TB2J 0.8.2.5__py3-none-any.whl → 0.8.2.8__py3-none-any.whl

TB2J/Oiju.py

@@ -45,10 +45,6 @@ def gen_exchange_Oiju(
     kmesh=[5, 5, 5],
     emin=-12.0,
     emax=0.0,
-    height=0.2,
-    nz1=50,
-    nz2=200,
-    nz3=50,
     exclude_orbs=[],
     Rmesh=[1, 1, 1],
     description="",
@@ -93,10 +89,6 @@ def gen_exchange_Oiju(
             kmesh=kmesh,
             emin=emin,
             emax=emax,
-            height=height,
-            nz1=nz1,
-            nz2=nz2,
-            nz3=nz3,
             exclude_orbs=exclude_orbs,
             Rmesh=Rmesh,
             description=description,
@@ -123,10 +115,6 @@ if __name__ == "__main__":
         kmesh=[4, 4, 4],
         emin=-12.0,
         emax=0.0,
-        height=0.1,
-        nz1=50,
-        nz2=200,
-        nz3=50,
         exclude_orbs=[],
         Rmesh=[1, 1, 1],
         description="",

TB2J/Oiju_epc.py

@@ -19,10 +19,6 @@ class OijuWannEPC(ExchangeCL2):
         kmesh=[4, 4, 4],
         emin=-15,  # integration lower bound, relative to fermi energy
         emax=0.05,  # integration upper bound. Should be 0 (fermi energy). But DFT codes define Fermi energy in various ways.
-        height=0.5,  # the delta in the (i delta) in green's function to prevent divergence
-        nz1=150,  # grid from emin to emin+(i delta)
-        nz2=300,  # grid from emin +(i delta) to emax+(i delta)
-        nz3=150,  # grid from emax + (i delta) to emax
         exclude_orbs=[],  #
         Rmesh=[0, 0, 0],  # Rmesh.
         description="",
@@ -40,10 +36,6 @@ class OijuWannEPC(ExchangeCL2):
             emin=-15,  # integration lower bound, relative to fermi energy
             emax=0.05,  # integration upper bound. Should be 0 (fermi energy).
             # But DFT codes define Fermi energy in various ways.
-            height=0.5,  # the delta in the (i delta) in green's function.
-            nz1=150,  # grid from emin to emin+(i delta)
-            nz2=300,  # grid from emin +(i delta) to emax+(i delta)
-            nz3=150,  # grid from emax + (i delta) to emax
             exclude_orbs=[],  #
             Rmesh=[0, 0, 0],  # Rmesh.
             description="",

TB2J/__init__.py

@@ -1 +1 @@
-__version__ = "0.8.2.5"
+__version__ = "0.8.2.8"

