TB2J 0.9.9.3__py3-none-any.whl → 0.9.9.6__py3-none-any.whl

TB2J/magnon/structure.py

@@ -0,0 +1,348 @@
+from warnings import warn
+
+import numpy as np
+
+valid_symbols = [
+    # 0
+    "Ae",
+    # 1
+    "H",
+    "He",
+    # 2
+    "Li",
+    "Be",
+    "B",
+    "C",
+    "N",
+    "O",
+    "F",
+    "Ne",
+    # 3
+    "Na",
+    "Mg",
+    "Al",
+    "Si",
+    "P",
+    "S",
+    "Cl",
+    "Ar",
+    # 4
+    "K",
+    "Ca",
+    "Sc",
+    "Ti",
+    "V",
+    "Cr",
+    "Mn",
+    "Fe",
+    "Co",
+    "Ni",
+    "Cu",
+    "Zn",
+    "Ga",
+    "Ge",
+    "As",
+    "Se",
+    "Br",
+    "Kr",
+    # 5
+    "Rb",
+    "Sr",
+    "Y",
+    "Zr",
+    "Nb",
+    "Mo",
+    "Tc",
+    "Ru",
+    "Rh",
+    "Pd",
+    "Ag",
+    "Cd",
+    "In",
+    "Sn",
+    "Sb",
+    "Te",
+    "I",
+    "Xe",
+    # 6
+    "Cs",
+    "Ba",
+    "La",
+    "Ce",
+    "Pr",
+    "Nd",
+    "Pm",
+    "Sm",
+    "Eu",
+    "Gd",
+    "Tb",
+    "Dy",
+    "Ho",
+    "Er",
+    "Tm",
+    "Yb",
+    "Lu",
+    "Hf",
+    "Ta",
+    "W",
+    "Re",
+    "Os",
+    "Ir",
+    "Pt",
+    "Au",
+    "Hg",
+    "Tl",
+    "Pb",
+    "Bi",
+    "Po",
+    "At",
+    "Rn",
+    # 7
+    "Fr",
+    "Ra",
+    "Ac",
+    "Th",
+    "Pa",
+    "U",
+    "Np",
+    "Pu",
+    "Am",
+    "Cm",
+    "Bk",
+    "Cf",
+    "Es",
+    "Fm",
+    "Md",
+    "No",
+    "Lr",
+    "Rf",
+    "Db",
+    "Sg",
+    "Bh",
+    "Hs",
+    "Mt",
+    "Ds",
+    "Rg",
+    "Cn",
+    "Nh",
+    "Fl",
+    "Mc",
+    "Lv",
+    "Ts",
+    "Og",
+]
+
+
+def get_attribute_array(array, attribute, dtype=float):
+    try:
+        the_array = np.array(array, dtype=dtype)
+    except (IndexError, ValueError, TypeError) as err:
+        typename = dtype.__name__
+        raise type(err)(
+            f"'{attribute}' must be an arraylike object of '{typename}' elements."
+        )
+
+    return the_array
+
+
+def validate_symbols(value):
+    try:
+        values_list = value.split()
+    except AttributeError:
+        try:
+            values_list = list(value)
+        except (ValueError, TypeError):
+            raise TypeError("'elements' must be an iterable of 'str' or 'int' entries.")
+
+    if all(isinstance(s, str) for s in values_list):
+        symbols = values_list
+        for symbol in symbols:
+            if symbol not in valid_symbols:
+                raise ValueError(f"Unrecognized element '{symbol}'.")
+    elif all(isinstance(i, (int, np.integer)) for i in values_list):
+        if any(i < 0 for i in values_list):
+            raise ValueError("Atomic numbers must be positive.")
+        try:
+            symbols = [valid_symbols[i] for i in values_list]
+        except IndexError:
+            raise ValueError("Atomic number exceeds 118.")
+    else:
+        raise ValueError("'elements' must be an iterable of 'str' or 'int' entries.")
+
+    return symbols
+
+
+class BaseMagneticStructure:
+    def __init__(
+        self,
+        atoms=None,
+        cell=None,
+        elements=None,
+        positions=None,
+        magmoms=None,
+        pbc=None,
+        collinear=True,
+    ):
+        if atoms is not None:
+            if any(arg is not None for arg in [cell, elements, positions]):
+                warn(
+                    "WARNING: 'atoms' overrides the 'cell', 'elements', and 'positions' arguments."
+                )
+            cell = atoms.cell.array
+            elements = atoms.numbers
+            positions = atoms.get_scaled_positions()
+            pbc = atoms.pbc if pbc is None else pbc
+        else:
+            if cell is None:
+                cell = np.zeros((3, 3))
+            if elements is None:
+                elements = ()
+            if positions is None:
+                positions = np.zeros((len(elements), 3))
+            if pbc is None:
+                pbc = (True, True, True)
+        if magmoms is None:
+            magmoms_shape = positions.shape[0] if collinear else positions.shape
+            magmoms = np.zeros(magmoms_shape)
+
+        self.cell = cell
