TB2J 0.9.5rc0__py3-none-any.whl → 0.9.6rc0__py3-none-any.whl

TB2J/abacus/MAE.py

@@ -1,320 +0,0 @@
-import numpy as np
-from TB2J.abacus.abacus_wrapper import AbacusWrapper, AbacusParser
-from TB2J.mathutils.rotate_spin import rotate_Matrix_from_z_to_axis
-from TB2J.kpoints import monkhorst_pack
-from TB2J.mathutils.fermi import fermi
-from TB2J.mathutils.kR_convert import R_to_k
-from scipy.linalg import eigh
-from copy import deepcopy
-from scipy.spatial.transform import Rotation
-import matplotlib.pyplot as plt
-from pathlib import Path
-from TB2J.abacus.occupations import Occupations
-
-# TODO List:
-# - [x] Add the class AbacusSplitSOCWrapper
-# - [x] Add the function to rotate the XC part
-# - [x] Compute the band energy at arbitrary angle
-
-
-def get_occupation(evals, kweights, nel, width=0.1):
-    occ = Occupations(nel=nel, width=width, wk=kweights, nspin=2)
-    return occ.occupy(evals)
-
-
-def get_density_matrix(evals=None, evecs=None, kweights=None, nel=None, width=0.1):
-    occ = get_occupation(evals, kweights, nel, width=width)
-    rho = np.einsum("kib, kb, kjb -> kij", evecs, occ, evecs.conj())
-    return rho
-
-
-def spherical_to_cartesian(theta, phi, normalize=True):
-    """
-    Convert spherical coordinates to cartesian
-    """
-    x = np.sin(theta) * np.cos(phi)
-    y = np.sin(theta) * np.sin(phi)
-    z = np.cos(theta)
-    vec = np.array([x, y, z])
-    if normalize:
-        vec = vec / np.linalg.norm(vec)
-    return vec
-
-
-class AbacusSplitSOCWrapper(AbacusWrapper):
-    """
-    Abacus wrapper with Hamiltonian split to SOC and non-SOC parts
-    """
-
-    def __init__(self, *args, **kwargs):
-        HR_soc = kwargs.pop("HR_soc", None)
-        # nbasis = HR_soc.shape[1]
-        # kwargs["nbasis"] = nbasis
-        super().__init__(*args, **kwargs)
-        self._HR_copy = deepcopy(self._HR)
-        self.HR_soc = HR_soc
-        self.soc_lambda = 1.0
-        self.nel = 16
-        self.width = 0.1
-
-    @property
-    def HR(self):
-        return self._HR + self.HR_soc * self.soc_lambda
-
-    def rotate_HR_xc(self, axis):
-        """
-        Rotate SOC part of Hamiltonian
-        """
-        for iR, R in enumerate(self.Rlist):
-            self._HR[iR] = rotate_Matrix_from_z_to_axis(self._HR_copy[iR], axis)
-
-    def rotate_Hk_xc(self, axis):
-        """
-        Rotate SOC part of Hamiltonian
-        """
-        for ik in range(len(self._Hk)):
-            self._Hk[ik] = rotate_Matrix_from_z_to_axis(self._Hk_copy[ik], axis)
-
-    def get_density_matrix(self, kpts, kweights=None):
-        rho = np.zeros((len(kpts), self.nbasis, self.nbasis), dtype=complex)
-        evals, evecs = self.solve_all(kpts)
-        occ = get_occupation(evals, kweights, self.nel, width=self.width)
-        rho = np.einsum(
-            "kib, kb, kjb -> kij", evecs, occ, evecs.conj()
-        )  # should multiply S to the the real DM.