TB2J/exchange.py

@@ -26,10 +26,6 @@ class ExchangeParams:
         emax=0.05,
         nz=100,
         # the delta in the (i delta) in green's function to prevent divergence
-        height=0.5,
-        nz1=150,  # grid from emin to emin+(i delta)
-        nz2=300,  # grid from emin +(i delta) to emax+(i delta)
-        nz3=150,  # grid from emax + (i delta) to emax
         exclude_orbs=[],  #
         ne=None,  # number of electrons in Wannier function.
         Rcut=None,  # Rcut.
@@ -44,12 +40,6 @@ class ExchangeParams:
         self.emin = emin
         self.emax = emax
         self.nz = nz
-        self.height = height
-        self.nz1 = nz1
-        self.nz2 = nz2
-        self.nz3 = nz3
-        if nz is None:
-            self.nz = nz1 + nz2 + nz3
         self.Rcut = Rcut
         self.basis = basis
         self.magnetic_elements = magnetic_elements
@@ -81,10 +71,6 @@ class Exchange(ExchangeParams):
         emax=0.05,
         nz=100,
         # the delta in the (i delta) in green's function to prevent divergence
-        height=0.5,
-        nz1=150,  # grid from emin to emin+(i delta)
-        nz2=300,  # grid from emin +(i delta) to emax+(i delta)
-        nz3=150,  # grid from emax + (i delta) to emax
         exclude_orbs=[],  #
         ne=None,  # number of electrons in Wannier function.
         Rcut=None,  # Rcut.
@@ -105,10 +91,6 @@ class Exchange(ExchangeParams):
             emin=emin,
             emax=emax,
             nz=nz,
-            height=height,
-            nz1=nz1,
-            nz2=nz2,
-            nz3=nz3,
             exclude_orbs=exclude_orbs,
             ne=ne,
             Rcut=Rcut,
@@ -164,11 +146,11 @@ class Exchange(ExchangeParams):
          emin --1-> emin + 1j*height --2-> emax+1j*height --3-> emax
         """
         self.contour = Contour(self.emin, self.emax)
-        if method.lower() == "rectangle":
-            self.contour.build_path_rectangle(
-                height=self.height, nz1=self.nz1, nz2=self.nz2, nz3=self.nz3
-            )
-        elif method.lower() == "semicircle":
+        # if method.lower() == "rectangle":
+        #    self.contour.build_path_rectangle(
+        #        height=self.height, nz1=self.nz1, nz2=self.nz2, nz3=self.nz3
+        #    )
+        if method.lower() == "semicircle":
             self.contour.build_path_semicircle(npoints=self.nz, endpoint=True)
         elif method.lower() == "legendre":
             self.contour.build_path_legendre(npoints=self.nz, endpoint=True)
@@ -362,7 +344,8 @@ class ExchangeNCL(Exchange):
         )
         self.norb = self.G.norb
         self.nbasis = self.G.nbasis
-        self.rho = np.zeros((self.nbasis, self.nbasis), dtype=complex)
+        # self.rho = np.zeros((self.nbasis, self.nbasis), dtype=complex)
+        self.rho = self.G.get_density_matrix().real
         self.A_ijR_list = defaultdict(lambda: [])
         self.A_ijR = defaultdict(lambda: np.zeros((4, 4), dtype=complex))
         self.A_ijR_orb = dict()
@@ -595,22 +578,22 @@ class ExchangeNCL(Exchange):
                 B = np.imag(val[3, 3])
                 self.B[keyspin] = Jprime, B
 
-    def get_N_e(self, GR, de):
-        """
-        calcualte density matrix for all R,i, j
-        """
-        self.N = defaultdict(lambda: 0.0)
-        for R, G in GR.items():
-            self.N[R] += -1.0 / np.pi * np.imag(G * de)
+    # def get_N_e(self, GR, de):
+    #    """
+    #    calcualte density matrix for all R,i, j
+    #    """
+    #    self.N = defaultdict(lambda: 0.0)
+    #    for R, G in GR.items():
+    #        self.N[R] += -1.0 / np.pi * np.imag(G * de)
 
-    def get_rho_e(self, rhoR):
-        """add component to density matrix from a green's function
-        :param GR: Green's funciton in real space.
-        """
-        return -1.0 / np.pi * rhoR[0, 0, 0]
+    # def get_rho_e(self, rhoR):
+    #    """add component to density matrix from a green's function
+    #    :param GR: Green's funciton in real space.
+    #    """
+    #    return -1.0 / np.pi * rhoR[0, 0, 0]
 
-    def get_total_charges(self):
-        return np.sum(np.imag(np.diag(self.rho)))
+    # def get_total_charges(self):
+    #    return np.sum(np.imag(np.diag(self.rho)))
 
     def get_rho_atom(self):
         """
@@ -623,9 +606,9 @@ class ExchangeNCL(Exchange):
             iorb = self.iorb(iatom)
             tmp = self.rho[np.ix_(iorb, iorb)]
             # *2 because there is a 1/2 in the paui_block_all function
-            rho[iatom] = np.array([np.trace(x) * 2 for x in pauli_block_all(tmp)])
-            self.charges[iatom] = np.imag(rho[iatom][0])
-            self.spinat[iatom, :] = np.imag(rho[iatom][1:])
+            rho[iatom] = np.array([np.trace(x) * 2 for x in pauli_block_all(tmp)]).real
+            self.charges[iatom] = rho[iatom][0]
+            self.spinat[iatom, :] = rho[iatom][1:]
         self.rho_dict = rho
         return self.rho_dict
 
@@ -676,7 +659,7 @@ class ExchangeNCL(Exchange):
         self.Ddict_NJT = Ddict_NJT
         return Ddict_NJT
 
-    def integrate(self, rhoRs, AijRs, AijRs_orb=None, method="simpson"):
+    def integrate(self, AijRs, AijRs_orb=None, method="simpson"):
         """
         AijRs: a list of AijR,
         wherer AijR: array of ((nR, n, n, 4,4), dtype=complex)
@@ -686,7 +669,7 @@ class ExchangeNCL(Exchange):
         elif method == "simpson":
             integrate = simpson_nonuniform
 
