TB2J 0.9.12.18__py3-none-any.whl → 0.9.12.22__py3-none-any.whl

TB2J/spinham/hamiltonian_terms.py

@@ -1,8 +1,10 @@
 """
 Hamiltonian terms
 """
-import numpy as np
+
 from collections import defaultdict
+
+import numpy as np
 import scipy.sparse as ssp
 
 
@@ -329,3 +331,40 @@ class DipDip(TwoBodyTerm):
 
     def __init__(self):
         pass
+
+
+class SIATensorTerm(SingleBodyTerm):
+    """
+    Single Ion Anisotropy tensor term.
+    $H_{SIA} = -\\sum_i \\vec{S}_i^T \\mathbf{A}_i \\vec{S}_i$
+    where A_i is a 3x3 anisotropy tensor for each atom i.
+    """
+
+    def __init__(self, sia_tensor_dict, ms=None):
+        super(SIATensorTerm, self).__init__(ms=ms)
+        self.sia_tensor_dict = sia_tensor_dict
+
+    def func_i(self, S, i):
+        return -np.dot(S[i], np.dot(self.sia_tensor_dict[i], S[i]))
+
+    def eff_field(self, S, Heff):
+        for i, A in self.sia_tensor_dict.items():
+            Heff[i] += np.dot(A + A.T, S[i])
+
+    def jacobian_i(self, S, i):
+        return np.dot(self.sia_tensor_dict[i] + self.sia_tensor_dict[i].T, S[i])
+
+    def calc_hessian(self):
+        self._hessian = ssp.lil_matrix(
+            (self.nmatoms * 3, self.nmatoms * 3), dtype=float
+        )
+        for i, A in self.sia_tensor_dict.items():
+            self._hessian[i * 3 : i * 3 + 3, i * 3 : i * 3 + 3] = A + A.T
+        self._hessian = ssp.csr_matrix(self._hessian)
+        return self._hessian
+
+    def calc_hessian_ijR(self):
+        self._hessian_ijR = {}
+        for i, A in self.sia_tensor_dict.items():
+            self._hessian_ijR[(i, i, (0, 0, 0))] = A + A.T
+        return self._hessian_ijR

TB2J/spinham/spin_xml.py

@@ -1,9 +1,11 @@
 import xml.etree.ElementTree as ET
-from ase.atoms import Atoms
+
 import numpy as np
-from ase.units import Bohr, eV, J
-from .constants import gyromagnetic_ratio
+from ase.atoms import Atoms
 from ase.data import atomic_masses
+from ase.units import Bohr, J, eV
+
+from .constants import gyromagnetic_ratio
 
 
 class BaseSpinModelParser(object):
@@ -25,6 +27,7 @@ class BaseSpinModelParser(object):
         self._exchange = {}
         self._dmi = {}
         self._bilinear = {}
+        self._sia_tensor = {}
         self._parse(fname)
         self.lattice = Atoms(
             positions=self.positions, masses=self.masses, cell=self.cell
@@ -79,6 +82,10 @@ class BaseSpinModelParser(object):
     def bilinear(self):
         return self._bilinear
 
+    @property
+    def sia_tensor(self):
+        return self._sia_tensor
+
     @property
     def has_exchange(self):
         return bool(len(self._exchange))
@@ -91,6 +98,10 @@ class BaseSpinModelParser(object):
     def has_bilinear(self):
         return bool(len(self._bilinear))
 
+    @property
+    def has_sia_tensor(self):
+        return bool(len(self._sia_tensor))
+
 
 class SpinXmlWriter(object):
     def _write(self, model, fname):
@@ -174,15 +185,14 @@ class SpinXmlWriter(object):
                 uni_term = ET.SubElement(uni, "spin_uniaxial_SIA_term")
                 ET.SubElement(uni_term, "i").text = "%d " % (i + 1)
                 ET.SubElement(uni_term, "amplitude").text = "%.5e" % (k1 * J / eV)
-                ET.SubElement(
-                    uni_term, "direction"
-                ).text = "%.5e \t %.5e \t %.5e " % tuple(model.k1dir[i])
+                ET.SubElement(uni_term, "direction").text = (
+                    "%.5e \t %.5e \t %.5e " % tuple(model.k1dir[i])
+                )
 
         if model.has_bilinear:
-            bi = ET.SubElement()
             bilinear = ET.SubElement(root, "spin_bilinear_list", units="eV")
             ET.SubElement(bilinear, "nterms").text = "%d" % len(model.bilinear_J_dict)
-            for key, val in model.bilinear_Jdict.items():
+            for key, val in model.bilinear_J_dict.items():
                 bilinear_term = ET.SubElement(bilinear, "spin_bilinear_term")
                 ET.SubElement(bilinear_term, "ijR").text = "%d %d %d %d %d" % (
                     key[0] + 1,
@@ -195,6 +205,17 @@ class SpinXmlWriter(object):
                     ["%.5e" % (x * J / eV) for x in val]
                 )
 
