TB2J 0.9.9rc19__py3-none-any.whl → 0.9.9rc20__py3-none-any.whl

TB2J/exchange_params.py

@@ -177,8 +177,7 @@ def add_exchange_args_to_parser(parser: argparse.ArgumentParser):
     )
 
     parser.add_argument(
-        "--np",
-        "--nproc",
+        "-np",
         help="number of cpu cores to use in parallel, default: 1",
         default=1,
         type=int,

TB2J/io_exchange/io_exchange.py

@@ -335,7 +335,7 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
             )
         return Jtensor
 
-    def get_full_Jtensor_for_one_R(self, R, iso_only=False):
+    def get_full_Jtensor_for_one_R_i3j3(self, R, iso_only=False):
         """
         Return the full exchange tensor of all i and j for cell R.
         param R (tuple of integers): cell index R
@@ -351,18 +351,46 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
                 )
         return Jmat
 
-    def get_full_Jtensor_for_Rlist(self, asr=False, iso_only=True):
-        n3 = self.nspin * 3
+    def get_full_Jtensor_for_one_R_ij33(self, R, iso_only=False):
+        """
+        Return the full exchange tensor of all i and j for cell R.
+        param R (tuple of integers): cell index R
+        returns:
+            Jmat: (nspin,nspin,3,3) matrix.
+        """
+        n = self.nspin
+        Jmat = np.zeros((n, n, 3, 3), dtype=float)
+        for i in range(self.nspin):
+            for j in range(self.nspin):
+                Jmat[i, j, :, :] = self.get_J_tensor(i, j, R, iso_only=iso_only)
+        return Jmat
+
+    def get_full_Jtensor_for_Rlist(self, asr=False, iso_only=True, order="i3j3"):
+        n = self.nspin
+        n3 = n * 3
         nR = len(self.Rlist)
-        Jmat = np.zeros((nR, n3, n3), dtype=float)
-        for iR, R in enumerate(self.Rlist):
-            Jmat[iR] = self.get_full_Jtensor_for_one_R(R, iso_only=iso_only)
-        if asr:
-            iR0 = np.argmin(np.linalg.norm(self.Rlist, axis=1))
-            assert np.linalg.norm(self.Rlist[iR0]) == 0
-            for i in range(n3):
-                sum_JRi = np.sum(np.sum(Jmat, axis=0)[i])
-                Jmat[iR0][i, i] -= sum_JRi
+        if order == "i3j3":
+            Jmat = np.zeros((nR, n3, n3), dtype=float)
+            for iR, R in enumerate(self.Rlist):
+                Jmat[iR] = self.get_full_Jtensor_for_one_R_i3j3(R, iso_only=iso_only)
+            if asr:
+                iR0 = np.argmin(np.linalg.norm(self.Rlist, axis=1))
+                assert np.linalg.norm(self.Rlist[iR0]) == 0
+                for i in range(n3):
+                    sum_JRi = np.sum(np.sum(Jmat, axis=0)[i])
+                    Jmat[iR0][i, i] -= sum_JRi
+
+        elif order == "ij33":
+            Jmat = np.zeros((nR, n, n, 3, 3), dtype=float)
+            Jmat[iR] = self.get_full_Jtensor_for_one_R_ij33(R, iso_only=iso_only)
+            if asr:
+                iR0 = np.argmin(np.linalg.norm(self.Rlist, axis=1))
+                assert np.linalg.norm(self.Rlist[iR0]) == 0
+                for i in range(n):
+                    sum_JRi = np.sum(np.sum(Jmat, axis=0)[i])
+                    Jmat[iR0][i, i] -= sum_JRi
+        else:
+            raise ValueError("order must be either 'i3j3' or 'ij33'.")
         return Jmat
 
     def write_pickle(self, path="TB2J_results", fname="TB2J.pickle"):

TB2J/magnon/io_exchange2.py

@@ -11,7 +11,7 @@ It includes classes and functions for:
 import numpy as np
 from scipy.spatial.transform import Rotation
 
-from ..mathutils import generate_grid, get_rotation_arrays, round_to_precision, uz
+from .magnon_math import generate_grid, get_rotation_arrays, round_to_precision, uz
 from .plot import BandsPlot
 from .structure import BaseMagneticStructure, get_attribute_array
 
