TB2J 0.8.2.8__py3-none-any.whl → 0.9.0.1__py3-none-any.whl

TB2J/rotate_atoms.py

@@ -5,19 +5,24 @@ import numpy as np
 from TB2J.tensor_rotate import Rxx, Rxy, Rxz, Ryx, Ryy, Ryz, Rzx, Rzy, Rzz
 
 
-def rotate_atom_xyz(atoms):
+def rotate_atom_xyz(atoms, noncollinear=False):
     """
-    given a atoms, return:
-    - 'z'->'x'
-    - 'z'->'y'
-    - 'z'->'z'
+    given a atoms, return rotated atoms:
+    atoms_1, ..., atoms_n,
+    where we considered n diffeerent roation axes.
+
+    When noncollinear == True, more rotated structures
+    will be generated.
     """
-    atoms_x = copy.deepcopy(atoms)
-    atoms_x.rotate(90, "y", rotate_cell=True)
-    atoms_y = copy.deepcopy(atoms)
-    atoms_y.rotate(90, "x", rotate_cell=True)
-    atoms_z = atoms
-    return atoms_x, atoms_y, atoms_z
+
+    rotation_axes = [(1, 0, 0), (0, 1, 0)]
+    if noncollinear:
+        rotation_axes += [(1, 1, 0), (1, 0, 1), (0, 1, 1)]
+    
+    for axis in rotation_axes:
+        rotated_atoms = copy.deepcopy(atoms)
+        rotated_atoms.rotate(90, axis, rotate_cell=True)
+        yield rotated_atoms
 
 
 def rotate_atom_spin_one_rotation(atoms, Rotation):
@@ -96,18 +101,15 @@ def check_ftype(ftype):
         print("=" * 40)
 
 
-def rotate_xyz(fname, ftype="xyz"):
+def rotate_xyz(fname, ftype="xyz", noncollinear=False):
     check_ftype(ftype)
     atoms = read(fname)
     atoms.set_pbc(True)
 
-    atoms_x, atoms_y, atoms_z = rotate_atom_xyz(atoms)
+    rotated = rotate_atom_xyz(atoms, noncollinear=noncollinear)
 
-    fname_x = f"atoms_x.{ftype}"
-    fname_y = f"atoms_y.{ftype}"
-    fname_z = f"atoms_z.{ftype}"
+    for i, rotated_atoms in enumerate(rotated):
+        write(f"atoms_{i+1}.{ftype}", rotated_atoms)
+    write(f"atoms_0.{ftype}", atoms)
 
-    write(fname_x, atoms_x)
-    write(fname_y, atoms_y)
-    write(fname_z, atoms_z)
-    print(f"The output has been written to {fname_x}, {fname_y}, {fname_z}")
+    print(f"The output has been written to the atoms_i.{ftype} files. atoms_0.{ftype} contains the reference structure.")

TB2J/rotate_siestaDM.py

@@ -0,0 +1,36 @@
+import sisl
+
+def rotate_siesta_DM(DM, noncollinear=False):
+    
+    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:
+        for line in File:
+            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):
+
+    fdf = sisl.get_sile(fdf_fname)
+    DM = fdf.read_density_matrix()
+    label = read_label(fdf_fname)
+
+    rotated = rotate_siesta_DM(DM, noncollinear=noncollinear)
+
+    for i, rotated_DM in enumerate(rotated):
+        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.")

TB2J/sisl_wrapper.py

@@ -10,7 +10,6 @@ from TB2J.mathutils import Lowdin
 
 class SislWrapper(AbstractTB):
     def __init__(self, sisl_hamiltonian, geom=None, spin=None):
-        self.is_siesta = False
         self.is_orthogonal = False
         self.ham = sisl_hamiltonian
         # k2Rfactor : H(k) = \int_R H(R) * e^(k2Rfactor * k.R)