+        if model.has_sia_tensor:
+            sia = ET.SubElement(root, "spin_sia_tensor_list", units="eV")
+            ET.SubElement(sia, "nterms").text = "%d" % len(model.sia_tensor_dict)
+            for i, tensor in model.sia_tensor_dict.items():
+                sia_term = ET.SubElement(sia, "spin_sia_tensor_term")
+                ET.SubElement(sia_term, "i").text = "%d" % (i + 1)
+                tensor_flat = tensor.flatten()
+                ET.SubElement(sia_term, "data").text = "\t".join(
+                    ["%.5e" % (x * J / eV) for x in tensor_flat]
+                )
+
         tree = ET.ElementTree(root)
         tree.write(fname)
 
@@ -295,3 +316,14 @@ class SpinXmlParser(BaseSpinModelParser):
             assert (
                 len(self._bilinear) == n_bil
             ), f"Number of bilinear terms {len(self._bil)} different from nterms in xml file {n_bil}"
+
+        sia = root.find("spin_sia_tensor_list")
+        if sia is not None:
+            n_sia = int(sia.find("nterms").text)
+            for si in sia.findall("spin_sia_tensor_term"):
+                i = int(si.find("i").text) - 1
+                val = [float(x) for x in si.find("data").text.strip().split()]
+                self._sia_tensor[i] = np.array(val).reshape((3, 3)) * eV / J
+            assert (
+                len(self._sia_tensor) == n_sia
+            ), f"Number of SIA tensor terms {len(self._sia_tensor)} different from nterms in xml file {n_sia}"

TB2J/symmetrize_J.py

@@ -1,5 +1,5 @@
 import copy
-from pathlib import Path
+from collections import defaultdict
 
 import numpy as np
 from sympair import SymmetryPairFinder
@@ -51,10 +51,16 @@ class TB2JSymmetrizer:
         for pairgroup in self.pgdict.pairlists:
             ijRs = pairgroup.get_all_ijR()
             ijRs_spin = [self.exc.ijR_index_atom_to_spin(*ijR) for ijR in ijRs]
-            Js = [self.exc.get_J(*ijR_spin) for ijR_spin in ijRs_spin]
-            Javg = np.average(Js)
-            for i, j, R in ijRs_spin:
-                symJdict[(R, i, j)] = Javg
+            Js = []
+            for ijR_spin in ijRs_spin:
+                i, j, R = ijR_spin
+                J = self.exc.get_J(i, j, R)
+                if J is not None:
+                    Js.append(J)
+            if Js:
+                Javg = np.average(Js)
+                for i, j, R in ijRs_spin:
+                    symJdict[(R, i, j)] = Javg
         self.new_exc.exchange_Jdict = symJdict
         if self.Jonly:
             self.new_exc.has_dmi = False
@@ -67,10 +73,10 @@ class TB2JSymmetrizer:
 
     def output(self, path="TB2J_symmetrized"):
         if path is None:
-            path = Path(".")
+            path = "TB2J_symmetrized"
         self.new_exc.write_all(path=path)
 
-    def run(self, path=None):
+    def run(self, path="TB2J_symmetrized"):
         print("** Symmetrizing exchange parameters.")
         self.symmetrize_J()
         print("** Outputing the symmetrized exchange parameters.")
@@ -93,11 +99,136 @@ def symmetrize_J(
     exc: exchange
     """
     if exc is None:
+        if path is None:
+            raise ValueError("Please provide the path to the exchange parameters.")
         exc = SpinIO.load_pickle(path=path, fname=fname)
     symmetrizer = TB2JSymmetrizer(exc, symprec=symprec, Jonly=Jonly)
     symmetrizer.run(path=output_path)
 