@@ -112,8 +112,12 @@ def Hermitize(array):
     result = np.zeros((n, n) + array.shape[1:], dtype=complex)
     u_indices = np.triu_indices(n)
 
-    result[*u_indices] = array
-    result.swapaxes(0, 1)[*u_indices] = array.swapaxes(-1, -2).conj()
+    # for python>=3.11
+    # result[*u_indices] = array
+    # result.swapaxes(0, 1)[*u_indices] = array.swapaxes(-1, -2).conj()
+    # for python<3.11
+    result[u_indices[0], u_indices[1]] = array
+    result.swapaxes(0, 1)[u_indices[0], u_indices[1]] = array.swapaxes(-1, -2).conj()
 
     return result
 
@@ -395,11 +399,14 @@ class ExchangeIO(BaseMagneticStructure):
         tensor = np.zeros(shape, dtype=float)
 
         if anisotropic and not self.collinear:
+            # anisotropic exchange tensor
             tensor += self._exchange_values[:, :, 9:].reshape(shape)
+            # DMI
             pos_indices = ([1, 2, 0], [2, 0, 1])
             neg_indices = ([2, 0, 1], [1, 2, 0])
             tensor[:, :, *pos_indices] += self._exchange_values[:, :, 6:9]
             tensor[:, :, *neg_indices] -= self._exchange_values[:, :, 6:9]
+        # isotropic exchange
         diag_indices = ([0, 1, 2], [0, 1, 2])
         tensor[:, :, *diag_indices] += self._exchange_values[:, :, 3, None]
 