+        self.elements = elements
+        self.positions = positions
+        self.collinear = collinear
+        self.magmoms = magmoms
+        self.pbc = pbc
+
+        self._Q = None
+        self._n = np.array([0, 0, 1])
+
+    @property
+    def cell(self):
+        return self._cell
+
+    @property
+    def reciprocal_cell(self):
+        return 2 * np.pi * np.linalg.inv(self._cell)
+
+    @cell.setter
+    def cell(self, value):
+        cell_array = get_attribute_array(value, "cell")
+        if cell_array.shape != (3, 3):
+            raise ValueError("'cell' must have a (3, 3) shape.")
+
+        self._cell = cell_array
+
+    @property
+    def elements(self):
+        return self._symbols
+
+    @elements.setter
+    def elements(self, value):
+        symbols = validate_symbols(value)
+        self._symbols = symbols
+
+    @property
+    def numbers(self):
+        return [valid_symbols.index(symbol) for symbol in self._symbols]
+
+    @property
+    def positions(self):
+        return self._positions
+
+    @property
+    def cartesian_positions(self):
+        return self._positions @ self._cell
+
+    @positions.setter
+    def positions(self, value):
+        natoms = len(self.elements)
+        posarray = get_attribute_array(value, "positions")
+        if posarray.shape != (natoms, 3):
+            raise ValueError(
+                "'positions' must have a (natoms, 3) shape, where natoms is the length of 'elements'. Make sure to set 'elements' first."
+            )
+
+        self._positions = posarray
+
+    @property
+    def magmoms(self):
+        return self._magmoms
+
+    @magmoms.setter
+    def magmoms(self, value):
+        magarray = get_attribute_array(value, "magmoms")
+        if self.collinear and magarray.shape != (len(self._positions),):
+            raise ValueError(
+                "'magmoms' must be a 1dim array with the same length as 'positions'. Make sure to set 'positions' first."
+            )
+        elif not self.collinear and magarray.shape != self._positions.shape:
+            raise ValueError(
+                "'magmoms' must have the same shape as 'positions'. Make sure to set 'positions' first."
+            )
+
+        self._magmoms = magarray
+
+    @property
+    def pbc(self):
+        return self._pbc
+
+    @pbc.setter
+    def pbc(self, value):
+        try:
+            periodic_boundary_conditions = tuple(bool(b) for b in value)
+        except (ValueError, TypeError):
+            raise TypeError("'pbc' must be an iterable of 'bool' entries.")
+
+        if len(periodic_boundary_conditions) != 3:
+            raise ValueError("'pbc' must be of length 3.")
+
+        self._pbc = periodic_boundary_conditions
+
+    @property
+    def propagation_vector(self):
+        return self._Q
+
+    @propagation_vector.setter
+    def propagation_vector(self, value):
+        Q = get_attribute_array(value, "propagation_vector")
+        if Q.shape != (3,):
+            raise ValueError(
+                "The 'propagation_vector' must be a vector with 3 numbers."
+            )
+
+        self._Q = Q
+
+    @property
+    def normal_vector(self):
+        return self._n
+
+    @normal_vector.setter
+    def normal_vector(self, value):
+        n = get_attribute_array(value, "normal_vector")
+        if n.shape != (3,):
+            raise ValueError("The 'normal_vector' must be a vector with 3 numbers.")
+
+        self._n = n
+
+    def to_ase(self):
+        from ase.atoms import Atoms
+
+        atoms = Atoms(
+            cell=self.cell,
+            positions=self.cartesian_positions,
+            numbers=[valid_symbols.index(symbol) for symbol in self.elements],
+            pbc=self.pbc,
+        )
+
+        return atoms
+
+    @classmethod
+    def from_structure_file(
+        cls, filename, magmoms=None, collinear=True, pbc=(True, True, True)
+    ):
+        from ase.io import read
+
+        atoms = read(filename)
+        atoms.pbc = pbc
+        obj = cls(atoms=atoms, magmoms=magmoms, collinear=collinear)
+
+        return obj