-        self.rho = integrate(self.contour.path, rhoRs)
+        # self.rho = integrate(self.contour.path, rhoRs)
         for iR, R in enumerate(self.R_ijatom_dict):
             for iatom, jatom in self.R_ijatom_dict[R]:
                 f = AijRs[(R, iatom, jatom)]
@@ -696,10 +679,10 @@ class ExchangeNCL(Exchange):
                         self.contour.path, AijRs_orb[(R, iatom, jatom)]
                     )
 
-    def get_AijR_rhoR(self, e):
-        GR, rhoR = self.G.get_GR(self.short_Rlist, energy=e, get_rho=True)
+    def get_AijR(self, e):
+        GR = self.G.get_GR(self.short_Rlist, energy=e, get_rho=False)
         AijR, AijR_orb = self.get_all_A(GR)
-        return AijR, AijR_orb, self.get_rho_e(rhoR)
+        return AijR, AijR_orb
 
     def save_AijR(self, AijRs, fname):
         result = dict(path=self.contour.path, AijRs=AijRs)
@@ -717,7 +700,6 @@ class ExchangeNCL(Exchange):
         """
         print("Green's function Calculation started.")
 
-        rhoRs = []
         AijRs = {}
 
         AijRs_orb = {}
@@ -726,11 +708,9 @@ class ExchangeNCL(Exchange):
 
         npole = len(self.contour.path)
         if self.np > 1:
-            # executor = ProcessPool(nodes=self.np)
-            # results = executor.map(self.get_AijR_rhoR, self.contour.path)
-            results = p_map(self.get_AijR_rhoR, self.contour.path, num_cpus=self.np)
+            results = p_map(self.get_AijR, self.contour.path, num_cpus=self.np)
         else:
-            results = map(self.get_AijR_rhoR, tqdm(self.contour.path, total=npole))
+            results = map(self.get_AijR, tqdm(self.contour.path, total=npole))
 
         for i, result in enumerate(results):
             for iR, R in enumerate(self.R_ijatom_dict):
@@ -750,7 +730,6 @@ class ExchangeNCL(Exchange):
                             AijRs_orb[(R, iatom, jatom)].append(
                                 result[1][R, iatom, jatom]
                             )
-            rhoRs.append(result[2])
         if self.np > 1:
             # executor.close()
             # executor.join()
@@ -758,8 +737,7 @@ class ExchangeNCL(Exchange):
             pass
 
         # self.save_AijRs(AijRs)
-        self.integrate(rhoRs, AijRs, AijRs_orb)
-
+        self.integrate(AijRs, AijRs_orb)
         self.get_rho_atom()
         self.A_to_Jtensor()
         self.A_to_Jtensor_orb()

TB2J/exchangeCL2.py

@@ -42,10 +42,10 @@ class ExchangeCL2(ExchangeCL):
             )
         self.norb = self.Gup.norb
         self.nbasis = self.Gup.nbasis + self.Gdn.nbasis
-        self.rho_up_list = []
-        self.rho_dn_list = []
-        self.rho_up = np.zeros((self.norb, self.norb), dtype=float)
-        self.rho_dn = np.zeros((self.norb, self.norb), dtype=float)
+        # self.rho_up_list = []
+        # self.rho_dn_list = []
+        self.rho_up = self.Gup.get_density_matrix()
+        self.rho_dn = self.Gdn.get_density_matrix()
         self.Jorb_list = defaultdict(lambda: [])
         self.JJ_list = defaultdict(lambda: [])
         self.JJ = defaultdict(lambda: 0.0j)
@@ -225,8 +225,6 @@ class ExchangeCL2(ExchangeCL):
             integrate = trapezoidal_nonuniform
         elif method == "simpson":
             integrate = simpson_nonuniform
-        self.rho_up = np.imag(integrate(self.contour.path, self.rho_up_list))
-        self.rho_dn = np.imag(integrate(self.contour.path, self.rho_dn_list))
         for R, ijpairs in self.R_ijatom_dict.items():
             for iatom, jatom in ijpairs:
                 self.Jorb[(R, iatom, jatom)] = integrate(
@@ -236,12 +234,11 @@ class ExchangeCL2(ExchangeCL):
                     self.contour.path, self.JJ_list[(R, iatom, jatom)]
                 )
 