 
+def _map_atoms_to_spinio(atoms, spinio, symprec=1e-3):
+    """
+    Map atoms from input structure to SpinIO structure.
+
+    Uses species and position matching within symprec tolerance.
+
+    Parameters
+    ----------
+    atoms : ase.Atoms
+        Input atomic structure.
+    spinio : SpinIO
+        The SpinIO object containing the reference structure.
+    symprec : float, optional
+        Position tolerance in Angstrom. Default is 1e-3.
+
+    Returns
+    -------
+    dict
+        Mapping from SpinIO atom index to input structure atom index.
+    """
+    mapping = {}
+    symbols_in = atoms.get_chemical_symbols()
+    pos_in = atoms.get_positions()
+    symbols_s = spinio.atoms.get_chemical_symbols()
+    pos_s_array = spinio.atoms.get_positions()
+
+    for i_in, (sym, pos) in enumerate(zip(symbols_in, pos_in)):
+        for i_s, (sym_s, pos_s) in enumerate(zip(symbols_s, pos_s_array)):
+            if sym == sym_s:
+                if np.linalg.norm(pos - pos_s) < symprec:
+                    mapping[i_s] = i_in
+                    break
+    return mapping
+
+
+def symmetrize_exchange(spinio, atoms, symprec=1e-3):
+    """
+    Symmetrize isotropic exchange based on a provided atomic structure.
+
+    The symmetry is detected from the provided atomic structure using spglib.
+    Exchange parameters for symmetry-equivalent atom pairs are averaged.
+
+    Parameters
+    ----------
+    spinio : SpinIO
+        The SpinIO object to modify.
+    atoms : ase.Atoms
+        Atomic structure that defines the target symmetry.
+        For example, provide a cubic structure to symmetrize to cubic symmetry.
+    symprec : float, optional
+        Symmetry precision in Angstrom. Default is 1e-3.
+
+    Notes
+    -----
+    - Only isotropic exchange (exchange_Jdict) is modified.
+    - DMI and anisotropic exchange are unchanged.
+    - The spinio.atoms structure is NOT modified; only exchange values change.
+    - Atoms are mapped between input and SpinIO structures by species and position.
+
+    Examples
+    --------
+    >>> from ase.io import read
+    >>> # Symmetrize to cubic symmetry
+    >>> cubic_structure = read('cubic_smfeo3.cif')
+    >>> symmetrize_exchange(spinio, atoms=cubic_structure)
+
+    >>> # Symmetrize to original Pnma symmetry (averaging within groups)
+    >>> symmetrize_exchange(spinio, atoms=spinio.atoms)
+    """
+    try:
+        from spglib import spglib as spg
+    except ImportError:
+        raise ImportError(
+            "spglib is required for symmetrization. Install it with: pip install spglib"
+        )
+
+    # Get symmetry dataset from the provided structure
+    lattice = atoms.get_cell()
+    positions = atoms.get_scaled_positions()
+    numbers = atoms.get_atomic_numbers()
+
+    dataset = spg.get_symmetry_dataset((lattice, positions, numbers), symprec=symprec)
+    if dataset is None:
+        raise ValueError(
+            "spglib could not detect symmetry from the provided structure. "
+            "Check that the structure is valid and try adjusting symprec."
+        )
+
+    equivalent_atoms = dataset["equivalent_atoms"]
+
+    # Map atoms between input structure and SpinIO structure
+    atom_mapping = _map_atoms_to_spinio(atoms, spinio, symprec=symprec)
+
+    # Group equivalent pairs and average J values
+    groups = defaultdict(list)
+
+    for (R, i, j), J in spinio.exchange_Jdict.items():
+        # Get corresponding atom indices in SpinIO
+        iatom = spinio.iatom(i)
+        jatom = spinio.iatom(j)
+
+        # Find matching atoms in input structure
+        i_in = atom_mapping.get(iatom)
+        j_in = atom_mapping.get(jatom)
+
+        if i_in is not None and j_in is not None:
+            # Key based on equivalent atom orbits
+            key = (equivalent_atoms[i_in], equivalent_atoms[j_in], R)
+            groups[key].append(J)
+
+    # Average and reassign
+    for (R, i, j), J in spinio.exchange_Jdict.items():
+        iatom = spinio.iatom(i)
+        jatom = spinio.iatom(j)
+        i_in = atom_mapping.get(iatom)
+        j_in = atom_mapping.get(jatom)
+
+        if i_in is not None and j_in is not None:
+            key = (equivalent_atoms[i_in], equivalent_atoms[j_in], R)
+            if key in groups:
+                spinio.exchange_Jdict[(R, i, j)] = np.mean(groups[key])
+
+
 def symmetrize_J_cli():
     from argparse import ArgumentParser
 

TB2J/tests/test_cli_remove_sublattice.py

@@ -0,0 +1,33 @@
+from unittest.mock import MagicMock, patch
+
+from TB2J.scripts.TB2J_edit import cmd_remove_sublattice
+
+
+def test_cmd_remove_sublattice():
+    # Mock args
+    args = MagicMock()
+    args.input = "dummy.pickle"
+    args.output = "output_dir"
+    args.sublattice = "Sm"
+
+    # Mock load, save, remove_sublattice
+    with patch("TB2J.io_exchange.edit.load") as mock_load, patch(
+        "TB2J.io_exchange.edit.save"
+    ) as mock_save, patch(
+        "TB2J.io_exchange.edit.remove_sublattice"
+    ) as mock_remove_sublattice:
+        # Setup mock return value
+        mock_spinio = MagicMock()
+        mock_load.return_value = mock_spinio
+
+        # Run command
+        cmd_remove_sublattice(args)
+
+        # Assertions
+        mock_load.assert_called_with("dummy.pickle")
+        mock_remove_sublattice.assert_called_with(mock_spinio, "Sm")
+        mock_save.assert_called_with(mock_spinio, "output_dir")
+
+
+if __name__ == "__main__":
+    test_cmd_remove_sublattice()

