TB2J 0.9.9rc19__tar.gz → 0.9.9.1__tar.gz

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc19
+Version: 0.9.9.1
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -21,10 +21,11 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: HamiltonIO>=0.2.1
+Requires-Dist: HamiltonIO>=0.1.10
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
 Requires-Dist: sisl>=0.9.0
+Requires-Dist: netcdf4
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/TB2J/Jdownfolder.py

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

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/TB2J/MAEGreen.py

@@ -1,6 +1,7 @@
 import gc
 from pathlib import Path
 
+import matplotlib.pyplot as plt
 import numpy as np
 import tqdm
 from HamiltonIO.abacus.abacus_wrapper import AbacusSplitSOCParser
@@ -31,9 +32,7 @@ class MAEGreen(ExchangeNCL):
         """
         super().__init__(**kwargs)
         self.natoms = len(self.atoms)
-        if angles is None or angles == "xyz":
-            self.set_angles_xyz()
-        elif angles == "axis":
+        if angles is None or angles == "axis":
             self.set_angles_axis()
         elif angles == "scan":
             self.set_angles_scan()
@@ -52,11 +51,6 @@ 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]
@@ -81,6 +75,7 @@ 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)
 
@@ -253,11 +248,11 @@ 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:
@@ -282,18 +277,18 @@ 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-0.9.9rc19 → tb2j-0.9.9.1}/TB2J/exchange_params.py

@@ -251,11 +251,6 @@ def add_exchange_args_to_parser(parser: argparse.ArgumentParser):
 
 
 def parser_argument_to_dict(args) -> dict:
-    ind_mag_atoms = args.index_magnetic_atoms
-    if ind_mag_atoms is not None:
-        ind_mag_atoms = [int(i) - 1 for i in ind_mag_atoms]
-    else:
-        ind_mag_atoms = None
     return {
         "efermi": args.efermi,
         "magnetic_elements": args.elements,
@@ -273,5 +268,5 @@ def parser_argument_to_dict(args) -> dict:
         "orb_decomposition": args.orb_decomposition,
         "output_path": args.output_path,
         "orth": args.orth,
-        "index_magnetic_atoms": ind_mag_atoms,
+        "index_magnetic_atoms": args.index_magnetic_atoms,
     }

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/TB2J/interfaces/siesta_interface.py

@@ -4,7 +4,6 @@ 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:
@@ -157,7 +156,7 @@ Warning: The DMI component parallel to the spin orientation, the Jani which has
                 atoms=model.atoms,
                 basis=basis,
                 efermi=None,
-                angles="axis",
+                angles="miller",
                 # magnetic_elements=magnetic_elements,
                 # include_orbs=include_orbs,
                 **exargs,
@@ -166,9 +165,9 @@ 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():
@@ -192,13 +191,3 @@ 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-0.9.9rc19 → tb2j-0.9.9.1}/TB2J/io_exchange/__init__.py

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

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/TB2J/io_exchange/io_exchange.py

@@ -8,13 +8,16 @@ write not only xml output.
 - tom's asd inputs.
 """
 
-# matplotlib.use("Agg")
-import gc
 import os
 import pickle
 from collections.abc import Iterable
 from datetime import datetime
 
+import matplotlib
+
+matplotlib.use("Agg")
+import gc
+
 import matplotlib.pyplot as plt
 import numpy as np
 

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/TB2J/mathutils/__init__.py

@@ -1,2 +1 @@
 from .lowdin import Lowdin
-from .magnons import *

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc19
+Version: 0.9.9.1
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -21,10 +21,11 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: HamiltonIO>=0.2.1
+Requires-Dist: HamiltonIO>=0.1.10
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
 Requires-Dist: sisl>=0.9.0
+Requires-Dist: netcdf4
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/TB2J.egg-info/SOURCES.txt

@@ -70,16 +70,11 @@ TB2J/io_exchange/io_tomsasd.py
 TB2J/io_exchange/io_txt.py
 TB2J/io_exchange/io_uppasd.py
 TB2J/io_exchange/io_vampire.py
-TB2J/magnon/__init__.py
-TB2J/magnon/io_exchange2.py
-TB2J/magnon/plot.py
-TB2J/magnon/structure.py
 TB2J/mathutils/__init__.py
 TB2J/mathutils/fermi.py
 TB2J/mathutils/fibonacci_sphere.py
 TB2J/mathutils/kR_convert.py
 TB2J/mathutils/lowdin.py
-TB2J/mathutils/magnons.py
 TB2J/mathutils/rotate_spin.py
 TB2J/spinham/__init__.py
 TB2J/spinham/base_parser.py
@@ -97,7 +92,6 @@ TB2J/wannier/w90_tb_parser.py
 scripts/TB2J_downfold.py
 scripts/TB2J_eigen.py
 scripts/TB2J_magnon.py
-scripts/TB2J_magnon2.py
 scripts/TB2J_magnon_dos.py
 scripts/TB2J_merge.py
 scripts/TB2J_rotate.py