-        return rho
-
-    def rotate_DM(self, rho, axis):
-        """
-        Rotate the density matrix
-        """
-        for ik in range(len(rho)):
-            rho[ik] = rotate_Matrix_from_z_to_axis(rho[ik], axis)
-        return rho
-
-
-class RotateHam:
-    def __init__(self, model, kmesh, gamma=True):
-        self.model = model
-        self.kpts = monkhorst_pack(kmesh, gamma_center=gamma)
-        self.kweights = np.ones(len(self.kpts), dtype=float) / len(self.kpts)
-
-    def get_band_energy2(self):
-        for ik, kpt in enumerate(self.kpts):
-            Hk, Sk = self.model.gen_ham(kpt)
-            evals, evecs = eigh(Hk, Sk)
-            rho = np.einsum(
-                "ib, b, jb -> ij",
-                evecs,
-                fermi(evals, self.model.efermi, width=0.05),
-                evecs.conj(),
-            )
-            eband1 = np.sum(evals * fermi(evals, self.model.efermi, width=0.05))
-            eband2 = np.trace(Hk @ rho)
-            print(eband1, eband2)
-
-    def get_band_energy(self, dm=False):
-        evals, evecs = self.model.solve_all(self.kpts)
-        occ = get_occupation(
-            evals, self.kweights, self.model.nel, width=self.model.width
-        )
-        eband = np.sum(evals * occ * self.kweights[:, np.newaxis])
-        # * fermi(evals, self.model.efermi, width=0.05)
-        if dm:
-            density_matrix = self.model.get_density_matrix(evecs)
-            return eband, density_matrix
-        else:
-            return eband
-
-    def calc_ref(self):
-        # calculate the Hk_ref, Sk_ref, Hk_soc_ref, and rho_ref
-        self.Sk_ref = R_to_k(self.kpts, self.model.Rlist, self.model.SR)
-        self.Hk_xc_ref = R_to_k(self.kpts, self.model.Rlist, self.model._HR_copy)
-        self.Hk_soc_ref = R_to_k(self.kpts, self.model.Rlist, self.model.HR_soc)
-        self.rho_ref = np.zeros(
-            (len(self.kpts), self.model.nbasis, self.model.nbasis), dtype=complex
-        )
-
-        evals = np.zeros((len(self.kpts), self.model.nbasis), dtype=float)
-        evecs = np.zeros(
-            (len(self.kpts), self.model.nbasis, self.model.nbasis), dtype=complex
-        )
-
-        for ik, kpt in enumerate(self.kpts):
-            # evals, evecs = eigh(self.Hk_xc_ref[ik]+self.Hk_soc_ref[ik], self.Sk_ref[ik])
-            evals[ik], evecs[ik] = eigh(self.Hk_xc_ref[ik], self.Sk_ref[ik])
-        occ = get_occupation(
-            evals, self.kweights, self.model.nel, width=self.model.width
-        )
-        # occ = fermi(evals, self.model.efermi, width=self.model.width)
-        self.rho_ref = np.einsum("kib, kb, kjb -> kij", evecs, occ, evecs.conj())
-
-    def get_band_energy_from_rho(self, axis):
-        """
-        This is wrong!! Should use second order perturbation theory to get the band energy instead.
-        """
-        eband = 0.0
-        for ik, k in enumerate(self.kpts):
-            rho = rotate_Matrix_from_z_to_axis(self.rho_ref[ik], axis)
-            Hk_xc = rotate_Matrix_from_z_to_axis(self.Hk_xc_ref[ik], axis)
-            Hk_soc = self.Hk_soc_ref[ik]
-            Htot = Hk_xc + Hk_soc * self.model.soc_lambda
-            # Sk = self.Sk_ref[ik]
-            # evals, evecs = eigh(Htot, Sk)
-            # rho2= np.einsum("ib, b, jb -> ij", evecs, fermi(evals, self.model.efermi, width=0.05), evecs.conj())
-            if ik == 0 and False:
-                pass
-                # print(f"{evecs[:4,0:4].real=}")
-                # print(f"{evals[:4]=}")
-                # print(f"{Hk_xc[:4,0:4].real=}")
-                # print(f"{Htot[:4,0:4].real=}")
-                # print(f"{Sk[:4,0:4].real=}")
-                # print(f"{rho[:4,0:4].real=}")
-                # print(f"{rho2[:4,0:4].real=}")
-            # eband1 = np.sum(evals * fermi(evals, self.model.efermi, width=0.05))
-            # eband2 = np.trace(Htot @ rho2).real
-            # eband3 = np.trace(Htot @ rho).real
-            # print(eband1, eband2, eband3)
-            e_soc = np.trace(Hk_soc @ rho) * self.kweights[ik] * self.model.soc_lambda
-            eband += e_soc