TB2J/tests/test_cli_toggle_exchange.py

@@ -0,0 +1,50 @@
+from unittest.mock import MagicMock, patch
+
+from TB2J.scripts.TB2J_edit import cmd_toggle_exchange
+
+
+def test_cmd_toggle_exchange():
+    args = MagicMock()
+    args.input = "dummy.pickle"
+    args.output = "output_dir"
+    args.enable = False
+    args.disable = True
+
+    with patch("TB2J.io_exchange.edit.load") as mock_load, patch(
+        "TB2J.io_exchange.edit.save"
+    ) as mock_save, patch("TB2J.io_exchange.edit.toggle_exchange") as mock_toggle:
+        mock_spinio = MagicMock()
+        mock_spinio.has_exchange = True
+        mock_load.return_value = mock_spinio
+
+        cmd_toggle_exchange(args)
+
+        mock_load.assert_called_with("dummy.pickle")
+        mock_toggle.assert_called_with(mock_spinio, enabled=False)
+        mock_save.assert_called_with(mock_spinio, "output_dir")
+
+
+def test_cmd_toggle_exchange_enable():
+    args = MagicMock()
+    args.input = "dummy.pickle"
+    args.output = "output_dir"
+    args.enable = True
+    args.disable = False
+
+    with patch("TB2J.io_exchange.edit.load") as mock_load, patch(
+        "TB2J.io_exchange.edit.save"
+    ) as mock_save, patch("TB2J.io_exchange.edit.toggle_exchange") as mock_toggle:
+        mock_spinio = MagicMock()
+        mock_spinio.has_exchange = False
+        mock_load.return_value = mock_spinio
+
+        cmd_toggle_exchange(args)
+
+        mock_load.assert_called_with("dummy.pickle")
+        mock_toggle.assert_called_with(mock_spinio, enabled=True)
+        mock_save.assert_called_with(mock_spinio, "output_dir")
+
+
+if __name__ == "__main__":
+    test_cmd_toggle_exchange()
+    test_cmd_toggle_exchange_enable()

{tb2j-0.9.12.18.dist-info → tb2j-0.9.12.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.12.18
+Version: 0.9.12.22
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author-email: Xu He <mailhexu@gmail.com>
 Maintainer-email: Xu He <mailhexu@gmail.com>
@@ -18,6 +18,9 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Operating System :: OS Independent
 Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Chemistry
@@ -26,7 +29,7 @@ Classifier: License :: OSI Approved :: BSD License
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: scipy
+Requires-Dist: scipy<1.17,>=1.9
 Requires-Dist: matplotlib
 Requires-Dist: ase>=3.19
 Requires-Dist: tqdm
@@ -34,10 +37,11 @@ Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
 Requires-Dist: HamiltonIO>=0.3.0
 Requires-Dist: pre-commit
-Requires-Dist: sympair>0.1.1
+Requires-Dist: sympair>=0.1.4
 Requires-Dist: tomli>=2.0.0
 Requires-Dist: tomli-w>=1.0.0
 Requires-Dist: typing_extensions
+Requires-Dist: sisl>=0.16.2
 Provides-Extra: siesta
 Requires-Dist: sisl>=0.9.0; extra == "siesta"
 Requires-Dist: netcdf4; extra == "siesta"

