TB2J 0.9.9.2__tar.gz → 0.9.9.3__tar.gz

{tb2j-0.9.9.2 → tb2j-0.9.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9.2
+Version: 0.9.9.3
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -21,7 +21,7 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: HamiltonIO>=0.1.10
+Requires-Dist: HamiltonIO>=0.2.1
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
 Requires-Dist: sisl>=0.9.0

{tb2j-0.9.9.2 → tb2j-0.9.9.3}/TB2J/exchange_params.py

@@ -251,6 +251,11 @@ 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,
@@ -268,5 +273,5 @@ def parser_argument_to_dict(args) -> dict:
         "orb_decomposition": args.orb_decomposition,
         "output_path": args.output_path,
         "orth": args.orth,
-        "index_magnetic_atoms": args.index_magnetic_atoms,
+        "index_magnetic_atoms": ind_mag_atoms,
     }

{tb2j-0.9.9.2 → tb2j-0.9.9.3}/TB2J/io_exchange/io_exchange.py

@@ -8,16 +8,13 @@ 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-0.9.9.2 → tb2j-0.9.9.3}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9.2
+Version: 0.9.9.3
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -21,7 +21,7 @@ Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
 Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
-Requires-Dist: HamiltonIO>=0.1.10
+Requires-Dist: HamiltonIO>=0.2.1
 Requires-Dist: pre-commit
 Requires-Dist: sympair>0.1.0
 Requires-Dist: sisl>=0.9.0

{tb2j-0.9.9.2 → tb2j-0.9.9.3}/TB2J.egg-info/requires.txt

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

{tb2j-0.9.9.2 → tb2j-0.9.9.3}/scripts/abacus2J.py

@@ -28,7 +28,11 @@ def run_abacus2J():
 
     args = parser.parse_args()
 
-    if args.elements is 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]
+
+    if args.elements is None and index_magnetic_atoms is None:
         print("Please input the magnetic elements, e.g. --elements Fe Ni")
         sys.exit()
 
@@ -49,7 +53,7 @@ def run_abacus2J():
         nproc=args.nproc,
         exclude_orbs=args.exclude_orbs,
         orb_decomposition=args.orb_decomposition,
-        index_magnetic_atoms=args.index_magnetic_atoms,
+        index_magnetic_atoms=index_magnetic_atoms,
         cutoff=args.cutoff,
     )
 

{tb2j-0.9.9.2 → tb2j-0.9.9.3}/scripts/siesta2J.py

@@ -47,6 +47,10 @@ 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,
@@ -66,7 +70,7 @@ def run_siesta2J():
         orb_decomposition=args.orb_decomposition,
         read_H_soc=args.split_soc,
         orth=args.orth,
-        index_magnetic_atoms=args.index_magnetic_atoms,
+        index_magnetic_atoms=index_magnetic_atoms,
     )
 
 

{tb2j-0.9.9.2 → tb2j-0.9.9.3}/scripts/wann2J.py

@@ -61,10 +61,14 @@ def run_wann2J():
     if args.efermi is None:
         print("Please input fermi energy using --efermi ")
         sys.exit()
-    if args.elements is None:
+    if args.elements is None and args.index_magnetic_atoms 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),
@@ -89,7 +93,7 @@ def run_wann2J():
         # qspace=args.qspace,
         write_density_matrix=args.write_dm,
         orb_decomposition=args.orb_decomposition,
-        index_magnetic_atoms=args.index_magnetic_atoms,
+        index_magnetic_atoms=index_magnetic_atoms,
     )
 
 

{tb2j-0.9.9.2 → tb2j-0.9.9.3}/setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from setuptools import find_packages, setup
 
-__version__ = "0.9.9.2"
+__version__ = "0.9.9.3"
 
 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. """
 
@@ -40,11 +40,11 @@ setup(
         "tqdm",
         "pathos",
         "packaging>=20.0",
-        "HamiltonIO>=0.1.10",
+        "HamiltonIO>=0.2.1",
         "pre-commit",
         "sympair>0.1.0",
         "sisl>=0.9.0",
-        "netcdf4"
+        "netcdf4",
     ],
     classifiers=[
         "Development Status :: 3 - Alpha",