-        return eband
-
-    def get_band_energy_vs_angles(
-        self,
-        thetas,
-        psis,
-    ):
-        es = []
-        # es2 = []
-        # e,rho = self.model.get_band_energy(dm=True)
-        # self.calc_ref()
-        # thetas = np.linspace(*angle_range, npoints)
-        for i, theta, phi in enumerate(zip(thetas, psis)):
-            axis = spherical_to_cartesian(theta, phi)
-            self.model.rotate_HR_xc(axis)
-            # self.get_band_energy2()
-            e = self.get_band_energy()
-            es.append(e)
-            # es2.append(e2)
-        return es
-
-
-def get_model_energy(model, kmesh, gamma=True):
-    ham = RotateHam(model, kmesh, gamma=gamma)
-    return ham.get_band_energy()
-
-
-class AbacusSplitSOCParser:
-    """
-    Abacus parser with Hamiltonian split to SOC and non-SOC parts
-    """
-
-    def __init__(self, outpath_nosoc=None, outpath_soc=None, binary=False):
-        self.outpath_nosoc = outpath_nosoc
-        self.outpath_soc = outpath_soc
-        self.binary = binary
-        self.parser_nosoc = AbacusParser(outpath=outpath_nosoc, binary=binary)
-        self.parser_soc = AbacusParser(outpath=outpath_soc, binary=binary)
-        spin1 = self.parser_nosoc.read_spin()
-        spin2 = self.parser_soc.read_spin()
-        if spin1 != "noncollinear" or spin2 != "noncollinear":
-            raise ValueError("Spin should be noncollinear")
-
-    def parse(self):
-        nbasis, Rlist, HR, SR = self.parser_nosoc.Read_HSR_noncollinear()
-        nbasis2, Rlist2, HR2, SR2 = self.parser_soc.Read_HSR_noncollinear()
-        # print(HR[0])
-        HR_soc = HR2 - HR
-        model = AbacusSplitSOCWrapper(HR, SR, Rlist, nbasis, nspin=2, HR_soc=HR_soc)
-        model.efermi = self.parser_soc.efermi
-        model.basis = self.parser_nosoc.basis
-        model.atoms = self.parser_nosoc.atoms
-        return model
-
-
-def abacus_get_MAE(
-    path_nosoc, path_soc, kmesh, thetas, psis, gamma=True, outfile="MAE.txt"
-):
-    """Get MAE from Abacus with magnetic force theorem. Two calculations are needed. First we do an calculation with SOC but the soc_lambda is set to 0. Save the density. The next calculatin we start with the density from the first calculation and set the SOC prefactor to 1. With the information from the two calcualtions, we can get the band energy with magnetic moments in the direction, specified in two list, thetas, and phis."""
-    parser = AbacusSplitSOCParser(
-        outpath_nosoc=path_nosoc, outpath_soc=path_soc, binary=False
-    )
-    model = parser.parse()
-    ham = RotateHam(model, kmesh, gamma=gamma)
-    es = []
-    for theta, psi in zip(thetas, psis):
-        axis = spherical_to_cartesian(theta, psi)
-        model.rotate_HR_xc(axis)
-        e = ham.get_band_energy()
-        es.append(ham.get_band_energy())
-    if outfile:
-        with open(outfile, "w") as f:
-            f.write("theta, psi, energy\n")
-            for theta, psi, e in zip(thetas, psis, es):
-                f.write(f"{theta}, {psi}, {e}\n")
-    return es
-
-
-def test_AbacusSplitSOCWrapper():
-    # path = Path("~/projects/2D_Fe").expanduser()
-    path = Path("~/projects/TB2Jflows/examples/2D_Fe/Fe_z").expanduser()
-    outpath_nosoc = f"{path}/soc0/OUT.ABACUS"
-    outpath_soc = f"{path}/soc1/OUT.ABACUS"
-    parser = AbacusSplitSOCParser(
-        outpath_nosoc=outpath_nosoc, outpath_soc=outpath_soc, binary=False
-    )
-    model = parser.parse()
-    kmesh = [6, 6, 1]
-
-    r = RotateHam(model, kmesh)
-    # thetas, es = r.get_band_energy_vs_theta(angle_range=(0, np.pi*2), rotation_axis="z", initial_direction=(1,0,0),  npoints=21)
-    thetas, es, es2 = r.get_band_energy_vs_theta(
-        angle_range=(0, np.pi * 2),
-        rotation_axis="y",
-        initial_direction=(0, 0, 1),
-        npoints=11,
-    )
-    # print the table of thetas and es, es2
-    print("theta, e, e2")
-    for theta, e, e2 in zip(thetas, es, es2):
-        print(f"{theta=}, {e=}, {e2=}")
-
-    plt.plot(thetas / np.pi, es - es[0], marker="o")
-    plt.plot(thetas / np.pi, es2 - es2[0], marker=".")