{tb2j-0.9.12.18.dist-info → tb2j-0.9.12.22.dist-info}/RECORD

@@ -1,8 +1,7 @@
-TB2J/.gitignore,sha256=0Q9EiAAZLJpONgoHwR1XcEskJykFEKfCc45KGH-C3zI,68
 TB2J/Jdownfolder.py,sha256=K8WrvU_5daH7eQgB53VymJPFRWZoOMlvQGgIca9GNt0,10885
 TB2J/Jtensor.py,sha256=WRhpp5N92a6lA1jeM1hc7jYUoTOLIdMnIIKpdOyzjR4,3192
-TB2J/MAE.py,sha256=fM8U-Dgp9HcQOEeC_kyZV1oVrygBvcux9BraUXVouvY,10994
-TB2J/MAEGreen.py,sha256=ytwu9mck0bourYG-e4_d2dcSmM2fxxzviHGowqShx-s,17011
+TB2J/MAE.py,sha256=IhNjh50vPLLqkDxVTGvmuh5Q5sLVqrDYCKOC6iaSLas,11104
+TB2J/MAEGreen.py,sha256=Yrtk9yg7X9Uc3UIMsyX8yHaaNZtKAAwt7js50keSZ8A,16938
 TB2J/Oiju.py,sha256=cNGv8N5uH_swGq7cnAt2OyiDfqtjLlLrwseGu0E4iaM,3383
 TB2J/Oiju_epc.py,sha256=oytM3NYW7nWmklrGgNlqwIpI_JYv_hb7ZnR4o9nYNog,6809
 TB2J/__init__.py,sha256=4snBkP_Q_-pFYbLHVoTWZ35Oo5zCX6tsPQ0_L8DKfFo,76
@@ -12,37 +11,32 @@ TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=qavPsWiyR3IFm8uJlioZZI0I2PlJV_vNTwXVwipJwy0,3310
 TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
-TB2J/exchange.py,sha256=kl-pmyNAu02FzAkeqy7nrXi97HQlmw7ByM2LllHVzsk,39547
-TB2J/exchangeCL2.py,sha256=pi547zshbo1SDegw32tpONKEc4RJ2w1urjgGc6opJQ8,22116
-TB2J/exchange_params.py,sha256=LxV9P9tui4FGqTa-lyahzKO0UcoGU2ZKyMPGVl0YsS4,9071
+TB2J/exchange.py,sha256=WF6HG1q4I84LxjTOTemRfMEB0ZWN37MzrLGD3bGjQtM,39835
+TB2J/exchangeCL2.py,sha256=RPAFQ_wNKcdH4joPSMhA2xK0_EMdY326FFtP_zCr2c4,22200
+TB2J/exchange_params.py,sha256=5MbEfGTdHcjKfLbTxs1I8TsosdYWQIyyHulguDl-gEg,9829
 TB2J/exchange_pert.py,sha256=jmFMtQbYa_uczM4VAeS6TijkIHRFIqEzZJswzE9Wfuo,8523
 TB2J/exchange_qspace.py,sha256=ZL68qBGFUaQ9BsSPsJaaoWOr9RssPiqX34R_9I3nk_8,8436
 TB2J/gpaw_wrapper.py,sha256=cnXwDDN-pcfxRI3o5OTNjgql8CkxylltFZy9bDxOffU,6813
-TB2J/green.py,sha256=cPX6rx5Ed-TYCt_yREq5kBsxbm7j7nMtsa8H5zTHVIw,18139
+TB2J/green.py,sha256=-YO0oq5hrfDut-7o-U8gRjvdywTDFqkdb2HVPihbez4,18537
 TB2J/greentest.py,sha256=2ISSfhor9ecSEOi_E6b4Cv26wEIQlwlzca0ru8z44_E,1603
-TB2J/io_merge.py,sha256=mgoc8ZUP_a_g-9KvWWISp25qo6aBJ8TQsDsBrMSB5nk,7509
+TB2J/io_merge.py,sha256=d92-oLi6nxJDqdjBx_QLC7L2b8DUATRnOX5oeJLWeOs,8526
 TB2J/kpoints.py,sha256=9L7tBarFBHoIhpuc9zuwA6HdnlgH834SQrPek4yRoWk,3191
 TB2J/myTB.py,sha256=6fP6ZlHxejUzgglr0b_hsxv137sQrltozladTKSczFo,17603
-TB2J/mycfr.py,sha256=ZF1PEE2khlKd_4gPyMkoNXepX3XqwWAL2kDbRJNVX-Y,3908
+TB2J/mycfr.py,sha256=vgk5NcWBSW9i0vtqnOYo1T734EFsAD8CL0YumtUYpe0,4045
 TB2J/orbital_magmom.py,sha256=JTwO9ZDgRRQndqR9aFIua4eTvwLMoGsTiY_HaIPMZ2I,889
 TB2J/orbmap.py,sha256=XLQjKMxCy2eADaM5eb2F_zG08V7lzpXJxp5uEtTeVYI,7194
 TB2J/pauli.py,sha256=XHXFBLiGYl0X67mcIgtwjKXrH0IN16ueoQS392x1AM0,6218
 TB2J/pert.py,sha256=RaCJfewl0doht4cjAnzzGKe-uj2le4aqe0iPKFrq9fo,1192
-TB2J/plot.py,sha256=AhZW7ThKYWVZR8L_T2WhvBoqtw1CkrwG1TxgExtvQYI,4079
+TB2J/plot.py,sha256=ghudgnxPEJA7ERtu7lynTg5Xjbwn9Q4Ne3heyF5Trbc,4763
 TB2J/rotate_atoms.py,sha256=taVNQh2OISHx-nuktRNOwDCbz2a_iKTIghCIT_ld250,3250
 TB2J/rotate_siestaDM.py,sha256=I4ytO8uFP8_GFyBs9-zMdiMSZS3Y3lj2dSLfNBNI2ZY,1078
 TB2J/sisl_wrapper.py,sha256=A5x1-tt8efUSPeGY5wM5m6-pJYQFXTCzQHVqD6RBa2g,14792
-TB2J/symmetrize_J.py,sha256=woZfqWe-NSDBpS_LZAgSXjd2Bkmy6JbVHE4URLfKjaQ,4476
+TB2J/symmetrize_J.py,sha256=rC91wXrw8w1aESb5-ATBpmoKs_71aEd2MtxfHvcyvDw,9003
 TB2J/tensor_rotate.py,sha256=ZAC52knugXNJHpvpqSrmrHVdCs04b9v5X2F7rXV2zn4,8059
 TB2J/thetaphi.py,sha256=Z7N3EOSM7rjHd7b9HxMYLPQO__uR0VwEiV9b471Yudc,399
 TB2J/utest.py,sha256=z_ahi7tpHQF9WlHNQihcQ7qzfezRJQXQt28eB1X_z64,3897
 TB2J/utils.py,sha256=DHkc7BK0KUGesfoAv1OxMgIw_iZzcFXh--3ybsFSd_c,12535
 TB2J/versioninfo.py,sha256=saxQPcaJfCExOjEj-fPln1CRbVMCFEV57JUQnf_b3zw,414
