TB2J 0.9.9rc17__py3-none-any.whl → 0.9.9rc19__py3-none-any.whl

TB2J/Jdownfolder.py

@@ -136,7 +136,7 @@ class JDownfolder_pickle:
         outpath,
         qmesh=[7, 7, 7],
         iso_only=False,
-        method="pwf",
+        method="lowdin",
         **kwargs,
     ):
         self.exc = SpinIO.load_pickle(path=inpath, fname="TB2J.pickle")
@@ -146,6 +146,7 @@ class JDownfolder_pickle:
         self.ligands = ligands
         self.outpath = outpath
         self.method = method
+        print("Using method:", self.method)
 
         # read atomic structure
         self.atoms = self.exc.atoms
@@ -176,7 +177,7 @@ class JDownfolder_pickle:
 
     def _downfold(self, **kwargs):
         JR2 = self.exc.get_full_Jtensor_for_Rlist(asr=True)
-        if self.method == "lowdin":
+        if self.method.lower() == "lowdin":
             d = JDownfolder(
                 JR2,
                 self.exc.Rlist,

TB2J/MAEGreen.py

@@ -1,7 +1,6 @@
 import gc
 from pathlib import Path
 
-import matplotlib.pyplot as plt
 import numpy as np
 import tqdm
 from HamiltonIO.abacus.abacus_wrapper import AbacusSplitSOCParser
@@ -32,7 +31,9 @@ class MAEGreen(ExchangeNCL):
         """
         super().__init__(**kwargs)
         self.natoms = len(self.atoms)
-        if angles is None or angles == "axis":
+        if angles is None or angles == "xyz":
+            self.set_angles_xyz()
+        elif angles == "axis":
             self.set_angles_axis()
         elif angles == "scan":
             self.set_angles_scan()
@@ -51,6 +52,11 @@ class MAEGreen(ExchangeNCL):
         self.es_atom = np.zeros((nangles, self.natoms), dtype=complex)
         self.es_atom_orb = DefaultDict(lambda: 0)
 
+    def set_angles_xyz(self):
+        """theta and phi are defined as the x, y, z, xy, yz, xz, xyz, x-yz, -xyz, -x-yz axis."""
+        self.thetas = [np.pi / 2, np.pi / 2, 0.0]
+        self.phis = [np.pi / 2, 0, 0.0]
+
     def set_angles_axis(self):
         """theta and phi are defined as the x, y, z, xy, yz, xz, xyz, x-yz, -xyz, -x-yz axis."""
         self.thetas = [0, np.pi / 2, np.pi / 2, np.pi / 2, np.pi, 0, np.pi / 2, 0, 0, 0]
@@ -75,7 +81,6 @@ class MAEGreen(ExchangeNCL):
         self.thetas = thetas
         self.phis = phis
         self.angle_pairs = list(zip(thetas, phis))
-        # remove duplicates of angles using sets.
         self.angle_pairs = list(set(self.angle_pairs))
         self.thetas, self.phis = zip(*self.angle_pairs)
 
@@ -248,11 +253,11 @@ class MAEGreen(ExchangeNCL):
         Path(output_path).mkdir(exist_ok=True)
         fname = f"{output_path}/MAE.dat"
         fname_orb = f"{output_path}/MAE_orb.dat"
-        fname_tensor = f"{output_path}/MAE_tensor.dat"
-        if figure3d is not None:
-            fname_fig3d = f"{output_path}/{figure3d}"
-        if figure_contourf is not None:
-            fname_figcontourf = f"{output_path}/{figure_contourf}"
+        # fname_tensor = f"{output_path}/MAE_tensor.dat"
+        # if figure3d is not None:
+        #    fname_fig3d = f"{output_path}/{figure3d}"
+        # if figure_contourf is not None:
+        #    fname_figcontourf = f"{output_path}/{figure_contourf}"
 
         # ouput with eigenvalues.
         if with_eigen:
@@ -277,18 +282,18 @@ class MAEGreen(ExchangeNCL):
                     f.write(f"{ea*1e3:.8f} ")
                 f.write("\n")
 
-        self.ani = self.fit_anisotropy_tensor()
-        with open(fname_tensor, "w") as f:
-            f.write("# Anisotropy tensor in meV\n")
-            f.write(f"{self.ani.tensor_strings(include_isotropic=False)}\n")
+        # self.ani = self.fit_anisotropy_tensor()
+        # with open(fname_tensor, "w") as f:
+        #    f.write("# Anisotropy tensor in meV\n")
+        #    f.write(f"{self.ani.tensor_strings(include_isotropic=False)}\n")
 
-        if figure3d is not None:
-            self.ani.plot_3d(figname=fname_fig3d, show=False)
+        # if figure3d is not None:
+        #    self.ani.plot_3d(figname=fname_fig3d, show=False)
 
-        if figure_contourf is not None:
-            self.ani.plot_contourf(figname=fname_figcontourf, show=False)
+        # if figure_contourf is not None:
+        #    self.ani.plot_contourf(figname=fname_figcontourf, show=False)
 
-        plt.close()
+        # plt.close()
         gc.collect()
 
         with open(fname_orb, "w") as f:

TB2J/interfaces/siesta_interface.py

@@ -4,6 +4,7 @@ import numpy as np
 
 from TB2J.exchange import ExchangeNCL
 from TB2J.exchangeCL2 import ExchangeCL2
+from TB2J.io_merge import merge
 from TB2J.MAEGreen import MAEGreen
 
 try:
@@ -156,7 +157,7 @@ Warning: The DMI component parallel to the spin orientation, the Jani which has
                 atoms=model.atoms,
                 basis=basis,
                 efermi=None,
-                angles="miller",
+                angles="axis",
                 # magnetic_elements=magnetic_elements,
                 # include_orbs=include_orbs,
                 **exargs,
@@ -165,9 +166,9 @@ Warning: The DMI component parallel to the spin orientation, the Jani which has
             # phis = [0, 0, 0, 0]
             # MAE.set_angles(thetas=thetas, phis=phis)
             MAE.run(output_path=f"{output_path}_anisotropy", with_eigen=False)
-            print(
-                f"MAE calculation finished. The results are in {output_path} directory."
-            )
+            # print(
+            #    f"MAE calculation finished. The results are in {output_path} directory."
+            # )
 
             angle = {"x": (np.pi / 2, 0), "y": (np.pi / 2, np.pi / 2), "z": (0, 0)}
             for key, val in angle.items():
@@ -191,3 +192,13 @@ Warning: The DMI component parallel to the spin orientation, the Jani which has
                 print(
                     f"All calculation finished. The results are in {output_path_full} directory."
                 )
+
+            merge(
+                "TB2J_results_x",
+                "TB2J_results_y",
+                "TB2J_results_z",
+                main_path=None,
+                save=True,
+                write_path="TB2J_results",
+            )
+            print("Final TB2J_results written to TB2J_results directory.")

{tb2j-0.9.9rc17.data → tb2j-0.9.9rc19.data}/scripts/TB2J_magnon2.py

@@ -1,3 +1,4 @@
+#!python
 from TB2J.magnon import plot_tb2j_magnon_bands
 
 

{tb2j-0.9.9rc17.dist-info → tb2j-0.9.9rc19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc17
+Version: 0.9.9rc19
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com

{tb2j-0.9.9rc17.dist-info → tb2j-0.9.9rc19.dist-info}/RECORD

@@ -1,7 +1,7 @@
-TB2J/Jdownfolder.py,sha256=xs0gmcKwOA3ejXqk3JPPgnYVu8CvkK8cteuvHuu1oSk,9603
+TB2J/Jdownfolder.py,sha256=n5BeQCYP4mD9JsAPeE1F3ZKKR3SUxADfDbaG_rzi77k,9658
 TB2J/Jtensor.py,sha256=t6OsqrSlYW6Im4H7ykVAW8Al_pFXN4C5yj2UEsV6r7g,3181
 TB2J/MAE.py,sha256=fM8U-Dgp9HcQOEeC_kyZV1oVrygBvcux9BraUXVouvY,10994
-TB2J/MAEGreen.py,sha256=pCX12GDNaOz8XgMlui8NjAERM43Ux3HyOKfiD80czXI,15306
+TB2J/MAEGreen.py,sha256=Iq4hlZrKEOycPvpV66_t13WIcJ1FJgBS79NleXYpFzw,15528
 TB2J/Oiju.py,sha256=cNGv8N5uH_swGq7cnAt2OyiDfqtjLlLrwseGu0E4iaM,3383
 TB2J/Oiju_epc.py,sha256=oytM3NYW7nWmklrGgNlqwIpI_JYv_hb7ZnR4o9nYNog,6809
 TB2J/__init__.py,sha256=hcEWkag_UvLm1ZSbjsgcTWkGVlR3Bwmzg1QYAwsvf-g,24
@@ -43,7 +43,7 @@ TB2J/interfaces/__init__.py,sha256=4tiLoXQ73Nlyi9L4j8jJXOYzXluVNPxQZkwfkQZEGHg,3
 TB2J/interfaces/gpaw_interface.py,sha256=GCDlJ-hRWfChvWwsgBDYSmVqO4sH9HAuGZTV9GqgN6c,1504
 TB2J/interfaces/lawaf_interface.py,sha256=PieLnmppdafOYsgeHznqOou1g9L1sam5jOm3KaObdqo,4408
 TB2J/interfaces/manager.py,sha256=PQMLEfMCT5GnDWSl2nI4JOgRPm_fysyR-6Y6l97xWcw,860
-TB2J/interfaces/siesta_interface.py,sha256=olvo2xdBOSNk3zn67nuKrxbW--EKPoWwEzKRBwJbrVY,7366
+TB2J/interfaces/siesta_interface.py,sha256=nCrVWKXua-QzikSPhrvdFVw3OpjeKYPzLzMa7Hqc6Yc,7714
 TB2J/interfaces/wannier90_interface.py,sha256=qzRgXUBb7t1Aiegrl_RV51BB8csdtVM0EP0Z4pjmTcs,4467
 TB2J/interfaces/abacus/__init__.py,sha256=leas71oCvM_HxrF4gnO5A_VKcJmDAgsI1BUctLU3OBw,177
 TB2J/interfaces/abacus/abacus_api.py,sha256=lNV4LNkLcKw7Zux4MQYM9wnh3eFTlcSqbf4Pb7pqhrk,7243
@@ -85,20 +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
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-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
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-tb2j-0.9.9rc17.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
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