{TB2J-0.8.2.8.data → TB2J-0.9.0.1.data}/scripts/TB2J_merge.py

@@ -2,7 +2,7 @@
 import argparse
 import os
 import sys
-from TB2J.io_merge import merge, merge2
+from TB2J.io_merge import merge
 
 
 def main():
@@ -28,11 +28,18 @@ def main():
         type=str,
         default="TB2J_results",
     )
+    parser.add_argument(
+        "--main_path",
+        help="The path containning the reference structure.",
+        type=str,
+        default=None
+    )
 
     args = parser.parse_args()
     # merge(*(args.directories), args.type.strip().lower(), path=args.output_path)
     # merge(*(args.directories), method=args.type.strip().lower(), path=args.output_path)
-    merge2(args.directories, args.type.strip().lower(), path=args.output_path)
+    #merge2(args.directories, args.type.strip().lower(), path=args.output_path)
+    merge(*args.directories, main_path=args.main_path, write_path=args.output_path)
 
 
 main()

{TB2J-0.8.2.8.data → TB2J-0.9.0.1.data}/scripts/TB2J_rotate.py

@@ -14,9 +14,14 @@ def main():
         default="xyz",
         type=str,
     )
+    parser.add_argument(
+        "--noncollinear",
+        action="store_true",
+        help="If present, six different configurations will be generated. These are required for non-collinear systems."
+    )
 
     args = parser.parse_args()
-    rotate_xyz(args.fname, ftype=args.ftype)
+    rotate_xyz(args.fname, ftype=args.ftype, noncollinear=args.noncollinear)
 
 
 if __name__ == "__main__":

TB2J-0.9.0.1.data/scripts/TB2J_rotateDM.py

@@ -0,0 +1,21 @@
+#!python
+import argparse
+from TB2J.rotate_siestaDM import rotate_DM
+
+def main():
+    parser = argparse.ArgumentParser(description="")
+    parser.add_argument(
+        "--fdf_fname", help="Name of the *.fdf siesta file."
+    )
+    parser.add_argument(
+        "--noncollinear",
+        action="store_true",
+        help="If present, six different configurations will be generated. These are required for non-collinear systems."
+    )
+
+    args = parser.parse_args()
+    rotate_DM(args.fdf_fname, noncollinear=args.noncollinear)
+
+
+if __name__ == "__main__":
+    main()

{TB2J-0.8.2.8.dist-info → TB2J-0.9.0.1.dist-info}/METADATA

@@ -1,12 +1,10 @@
 Metadata-Version: 2.1
 Name: TB2J
-Version: 0.8.2.8
+Version: 0.9.0.1
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
-Home-page: UNKNOWN
 Author: Xu He
 Author-email: mailhexu@gmail.com
 License: BSD-2-clause
-Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
@@ -16,14 +14,13 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: License :: OSI Approved :: BSD License
 Requires-Python: >=3.6
 License-File: LICENSE
-Requires-Dist: ase (>=3.19)
+Requires-Dist: numpy >1.16.5
+Requires-Dist: scipy
 Requires-Dist: matplotlib
-Requires-Dist: numpy (>1.16.5)
-Requires-Dist: packaging (>=20.0)
+Requires-Dist: ase >=3.19
+Requires-Dist: tqdm
 Requires-Dist: pathos
+Requires-Dist: packaging >=20.0
 Requires-Dist: pre-commit
-Requires-Dist: scipy
-Requires-Dist: tqdm
 
 TB2J is a Python package aimed to compute automatically the magnetic interactions (superexchange  and Dzyaloshinskii-Moriya) between atoms of magnetic crystals from DFT Hamiltonian based on Wannier functions or Linear combination of atomic orbitals. It uses the Green's function method and take the local rigid spin rotation as a perturbation. The package can take the output from Wannier90, which is interfaced with many density functional theory codes or from codes based on localised orbitals. A minimal user input is needed, which allows for an easily integration into a high-throughput workflows. 
-

