TB2J 0.9.9rc17__tar.gz → 0.9.9rc18__tar.gz

{tb2j-0.9.9rc17 → tb2j-0.9.9rc18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc17
+Version: 0.9.9rc18
 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 → tb2j-0.9.9rc18}/TB2J/MAEGreen.py

@@ -32,7 +32,9 @@ 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 +53,12 @@ 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 +83,6 @@ 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)
 
@@ -277,18 +284,18 @@ 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-0.9.9rc17 → tb2j-0.9.9rc18}/TB2J/interfaces/siesta_interface.py

@@ -5,6 +5,7 @@ import numpy as np
 from TB2J.exchange import ExchangeNCL
 from TB2J.exchangeCL2 import ExchangeCL2
 from TB2J.MAEGreen import MAEGreen
+from TB2J.io_merge import merge
 
 try:
     from HamiltonIO.siesta import SislParser
@@ -156,18 +157,18 @@ 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,
             )
-            # thetas = [0, np.pi / 2, np.pi, 3 * np.pi / 2]
-            # phis = [0, 0, 0, 0]
-            # MAE.set_angles(thetas=thetas, phis=phis)
+            #thetas = [0, np.pi / 2, np.pi, 3 * np.pi / 2]
+            #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 +192,9 @@ 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 → tb2j-0.9.9rc18}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc17
+Version: 0.9.9rc18
 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 → tb2j-0.9.9rc18}/setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from setuptools import find_packages, setup
 
-__version__ = "0.9.9rc17"
+__version__ = "0.9.9rc18"
 
 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. """