TB2J 0.9.9rc19__py3-none-any.whl → 0.9.9.2__py3-none-any.whl

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/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/__init__.py

@@ -1 +1 @@
-__version__ = "0.9.0.1"
+__version__ = "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/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/io_exchange/__init__.py

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

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/mathutils/__init__.py

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

{tb2j-0.9.9rc19.data → tb2j-0.9.9.2.data}/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.data → tb2j-0.9.9.2.data}/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.data → tb2j-0.9.9.2.data}/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.dist-info → tb2j-0.9.9.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc19
+Version: 0.9.9.2
 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.dist-info → tb2j-0.9.9.2.dist-info}/RECORD

@@ -1,10 +1,10 @@
-TB2J/Jdownfolder.py,sha256=n5BeQCYP4mD9JsAPeE1F3ZKKR3SUxADfDbaG_rzi77k,9658
+TB2J/Jdownfolder.py,sha256=xs0gmcKwOA3ejXqk3JPPgnYVu8CvkK8cteuvHuu1oSk,9603
 TB2J/Jtensor.py,sha256=t6OsqrSlYW6Im4H7ykVAW8Al_pFXN4C5yj2UEsV6r7g,3181
 TB2J/MAE.py,sha256=fM8U-Dgp9HcQOEeC_kyZV1oVrygBvcux9BraUXVouvY,10994
-TB2J/MAEGreen.py,sha256=Iq4hlZrKEOycPvpV66_t13WIcJ1FJgBS79NleXYpFzw,15528
+TB2J/MAEGreen.py,sha256=pCX12GDNaOz8XgMlui8NjAERM43Ux3HyOKfiD80czXI,15306
 TB2J/Oiju.py,sha256=cNGv8N5uH_swGq7cnAt2OyiDfqtjLlLrwseGu0E4iaM,3383
 TB2J/Oiju_epc.py,sha256=oytM3NYW7nWmklrGgNlqwIpI_JYv_hb7ZnR4o9nYNog,6809
-TB2J/__init__.py,sha256=hcEWkag_UvLm1ZSbjsgcTWkGVlR3Bwmzg1QYAwsvf-g,24
+TB2J/__init__.py,sha256=bhvNrEcDHXt9O-K1rdRAtMHwmvdSm_-Y28VwdCZFsik,24
 TB2J/anisotropy.py,sha256=0zmvXkmDmakbBOwGYLa3IIkv5cE99SHLAQJsGoZz7JQ,25463
 TB2J/basis.py,sha256=DFo6_QUwjBwisP6zGxvoO0lpGTMDPAOkiL9giNCjOjA,1558
 TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
@@ -13,7 +13,7 @@ TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
 TB2J/exchange.py,sha256=HSvB_keITEeaoNG661feoEcCwjkQlavQQiIi1ONsI3Y,27035
 TB2J/exchangeCL2.py,sha256=P7bklMXVYX_tn9DbjEPqeTir1SeZyfPBIP1fhWUzLmY,11419
-TB2J/exchange_params.py,sha256=d1nFBFwut9SvxUmPRzPzRxD6y0KAP2IvGoEOQ2Jec9U,8049
+TB2J/exchange_params.py,sha256=eEO7DX9Hy9HiQ_ZyAvsBcc7KhB6jeKJKZzrhf74YKMk,7882
 TB2J/exchange_pert.py,sha256=jmFMtQbYa_uczM4VAeS6TijkIHRFIqEzZJswzE9Wfuo,8523
 TB2J/exchange_qspace.py,sha256=ZL68qBGFUaQ9BsSPsJaaoWOr9RssPiqX34R_9I3nk_8,8436
 TB2J/gpaw_wrapper.py,sha256=aJ--9Dtyq7jOP1Hkh-Sh1nWcfXm6zKcljOCO0DNCAr0,6890
@@ -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=nCrVWKXua-QzikSPhrvdFVw3OpjeKYPzLzMa7Hqc6Yc,7714
+TB2J/interfaces/siesta_interface.py,sha256=olvo2xdBOSNk3zn67nuKrxbW--EKPoWwEzKRBwJbrVY,7366
 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
@@ -54,23 +54,18 @@ TB2J/interfaces/abacus/stru_api.py,sha256=Ac03ikHRsZRXqTul4IUge7D2iG_xLh4_oyYfeP
 TB2J/interfaces/abacus/test_density_matrix.py,sha256=bMWWJYtDS57SpPZ-eZXZ9Hr_UK4mv8ZHM7SzItG3IVA,774
