TB2J 0.9.9.4__py3-none-any.whl → 0.9.9.7__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/exchange.py

@@ -157,7 +157,6 @@ class Exchange(ExchangeParams):
                     or f"{sym}{tag}" in self.magnetic_elements
                 ):
                     self.ind_mag_atoms.append(atom_idx)
-        print(f"Magnetic atoms: {self.ind_mag_atoms}")
 
     def _validate_orbital_assignments(self):
         """Validate that magnetic atoms have proper orbital assignments."""
@@ -333,6 +332,7 @@ class ExchangeNCL(Exchange):
 
     def get_H_atom(self, iatom):
         orbs = self.iorb(iatom)
+        print(orbs)
         # return self.HR0[self.orb_slice[iatom], self.orb_slice[iatom]]
         return self.HR0[np.ix_(orbs, orbs)]
 

TB2J/exchange_params.py

@@ -177,8 +177,7 @@ def add_exchange_args_to_parser(parser: argparse.ArgumentParser):
     )
 
     parser.add_argument(
-        "--np",
-        "--nproc",
+        "-np",
         help="number of cpu cores to use in parallel, default: 1",
         default=1,
         type=int,

TB2J/interfaces/abacus/abacus_wrapper.py

@@ -160,8 +160,6 @@ class AbacusParser:
         self.read_atoms()
         self.efermi = self.read_efermi()
         self.nel = self.read_nel()
-        print(f"efermi: {self.efermi}")
-        print(f"nel: {self.nel}")
         self.read_basis()
 
     def read_spin(self):
@@ -192,7 +190,6 @@ class AbacusParser:
     def read_basis(self):
         fname = str(Path(self.outpath) / "Orbital")
         self.basis = parse_abacus_orbital(fname)
-        print(self.basis)
         return self.basis
 
     def read_HSR_collinear(self, binary=None):

TB2J/interfaces/abacus/gen_exchange_abacus.py

@@ -30,6 +30,7 @@ def gen_exchange_abacus(
     nproc=1,
     output_path="TB2J_results",
     orb_decomposition=False,
+    index_magnetic_atoms=None,
     description=None,
 ):
     outpath = Path(path) / f"OUT.{suffix}"
@@ -64,6 +65,7 @@ data directory: {outpath}
             use_cache=use_cache,
             output_path=output_path,
             orb_decomposition=orb_decomposition,
+            index_magnetic_atoms=index_magnetic_atoms,
             description=description,
         )
         exchange.run(path=output_path)
@@ -90,6 +92,7 @@ data directory: {outpath}
             nproc=nproc,
             use_cache=use_cache,
             orb_decomposition=orb_decomposition,
+            index_magnetic_atoms=index_magnetic_atoms,
             description=description,
         )
         exchange.run()

TB2J/interfaces/abacus/orbital_api.py

@@ -45,6 +45,7 @@ def parse_abacus_orbital(fname):
             z = int(z)
             orbs.append(AbacusOrbital(iatom, sym, ispin, element, n, l, m, z))
             line = myfile.readline()
+    print(orbs)
     return orbs
 
 

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,
@@ -165,13 +166,12 @@ 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():
-                # model = parser.get_model()
                 theta, phi = val
                 model.set_so_strength(1.0)
                 model.set_Hsoc_rotation_angle([theta, phi])
@@ -182,8 +182,6 @@ Warning: The DMI component parallel to the spin orientation, the Jani which has
                     atoms=model.atoms,
                     basis=basis,
                     efermi=None,  # set to None, compute from efermi.
-                    # magnetic_elements=magnetic_elements,
-                    # include_orbs=include_orbs,
                     **exargs,
                 )
                 exchange.run(path=output_path_full)
@@ -191,3 +189,13 @@ 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/io_exchange/__init__.py

@@ -1 +1,3 @@
 from .io_exchange import SpinIO
+
+__all__ = ["SpinIO"]

TB2J/io_exchange/io_exchange.py

@@ -335,7 +335,7 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
             )
         return Jtensor
 
-    def get_full_Jtensor_for_one_R(self, R, iso_only=False):
+    def get_full_Jtensor_for_one_R_i3j3(self, R, iso_only=False):
         """
         Return the full exchange tensor of all i and j for cell R.
         param R (tuple of integers): cell index R
@@ -351,18 +351,46 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
                 )
         return Jmat
 
-    def get_full_Jtensor_for_Rlist(self, asr=False, iso_only=True):
-        n3 = self.nspin * 3
+    def get_full_Jtensor_for_one_R_ij33(self, R, iso_only=False):
+        """
+        Return the full exchange tensor of all i and j for cell R.
+        param R (tuple of integers): cell index R
+        returns:
+            Jmat: (nspin,nspin,3,3) matrix.
+        """
+        n = self.nspin
+        Jmat = np.zeros((n, n, 3, 3), dtype=float)
+        for i in range(self.nspin):
+            for j in range(self.nspin):
+                Jmat[i, j, :, :] = self.get_J_tensor(i, j, R, iso_only=iso_only)
+        return Jmat
+
+    def get_full_Jtensor_for_Rlist(self, asr=False, iso_only=True, order="i3j3"):
+        n = self.nspin
+        n3 = n * 3
         nR = len(self.Rlist)
-        Jmat = np.zeros((nR, n3, n3), dtype=float)
-        for iR, R in enumerate(self.Rlist):
-            Jmat[iR] = self.get_full_Jtensor_for_one_R(R, iso_only=iso_only)
-        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
+        if order == "i3j3":
+            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, iso_only=iso_only)
+            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
+
+        elif order == "ij33":
+            Jmat = np.zeros((nR, n, n, 3, 3), dtype=float)
+            Jmat[iR] = self.get_full_Jtensor_for_one_R_ij33(R, iso_only=iso_only)
+            if asr:
+                iR0 = np.argmin(np.linalg.norm(self.Rlist, axis=1))
+                assert np.linalg.norm(self.Rlist[iR0]) == 0
+                for i in range(n):
+                    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'.")
         return Jmat
 
     def write_pickle(self, path="TB2J_results", fname="TB2J.pickle"):

TB2J/magnon/__init__.py

@@ -0,0 +1,3 @@
+from .io_exchange2 import ExchangeIO, plot_tb2j_magnon_bands
+
+__all__ = ["ExchangeIO", "plot_tb2j_magnon_bands"]