(magnetic_elements)
-    print(include_orbs)
 
     fdf = sisl.get_sile(fdf_fname)
-    geom = fdf.read_geometry()
+    # geom = fdf.read_geometry()
     H = fdf.read_hamiltonian()
+    geom = H.geometry
     if H.spin.is_colinear:
         print("Reading Siesta hamiltonian: colinear spin.")
         tbmodel_up = SislWrapper(H, spin=0, geom=geom)

TB2J/sisl_wrapper.py

@@ -33,7 +33,7 @@ class SislWrapper(AbstractTB):
         self.positions = g.xyz
         self.cell = np.array(g.sc.cell)
         for ia, a in enumerate(_atoms):
-            atomic_numbers.append(a.Z)
+            atomic_numbers.append(a.Z % 200)
         self.atoms = Atoms(
             numbers=atomic_numbers, cell=self.cell, positions=self.positions
         )
@@ -276,9 +276,11 @@ class SislWFSXWrapper(SislWrapper):
         energy shift to be applied to all energies. If `None` no shift is applied. (default: None)
     """
 
-    def __init__(self, geom, wfsx_sile, spin, ispin=None, shift_fermi=None):
+    def __init__(
+        self, sisl_hamiltonian, geom, wfsx_sile, spin, ispin=None, shift_fermi=None
+    ):
         # super().__init__(geom, spin=spin, ispin=ispin, shift_fermi=shift_fermi)
-        super().__init__(sisl_hamiltonian, geom=None, spin=None)
+        super().__init__(sisl_hamiltonian, geom=geom, spin=spin)
         self.geom = geom
         self.wfsx_sile = wfsx_sile
         self.read_all()

TB2J/wannier/w90_parser.py

@@ -137,7 +137,6 @@ def parse_atoms(fname):
     if match.group("suffix").upper() == "FRAC":
         atoms = Atoms(symbols=symbols, cell=cell, scaled_positions=taus)
         atoms.set_tags(tags)
-        print(atoms.get_tags)
     else:
         if match.group("units") is not None:
             factor = unit_dict[match.group("units").upper()]

{TB2J-0.8.2.2.dist-info → TB2J-0.8.2.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: TB2J
-Version: 0.8.2.2
+Version: 0.8.2.4
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Home-page: UNKNOWN
 Author: Xu He

