TB2J 0.9.9.14__tar.gz → 0.9.9.16__tar.gz

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9.14
+Version: 0.9.9.16
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -24,16 +24,24 @@ Requires-Dist: packaging>=20.0
 Requires-Dist: HamiltonIO>=0.2.4
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
-Requires-Dist: sisl>=0.9.0
 Requires-Dist: tomli>=2.0.0
 Requires-Dist: tomli-w>=1.0.0
-Requires-Dist: netcdf4
+Provides-Extra: siesta
+Requires-Dist: sisl>=0.9.0; extra == "siesta"
+Requires-Dist: netcdf4; extra == "siesta"
+Provides-Extra: lawaf
+Requires-Dist: lawaf==0.2.3; extra == "lawaf"
+Provides-Extra: all
+Requires-Dist: sisl>=0.9.0; extra == "all"
+Requires-Dist: netcdf4; extra == "all"
+Requires-Dist: lawaf==0.2.3; extra == "all"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
 Dynamic: description
 Dynamic: license
 Dynamic: license-file
+Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/TB2J/Jdownfolder.py

@@ -94,7 +94,7 @@ class PWFDownfolder:
             # anchors={(0, 0, 0): (-1, -2, -3, -4)},
             # anchors={(0, 0, 0): ()},
             # use_proj=True,
-            enhance_Amn=0.0,
+            enhance_Amn=1.4,
         )
         params.update(kwargs)
         wann.set_parameters(**params)
@@ -176,7 +176,7 @@ class JDownfolder_pickle:
         self.nsite = self.nM + self.nL
 
     def _downfold(self, **kwargs):
-        JR2 = self.exc.get_full_Jtensor_for_Rlist(asr=True)
+        JR2 = self.exc.get_full_Jtensor_for_Rlist(order="i3j3_2D", asr=True)
         if self.method.lower() == "lowdin":
             d = JDownfolder(
                 JR2,

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/TB2J/Jtensor.py

@@ -64,8 +64,9 @@ def decompose_J_tensor(Jtensor):
     :returns:
 
     """
+    Jtensor = Jtensor.real
     Jiso = np.average(np.diag(Jtensor))
-    Dm = (Jtensor - Jtensor.T) / 2.0
+    Dm = (Jtensor - Jtensor.T).real / 2.0
     D = np.array((Dm[1, 2], Dm[2, 0], Dm[0, 1]), dtype=float)
     Jani = (Jtensor + Jtensor.T) / 2 - np.eye(3) * Jiso
     return Jiso, D, Jani

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/TB2J/io_exchange/io_exchange.py

@@ -430,8 +430,20 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
                 for i in range(n):
                     sum_JRi = np.sum(np.sum(Jmat, axis=0)[i])
                     Jmat[iR0][i, i] -= sum_JRi
+        elif order == "i3j3_2D":
+            Jmat = np.zeros((nR, n3, n3), dtype=float)
+            for iR, R in enumerate(self.Rlist):
+                Jmat[iR] = self.get_full_Jtensor_for_one_R_i3j3(
+                    R, Jiso=Jiso, Jani=Jani, DMI=DMI
+                ).reshape((n3, n3))
+            if asr:
+                iR0 = np.argmin(np.linalg.norm(self.Rlist, axis=1))
+                assert np.linalg.norm(self.Rlist[iR0]) == 0
+                for i in range(n3):
+                    sum_JRi = np.sum(np.sum(Jmat, axis=0)[i])
+                    Jmat[iR0][i, i] -= sum_JRi
         else:
-            raise ValueError("order must be either 'i3j3' or 'ij33'.")
+            raise ValueError("order must be either 'i3j3' or 'ij33', or 'i3j3_2D'.")
         return Jmat
 
     def write_pickle(self, path="TB2J_results", fname="TB2J.pickle"):

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/TB2J/io_exchange/io_vampire.py

@@ -60,7 +60,7 @@ def write_vampire_unitcell_file(cls, fname):
                     val = np.real(Jtensor[i, j] * 2.0 / J)
                     if np.abs(val) < 1e-30:
                         val = 0.0
-                    myfile.write(f"{val:<012.5e} ")
+                    myfile.write(f"{val:< 12.5e} ")
             myfile.write("\n")
 
 