-TB2J/agent_files/debug_spinphon_fd/debug_main.py,sha256=e8wUIgQLRxhi3EuSHKsC_w7fGhlEo72Kzd5Rt1eAFMo,6610
-TB2J/agent_files/debug_spinphon_fd/test_compute_dJdx.py,sha256=QyFmwtc-U9Kv0yaS9j6P8XacrCynGZwJxUeJMeNV2bw,10241
-TB2J/agent_files/debug_spinphon_fd/test_ispin0_only.py,sha256=WV9FXUH2zO9rmT3h3jnaasZVRoFMEYOExZQB5g6JlOE,4586
-TB2J/agent_files/debug_spinphon_fd/test_no_d2j.py,sha256=-f6gG6ODBd1m-Iz3jPZixhPuYZKftqG16zYm2d0GBSQ,1100
-TB2J/agent_files/debug_spinphon_fd/test_with_d2j.py,sha256=Yiibt58FfFb5oS75CtHbsvtf8rJi98Pqrj2vuOxBBFs,982
 TB2J/downfold/Hdownfolder.py,sha256=EmNy5SCxR-5u64Yprec3PX7H3tvaMj0-jOnsVolDRbs,8152
 TB2J/external/__init__.py,sha256=yD_ZIMi76H49rj6GAQpiB7UlKa3TgSaMkkLHT6M-8w8,137
 TB2J/external/p_tqdm.py,sha256=ug1jy3-43r8iW7bC37xzPSIe0EjYKH_GUluGzMiQiDw,5831
@@ -55,23 +49,22 @@ TB2J/interfaces/wannier90_interface.py,sha256=IlHjo1RPGBcmso14r3DIZHp-nHNlOmm3Gc
 TB2J/interfaces/abacus/__init__.py,sha256=leas71oCvM_HxrF4gnO5A_VKcJmDAgsI1BUctLU3OBw,177
 TB2J/interfaces/abacus/abacus_api.py,sha256=lNV4LNkLcKw7Zux4MQYM9wnh3eFTlcSqbf4Pb7pqhrk,7243
 TB2J/interfaces/abacus/abacus_wrapper.py,sha256=bQFnvvy-0hruTavH_VspMk1wD32t2UFybEkCgwkwle0,11941
-TB2J/interfaces/abacus/gen_exchange_abacus.py,sha256=v-AUHGkJWeMNf4D5A4wOpCjM6DygQsFB6SWu-BGdTxM,3262
+TB2J/interfaces/abacus/gen_exchange_abacus.py,sha256=haj9m6rbHIfeSRzUgZADFsY1Tf-3n-jPWVPuxfaXhOg,3315
 TB2J/interfaces/abacus/orbital_api.py,sha256=QEAyy4y_uM5GnwRyLvmShjd_z5A2fwqk7L8yj0Y2Mgc,1577
 TB2J/interfaces/abacus/stru_api.py,sha256=Hb9MCo_4d_DVEEhntvBNAFw5KQ46TkAADn4z7CT6qOk,67801
 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/__init__.py,sha256=n6ukJTXzAlP1bGk_BRRZHbSdcex-uP4CzRNndS8S080,335
+TB2J/io_exchange/edit.py,sha256=m5Z6JMLSXkXiDH_MlwjrCPQnFsxX5DM9QHdzXwpoMvo,19157
 TB2J/io_exchange/io_espins.py,sha256=M5VP2z6QY88RtzP06ebqHoQy5ywchojz8gr9Uw9rATk,10615
-TB2J/io_exchange/io_exchange.py,sha256=VUCog9y120d3Zved-lJ-qIb0pazx1IdAs8SHl3B_MfM,24931
+TB2J/io_exchange/io_exchange.py,sha256=QLYcmnsZrLGatbaIEdgYdxWgIU-imms7q4DN1LyHxA4,31198
 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=jFScdZ5W5_VNSEWYq6WDNKWeshZ0wxFfEzyjfvvU9MA,10601
+TB2J/io_exchange/io_tomsasd.py,sha256=rGWgO2aUgEIKvWccQjlG1SQx5dk345qHrBXddKx2JYo,4186
+TB2J/io_exchange/io_txt.py,sha256=r7Uh1HGfAfkHppMR6pLsx2kMmMJDOR48hk75_ffBd7o,13136
 TB2J/io_exchange/io_uppasd.py,sha256=qhGhHbp3cZmwuBo1SrEBQulrPjEWPD3yRgVs-juQ7Fs,3268
-TB2J/io_exchange/io_vampire.py,sha256=nheRskvFdjEnWT8BRZ5ckZjC0dosno_PXB9erKPq_T4,5862
+TB2J/io_exchange/io_vampire.py,sha256=1dvCxzAUcs5xfeLiFfrhyiWC75-RmrLOdOjF3f9iQSo,5883
 TB2J/magnon/__init__.py,sha256=Q69duroGIIotgW_71ZdHYarSiJLGAu9NPYgEacUk6eI,117
 TB2J/magnon/io_exchange2.py,sha256=EcC3x6H13qq61WBsr__xKzHDtSvy_dMz1tEdUaqSG2I,23265
-TB2J/magnon/magnon3.py,sha256=ecMCCAZiBCPyEPdNI60h5rV0nRyjFeB40FIX8-o87kE,31801
+TB2J/magnon/magnon3.py,sha256=nl_jR7uO1TlyUDRUoEn7H2y8tuGJ_P2Lj7MceGoqM0w,32371
 TB2J/magnon/magnon_band.py,sha256=ZLHK1qf2Clu9jlcvBwBCBEi1MrPfy2BWrow8JJ2v5pk,6103
 TB2J/magnon/magnon_dos.py,sha256=uztzsxCmFZpDHl-JziaUb_NNwBeZw9-L2ozd3XNTvxI,8506
 TB2J/magnon/magnon_io.py,sha256=H4bmzCcnh1D3Sb6UBIIKWa6jIrA20dg9lX4wfLXHEjo,1241
@@ -85,13 +78,15 @@ TB2J/mathutils/fermi.py,sha256=72tZ5CptGmYaBUD0xLWltuH7LBXcrMUwODyW6-WqlzI,638
 TB2J/mathutils/fibonacci_sphere.py,sha256=1rqf5n3a9aDjSydA4qGkR1eIeLJKuoblA73cchWJzNg,2342
 TB2J/mathutils/kR_convert.py,sha256=p_9XWJVNanTzTK2rI6KRjTkbSq42la6N448-zJOsMwY,2671