-    def get_AijR_rhoR(self, e):
-        GR_up, rho_up = self.Gup.get_GR(self.short_Rlist, energy=e, get_rho=True)
-        GR_dn, rho_dn = self.Gdn.get_GR(self.short_Rlist, energy=e, get_rho=True)
-        rup, rdn = self.get_rho_e(rho_up, rho_dn)
+    def get_AijR(self, e):
+        GR_up = self.Gup.get_GR(self.short_Rlist, energy=e, get_rho=False)
+        GR_dn = self.Gdn.get_GR(self.short_Rlist, energy=e, get_rho=False)
         Jorb_list, JJ_list = self.get_all_A(GR_up, GR_dn)
-        return rup, rdn, Jorb_list, JJ_list
+        return Jorb_list, JJ_list
 
     def calculate_all(self):
         """
@@ -251,15 +248,13 @@ class ExchangeCL2(ExchangeCL):
 
         npole = len(self.contour.path)
         if self.np == 1:
-            results = map(self.get_AijR_rhoR, tqdm(self.contour.path, total=npole))
+            results = map(self.get_AijR, tqdm(self.contour.path, total=npole))
         else:
             # pool = ProcessPool(nodes=self.np)
             # results = pool.map(self.get_AijR_rhoR ,self.contour.path)
-            results = p_map(self.get_AijR_rhoR, self.contour.path, num_cpus=self.np)
+            results = p_map(self.get_AijR, self.contour.path, num_cpus=self.np)
         for i, result in enumerate(results):
-            rup, rdn, Jorb_list, JJ_list = result
-            self.rho_up_list.append(rup)
-            self.rho_dn_list.append(rdn)
+            Jorb_list, JJ_list = result
             for iR, R in enumerate(self.R_ijatom_dict):
                 for iatom, jatom in self.R_ijatom_dict[R]:
                     key = (R, iatom, jatom)

TB2J/exchange_pert.py

@@ -194,7 +194,7 @@ class ExchangePert(ExchangeNCL):
             e = self.contour.elist[ie]
             de = self.contour.de[ie]
             GR, dGdx = self.G.get_GR_and_dGRdx(self.Rlist, energy=e, dHdx=self.dHdx)
-            self.get_rho_e(GR, de)
+            # self.get_rho_e(GR, de)
             self.get_all_A(GR, dGdx, de)
             if self.calc_NJt:
                 self.get_N_e(GR, de)

TB2J/green.py

@@ -225,12 +225,22 @@ class TBGreen:
 
     def get_density_matrix(self):
         rho = np.zeros((self.nbasis, self.nbasis), dtype=complex)
-        for ik, _ in enumerate(self.kpts):
-            rho += (
-                (self.get_evecs(ik) * fermi(self.evals[ik], self.efermi))
-                @ self.get_evecs(ik).T.conj()
-                * self.kweights[ik]
-            )
+        if self.is_orthogonal:
+            for ik, _ in enumerate(self.kpts):
+                rho += (
+                    (self.get_evecs(ik) * fermi(self.evals[ik], self.efermi))
+                    @ self.get_evecs(ik).T.conj()
+                    * self.kweights[ik]
+                )
+        else:
+            for ik, _ in enumerate(self.kpts):
+                rho += (
+                    (self.get_evecs(ik) * fermi(self.evals[ik], self.efermi))
+                    @ self.get_evecs(ik).T.conj()
+                    @ self.get_Sk(ik)
+                    * self.kweights[ik]
+                )
+
         return rho
 
     def get_rho_R(self, Rlist):
@@ -238,9 +248,6 @@ class TBGreen:
         rho_R = np.zeros((nR, self.nbasis, self.nbasis), dtype=complex)
         for ik, kpt in enumerate(self.kpts):
             evec = self.get_evecs(ik)
-            # rhok=(evec * fermi(self.evals[ik], self.efermi)
-            #        ) @ evec.T.conj()
-            # print(fermi(self.evals[ik] , self.efermi))
             rhok = np.einsum(
                 "ib,b, bj-> ij", evec, fermi(self.evals[ik], self.efermi), evec.conj().T
             )