-    plt.savefig("E_along_z_x_z.png")
-    plt.show()
-
-
-def abacus_get_MAE_cli():
-    import argparse
-
-    parser = argparse.ArgumentParser(
-        description="Get MAE from Abacus with magnetic force theorem. Two calculations are needed. First we do an calculation with SOC but the soc_lambda is set to 0. Save the density. The next calculatin we start with the density from the first calculation and set the SOC prefactor to 1. With the information from the two calcualtions, we can get the band energy with magnetic moments in the direction, specified in two list, thetas, and phis. "
-    )
-    parser.add_argument("path_nosoc", type=str, help="Path to the  calculation with ")
-    parser.add_argument("path_soc", type=str, help="Path to the SOC calculation")
-    parser.add_argument("thetas", type=float, nargs="+", help="Thetas")
-    parser.add_argument("psis", type=float, nargs="+", help="Phis")
-    parser.add_argument("kmesh", type=int, nargs=3, help="K-mesh")
-    parser.add_argument(
-        "--gamma", action="store_true", help="Use Gamma centered kpoints"
-    )
-    parser.add_argument(
-        "--outfile",
-        type=str,
-        help="The angles and the energey will be saved in this file.",
-    )
-    args = parser.parse_args()
-    abacus_get_MAE(
-        args.path_nosoc,
-        args.path_soc,
-        args.kmesh,
-        args.thetas,
-        args.psis,
-        gamma=args.gamma,
-        outfile=args.outfile,
-    )
-
-
-if __name__ == "__main__":
-    abacus_get_MAE_cli()

TB2J/abacus/__init__.py

@@ -1 +0,0 @@
-from .abacus_wrapper import AbacusWrapper, AbacusParser

TB2J/abacus/occupations.py

@@ -1,278 +0,0 @@
-"""
-This file is stolen from the hotbit programm, with some modification.
-"""
-
-import numpy as np
-from scipy.optimize import brentq
-import sys
-
-from ase.dft.dos import DOS
-from scipy import integrate
-
-# import numba
-
-# from numba import float64, int32
-
-MAX_EXP_ARGUMENT = np.log(sys.float_info.max)
-
-# @numba.vectorize(nopython=True)
-# def myfermi(e, mu, width, nspin):
-#    x = (e - mu) / width
-#    if x < -10:
-#        ret = 2.0 / nspin
-#    elif x > 10:
-#        ret = 0.0
-#    else:
-#        ret = 2.0 / nspin / (math.exp(x) + 1)
-#    return ret
-
-
-def myfermi(e, mu, width, nspin):
-    x = (e - mu) / width
-    return np.where(x < 10, 2.0 / (nspin * (np.exp(x) + 1.0)), 0.0)
-
-
-class Occupations(object):
-    def __init__(self, nel, width, wk, nspin=1):
-        """
-        Initialize parameters for occupations.
-        :param nel: Number of electrons
-        :param width: Fermi-broadening
-        :param wk: k-point weights. eg. If only gamma, [1.0]
-        :param nspin(optional): number of spin, if spin=1 multiplicity=2 else, multiplicity=1.