 TB2J/mathutils/lowdin.py,sha256=RYbm9OcnFnjcZFdC5YcNUsI9cOJmoDLsWSSCaP0GqKQ,499
-TB2J/mathutils/rotate_spin.py,sha256=sPTnwJThfohCHIY7EuzBV2K3mIXcJI5y1QBytGmEKR4,8229
+TB2J/mathutils/rotate_spin.py,sha256=lmb5vYhVe52q5vBPmz9RKvfoKQpBw0nnRTnHTBb7sHw,8238
 TB2J/scripts/TB2J_downfold.py,sha256=f1CPuka_uOcvwBKDWAaseRZ04Bqyx_Cor5PvU6LyIsU,2600
+TB2J/scripts/TB2J_edit.py,sha256=EIQR2Hyqe3bkgaIHKRKpEvkB8tMO_hADfPqKZhnU-Aw,12870
 TB2J/scripts/TB2J_eigen.py,sha256=LVFoe1xntAnaljRBbVywBSxq0bSQs0tR7ECf8Zf0CS0,1174
 TB2J/scripts/TB2J_magnon.py,sha256=fz9nOv5dMy1e0Dac3eGtiNODvdfTnfLlM7jvYbShiN0,3116
 TB2J/scripts/TB2J_magnon2.py,sha256=mfDrkjK9DpXeKl6jLdACzAD6ArAWBCmC-TPb-vCWpJs,1934
 TB2J/scripts/TB2J_magnon_dos.py,sha256=xQlI6u31Oyv9Yua73_Qa5cF1cnvg1PNrTy1VXs4dcBk,107
 TB2J/scripts/TB2J_merge.py,sha256=Qzo1cZPxCy_-RwcxB6R1u4vnTt8BA_cIoVIEs8nHwS4,2109
+TB2J/scripts/TB2J_plot_exchange.py,sha256=WSQG6vNbCeJfDawHudiBxtBDFnpTkQdphSv6Uaq5udc,1251
 TB2J/scripts/TB2J_plot_magnon_bands.py,sha256=x5WkiI-pkVHqCTa2e5qNWaeAvyXmchqY8BMeTW13dFs,636
 TB2J/scripts/TB2J_rotate.py,sha256=WneOj6NBMDzVlpLXnq9tZqnJqTATfv_zmgl4EltD118,859
 TB2J/scripts/TB2J_rotateDM.py,sha256=lH71mkg0BKDGVLoK7VvmIPkf2mCjyc0V5l9rZZgyfP4,570
@@ -102,19 +97,21 @@ TB2J/scripts/wann2J.py,sha256=djLBG3t4oEimokMG6TIFHyjp8u8DtnizN9coQXOTN7U,3254
 TB2J/spinham/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 TB2J/spinham/base_parser.py,sha256=oQRHvFE_BlUtTaTZykKgvicu40oXcbICB-D1aAt-qlA,2196
 TB2J/spinham/constants.py,sha256=y4-hRyl5EAR42k24Oa5XhAsUQtKVn1MAgyqNf-p3PrM,762
-TB2J/spinham/hamiltonian.py,sha256=x7ACIdZhblGMStsENk8lpqYGnT2YeIZEN2ikjC1H5Uk,16597
-TB2J/spinham/hamiltonian_terms.py,sha256=7e84tfEjvAfZltUkrSWi1sUEiW_itLKy83lxi5iBpcQ,9714
+TB2J/spinham/hamiltonian.py,sha256=pYP8Fbn5k3oIq-amLmWh8FoFNozKrgrbOvKuaIh-bqI,22093
+TB2J/spinham/hamiltonian_terms.py,sha256=OVFiedRDzqWSBjUbvKWipNzqiFeyP1mKM7qnN8RPPc8,10975
 TB2J/spinham/plot.py,sha256=tLLNqFAATVrP1kmSVLPKzn686i-CUyqu4qgOcs-okHI,6599
 TB2J/spinham/qsolver.py,sha256=Sr9I3aGfVNYn5wzwPx1QonHe6ZZUXBAujWRa7nTA5u4,4986
 TB2J/spinham/spin_api.py,sha256=oN3AKg1WQl0YzR4f5ealcJOaVoAy8d7HodIwrbXvQeY,2219
-TB2J/spinham/spin_xml.py,sha256=mneeZzkCE5andvIlur_6VK3XzWvoL-PVqSoWKXtDYTM,11033
+TB2J/spinham/spin_xml.py,sha256=BEIuXWddOq-EDwlJypiHNUIznBoFujqENisIr2FOZJE,12346
 TB2J/spinham/supercell.py,sha256=y17uUC6r3gQb278FhxIW4CABihfLTvKFj6flyXrCPR8,12217
+TB2J/tests/test_cli_remove_sublattice.py,sha256=R6IKrgDi1iilPg4horb9thSgTSayraTA5Q6rhr4g-RA,963
+TB2J/tests/test_cli_toggle_exchange.py,sha256=oL9jaYS-Qb2lUgGc5jqk9FmPGofAejiyZ0Cp1aPet0o,1592
 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=XPh0PNgX_fKYQodDOzZj6DKsvgULMQERU8Kjh4U2xZY,4563
-tb2j-0.9.12.18.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-tb2j-0.9.12.18.dist-info/METADATA,sha256=bE2PpSMQlLu4gllLxfmcIbHPgT_X8NbQ5b5L6kjObbs,4145
-tb2j-0.9.12.18.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-tb2j-0.9.12.18.dist-info/entry_points.txt,sha256=QlTwH3gCmaKBW48nr0FwGTd5LTThTiemw_36u7e1B7o,770
-tb2j-0.9.12.18.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
-tb2j-0.9.12.18.dist-info/RECORD,,
+tb2j-0.9.12.22.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
+tb2j-0.9.12.22.dist-info/METADATA,sha256=k1qU2PLNeSznexKr0d1BzgKs2u5pOZ4XjJkuBZoDIew,4338
+tb2j-0.9.12.22.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+tb2j-0.9.12.22.dist-info/entry_points.txt,sha256=MkVo66rLBjbfup6lQoEepI525v50Wojkz2_rMQpUL7Y,874
+tb2j-0.9.12.22.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
+tb2j-0.9.12.22.dist-info/RECORD,,