TB2J/mathutils/__init__.py

@@ -1 +1,3 @@
 from .lowdin import Lowdin
+
+__all__ = ["Lowdin"]

TB2J/mathutils/fibonacci_sphere.py

@@ -50,7 +50,7 @@ def test_fibonacci_sphere():
     import matplotlib.pyplot as plt
 
     # Generate points on the sphere
-    samples = 20000
+    samples = 200
     theta, phi = fibonacci_sphere(samples)
     # theta, phi = fibonacci_semisphere(samples)
 

TB2J/mathutils/rotate_spin.py

@@ -11,7 +11,6 @@ def rotate_Matrix_from_z_to_axis(M, axis, normalize=True):
     """
     MI, Mx, My, Mz = pauli_block_all(M)
     axis = axis / np.linalg.norm(axis)
-    # M_new = s0* MI +  Mz * (axis[0] * s1 + axis[1] * s2 + axis[2] * s3) *2
     M_new = gather_pauli_blocks(MI, Mz * axis[0], Mz * axis[1], Mz * axis[2])
     return M_new
 
@@ -96,7 +95,6 @@ def rotate_spinor_matrix_einsum(M, theta, phi):
     n1 = np.product(shape[:-1]) // 2
     n2 = M.shape[-1] // 2
     Mnew = np.reshape(M, (n1, 2, n2, 2))  # .swapaxes(1, 2)
-    # print("Mnew:", Mnew)
     U = rotation_matrix(theta, phi)
     UT = U.conj().T
     Mnew = np.einsum(
@@ -132,7 +130,6 @@ def rotate_spinor_matrix_reshape(M, theta, phi):
     """
     N = M.shape[0] // 2
     Mnew = np.reshape(M, (N, 2, N, 2)).swapaxes(1, 2)
-    # print("Mnew:", Mnew)
     U = rotation_matrix(theta, phi)
     UT = U.conj().T
     Mnew = UT @ Mnew @ U

TB2J/symmetrize_J.py

@@ -102,7 +102,7 @@ def symmetrize_J_cli():
     from argparse import ArgumentParser
 
     parser = ArgumentParser(
-        description="Symmetrize exchange parameters. Currently, it take the crystal symmetry into account and  not the magnetic moment into account."
+        description="Symmetrize exchange parameters. Currently, it take the crystal symmetry into account and  not the magnetic moment."
     )
     parser.add_argument(
         "-i",