-        """
-        self.nel = nel
-        self.width = width
-        self.wk = wk
-        self.nk = len(wk)
-        self.nspin = nspin
-
-    def get_mu(self):
-        """Return the Fermi-level (or chemical potential)."""
-        return self.mu
-
-    def fermi(self, mu):
-        """
-        Occupy states with given chemical potential.
-        Occupations are 0...2; without k-point weights
-        """
-        return myfermi(self.e, mu, self.width, self.nspin)
-
-    def root_function(self, mu):
-        """This function is exactly zero when mu is right."""
-        f = self.fermi(mu)
-        return np.einsum("i, ij->", self.wk, f) - self.nel
-
-    def occupy(self, e, xtol=1e-11):
-        """
-        Calculate occupation numbers with given Fermi-broadening.
-
-        @param e: e[ind_k,ind_orb] energy of k-point, state a
-            Note added by hexu:  With spin=2,e[k,a,sigma], it also work. only the *2 should be removed.
-        @param wk: wk[:] weights for k-points
-        @param width: The Fermi-broadening
-
-        Returns: fermi[ind_k, ind_orb]
-        """
-        self.e = e
-        eflat = e.flatten()
-        ind = np.argsort(eflat)
-        e_sorted = eflat[ind]
-        if self.nspin == 1:
-            m = 2
-        elif self.nspin == 2:
-            m = 1
-        n_sorted = (self.wk[:, None, None] * np.ones_like(e) * m).flatten()[ind]
-
-        sum = n_sorted.cumsum()
-        if self.nel < sum[0]:
-            ifermi = 0
-        elif self.nel > sum[-1]:
-            raise ("number of electrons larger than number of orbital*spin")
-        else:
-            ifermi = np.searchsorted(sum, self.nel)
-        try:
-            if ifermi == 0:
-                elo = e_sorted[0]
-            else:
-                elo = e_sorted[ifermi - 1]
-            if ifermi == len(e_sorted) - 1:
-                ehi = e_sorted[-1]
-            else:
-                ehi = e_sorted[ifermi + 1]
-            guess = e_sorted[ifermi]
-            dmu = np.max((self.width, guess - elo, ehi - guess))
-            mu = brentq(self.root_function, guess - dmu, guess + dmu, xtol=xtol)
-            # mu = brent(
-            #    self.root_function,
-            #    brack=(guess - elo, guess, guess + dmu),
-            #    tol=xtol)
-        except Exception as E:
-            # probably a bad guess
-            print("Error in finding Fermi level: ", E)
-            dmu = self.width
-            if self.nel < 1e-3:
-                mu = min(e_sorted) - dmu * 20
-            elif self.nel - sum[-1] > -1e-3:
-                mu = max(e_sorted) + dmu * 20
-            else:
-                # mu = brent(
-                #         self.root_function,
-                #         brack=(e_sorted[0] - dmu * 10,
-                #                guess,
-                #                e_sorted[-1] + dmu * 10),
-                #         tol=xtol)
-                mu = brentq(
-                    self.root_function,
-                    e_sorted[0] - dmu * 20,
-                    e_sorted[-1] + dmu * 20,
-                    xtol=xtol,
-                )
-
-        if np.abs(self.root_function(mu)) > xtol * 1e4:
-            # raise RuntimeError(
-            #    'Fermi level could not be assigned reliably. Has the system fragmented?'
-            # )
-            print(
-                "Fermi level could not be assigned reliably. Has the system fragmented?"
-            )
-
-        f = self.fermi(mu)
-        # rho=(self.eigenvecs*f).dot(self.eigenvecs.transpose())
-
-        self.mu, self.f = mu, f
-        return f
-
-    def plot(self):
-        import pylab as pl
-
-        for ik in range(self.nk):
-            pl.plot(self.e[ik, :], self.f[ik, :])
-            pl.scatter(self.e[ik, :], self.f[ik, :])
-        pl.title("occupations")
-        pl.xlabel("energy (Ha)")
-        pl.ylabel("occupation")
-        pl.show()
-
-
-class GaussOccupations(Occupations):
-    def get_mu(self):
-        return self.mu
-
-    def delta(self, energy):
-        """Return a delta-function centered at 'energy'."""