TB2J/magnon/magnon3.py

@@ -0,0 +1,204 @@
+import numpy as np
+from scipy.spatial.transform import Rotation
+
+from TB2J.io_exchange import SpinIO
+
+from ..mathutils import Hermitize, get_rotation_arrays, uz
+from .plot import BandsPlot
+
+
+class Magnon:
+    """ """
+
+    def __init__(self, exc: SpinIO, iso_only=False, asr=False):
+        self.exc = exc
+        self.nspin = exc.get_nspin()
+        self.ind_atoms = exc.ind_atoms
+        self.magmom = np.array([exc.spinat[exc.iatom(i)] for i in range(self.nspin)])
+        self.Rlist = exc.Rlist
+        self.JR = exc.get_full_Jtensor_for_Rlist(asr=asr, iso_only=iso_only)
+        self._Q = None
+        self._uz = np.array([[0.0, 0.0, 1.0]], dtype=float)
+        self._n = np.array([0, 0, 1], dtype=float)
+
+    def set_propagation_vector(self, Q):
+        self._Q = np.array(Q)
+
+    @property
+    def Q(self):
+        if self._Q is None:
+            raise ValueError("Propagation vector Q is not set.")
+        return self._Q
+
+    @Q.setter
+    def Q(self, value):
+        if not isinstance(value, (list, np.ndarray)):
+            raise TypeError("Propagation vector Q must be a list or numpy array.")
+        if len(value) != 3:
+            raise ValueError("Propagation vector Q must have three components.")
+        self._Q = np.array(value)
+
+    def Jq(self, kpoints):
+        """
+        Compute the exchange interactions in reciprocal space.
+
+        Parameters
+        ----------
+        kpoints : array_like
+            k-points at which to evaluate the exchange interactions
+        """
+        Rlist = np.array(self.Rlist)
+        JR = self.JR
+
+        for iR, R in enumerate(Rlist):
+            if self._Q is not None:
+                phi = 2 * np.pi * R @ self._Q
+                rv = phi * self._n
+                Rmat = Rotation.from_rotvec(rv).as_matrix()
+                JR[iR] = np.einsum("rijxy, yz -> rixzy", JR[iR], Rmat)
+
+        nkpt = kpoints.shape[0]
+        Jq = np.zeros((nkpt, self.nspin, self.nspin, 3, 3), dtype=complex)
+
+        for iR, R in enumerate(Rlist):
+            for iqpt, qpt in enumerate(kpoints):
+                phase = 2 * np.pi * R @ qpt
+                Jq[iqpt] += np.exp(1j * phase) * JR[iR]
+
+                # Hermitian
+                Jq[iqpt, :, :, :, :] += np.conj(Jq[iqpt, :, :, :, :].swapaxes(-1, -2))
+
+        # should we divide
+
+        # if self._Q is not None:
+        #    phi = 2 * np.pi * vectors.round(3).astype(int) @ self._Q
+        #    rv = np.einsum("ij,k->ijk", phi, self._n)
+        #    R = (
+        #        Rotation.from_rotvec(rv.reshape(-1, 3))
+        #        .as_matrix()
+        #        .reshape(vectors.shape[:2] + (3, 3))
+        #    )
+        #    np.einsum("nmij,nmjk->nmik", tensor, R, out=tensor)
+
+        # exp_summand = np.exp(2j * np.pi * vectors @ kpoints.T)
+        # Jexp = exp_summand[:, :, :, None, None] * tensor[:, :, None]
+        # Jq = np.sum(Jexp, axis=1)
+
+        # pairs = np.array(self._pairs)
+        # idx = np.where(pairs[:, 0] == pairs[:, 1])
+        # Jq[idx] /= 2
+
+        return Jq
+
+    def Hq(self, kpoints, anisotropic=True, u=uz):
+        """
+        Compute the magnon Hamiltonian in reciprocal space.
+
+        Parameters
+        ----------
+        kpoints : array_like
+            k-points at which to evaluate the Hamiltonian
+        anisotropic : bool, optional
+            Whether to include anisotropic interactions, default True
+        u : array_like, optional
+            Reference direction for spin quantization axis
+
+        Returns
+        -------
+        numpy.ndarray
+            Magnon Hamiltonian matrix at each k-point
+        """
+        magmoms = self.magmom.copy()
+        magmoms /= np.linalg.norm(magmoms, axis=-1)[:, None]
+
+        U, V = get_rotation_arrays(magmoms, u=u)
+
+        J0 = self.Jq(np.zeros((1, 3)), anisotropic=anisotropic)
+        J0 = -Hermitize(J0)[:, :, 0]
+        Jq = -Hermitize(self.Jq(kpoints, anisotropic=anisotropic))
+
+        C = np.diag(np.einsum("ix,ijxy,jy->i", V, 2 * J0, V))
+        B = np.einsum("ix,ijkxy,jy->kij", U, Jq, U)
+        A1 = np.einsum("ix,ijkxy,jy->kij", U, Jq, U.conj())
+        A2 = np.einsum("ix,ijkxy,jy->kij", U.conj(), Jq, U)
+
+        return np.block([[A1 - C, B], [B.swapaxes(-1, -2).conj(), A2 - C]])
+
+    def _magnon_energies(self, kpoints, anisotropic=True, u=uz):
+        H = self.Hq(kpoints, anisotropic=anisotropic, u=u)
+        n = H.shape[-1] // 2
+        I = np.eye(n)
+
+        min_eig = 0.0
+        try:
+            K = np.linalg.cholesky(H)
+        except np.linalg.LinAlgError:
+            try:
+                K = np.linalg.cholesky(H + 1e-6 * np.eye(2 * n))
+            except np.linalg.LinAlgError:
+                from warnings import warn
+
+                min_eig = np.min(np.linalg.eigvalsh(H))
+                K = np.linalg.cholesky(H - (min_eig - 1e-6) * np.eye(2 * n))
+                warn(
+                    f"WARNING: The system may be far from the magnetic ground-state. Minimum eigenvalue: {min_eig}. The magnon energies might be unphysical."
+                )
+
+        g = np.block([[1 * I, 0 * I], [0 * I, -1 * I]])
+        KH = K.swapaxes(-1, -2).conj()
+
+        return np.linalg.eigvalsh(KH @ g @ K)[:, n:] + min_eig
+
+    def get_magnon_bands(
+        self,
+        kpoints: np.array = np.array([]),
+        path: str = None,
+        npoints: int = 300,
+        special_points: dict = None,
+        tol: float = 2e-4,
+        pbc: tuple = None,
+        cartesian: bool = False,
+        labels: list = None,
+        anisotropic: bool = True,
+        u: np.array = uz,
+    ):
+        pbc = self._pbc if pbc is None else pbc
+
+        if kpoints.size == 0:
+            from ase.cell import Cell
+
+            bandpath = Cell(self._cell).bandpath(
+                path=path,
+                npoints=npoints,
+                special_points=special_points,
+                eps=tol,
+                pbc=pbc,
+            )
+            kpoints = bandpath.kpts
+            spk = bandpath.special_points
+            spk[r"$\Gamma$"] = spk.pop("G", np.zeros(3))
+            labels = [
+                (i, symbol)
+                for symbol in spk
+                for i in np.where((kpoints == spk[symbol]).all(axis=1))[0]
+            ]
+        elif cartesian:
+            kpoints = np.linalg.solve(self._cell.T, kpoints.T).T
+
+        bands = self._magnon_energies(kpoints, anisotropic=anisotropic, u=u)
+
+        return labels, bands
+
+    def plot_magnon_bands(self, **kwargs):
+        """
+        Plot magnon band structure.
+
+        Parameters
+        ----------
+        **kwargs
+            Additional keyword arguments passed to get_magnon_bands and plotting functions
+        """
+        filename = kwargs.pop("filename", None)
+        kpath, bands = self.get_magnon_bands(**kwargs)
+        bands_plot = BandsPlot(bands, kpath)
+        bands_plot.plot(filename=filename)