 TB2J/interfaces/abacus/test_read_HRSR.py,sha256=W1oO_yigT50Yb5_u-KB_IfTpM7kArGkBuMSMs0H4CTs,1235
 TB2J/interfaces/abacus/test_read_stru.py,sha256=hoKPHVco8vwzC7Gao4bOPCdAPhh29x-9DTJJqRr7AYM,788
-TB2J/io_exchange/__init__.py,sha256=LqEnG67qDVKt4hCUywDEQvUIJ7jsQjmtueOW_J16NOE,54
-TB2J/io_exchange/io_exchange.py,sha256=6fefcfYAyRojkCJA5bFwAa2Hjwx6epysfyX8Snj9DWc,20102
+TB2J/io_exchange/__init__.py,sha256=KfGHum7B8E4G_KKfillqw0lErtoyKEuFUUttHLs-mg4,32
+TB2J/io_exchange/io_exchange.py,sha256=gaT0fXD3EzPsMgE_VX9gvcf7nEGY3KVYN8xxTAPzxc0,20120
 TB2J/io_exchange/io_multibinit.py,sha256=8PDmWxzGuv-GwJosj2ZTmiyNY_duFVWJ4ekCuSqGdd8,6739
 TB2J/io_exchange/io_tomsasd.py,sha256=NqkAC1Fl-CUnFA21eBzSy_S5F_oeQFJysw4UukQbN8o,4173
 TB2J/io_exchange/io_txt.py,sha256=BMr1eSILlKpgtjvDx7uw2VMAkEKSvGEPNxpaT_zev0I,10547
 TB2J/io_exchange/io_uppasd.py,sha256=bI4iPEgnK4TvCZNvb6x2xYXgjW7pEehCqmcizy2pqFU,3301
 TB2J/io_exchange/io_vampire.py,sha256=UllC4twf06_q2vBCnAYFzEDGvS8mSefwQXDquBuyc0M,5583
-TB2J/magnon/__init__.py,sha256=jdUFkOlhrpHRmKavAXVcFdZgtY7lKZVzMPFlLmmCErM,113
-TB2J/magnon/io_exchange2.py,sha256=vKKQXhPSvoeKNIc0Kh0GaTFph36jSW0Z46nAAbSEcAg,22993
-TB2J/magnon/plot.py,sha256=kwq9LL0FRVo-SLYNkE-ghlyjz8DZD-c4LAWg8si5GJo,1674
-TB2J/magnon/structure.py,sha256=rKefzXgQlEjVvV-A7E2IogVDWwf5egZr3Wxxu6HuJU4,7685
-TB2J/mathutils/__init__.py,sha256=u3QCXBUmKOtJc5PWMFS65e1WhP43UpSf48S7aJZCohc,50
+TB2J/mathutils/__init__.py,sha256=tQLBfHkZqdVfVxPOahy42qMUkFYnFFFhM-uc4QsYFxI,27
 TB2J/mathutils/fermi.py,sha256=72tZ5CptGmYaBUD0xLWltuH7LBXcrMUwODyW6-WqlzI,638
 TB2J/mathutils/fibonacci_sphere.py,sha256=l0USn25ZCAWF6l4UleyWaeLthsj9TThV9iWmfi6DbaM,2344
 TB2J/mathutils/kR_convert.py,sha256=p_9XWJVNanTzTK2rI6KRjTkbSq42la6N448-zJOsMwY,2671
 TB2J/mathutils/lowdin.py,sha256=RYbm9OcnFnjcZFdC5YcNUsI9cOJmoDLsWSSCaP0GqKQ,499
-TB2J/mathutils/magnons.py,sha256=o9O7OR39RK1cl46MtiUO9Kd1IZYDOR3ANe82FZ7laY8,1085
 TB2J/mathutils/rotate_spin.py,sha256=lbGzve_36FyNjanXqdxYDb102kA4_5OycRlBcm-tH-g,8360
 TB2J/spinham/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 TB2J/spinham/base_parser.py,sha256=oQRHvFE_BlUtTaTZykKgvicu40oXcbICB-D1aAt-qlA,2196
@@ -85,20 +80,19 @@ 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
-tb2j-0.9.9rc19.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
-tb2j-0.9.9rc19.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-tb2j-0.9.9rc19.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-tb2j-0.9.9rc19.data/scripts/TB2J_magnon2.py,sha256=tMa7Fg_Wd2UytnrH3C_AsgGM7BciUW0iy6NiPlWvar8,1920
-tb2j-0.9.9rc19.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-tb2j-0.9.9rc19.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
-tb2j-0.9.9rc19.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
-tb2j-0.9.9rc19.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
-tb2j-0.9.9rc19.data/scripts/abacus2J.py,sha256=VD1ldQP-PIMyxo3Rzzwk_06fJEbbU7oiU3aRXNHK0a0,1826
-tb2j-0.9.9rc19.data/scripts/siesta2J.py,sha256=QJ6c0DbqxaqYEesxiL5R9nK9-flNLrr7hajKfCwirYc,2318
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TB2J/magnon/__init__.py

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