{TB2J-0.8.2.8.dist-info → TB2J-0.9.0.1.dist-info}/RECORD

@@ -2,39 +2,38 @@ TB2J/Jdownfolder.py,sha256=Nw2ixvn2Uq-o1wficz6rdaYHjfRN3U_kQCvrNJGNb68,6980
 TB2J/Jtensor.py,sha256=0fhfOcfVQGu75gytEnApKWTJZfg9ksKJ0anJgco5wRQ,3179
 TB2J/Oiju.py,sha256=cNGv8N5uH_swGq7cnAt2OyiDfqtjLlLrwseGu0E4iaM,3383
 TB2J/Oiju_epc.py,sha256=oytM3NYW7nWmklrGgNlqwIpI_JYv_hb7ZnR4o9nYNog,6809
-TB2J/__init__.py,sha256=am9nQoXsrjfFlI37cMwyeG0iWxg4QrTRX090gUPnDJ4,24
+TB2J/__init__.py,sha256=hcEWkag_UvLm1ZSbjsgcTWkGVlR3Bwmzg1QYAwsvf-g,24
 TB2J/basis.py,sha256=DFo6_QUwjBwisP6zGxvoO0lpGTMDPAOkiL9giNCjOjA,1558
 TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=aw8LX6wVFCRPhcpkzuI0jGnHisvk4cezvUhkF_6Yx94,2633
-TB2J/cut_cell.py,sha256=kr9WeQhBQLm8QXL2B3NcsSYmSw-OAtJk3f9wksAOZbs,2952
 TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
-TB2J/exchange.py,sha256=UmZU5h91BPql3ylNALvzMJWTxkfzObZ1OVMxj2Hmp7A,29570
+TB2J/exchange.py,sha256=dsXQhlxXaBurxa7z3YkBjqmEFFtfEy1xaHf0VT3eKZE,29581
 TB2J/exchangeCL2.py,sha256=TIr-d2X56AiGe4qEhyXyZhRuwXvQG6clJMwDmjnTOaE,10985
 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
 TB2J/green.py,sha256=X-D8UZcIyz6zh_0W9VgUUv5yXPP3KWJ6C03m6CMWE3o,13377
 TB2J/greentest.py,sha256=2ISSfhor9ecSEOi_E6b4Cv26wEIQlwlzca0ru8z44_E,1603
-TB2J/io_merge.py,sha256=2dYrQFHSnb_8fwbQiVod9GyaT-BotawA26eagXWUyMg,15265
+TB2J/io_merge.py,sha256=t85k3L6IL9X5ys-PWK7CzResb3xJsyqM3LAlKPUe9vM,6825
 TB2J/kpoints.py,sha256=6XK2KqTncidEq3o9GuO6VEZRPNTRtWeXg9QfcV-9smI,532
 TB2J/manager.py,sha256=4-4x9jJRHpUEqJuhc5HqpXfh2-Ze5G9Wg8gOtn-AqR4,15372
 TB2J/mathutils.py,sha256=tHA6q3KPDpXLIbZHdDZ2NU5s886VVM_oEG490zQ6Ris,300
-TB2J/myTB.py,sha256=cm9Kkyzi686QyoxrR3lm4rsSnE6Imee3-j2xM78XnGI,17721
+TB2J/myTB.py,sha256=ok_B4my29bOIghMSZfx0Es6G8FaXaIiLP4gPxTdSj00,17659
 TB2J/orbmap.py,sha256=RCMJkOPGbfPrcZzcc5ia1ZMKBQWxGcyj8W1ve8BJaEw,6669
 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=BMYaj7-nVxKhYENEwafsyZHcRm1Z66p5Yr-zsxdiFcY,14823
-TB2J/supercell.py,sha256=4hgLGPBLRUDhtD-eF29v46ex7fHdkH-OENjS2wGLFww,19588
+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/tensor_rotate.py,sha256=4-DfT_Mg5e40fbd74M5W0D5DqmUq-kVOOLDkkkI834A,8083
 TB2J/utest.py,sha256=z_ahi7tpHQF9WlHNQihcQ7qzfezRJQXQt28eB1X_z64,3897
 TB2J/utils.py,sha256=_ARYKAeWfP1p5w0mEl-d7KwNfXoqC85TveYl0iCBD3c,9880
 TB2J/versioninfo.py,sha256=wZwS9QDFRVDe7rf8JyPDDI8UGdTQiO6Pb_sWv8GAegA,337
 TB2J/abacus/__init__.py,sha256=5sHiDnF2L-Y80QeET9zOiS83a5T_TQAXvnIhcYB6wNU,56
 TB2J/abacus/abacus_api.py,sha256=D_NyXW-Pno92d3RVHByx0l1HDPHQAvXsmQVt8cfIGR8,7267
-TB2J/abacus/abacus_wrapper.py,sha256=Pqm1MMcD5oQ1Pd4x0EkBh6yRindAps0FIf8LNGOlQok,8492
+TB2J/abacus/abacus_wrapper.py,sha256=QR3ZW6v-d7dgneKwBO5s9FfCjBp-fkWMEaTO4SlcROA,8461
 TB2J/abacus/gen_exchange_abacus.py,sha256=lKZqkWMnLQtaSwgn8O5Fzr-pV6tzwoMqfZU_vbET6gU,2973
 TB2J/abacus/orbital_api.py,sha256=l48Hn5z7TA0TH7Is4NDmz74b6B9L2ztYO4dRR37U4mQ,1562
 TB2J/abacus/stru_api.py,sha256=aBKKlZ2hvAZChVCfNxRdxH51rfHKqZn6kOlazY-yW8k,67888
@@ -45,7 +44,6 @@ 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=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