TB2J/{mathutils/magnons.py → magnon/magnon_math.py}

@@ -19,6 +19,14 @@ def generate_grid(kmesh, sort=True):
     return grid
 
 
+# def JR_to_Jq(JR, Rlist, qpt, vecn):
+#    for iR, R in enumerate(Rlist):
+#        phase = 2 * np.pi * R @ qpt
+#        rv = phase * vecn
+#        Rot = Rotation.from_rotvec(rv.reshape(-1, 3)).as_matrix().reshape(R.shape[0], 3, 3)
+#
+
+
 def get_rotation_arrays(magmoms, u=uz):
     dim = magmoms.shape[0]
     v = magmoms

TB2J/mathutils/__init__.py

@@ -1,2 +1,3 @@
 from .lowdin import Lowdin
-from .magnons import *
+
+__all__ = ["Lowdin"]

{tb2j-0.9.9rc19.data → tb2j-0.9.9rc20.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-0.9.9rc19.dist-info → tb2j-0.9.9rc20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc19
+Version: 0.9.9rc20
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com

{tb2j-0.9.9rc19.dist-info → tb2j-0.9.9rc20.dist-info}/RECORD

@@ -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
@@ -55,22 +55,23 @@ TB2J/interfaces/abacus/test_density_matrix.py,sha256=bMWWJYtDS57SpPZ-eZXZ9Hr_UK4
 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/io_exchange.py,sha256=6fefcfYAyRojkCJA5bFwAa2Hjwx6epysfyX8Snj9DWc,20102
+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
 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/magnon/__init__.py,sha256=jdUFkOlhrpHRmKavAXVcFdZgtY7lKZVzMPFlLmmCErM,113
-TB2J/magnon/io_exchange2.py,sha256=vKKQXhPSvoeKNIc0Kh0GaTFph36jSW0Z46nAAbSEcAg,22993
+TB2J/magnon/io_exchange2.py,sha256=EcC3x6H13qq61WBsr__xKzHDtSvy_dMz1tEdUaqSG2I,23265
+TB2J/magnon/magnon3.py,sha256=AsPTsbaMxvoPHvgi1nKSxqeN32QIJccm0os65u6o4uQ,6784
+TB2J/magnon/magnon_math.py,sha256=hJ2k24eR4TzdaFMxfxgCr10lWV4GEcfaf2WxhWj-uUk,1320
 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/__init__.py,sha256=E70Mx8mLXh3DJGmdN3TLWmGYMcsbvKxmgxUbAI6Mzmo,49
 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
@@ -85,20 +86,20 @@ 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
-tb2j-0.9.9rc19.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
-tb2j-0.9.9rc19.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-tb2j-0.9.9rc19.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-tb2j-0.9.9rc19.data/scripts/TB2J_magnon2.py,sha256=tMa7Fg_Wd2UytnrH3C_AsgGM7BciUW0iy6NiPlWvar8,1920
-tb2j-0.9.9rc19.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-tb2j-0.9.9rc19.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
-tb2j-0.9.9rc19.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
-tb2j-0.9.9rc19.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
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