TB2J/manager.py

@@ -27,10 +27,6 @@ def gen_exchange(
     emin=-12.0,
     emax=0.0,
     nz=100,
-    height=0.2,
-    nz1=50,
-    nz2=200,
-    nz3=50,
     exclude_orbs=[],
     Rcut=None,
     ne=None,
@@ -113,10 +109,6 @@ Warning: Please check if the noise level of Wannier function Hamiltonian to make
                 emin=emin,
                 emax=emax,
                 nz=nz,
-                height=height,
-                nz1=nz1,
-                nz2=nz2,
-                nz3=nz3,
                 exclude_orbs=exclude_orbs,
                 Rcut=Rcut,
                 ne=ne,
@@ -137,10 +129,6 @@ Warning: Please check if the noise level of Wannier function Hamiltonian to make
                 emin=emin,
                 emax=emax,
                 nz=nz,
-                height=height,
-                nz1=nz1,
-                nz2=nz2,
-                nz3=nz3,
                 exclude_orbs=exclude_orbs,
                 Rcut=Rcut,
                 ne=ne,
@@ -185,10 +173,6 @@ Warning: Please check if the noise level of Wannier function Hamiltonian to make
             emin=emin,
             emax=emax,
             nz=nz,
-            height=height,
-            nz1=nz1,
-            nz2=nz2,
-            nz3=nz3,
             exclude_orbs=exclude_orbs,
             Rcut=Rcut,
             ne=ne,
@@ -237,10 +221,6 @@ Warning: Please check if the noise level of Wannier function Hamiltonian to make
             emin=emin,
             emax=emax,
             nz=nz,
-            height=height,
-            nz1=nz1,
-            nz2=nz2,
-            nz3=nz3,
             exclude_orbs=exclude_orbs,
             Rcut=Rcut,
             ne=ne,

TB2J/spinham/h_matrix.py

@@ -0,0 +1,68 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import aiida
+from aiida_tb2j.data import ExchangeData
+
+def plot_dispersion(bands, kpoint_labels, color='blue', title=None):
+
+    fig, axs = plt.subplots(1, 1, constrained_layout=True)
+    fig.set_size_inches(6, 6/1.618)
+
+    '''
+    Plot the bands
+    '''
+    kpoints = np.arange(len(bands))
+    axs.plot(kpoints, bands, color=color, linewidth=1.5)
+
+    '''
+    Plot the symmetry points
+    '''
+    bmin = bands.min(); bmax = bands.max()
+    ymin = bmin - 0.05*np.abs(bmin-bmax); ymax = bmax + 0.05*np.abs(bmax-bmin);
+    axs.set_xticks(kpoint_labels[0], kpoint_labels[1], fontsize=10)
+    axs.vlines(x=kpoint_labels[0], ymin=ymin, ymax=ymax, color='black', linewidth=0.5)
+    axs.set_xlim([0, len(kpoints)])
+    axs.set_ylim([ymin, ymax])
+
+    if title is not None:
+        plt.title(title, fontsize=10)
+
+    plt.show()
+
+
+if __name__ == "__main__":
+    
+    from argparse import ArgumentParser
+
+    parser = ArgumentParser()
+    parser.add_argument('-f', '--pickle_filename', type=str, help="Path of the 'TB2J.pickle' file.", required=True)
+    args = parser.parse_args()
+    
+    '''
+    Right now the implementation depends on AiiDA and so we must create and load an AiiDA profile,
+    even if we do not store any information on a data base.
+    '''
+    aiida.load_profile()
+    '''
+    Create an ExchangeData object with the informations from the TB2J.pickle file
+    '''
+    exchange = ExchangeData.load_tb2j(pickle_file=args.pickle_filename, isotropic=False, pbc=(True, True, True))
+    '''
+    Compute the magnon band structure along a high symmetry path generated with
+    the ASE package. The informations is stored in an AiiDA BandsData object.
+    Here tol is the symmetry tolerance to determine the space group of the system.
+    They are in units of eV
+    '''
+    magnon_data = exchange.get_magnon_bands(npoints=300, tol=1e-1, with_DMI=True, with_Jani=True)
+    magnon_bands = 1000*magnon_data.get_bands() # Convert to meV
+    raw_labels = [(k, '$\Gamma$') if s == 'GAMMA' else (k, s) for k, s in magnon_data.labels]
+    kpoint_labels = list( zip( *raw_labels ) )
+    plot_dispersion(magnon_bands, kpoint_labels, color='blue', title='Magnon Bands')
+    '''
+    We can also obtain the dynamical matrix h instead of the actual magnon bands. The result
+    is stored in a numpy array with shape (number of kpoints, 2*natoms, 2*natoms)
+    '''
+    kpoints = magnon_data.get_kpoints() # The shape of the kpoints must be (nkpoints, 3)
+    h_matrix = 1000*exchange._H_matrix(kpoints, with_DMI=True, with_Jani=True) # Convert to meV
+    h_dispersion = np.linalg.eigvalsh(h_matrix) # We can also get the eigenvectors with np.linalg.eigh
+    plot_dispersion(h_dispersion, kpoint_labels, color='red', title='h matrix dispersion')