{tb2j-0.9.12.18.dist-info → tb2j-0.9.12.22.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{tb2j-0.9.12.18.dist-info → tb2j-0.9.12.22.dist-info}/entry_points.txt

@@ -1,9 +1,11 @@
 [console_scripts]
 TB2J_downfold.py = TB2J.scripts.TB2J_downfold:main
+TB2J_edit.py = TB2J.scripts.TB2J_edit:main
 TB2J_eigen.py = TB2J.scripts.TB2J_eigen:write_eigen_info
 TB2J_magnon.py = TB2J.scripts.TB2J_magnon:plot_magnon
 TB2J_magnon_dos.py = TB2J.plot:command_line_plot_magnon_dos
 TB2J_merge.py = TB2J.scripts.TB2J_merge:main
+TB2J_plot_exchange.py = TB2J.scripts.TB2J_plot_exchange:main
 TB2J_plot_magnon_bands.py = TB2J.magnon.magnon3:plot_magnon_bands_cli
 TB2J_plot_magnon_dos.py = TB2J.magnon.plot_magnon_dos_cli:main
 TB2J_rotate.py = TB2J.scripts.TB2J_rotate:main

TB2J/.gitignore

@@ -1,5 +0,0 @@
-*.o
-*.x
-*.mod
-exchanges.sublime-project
-exchanges.sublime-workspace