TB2J 0.9.9rc16__py3-none-any.whl → 0.9.9rc18__py3-none-any.whl

TB2J/magnon/plot.py

@@ -0,0 +1,58 @@
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+class BandsPlot:
+    _UNITS = "meV"
+    _NSYSTEMS = 1
+
+    def __init__(self, bands, kpath, **kwargs):
+        self.bands = bands
+        self.kpath = kpath
+        self.bands *= 1000
+
+        plot_options = kwargs
+        self.linewidth = plot_options.pop("linewidth", 1.5)
+        self.color = plot_options.pop("color", "blue")
+        self.fontsize = plot_options.pop("fontsize", 12)
+        self.ticksize = plot_options.pop("ticksize", 10)
+        self.plot_options = plot_options
+
+    def plot(self, filename=None):
+        fig, axs = plt.subplots(1, self._NSYSTEMS, constrained_layout=True)
+
+        kdata = np.arange(self.bands.shape[0])
+        for band in self.bands.T:
+            axs.plot(
+                kdata,
+                band,
+                linewidth=self.linewidth,
+                color=self.color,
+                **self.plot_options,
+            )
+
+        bmin, bmax = self.bands.min(), self.bands.max()
+        ymin, ymax = (
+            bmin - 0.05 * np.abs(bmin - bmax),
+            bmax + 0.05 * np.abs(bmax - bmin),
+        )
+
+        axs.set_ylim([ymin, ymax])
+        axs.set_xlim([0, kdata[-1]])
+
+        kpoint_labels = list(zip(*self.kpath))
+        axs.set_xticks(*kpoint_labels, fontsize=self.ticksize)
+        axs.vlines(
+            x=kpoint_labels[0],
+            ymin=ymin,
+            ymax=ymax,
+            color="black",
+            linewidth=self.linewidth / 5,
+        )
+
+        axs.set_ylabel(f"Energy ({self._UNITS})", fontsize=self.fontsize)
+
+        if filename is None:
+            plt.show()
+        else:
+            fig.save(filename, dpi=300, bbox_inches="tight")

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

TB2J/mathutils/magnons.py

@@ -0,0 +1,45 @@
+import numpy as np
+
+__all__ = ["generate_grid", "get_rotation_arrays", "round_to_precision", "uz", "I"]
+
+I = np.eye(3)
+uz = np.array([[0.0, 0.0, 1.0]])
+
+
+def generate_grid(kmesh, sort=True):
+    half_grid = [int(n / 2) for n in kmesh]
+    grid = np.stack(
+        np.meshgrid(*[np.arange(-n, n + 1) for n in half_grid]), axis=-1
+    ).reshape(-1, 3)
+
+    if sort:
+        idx = np.linalg.norm(grid, axis=-1).argsort()
+        grid = grid[idx]
+
+    return grid
+
+
+def get_rotation_arrays(magmoms, u=uz):
+    dim = magmoms.shape[0]
+    v = magmoms
+    n = np.cross(u, v)
+    n /= np.linalg.norm(n, axis=-1).reshape(dim, 1)
+    z = np.repeat(u, dim, axis=0)
+    A = np.stack([z, np.cross(n, z), n], axis=1)
+    B = np.stack([v, np.cross(n, v), n], axis=1)
+    R = np.einsum("nki,nkj->nij", A, B)
+
+    Rnan = np.isnan(R)
+    if Rnan.any():
+        nanidx = np.where(Rnan)[0]
+        R[nanidx] = I
+        R[nanidx, 2] = v[nanidx]
+
+    U = R[:, 0] + 1j * R[:, 1]
+    V = R[:, 2]
+
+    return U, V
+
+
+def round_to_precision(array, precision):
+    return precision * np.round(array / precision)

tb2j-0.9.9rc18.data/scripts/TB2J_magnon2.py

@@ -0,0 +1,77 @@
+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-0.9.9rc16.data → tb2j-0.9.9rc18.data}/scripts/abacus2J.py

@@ -29,8 +29,8 @@ def run_abacus2J():
     args = parser.parse_args()
 
     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 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")

{tb2j-0.9.9rc16.dist-info → tb2j-0.9.9rc18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc16
+Version: 0.9.9rc18
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com

{tb2j-0.9.9rc16.dist-info → tb2j-0.9.9rc18.dist-info}/RECORD

@@ -1,7 +1,7 @@
 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=pCX12GDNaOz8XgMlui8NjAERM43Ux3HyOKfiD80czXI,15306
+TB2J/MAEGreen.py,sha256=IhclMJU6TOp97fYogXWq-3dyyAW8iDJqu1FGRDdi6hM,15551
 TB2J/Oiju.py,sha256=cNGv8N5uH_swGq7cnAt2OyiDfqtjLlLrwseGu0E4iaM,3383
 TB2J/Oiju_epc.py,sha256=oytM3NYW7nWmklrGgNlqwIpI_JYv_hb7ZnR4o9nYNog,6809
 TB2J/__init__.py,sha256=hcEWkag_UvLm1ZSbjsgcTWkGVlR3Bwmzg1QYAwsvf-g,24
@@ -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=olvo2xdBOSNk3zn67nuKrxbW--EKPoWwEzKRBwJbrVY,7366
+TB2J/interfaces/siesta_interface.py,sha256=DACmRG89IKt_MHfmZDTORCjaUhQ6LRloLzoE1x-5IQM,7625
 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
@@ -54,18 +54,23 @@ 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=KfGHum7B8E4G_KKfillqw0lErtoyKEuFUUttHLs-mg4,32
+TB2J/io_exchange/__init__.py,sha256=LqEnG67qDVKt4hCUywDEQvUIJ7jsQjmtueOW_J16NOE,54
 TB2J/io_exchange/io_exchange.py,sha256=6fefcfYAyRojkCJA5bFwAa2Hjwx6epysfyX8Snj9DWc,20102
 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/mathutils/__init__.py,sha256=tQLBfHkZqdVfVxPOahy42qMUkFYnFFFhM-uc4QsYFxI,27
+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/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
@@ -80,19 +85,20 @@ 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
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{tb2j-0.9.9rc16.dist-info → tb2j-0.9.9rc18.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any