 TB2J/io_exchange/io_txt.py,sha256=BMr1eSILlKpgtjvDx7uw2VMAkEKSvGEPNxpaT_zev0I,10547
 TB2J/io_exchange/io_uppasd.py,sha256=bI4iPEgnK4TvCZNvb6x2xYXgjW7pEehCqmcizy2pqFU,3301
@@ -53,10 +51,8 @@ TB2J/io_exchange/io_vampire.py,sha256=UllC4twf06_q2vBCnAYFzEDGvS8mSefwQXDquBuyc0
 TB2J/spinham/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 TB2J/spinham/base_parser.py,sha256=oQRHvFE_BlUtTaTZykKgvicu40oXcbICB-D1aAt-qlA,2196
 TB2J/spinham/constants.py,sha256=y4-hRyl5EAR42k24Oa5XhAsUQtKVn1MAgyqNf-p3PrM,762
-TB2J/spinham/h_matrix.py,sha256=MfHIz6RViKkEB3Mu-WcwNx5uk7A5sjAlbqVG9wYA4xk,2784
 TB2J/spinham/hamiltonian.py,sha256=OfsjlGIgFwpXaohopZcgPamSfjm3X46_zc245eyTr_A,16607
 TB2J/spinham/hamiltonian_terms.py,sha256=7e84tfEjvAfZltUkrSWi1sUEiW_itLKy83lxi5iBpcQ,9714
-TB2J/spinham/obtain_J.py,sha256=sg8tiCRRLEN57Olb3MHIuqkDhAkmu-w87AkM00ylXtA,2401
 TB2J/spinham/plot.py,sha256=tLLNqFAATVrP1kmSVLPKzn686i-CUyqu4qgOcs-okHI,6599
 TB2J/spinham/qsolver.py,sha256=Sr9I3aGfVNYn5wzwPx1QonHe6ZZUXBAujWRa7nTA5u4,4986
 TB2J/spinham/spin_api.py,sha256=oN3AKg1WQl0YzR4f5ealcJOaVoAy8d7HodIwrbXvQeY,2219
@@ -65,17 +61,18 @@ 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-0.8.2.8.data/scripts/TB2J_downfold.py,sha256=F9oImXFysejCMP7eIBjbCX2jdHFOCvDW5beF1sG-UM8,1854
-TB2J-0.8.2.8.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-TB2J-0.8.2.8.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-TB2J-0.8.2.8.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-TB2J-0.8.2.8.data/scripts/TB2J_merge.py,sha256=uZKLM__EyCHwxrQvx3Wd73dOEADp_SqfYC8KQvA-N9g,1622
-TB2J-0.8.2.8.data/scripts/TB2J_rotate.py,sha256=XPacPb7-DaFafBXFdWuNW_eNbjd5XPdNhBRNYhge_cg,634
-TB2J-0.8.2.8.data/scripts/abacus2J.py,sha256=M4B07lvTCDczTPTqvnDh_PERzCARAd09TLKv4aIdSQM,4408
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-TB2J-0.8.2.8.dist-info/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-TB2J-0.8.2.8.dist-info/METADATA,sha256=GayTSi2vZJDVZpowe31iXUsOHyUHO5b-hYG_2_H_MnA,1464
-TB2J-0.8.2.8.dist-info/WHEEL,sha256=G16H4A3IeoQmnOrYV4ueZGKSjhipXx8zc8nu9FGlvMA,92
-TB2J-0.8.2.8.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
-TB2J-0.8.2.8.dist-info/RECORD,,
+TB2J-0.9.0.1.data/scripts/TB2J_downfold.py,sha256=F9oImXFysejCMP7eIBjbCX2jdHFOCvDW5beF1sG-UM8,1854
+TB2J-0.9.0.1.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
+TB2J-0.9.0.1.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
+TB2J-0.9.0.1.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
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+TB2J-0.9.0.1.data/scripts/siesta2J.py,sha256=hBzS7ZgoHM3oXlTCQd-xVA07Ks2FiIwyRpQWUFITRPE,4303
+TB2J-0.9.0.1.data/scripts/wann2J.py,sha256=2t2hWwyELskYCwkGDziCgiIAnfr6odLLJ6cQBJ2RQwQ,5714
+TB2J-0.9.0.1.dist-info/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
+TB2J-0.9.0.1.dist-info/METADATA,sha256=ky_ng24tVY8IC_GQn9420M7jzPnCpUiNcp-QtFkUbsk,1420
+TB2J-0.9.0.1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+TB2J-0.9.0.1.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
+TB2J-0.9.0.1.dist-info/RECORD,,