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9.14
+Version: 0.9.9.16
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -24,16 +24,24 @@ Requires-Dist: packaging>=20.0
 Requires-Dist: HamiltonIO>=0.2.4
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
-Requires-Dist: sisl>=0.9.0
 Requires-Dist: tomli>=2.0.0
 Requires-Dist: tomli-w>=1.0.0
-Requires-Dist: netcdf4
+Provides-Extra: siesta
+Requires-Dist: sisl>=0.9.0; extra == "siesta"
+Requires-Dist: netcdf4; extra == "siesta"
+Provides-Extra: lawaf
+Requires-Dist: lawaf==0.2.3; extra == "lawaf"
+Provides-Extra: all
+Requires-Dist: sisl>=0.9.0; extra == "all"
+Requires-Dist: netcdf4; extra == "all"
+Requires-Dist: lawaf==0.2.3; extra == "all"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
 Dynamic: description
 Dynamic: license
 Dynamic: license-file
+Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/TB2J.egg-info/requires.txt

@@ -8,7 +8,17 @@ packaging>=20.0
 HamiltonIO>=0.2.4
 pre-commit
 sympair>0.1.0
-sisl>=0.9.0
 tomli>=2.0.0
 tomli-w>=1.0.0
+
+[all]
+sisl>=0.9.0
+netcdf4
+lawaf==0.2.3
+
+[lawaf]
+lawaf==0.2.3
+
+[siesta]
+sisl>=0.9.0
 netcdf4

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/scripts/TB2J_downfold.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 import argparse
-import os
-import sys
+
 from TB2J.Jdownfolder import JDownfolder_pickle
+from TB2J.versioninfo import print_license
 
 
 def main():
@@ -73,6 +73,15 @@ def main():
     if len(args.ligands) == []:
         print("List of ligand elements cannot be empty")
 
+    print_license()
+    print("Input path:", args.inpath)
+    print("Output path:", args.outpath)
+    print("Magnetic cation elements:", args.metals)
+    print("Ligand elements:", args.ligands)
+    print("k-mesh:", args.qmesh)
+    print("Downfolding method:", args.method)
+    print("Downfolding only isotropic part:", args.iso_only)
+    print("Begining downfolding the exchange parameters:")
     JDownfolder_pickle(
         inpath=args.inpath,
         metals=args.metals,
@@ -82,6 +91,7 @@ def main():
         iso_only=args.iso_only,
         method=args.method,
     )
+    print("Downfolding finished. Results are saved in:", args.outpath)
 
 
 main()

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/scripts/TB2J_merge.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 import argparse
-import os
-import sys
+
 from TB2J.io_merge import merge
+from TB2J.version_info import print_license
 
 
 def main():
@@ -32,14 +32,18 @@ def main():
         "--main_path",
         help="The path containning the reference structure.",
         type=str,
-        default=None
+        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)
+    print_license()
+    print("Merging the TB2J results from the following directories: ", args.directories)
     merge(*args.directories, main_path=args.main_path, write_path=args.output_path)
+    print("Merging completed. The results are saved in:", args.output_path)
 
 
-main()
+if __name__ == "__main__":
+    main()

tb2j-0.9.9.16/scripts/TB2J_plot_magnon_bands.py

@@ -0,0 +1,27 @@
+#!/usr/bin/env python3
+
+
+if __name__ == "__main__":
+    # add a warning messege that this functionality is under development and should not be used in production.
+    # make it visually distinct, e.g. with a different color or formatting.
+    import warnings
+
+    from TB2J.magnon.magnon3 import main
+
+    warnings.warn(
+        """ 
+        # !!!!!!!!!!!!!!!!!! WARNING: =============================
+        # 
+        # This functionality is under development and should not be used in production.
+        # It is provided for testing and development purposes only.
+        # Please use with caution and report any issues to the developers.
+        #
+        # This warning will be removed in future releases.
+        # =====================================
+
+        """,
+        UserWarning,
+        stacklevel=2,
+    )
+    # Call the main function from the magnons module
+    main()

{tb2j-0.9.9.14 → tb2j-0.9.9.16}/setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from setuptools import find_packages, setup
 
-__version__ = "0.9.9.14"
+__version__ = "0.9.9.16"
 
 long_description = """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. """
 
@@ -46,11 +46,14 @@ setup(
         "HamiltonIO>=0.2.4",
         "pre-commit",
         "sympair>0.1.0",
-        "sisl>=0.9.0",
         "tomli>=2.0.0",
         "tomli-w>=1.0.0",
-        "netcdf4",
     ],
+    extras_require={
+        "siesta": ["sisl>=0.9.0", "netcdf4"],
+        "lawaf": ["lawaf==0.2.3"],
+        "all": ["sisl>=0.9.0", "netcdf4", "lawaf==0.2.3"],
+    },
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Programming Language :: Python :: 3",

tb2j-0.9.9.14/scripts/TB2J_plot_magnon_bands.py

@@ -1,7 +0,0 @@
-#!/usr/bin/env python3
-
-
-if __name__ == "__main__":
-    from TB2J.magnon.magnon3 import main
-
-    main()