-        x = -(((self.e - energy) / self.width) ** 2)
-        return np.exp(x) / (np.sqrt(np.pi) * self.width)
-
-    def get_dos(self, npts=500):
-        eflat = self.e.flatten()
-        ind = np.argsort(eflat)
-        ##e_sorted = eflat[ind]
-        if self.nspin == 1:
-            m = 2
-        elif self.nspin == 2:
-            m = 1
-        # n_sorted = (self.wk * np.ones_like(self.e) * m).flatten()[ind]
-        dos = np.zeros(npts)
-        for w, e_n in zip(self.w_k, self.e_skn[0]):
-            for e in e_n:
-                dos += w * self.delta(e)
-
-    def root_function(self, mu):
-        pass
-
-    # @profile
-    def occupy(self, e, xtol=1e-8, guess=0.0):
-        self.e = e
-        dos = myDOS(kweights=self.wk, eigenvalues=e, width=self.width, npts=501)
-        edos = dos.get_energies()
-        d = dos.get_dos()
-        idos = integrate.cumtrapz(d, edos, initial=0) - self.nel
-        # f_idos = interpolate.interp1d(edos, idos)
-        # ret = optimize.fmin(f_idos, x0=edos[400], xtol=xtol, disp=True)
-        ifermi = np.searchsorted(idos, 0.0)
-        # self.mu = ret[0]
-        self.mu = edos[ifermi]
-        self.f = self.fermi(self.mu)
-        return self.f
-
-
-class myDOS(DOS):
-    def __init__(
-        self, kweights, eigenvalues, nspin=1, width=0.1, window=None, npts=1001
-    ):
-        """Electronic Density Of States object.
-
-        calc: calculator object
-            Any ASE compliant calculator object.
-        width: float
-            Width of guassian smearing.  Use width=0.0 for linear tetrahedron
-            interpolation.
-        window: tuple of two float
-            Use ``window=(emin, emax)``.  If not specified, a window
-            big enough to hold all the eigenvalues will be used.
-        npts: int
-            Number of points.
-
-        """
-        self.npts = npts
-        self.width = width
-        # self.w_k = calc.get_k_point_weights()
-        self.w_k = kweights
-        self.nspins = nspin
-        # self.e_skn = np.array([[calc.get_eigenvalues(kpt=k, spin=s)
-        #                        for k in range(len(self.w_k))]
-        #                       for s in range(self.nspins)])
-        # self.e_skn -= calc.get_fermi_level()
-        self.e_skn = np.array([eigenvalues.T])  # eigenvalues: iband, ikpt
-
-        if window is None:
-            emin = None
-            emax = None
-        else:
-            emin, emax = window
-
-        if emin is None:
-            emin = self.e_skn.min() - 10 * self.width
-        if emax is None:
-            emax = self.e_skn.max() + 10 * self.width
-
-        self.energies = np.linspace(emin, emax, npts)
-
-        # if width == 0.0: # To use tetrahedron method
-        #    bzkpts = calc.get_bz_k_points()
-        #    size, offset = get_monkhorst_pack_size_and_offset(bzkpts)
-        #    bz2ibz = calc.get_bz_to_ibz_map()
-        #    shape = (self.nspins,) + tuple(size) + (-1,)
-        #    self.e_skn = self.e_skn[:, bz2ibz].reshape(shape)
-        #    self.cell = calc.atoms.cell
-
-    def get_idos(self):
-        e, d = self.get_dos()
-        return np.trapz(d, e)
-
-    def delta(self, energy):
-        """Return a delta-function centered at 'energy'."""
-        x = -(((self.energies - energy) / self.width) ** 2)
-        return np.exp(x) / (np.sqrt(np.pi) * self.width)
-
-    def get_dos(self, spin=None):
-        """Get array of DOS values.
-
-        The *spin* argument can be 0 or 1 (spin up or down) - if not
-        specified, the total DOS is returned.