{TB2J-0.8.2.8.dist-info → TB2J-0.9.0.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.37.1)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

TB2J/cut_cell.py

@@ -1,82 +0,0 @@
-import numpy as np
-from TB2J.supercell import find_primitive_cell, map_to_primitive
-from TB2J.io_exchange.io_exchange import SpinIO, gen_distance_dict
-
-
-def cut_cell(path, output_path, sc_matrix, origin_atom_id, thr=1e-5):
-    """
-    Cut the exchange parameters
-    :param path: the original TB2J_results path
-    :param output_path: the output path.
-    :param sc_matrix: the matrix which maps the primitive cell to supercell.
-    :param origin: the origin of the primitive cell.
-    :param thr: the atoms which the reduced position is within -thr to 1.0+thr are considered as inside the primitive atoms
-    :returns:
-    """
-    sc_matrix = np.asarray(sc_matrix, dtype=int)
-    sc_excparams = SpinIO.load_pickle(path=path, fname='TB2J.pickle')
-    sc_atoms = sc_excparams.atoms
-    uc_atoms, ids = find_primitive_cell(sc_atoms,
-                                        sc_matrix,
-                                        origin_atom_id=origin_atom_id,
-                                        thr=thr,
-                                        perfect=False)
-    uc_charges = sc_excparams.charges[ids]
-    uc_spinat = sc_excparams.spinat[ids]
-    indmap, Rmap = map_to_primitive(sc_atoms, uc_atoms)
-
-    # TODO index_spin: {iatom: ispin}
-
-    # list of iatom for each spin index.
-    uc_index_spin = [sc_excparams.index_spin[i] for i in ids]
-
-    uc_ind_atoms = {}
-    for iatom, ispin in enumerate(uc_index_spin):
-        if ispin >= 0:
-            uc_ind_atoms[ispin] = iatom
-
-    uc_Jdict = {}
-    uc_Rset = set()
-    for key, val in sc_excparams.exchange_Jdict.items():
-        R, ispin, jspin = key
-        iatom = sc_excparams.ind_atoms[ispin]
-        jatom = sc_excparams.ind_atoms[jspin]
-        uc_ispin = uc_index_spin[indmap[iatom]]
-        uc_jspin = uc_index_spin[indmap[jatom]]
-        uc_R = R @ sc_matrix + Rmap[jatom] - Rmap[iatom]
-        uc_R = tuple(uc_R)
-        if iatom in ids:
-            #print(f"{iatom=}, {indmap[iatom]=},{uc_ispin=}, {uc_jspin=}, {uc_R=} ")
-            uc_Jdict[(uc_R, uc_ispin, uc_jspin)] = val
-            uc_Rset.add(uc_R)
-
-    uc_distance_dict = gen_distance_dict(uc_ind_atoms, uc_atoms, list(uc_Rset))
-
-    assert sc_excparams.colinear, "Cut supercell for non-collinear spin is not yet implemented."
-
-    uc_exc = SpinIO(uc_atoms,
-                    spinat=uc_spinat,
-                    charges=uc_charges,
-                    index_spin=uc_index_spin,
-                    colinear=sc_excparams.colinear,
-                    distance_dict=uc_distance_dict,
-                    exchange_Jdict=uc_Jdict,
-                    description="Cutted")
-
-    uc_exc.write_all(output_path)
-
-
-def run_cut_cell(
-    path="TB2J_results",
-    output_path="./TB2J_cutted",
-    sc_matrix=np.array([[1, 1, 0], [-1, 1, 0], [0, 0, 2]]),
-):
-    cut_cell(path,
-             output_path,
-             np.array(sc_matrix),
-             origin_atom_id=0,
-             thr=1e-19)
-
-
-if __name__ == "__main__":
-    run_cut_cell()