tb2j-0.9.9.6.data/scripts/TB2J_magnon2.py

@@ -0,0 +1,78 @@
+#!python
+from TB2J.magnon import plot_tb2j_magnon_bands
+
+
+def plot_tb2j_magnon_bands_cli():
+    """Command line interface for plotting magnon band structures from TB2J data."""
+    import argparse
+
+    parser = argparse.ArgumentParser(
+        description="Plot magnon band structure from TB2J data",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+
+    parser.add_argument(
+        "-f", "--file", default="TB2J.pickle", help="Path to TB2J pickle file"
+    )
+
+    parser.add_argument(
+        "-p",
+        "--path",
+        help="High-symmetry k-point path (e.g., 'GXMG' for square lattice)",
+    )
+
+    parser.add_argument(
+        "-n",
+        "--npoints",
+        type=int,
+        default=300,
+        help="Number of k-points for band structure calculation",
+    )
+
+    parser.add_argument(
+        "-a",
+        "--anisotropic",
+        action="store_true",
+        help="Include anisotropic interactions",
+    )
+
+    parser.add_argument(
+        "-q",
+        "--quadratic",
+        action="store_true",
+        help="Include biquadratic interactions",
+    )
+
+    parser.add_argument("-o", "--output", help="Output filename for the plot")
+
+    parser.add_argument(
+        "--no-pbc",
+        nargs="+",
+        type=int,
+        choices=[0, 1, 2],
+        help="Disable periodic boundary conditions in specified directions (0=x, 1=y, 2=z)",
+    )
+
+    args = parser.parse_args()
+
+    # Set up periodic boundary conditions
+    pbc = [True, True, True]
+    if args.no_pbc:
+        for direction in args.no_pbc:
+            pbc[direction] = False
+    pbc = tuple(pbc)
+
+    # Plot the bands
+    plot_tb2j_magnon_bands(
+        pickle_file=args.file,
+        path=args.path,
+        npoints=args.npoints,
+        anisotropic=args.anisotropic,
+        quadratic=args.quadratic,
+        pbc=pbc,
+        filename=args.output,
+    )
+
+
+if __name__ == "__main__":
+    plot_tb2j_magnon_bands_cli()

{tb2j-0.9.9.3.data → tb2j-0.9.9.6.data}/scripts/abacus2J.py

@@ -50,7 +50,7 @@ def run_abacus2J():
         description=args.description,
         output_path=args.output_path,
         use_cache=args.use_cache,
-        nproc=args.nproc,
+        nproc=args.np,
         exclude_orbs=args.exclude_orbs,
         orb_decomposition=args.orb_decomposition,
         index_magnetic_atoms=index_magnetic_atoms,

{tb2j-0.9.9.3.dist-info → tb2j-0.9.9.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9.3
+Version: 0.9.9.6
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com
@@ -25,7 +25,6 @@ Requires-Dist: HamiltonIO>=0.2.1
 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-0.9.9.3.dist-info → tb2j-0.9.9.6.dist-info}/RECORD