{TB2J-0.8.2.2.dist-info → TB2J-0.8.2.4.dist-info}/RECORD

@@ -2,7 +2,7 @@ TB2J/Jdownfolder.py,sha256=Nw2ixvn2Uq-o1wficz6rdaYHjfRN3U_kQCvrNJGNb68,6980
 TB2J/Jtensor.py,sha256=0fhfOcfVQGu75gytEnApKWTJZfg9ksKJ0anJgco5wRQ,3179
 TB2J/Oiju.py,sha256=yQMfxQGnOSLbuTS22upkEFsJ9UAZk7wFaWynvg1NVdA,3595
 TB2J/Oiju_epc.py,sha256=sqjLIuWWT-d0uH2O7-6mobsUYQjHP5GyGlmdYqvkXFk,7332
-TB2J/__init__.py,sha256=0PDNS-YmjRhQMV1bITOLZQMM9tTUOBtkaUk28c8sLrE,24
+TB2J/__init__.py,sha256=m465wDULhkXiTAOlCtUHRpsYNAwwcrwD6KQMBsD8uY4,24
 TB2J/basis.py,sha256=DFo6_QUwjBwisP6zGxvoO0lpGTMDPAOkiL9giNCjOjA,1558
 TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=aw8LX6wVFCRPhcpkzuI0jGnHisvk4cezvUhkF_6Yx94,2633
@@ -18,7 +18,7 @@ TB2J/green.py,sha256=aaXFZn8B60kjsvThoBk0fVi5jm5RJBb-LT4E9XCFo2w,13169
 TB2J/greentest.py,sha256=2ISSfhor9ecSEOi_E6b4Cv26wEIQlwlzca0ru8z44_E,1603
 TB2J/io_merge.py,sha256=2dYrQFHSnb_8fwbQiVod9GyaT-BotawA26eagXWUyMg,15265
 TB2J/kpoints.py,sha256=6XK2KqTncidEq3o9GuO6VEZRPNTRtWeXg9QfcV-9smI,532
-TB2J/manager.py,sha256=hiryBJ5b2LMmZ34GXc-gbk3WhWHh6Tjy5OXD-lposVo,15846
+TB2J/manager.py,sha256=x5BerzE7HU70U6bUZZEyqsI1_YYzvSbbnJ6wqTIHRb8,15817
 TB2J/mathutils.py,sha256=tHA6q3KPDpXLIbZHdDZ2NU5s886VVM_oEG490zQ6Ris,300
 TB2J/myTB.py,sha256=cm9Kkyzi686QyoxrR3lm4rsSnE6Imee3-j2xM78XnGI,17721
 TB2J/orbmap.py,sha256=RCMJkOPGbfPrcZzcc5ia1ZMKBQWxGcyj8W1ve8BJaEw,6669
@@ -26,7 +26,7 @@ TB2J/pauli.py,sha256=_FIF62jq2CkQdWC473a3S2F6NmzCdeCnglO9PjNVmMI,4120
 TB2J/pert.py,sha256=RaCJfewl0doht4cjAnzzGKe-uj2le4aqe0iPKFrq9fo,1192
 TB2J/plot.py,sha256=AnFIFWE2vlmj7Z6f_7-dX_O1stJN-qbuiurPj43dUCM,4104
 TB2J/rotate_atoms.py,sha256=-fxlQN7LbyQAbGUCUBqDJ5ENR0pT8MLBd-5sLxaX_vI,3031
-TB2J/sisl_wrapper.py,sha256=szeNB_VrRklcMCfWrwnI1Vsv5wqJ92EwwlrWNrIPHM0,14785
+TB2J/sisl_wrapper.py,sha256=BMYaj7-nVxKhYENEwafsyZHcRm1Z66p5Yr-zsxdiFcY,14823
 TB2J/supercell.py,sha256=4hgLGPBLRUDhtD-eF29v46ex7fHdkH-OENjS2wGLFww,19588
 TB2J/tensor_rotate.py,sha256=4-DfT_Mg5e40fbd74M5W0D5DqmUq-kVOOLDkkkI834A,8083
 TB2J/utest.py,sha256=z_ahi7tpHQF9WlHNQihcQ7qzfezRJQXQt28eB1X_z64,3897
@@ -43,7 +43,7 @@ TB2J/abacus/test_read_stru.py,sha256=CpK4zWhlCVAMCmYQmp9Hy-A40OblZQLFpo5JokpNcWQ
 TB2J/external/__init__.py,sha256=yD_ZIMi76H49rj6GAQpiB7UlKa3TgSaMkkLHT6M-8w8,137
 TB2J/external/p_tqdm.py,sha256=ug1jy3-43r8iW7bC37xzPSIe0EjYKH_GUluGzMiQiDw,5831
 TB2J/io_exchange/__init__.py,sha256=KfGHum7B8E4G_KKfillqw0lErtoyKEuFUUttHLs-mg4,32
-TB2J/io_exchange/io_exchange.py,sha256=eJRQM1-ikuNJTfCAB0tgTFwvMA_TiWkGlevVu5CeeAk,19408
+TB2J/io_exchange/io_exchange.py,sha256=RxCZ7OOxhiIzGrIidCOqxNbgLsrHUfCqDVinMvrPdmI,19354
 TB2J/io_exchange/io_multibinit.py,sha256=8PDmWxzGuv-GwJosj2ZTmiyNY_duFVWJ4ekCuSqGdd8,6739
 TB2J/io_exchange/io_pickle.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 TB2J/io_exchange/io_tomsasd.py,sha256=NqkAC1Fl-CUnFA21eBzSy_S5F_oeQFJysw4UukQbN8o,4173