TB2J/spinham/h_matrix.py

@@ -1,68 +0,0 @@
-import numpy as np
-import matplotlib.pyplot as plt
-import aiida
-from aiida_tb2j.data import ExchangeData
-
-def plot_dispersion(bands, kpoint_labels, color='blue', title=None):
-
-    fig, axs = plt.subplots(1, 1, constrained_layout=True)
-    fig.set_size_inches(6, 6/1.618)
-
-    '''
-    Plot the bands
-    '''
-    kpoints = np.arange(len(bands))
-    axs.plot(kpoints, bands, color=color, linewidth=1.5)
-
-    '''
-    Plot the symmetry points
-    '''
-    bmin = bands.min(); bmax = bands.max()
-    ymin = bmin - 0.05*np.abs(bmin-bmax); ymax = bmax + 0.05*np.abs(bmax-bmin);
-    axs.set_xticks(kpoint_labels[0], kpoint_labels[1], fontsize=10)
-    axs.vlines(x=kpoint_labels[0], ymin=ymin, ymax=ymax, color='black', linewidth=0.5)
-    axs.set_xlim([0, len(kpoints)])
-    axs.set_ylim([ymin, ymax])
-
-    if title is not None:
-        plt.title(title, fontsize=10)
-
-    plt.show()
-
-
-if __name__ == "__main__":
-    
-    from argparse import ArgumentParser
-
-    parser = ArgumentParser()
-    parser.add_argument('-f', '--pickle_filename', type=str, help="Path of the 'TB2J.pickle' file.", required=True)
-    args = parser.parse_args()
-    
-    '''
-    Right now the implementation depends on AiiDA and so we must create and load an AiiDA profile,
-    even if we do not store any information on a data base.
-    '''
-    aiida.load_profile()
-    '''
-    Create an ExchangeData object with the informations from the TB2J.pickle file
-    '''
-    exchange = ExchangeData.load_tb2j(pickle_file=args.pickle_filename, isotropic=False, pbc=(True, True, True))
-    '''
-    Compute the magnon band structure along a high symmetry path generated with
-    the ASE package. The informations is stored in an AiiDA BandsData object.
-    Here tol is the symmetry tolerance to determine the space group of the system.
-    They are in units of eV
-    '''
-    magnon_data = exchange.get_magnon_bands(npoints=300, tol=1e-1, with_DMI=True, with_Jani=True)
-    magnon_bands = 1000*magnon_data.get_bands() # Convert to meV
-    raw_labels = [(k, '$\Gamma$') if s == 'GAMMA' else (k, s) for k, s in magnon_data.labels]
-    kpoint_labels = list( zip( *raw_labels ) )
-    plot_dispersion(magnon_bands, kpoint_labels, color='blue', title='Magnon Bands')
-    '''
-    We can also obtain the dynamical matrix h instead of the actual magnon bands. The result
-    is stored in a numpy array with shape (number of kpoints, 2*natoms, 2*natoms)
-    '''
-    kpoints = magnon_data.get_kpoints() # The shape of the kpoints must be (nkpoints, 3)
-    h_matrix = 1000*exchange._H_matrix(kpoints, with_DMI=True, with_Jani=True) # Convert to meV
-    h_dispersion = np.linalg.eigvalsh(h_matrix) # We can also get the eigenvectors with np.linalg.eigh
-    plot_dispersion(h_dispersion, kpoint_labels, color='red', title='h matrix dispersion')