-        """
-
-        if spin is None:
-            if self.nspins == 2:
-                # Spin-polarized calculation, but no spin specified -
-                # return the total DOS:
-                return self.get_dos(spin=0) + self.get_dos(spin=1)
-            else:
-                spin = 0
-
-        dos = np.zeros(self.npts)
-        for w, e_n in zip(self.w_k, self.e_skn[spin]):
-            for e in e_n:
-                dos += w * self.delta(e)
-        return dos

TB2J/cut_cell.py

@@ -1,82 +0,0 @@
-import numpy as np
-from TB2J.supercell import find_primitive_cell, map_to_primitive
-from TB2J.io_exchange.io_exchange import SpinIO, gen_distance_dict
-
-
-def cut_cell(path, output_path, sc_matrix, origin_atom_id, thr=1e-5):
-    """
-    Cut the exchange parameters
-    :param path: the original TB2J_results path
-    :param output_path: the output path.
-    :param sc_matrix: the matrix which maps the primitive cell to supercell.
-    :param origin: the origin of the primitive cell.
-    :param thr: the atoms which the reduced position is within -thr to 1.0+thr are considered as inside the primitive atoms
-    :returns:
-    """
-    sc_matrix = np.asarray(sc_matrix, dtype=int)
-    sc_excparams = SpinIO.load_pickle(path=path, fname='TB2J.pickle')
-    sc_atoms = sc_excparams.atoms
-    uc_atoms, ids = find_primitive_cell(sc_atoms,
-                                        sc_matrix,
-                                        origin_atom_id=origin_atom_id,
-                                        thr=thr,
-                                        perfect=False)
-    uc_charges = sc_excparams.charges[ids]
-    uc_spinat = sc_excparams.spinat[ids]
-    indmap, Rmap = map_to_primitive(sc_atoms, uc_atoms)
-
-    # TODO index_spin: {iatom: ispin}
-
-    # list of iatom for each spin index.
-    uc_index_spin = [sc_excparams.index_spin[i] for i in ids]
-
-    uc_ind_atoms = {}
-    for iatom, ispin in enumerate(uc_index_spin):
-        if ispin >= 0:
-            uc_ind_atoms[ispin] = iatom
-
-    uc_Jdict = {}
-    uc_Rset = set()
-    for key, val in sc_excparams.exchange_Jdict.items():
-        R, ispin, jspin = key
-        iatom = sc_excparams.ind_atoms[ispin]
-        jatom = sc_excparams.ind_atoms[jspin]
-        uc_ispin = uc_index_spin[indmap[iatom]]
-        uc_jspin = uc_index_spin[indmap[jatom]]
-        uc_R = R @ sc_matrix + Rmap[jatom] - Rmap[iatom]
-        uc_R = tuple(uc_R)
-        if iatom in ids:
-            #print(f"{iatom=}, {indmap[iatom]=},{uc_ispin=}, {uc_jspin=}, {uc_R=} ")
-            uc_Jdict[(uc_R, uc_ispin, uc_jspin)] = val
-            uc_Rset.add(uc_R)
-
-    uc_distance_dict = gen_distance_dict(uc_ind_atoms, uc_atoms, list(uc_Rset))
-
-    assert sc_excparams.colinear, "Cut supercell for non-collinear spin is not yet implemented."
-
-    uc_exc = SpinIO(uc_atoms,
-                    spinat=uc_spinat,
-                    charges=uc_charges,
-                    index_spin=uc_index_spin,
-                    colinear=sc_excparams.colinear,
-                    distance_dict=uc_distance_dict,
-                    exchange_Jdict=uc_Jdict,
-                    description="Cutted")
-
-    uc_exc.write_all(output_path)
-
-
-def run_cut_cell(
-    path="TB2J_results",
-    output_path="./TB2J_cutted",
-    sc_matrix=np.array([[1, 1, 0], [-1, 1, 0], [0, 0, 2]]),
-):
-    cut_cell(path,
-             output_path,
-             np.array(sc_matrix),
-             origin_atom_id=0,
-             thr=1e-19)
-
-
-if __name__ == "__main__":
-    run_cut_cell()