TB2J 0.9.9rc12__tar.gz → 0.9.9rc16__tar.gz

{tb2j-0.9.9rc12 → tb2j-0.9.9rc16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc12
+Version: 0.9.9rc16
 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-0.9.9rc12 → tb2j-0.9.9rc16}/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-0.9.9rc12 → tb2j-0.9.9rc16}/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-0.9.9rc12 → tb2j-0.9.9rc16}/TB2J/rotate_atoms.py

@@ -15,7 +15,6 @@ def rotate_atom_xyz(atoms, noncollinear=False):
     will be generated.
     """
 
-    yield atoms
     rotation_axes = [(1, 0, 0), (0, 1, 0)]
     if noncollinear:
         rotation_axes += [(1, 1, 0), (1, 0, 1), (0, 1, 1)]
@@ -24,7 +23,6 @@ def rotate_atom_xyz(atoms, noncollinear=False):
         rotated_atoms = copy.deepcopy(atoms)
         rotated_atoms.rotate(90, axis, rotate_cell=True)
         yield rotated_atoms
-    yield atoms 
 
 
 def rotate_atom_spin_one_rotation(atoms, Rotation):
@@ -111,5 +109,7 @@ def rotate_xyz(fname, ftype="xyz", noncollinear=False):
     rotated = rotate_atom_xyz(atoms, noncollinear=noncollinear)
 
     for i, rotated_atoms in enumerate(rotated):
-        write(f"atoms_{i}.{ftype}", rotated_atoms)
+        write(f"atoms_{i+1}.{ftype}", rotated_atoms)
+    write(f"atoms_0.{ftype}", atoms)
+
     print(f"The output has been written to the atoms_i.{ftype} files. atoms_0.{ftype} contains the reference structure.")

{tb2j-0.9.9rc12 → tb2j-0.9.9rc16}/TB2J.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc12
+Version: 0.9.9rc16
 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-0.9.9rc12 → tb2j-0.9.9rc16}/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-0.9.9rc12 → tb2j-0.9.9rc16}/docs/src/ecosystem.md

@@ -28,11 +28,9 @@ TB2J can provide the input files containing the parameters for Heisenberg models
 
 * [AiiDA\_TB2J\_plugin](https://github.com/antelmor/aiida_tb2j_plugin/tree/groundstate2/aiida_tb2j): AiiDA\_TB2J\_plugin is a AiiDA plugin for high-throughput Siesta-TB2J calculations within the framework of [AiiDA](https://www.aiida.net/). 
 
-#### Codes for Linear Spin Wave method and magnon band structure
-
-* [RAD-tools](https://rad-tools.org/): RAD-tools is a python package for the spin Hamiltonian analysis (with built-in notation changes) and magnon band structure calculation. It is interfaced directly with the TB2J .txt output ("exchange.out") and can compute the magnon band structure via the [linear spin wave theory](https://rad-tools.org/en/stable/user-guide/library/magnon-dispersion.html) for **ferromagnetic**, **antiferromagnetic** and **spiral** magnetic structures. Documentation of the usage can be found on the package website: if you know python -  [use as library](https://rad-tools.org/en/stable/user-guide/module/magnons/index.html) or if you do not know python - [use console interface](https://rad-tools.org/en/stable/user-guide/scripts/rad-plot-tb2j-magnons.html).
-
+#### Codes for Spin Wave methods
 
+* [magnopy](https://magnopy.org/): magnopy is an open-source python package that analyses spin Hamiltonian (with built-in manipulation of notation) on periodic lattices at several levels of spin wave theory. It is interfaced directly with the TB2J's text output ("exchange.out") and can output magnon band structure, among other thing. It can be used as a python library of within the command line interface.
   
 
 #### Related software without already-built interface with TB2J

{tb2j-0.9.9rc12 → tb2j-0.9.9rc16}/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 not index_magnetic_atoms is 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-0.9.9rc12 → tb2j-0.9.9rc16}/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-0.9.9rc12 → tb2j-0.9.9rc16}/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-0.9.9rc12 → tb2j-0.9.9rc16}/setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from setuptools import find_packages, setup
 
-__version__ = "0.9.9rc12"
+__version__ = "0.9.9rc16"
 
 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. """
 
@@ -40,7 +40,7 @@ setup(
         "tqdm",
         "pathos",
         "packaging>=20.0",
-        "HamiltonIO>=0.1.10",
+        "HamiltonIO>=0.2.1",
         "pre-commit",
         "sympair>0.1.0",
         "sisl>=0.9.0",