@@ -61,19 +61,19 @@ TB2J/spinham/spin_api.py,sha256=oN3AKg1WQl0YzR4f5ealcJOaVoAy8d7HodIwrbXvQeY,2219
 TB2J/spinham/spin_xml.py,sha256=mneeZzkCE5andvIlur_6VK3XzWvoL-PVqSoWKXtDYTM,11033
 TB2J/spinham/supercell.py,sha256=y17uUC6r3gQb278FhxIW4CABihfLTvKFj6flyXrCPR8,12217
 TB2J/wannier/__init__.py,sha256=7ojCbM84PYv1X1Tbo4NHI-d3gWmQsZB_xiYqbfxVV1E,80
-TB2J/wannier/w90_parser.py,sha256=96mOsWOgaxt0DsQXZLIPHlAFQeuTkP3DQNhNsWYiKm4,4650
+TB2J/wannier/w90_parser.py,sha256=dbd63LuKyv2DVUzqRINGsbDzEsOxsQyE8_Ear_LQIRg,4620
 TB2J/wannier/w90_tb_parser.py,sha256=qt8pnuprmPp9iIAYwPkPbmEzk6ZPgMq2xognoQp7vwc,4610
-TB2J-0.8.2.2.data/scripts/TB2J_downfold.py,sha256=F9oImXFysejCMP7eIBjbCX2jdHFOCvDW5beF1sG-UM8,1854
-TB2J-0.8.2.2.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-TB2J-0.8.2.2.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-TB2J-0.8.2.2.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-TB2J-0.8.2.2.data/scripts/TB2J_merge.py,sha256=uZKLM__EyCHwxrQvx3Wd73dOEADp_SqfYC8KQvA-N9g,1622
-TB2J-0.8.2.2.data/scripts/TB2J_rotate.py,sha256=XPacPb7-DaFafBXFdWuNW_eNbjd5XPdNhBRNYhge_cg,634
-TB2J-0.8.2.2.data/scripts/abacus2J.py,sha256=M4B07lvTCDczTPTqvnDh_PERzCARAd09TLKv4aIdSQM,4408
-TB2J-0.8.2.2.data/scripts/siesta2J.py,sha256=Q_kvdgE34JJKVUMgBCSe07kARge0XULJ9B6z8hQFu6M,4706
-TB2J-0.8.2.2.data/scripts/wann2J.py,sha256=0g8Y5RbsYgV7iuoRQEeOnpaBy3oNpRfiw1dy6lWD13E,6520
-TB2J-0.8.2.2.dist-info/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-TB2J-0.8.2.2.dist-info/METADATA,sha256=jAzW_RKP6M5nAZgBaO2HfFHAYxESe2FY7iQm2FdTAgE,1464
-TB2J-0.8.2.2.dist-info/WHEEL,sha256=G16H4A3IeoQmnOrYV4ueZGKSjhipXx8zc8nu9FGlvMA,92
-TB2J-0.8.2.2.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
-TB2J-0.8.2.2.dist-info/RECORD,,
+TB2J-0.8.2.4.data/scripts/TB2J_downfold.py,sha256=F9oImXFysejCMP7eIBjbCX2jdHFOCvDW5beF1sG-UM8,1854
+TB2J-0.8.2.4.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
+TB2J-0.8.2.4.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
+TB2J-0.8.2.4.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
+TB2J-0.8.2.4.data/scripts/TB2J_merge.py,sha256=uZKLM__EyCHwxrQvx3Wd73dOEADp_SqfYC8KQvA-N9g,1622
+TB2J-0.8.2.4.data/scripts/TB2J_rotate.py,sha256=XPacPb7-DaFafBXFdWuNW_eNbjd5XPdNhBRNYhge_cg,634
+TB2J-0.8.2.4.data/scripts/abacus2J.py,sha256=M4B07lvTCDczTPTqvnDh_PERzCARAd09TLKv4aIdSQM,4408
+TB2J-0.8.2.4.data/scripts/siesta2J.py,sha256=Q_kvdgE34JJKVUMgBCSe07kARge0XULJ9B6z8hQFu6M,4706
+TB2J-0.8.2.4.data/scripts/wann2J.py,sha256=0g8Y5RbsYgV7iuoRQEeOnpaBy3oNpRfiw1dy6lWD13E,6520
+TB2J-0.8.2.4.dist-info/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
+TB2J-0.8.2.4.dist-info/METADATA,sha256=a6ajzd11aBwUKoAF3NzJN74ejMVOrNMIU2jt36HAmz0,1464
+TB2J-0.8.2.4.dist-info/WHEEL,sha256=G16H4A3IeoQmnOrYV4ueZGKSjhipXx8zc8nu9FGlvMA,92
+TB2J-0.8.2.4.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
+TB2J-0.8.2.4.dist-info/RECORD,,