TB2J/spinham/obtain_J.py

@@ -1,79 +0,0 @@
-import numpy as np
-from aiida_tb2j.data import ExchangeData
-from aiida_tb2j.data.exchange import get_rotation_arrays
-from itertools import combinations_with_replacement
-
-ux, uy, uz = np.eye(3).reshape((3, 1, 3))
-
-def combine_arrays(u, v):
-
-    return np.concatenate([u*v, np.roll(u, -1, axis=-1)*v, np.roll(v, -1, axis=-1)*u], axis=-1)
-
-def get_coefficients(magmoms, indices):
-
-    i, j = indices
-
-    U, V = zip(*[get_rotation_arrays(magmoms, u=u) for u in [ux, uy, uz]])
-    U = np.stack(U).swapaxes(0, 1)
-    V = np.stack(V).swapaxes(0, 1)
-
-    uc = combine_arrays(U[i], U[j].conj())
-    ur = combine_arrays(U[i], U[j])
-    uc2 = combine_arrays(U[i].conj(), U[j])
-    u = np.concatenate([uc, ur, uc2], axis=1)
-
-    return u, V
-
-def get_C(H0, u, V):
-
-    n = int(H0.shape[-1]/2)
-    upi = np.triu_indices(n)
-    dig = np.diag_indices(n)
-    
-    i, j = upi
-    AB0 = H0[:, [i, i, i+n], [j, j+n, j+n]]
-    AB0 = np.swapaxes(AB0, 0, 2).reshape(len(i), 9)
-    J0_flat = np.linalg.solve(u, AB0)
-
-    J0 = np.empty((n, n, 3, 3), dtype=complex)
-    J0[*upi] = J0_flat[:, [0, 6, 5, 3, 1, 7, 8, 4, 2]].reshape(-1, 3, 3)
-    J0 += J0.swapaxes(0, 1)
-    J0[*dig] = 0.0
-
-    C = np.array([np.diag(a) for a in np.einsum('imx,ijxy,jmy->mi', V, 2*J0, V)]) 
-
-    return C
-
-def get_J(H, kpoints, exchange):
-
-    n = int(H.shape[-1]/2)
-    upi = np.triu_indices(n)
-    dig = np.diag_indices(n)
-    i, j = upi
-
-    magmoms = exchange.magmoms()[np.unique(exchange.pairs)]
-    magmoms /= np.linalg.norm(magmoms, axis=-1).reshape(-1, 1)
-    u, V = get_coefficients(magmoms, indices=upi)
-
-    H0 = np.stack([1000*exchange._H_matrix(kpoints=np.zeros((1, 3)), with_DMI=True, with_Jani=True, u=u) for u in [ux, uy, uz]])[:, 0, :, :]
-    C = get_C(H0, u, V)
-    H[:, :, :n, :n] += C.reshape(3, 1, n, n)
-    H[:, :, n:, n:] += C.reshape(3, 1, n, n)
-
-    AB = H[:, :, [i, i, i+n], [j, j+n, j+n]]
-    AB[:, :, 2, :] = AB[:, ::-1, 2, :]
-    AB = np.moveaxis(AB, [2, 3], [1, 0]).reshape(len(i), 9, -1)
-
-    vectors = exchange.get_vectors()
-    exp_summand = np.exp( -2j*np.pi*vectors @ kpoints.T )
-    nAB = np.einsum('nik,ndk->nid', AB, exp_summand) / len(kpoints)
-    
-    ii = np.where(i == j)
-    i0 = np.where(np.linalg.norm(vectors, axis=-1) == 0.0)
-    J = np.linalg.solve(u, nAB).swapaxes(1, 2)
-    J = J[:, :, [0, 6, 5, 3, 1, 7, 8, 4, 2]].reshape(len(i), -1, 3, 3)
-    J *= -1
-    J[ii] *= 2
-    J[i0] *= 0
-
-    return J