@@ -1,10 +1,10 @@
-TB2J/Jdownfolder.py,sha256=xs0gmcKwOA3ejXqk3JPPgnYVu8CvkK8cteuvHuu1oSk,9603
+TB2J/Jdownfolder.py,sha256=n5BeQCYP4mD9JsAPeE1F3ZKKR3SUxADfDbaG_rzi77k,9658
 TB2J/Jtensor.py,sha256=t6OsqrSlYW6Im4H7ykVAW8Al_pFXN4C5yj2UEsV6r7g,3181
 TB2J/MAE.py,sha256=fM8U-Dgp9HcQOEeC_kyZV1oVrygBvcux9BraUXVouvY,10994
-TB2J/MAEGreen.py,sha256=pCX12GDNaOz8XgMlui8NjAERM43Ux3HyOKfiD80czXI,15306
+TB2J/MAEGreen.py,sha256=Iq4hlZrKEOycPvpV66_t13WIcJ1FJgBS79NleXYpFzw,15528
 TB2J/Oiju.py,sha256=cNGv8N5uH_swGq7cnAt2OyiDfqtjLlLrwseGu0E4iaM,3383
 TB2J/Oiju_epc.py,sha256=oytM3NYW7nWmklrGgNlqwIpI_JYv_hb7ZnR4o9nYNog,6809
-TB2J/__init__.py,sha256=bhvNrEcDHXt9O-K1rdRAtMHwmvdSm_-Y28VwdCZFsik,24
+TB2J/__init__.py,sha256=hcEWkag_UvLm1ZSbjsgcTWkGVlR3Bwmzg1QYAwsvf-g,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=VW9nGVio6M_Ub9-36L_LExhjgdD1E_joYpI8AxmM360,8029
 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
@@ -31,7 +31,7 @@ TB2J/plot.py,sha256=AnFIFWE2vlmj7Z6f_7-dX_O1stJN-qbuiurPj43dUCM,4104
 TB2J/rotate_atoms.py,sha256=Dwptn-wdDW4zYzjYb95yxTzuZOe9WPuLjh3d3-YcSs0,3277
 TB2J/rotate_siestaDM.py,sha256=I4ytO8uFP8_GFyBs9-zMdiMSZS3Y3lj2dSLfNBNI2ZY,1078
 TB2J/sisl_wrapper.py,sha256=A5x1-tt8efUSPeGY5wM5m6-pJYQFXTCzQHVqD6RBa2g,14792
-TB2J/symmetrize_J.py,sha256=IypvLL0JxExq-cmqc4o0nLL8psE7OC9ijj9YMcsqJeA,4487
+TB2J/symmetrize_J.py,sha256=pv65f7TXW371kfnByIkg885XFEGg4UmWlzqY7cOUNAk,4474
 TB2J/tensor_rotate.py,sha256=4-DfT_Mg5e40fbd74M5W0D5DqmUq-kVOOLDkkkI834A,8083
 TB2J/thetaphi.py,sha256=Z7N3EOSM7rjHd7b9HxMYLPQO__uR0VwEiV9b471Yudc,399
 TB2J/utest.py,sha256=z_ahi7tpHQF9WlHNQihcQ7qzfezRJQXQt28eB1X_z64,3897
@@ -43,30 +43,37 @@ 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=olvo2xdBOSNk3zn67nuKrxbW--EKPoWwEzKRBwJbrVY,7366
+TB2J/interfaces/siesta_interface.py,sha256=nkb8CTjHtv3DgMok4njyiaE-vDGDJFCjLHat71R_Z48,7561
 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
 TB2J/interfaces/abacus/abacus_wrapper.py,sha256=8ZA8oA_YWvRF0Uj_SX1q1vl8ZyEVhHC_tu37JhV02gg,12041
-TB2J/interfaces/abacus/gen_exchange_abacus.py,sha256=N8H-iwyOmOJIo2ZC_owmyrXLhcr_QmZzTI4yxhxYZns,3121
+TB2J/interfaces/abacus/gen_exchange_abacus.py,sha256=v-AUHGkJWeMNf4D5A4wOpCjM6DygQsFB6SWu-BGdTxM,3262
 TB2J/interfaces/abacus/orbital_api.py,sha256=SpSm5fhyqLYbprNd6Lxx0oR1Fw5TUJHfNc-0x_4FW1U,1561
 TB2J/interfaces/abacus/stru_api.py,sha256=Ac03ikHRsZRXqTul4IUge7D2iG_xLh4_oyYfeP9tzGE,67881
 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=KfGHum7B8E4G_KKfillqw0lErtoyKEuFUUttHLs-mg4,32
-TB2J/io_exchange/io_exchange.py,sha256=6fefcfYAyRojkCJA5bFwAa2Hjwx6epysfyX8Snj9DWc,20102
+TB2J/io_exchange/__init__.py,sha256=LqEnG67qDVKt4hCUywDEQvUIJ7jsQjmtueOW_J16NOE,54
+TB2J/io_exchange/io_exchange.py,sha256=YEFJT8nPy-aGUgGRhIgrC73pf6IQfL7bgGovUkGKv60,21273
 TB2J/io_exchange/io_multibinit.py,sha256=8PDmWxzGuv-GwJosj2ZTmiyNY_duFVWJ4ekCuSqGdd8,6739
 TB2J/io_exchange/io_tomsasd.py,sha256=NqkAC1Fl-CUnFA21eBzSy_S5F_oeQFJysw4UukQbN8o,4173
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