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/TB2J.egg-info/requires.txt

@@ -5,7 +5,8 @@ ase>=3.19
 tqdm
 pathos
 packaging>=20.0
-HamiltonIO>=0.2.1
+HamiltonIO>=0.1.10
 pre-commit
 sympair>0.1.0
 sisl>=0.9.0
+netcdf4

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/scripts/abacus2J.py

@@ -28,11 +28,7 @@ def run_abacus2J():
 
     args = parser.parse_args()
 
-    index_magnetic_atoms = args.index_magnetic_atoms
-    if index_magnetic_atoms is not None:
-        index_magnetic_atoms = [i - 1 for i in index_magnetic_atoms]
-
-    if args.elements is None and index_magnetic_atoms is None:
+    if args.elements is None:
         print("Please input the magnetic elements, e.g. --elements Fe Ni")
         sys.exit()
 
@@ -53,7 +49,7 @@ def run_abacus2J():
         nproc=args.nproc,
         exclude_orbs=args.exclude_orbs,
         orb_decomposition=args.orb_decomposition,
-        index_magnetic_atoms=index_magnetic_atoms,
+        index_magnetic_atoms=args.index_magnetic_atoms,
         cutoff=args.cutoff,
     )
 

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/scripts/siesta2J.py

@@ -47,10 +47,6 @@ def run_siesta2J():
     #    else:
     #        include_orbs[element] = None
 
-    index_magnetic_atoms = args.index_magnetic_atoms
-    if index_magnetic_atoms is not None:
-        index_magnetic_atoms = [i - 1 for i in index_magnetic_atoms]
-
     gen_exchange_siesta(
         fdf_fname=args.fdf_fname,
         kmesh=args.kmesh,
@@ -70,7 +66,7 @@ def run_siesta2J():
         orb_decomposition=args.orb_decomposition,
         read_H_soc=args.split_soc,
         orth=args.orth,
-        index_magnetic_atoms=index_magnetic_atoms,
+        index_magnetic_atoms=args.index_magnetic_atoms,
     )
 
 

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/scripts/wann2J.py

@@ -61,14 +61,10 @@ def run_wann2J():
     if args.efermi is None:
         print("Please input fermi energy using --efermi ")
         sys.exit()
-    if args.elements is None and args.index_magnetic_atoms is None:
+    if args.elements is None:
         print("Please input the magnetic elements, e.g. --elements Fe Ni")
         sys.exit()
 
-    index_magnetic_atoms = args.index_magnetic_atoms
-    if index_magnetic_atoms is not None:
-        index_magnetic_atoms = [i - 1 for i in index_magnetic_atoms]
-
     gen_exchange(
         path=args.path,
         colinear=(not args.spinor),
@@ -93,7 +89,7 @@ def run_wann2J():
         # qspace=args.qspace,
         write_density_matrix=args.write_dm,
         orb_decomposition=args.orb_decomposition,
-        index_magnetic_atoms=index_magnetic_atoms,
+        index_magnetic_atoms=args.index_magnetic_atoms,
     )
 
 

{tb2j-0.9.9rc19 → tb2j-0.9.9.1}/setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from setuptools import find_packages, setup
 
-__version__ = "0.9.9rc19"
+__version__ = "0.9.9.1"
 
 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. """
 
@@ -22,7 +22,6 @@ setup(
         "scripts/TB2J_rotateDM.py",
         "scripts/TB2J_merge.py",
         "scripts/TB2J_magnon.py",
-        "scripts/TB2J_magnon2.py",
         "scripts/TB2J_magnon_dos.py",
         "scripts/TB2J_downfold.py",
         "scripts/TB2J_eigen.py",
@@ -41,10 +40,11 @@ setup(
         "tqdm",
         "pathos",
         "packaging>=20.0",
-        "HamiltonIO>=0.2.1",
+        "HamiltonIO>=0.1.10",
         "pre-commit",
         "sympair>0.1.0",
         "sisl>=0.9.0",
+        "netcdf4"
     ],
     classifiers=[
         "Development Status :: 3 - Alpha",

tb2j-0.9.9rc19/TB2J/magnon/__init__.py

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