TB2J/spinham/obtain_J.py

@@ -0,0 +1,79 @@
+import numpy as np
+from aiida_tb2j.data import ExchangeData
+from aiida_tb2j.data.exchange import get_rotation_arrays
+from itertools import combinations_with_replacement
+
+ux, uy, uz = np.eye(3).reshape((3, 1, 3))
+
+def combine_arrays(u, v):
+
+    return np.concatenate([u*v, np.roll(u, -1, axis=-1)*v, np.roll(v, -1, axis=-1)*u], axis=-1)
+
+def get_coefficients(magmoms, indices):
+
+    i, j = indices
+
+    U, V = zip(*[get_rotation_arrays(magmoms, u=u) for u in [ux, uy, uz]])
+    U = np.stack(U).swapaxes(0, 1)
+    V = np.stack(V).swapaxes(0, 1)
+
+    uc = combine_arrays(U[i], U[j].conj())
+    ur = combine_arrays(U[i], U[j])
+    uc2 = combine_arrays(U[i].conj(), U[j])
+    u = np.concatenate([uc, ur, uc2], axis=1)
+
+    return u, V
+
+def get_C(H0, u, V):
+
+    n = int(H0.shape[-1]/2)
+    upi = np.triu_indices(n)
+    dig = np.diag_indices(n)
+    
+    i, j = upi
+    AB0 = H0[:, [i, i, i+n], [j, j+n, j+n]]
+    AB0 = np.swapaxes(AB0, 0, 2).reshape(len(i), 9)
+    J0_flat = np.linalg.solve(u, AB0)
+
+    J0 = np.empty((n, n, 3, 3), dtype=complex)
+    J0[*upi] = J0_flat[:, [0, 6, 5, 3, 1, 7, 8, 4, 2]].reshape(-1, 3, 3)
+    J0 += J0.swapaxes(0, 1)
+    J0[*dig] = 0.0
+
+    C = np.array([np.diag(a) for a in np.einsum('imx,ijxy,jmy->mi', V, 2*J0, V)]) 
+
+    return C
+
+def get_J(H, kpoints, exchange):
+
+    n = int(H.shape[-1]/2)
+    upi = np.triu_indices(n)
+    dig = np.diag_indices(n)
+    i, j = upi
+
+    magmoms = exchange.magmoms()[np.unique(exchange.pairs)]
+    magmoms /= np.linalg.norm(magmoms, axis=-1).reshape(-1, 1)
+    u, V = get_coefficients(magmoms, indices=upi)
+
+    H0 = np.stack([1000*exchange._H_matrix(kpoints=np.zeros((1, 3)), with_DMI=True, with_Jani=True, u=u) for u in [ux, uy, uz]])[:, 0, :, :]
+    C = get_C(H0, u, V)
+    H[:, :, :n, :n] += C.reshape(3, 1, n, n)
+    H[:, :, n:, n:] += C.reshape(3, 1, n, n)
+
+    AB = H[:, :, [i, i, i+n], [j, j+n, j+n]]
+    AB[:, :, 2, :] = AB[:, ::-1, 2, :]
+    AB = np.moveaxis(AB, [2, 3], [1, 0]).reshape(len(i), 9, -1)
+
+    vectors = exchange.get_vectors()
+    exp_summand = np.exp( -2j*np.pi*vectors @ kpoints.T )
+    nAB = np.einsum('nik,ndk->nid', AB, exp_summand) / len(kpoints)
+    
+    ii = np.where(i == j)
+    i0 = np.where(np.linalg.norm(vectors, axis=-1) == 0.0)
+    J = np.linalg.solve(u, nAB).swapaxes(1, 2)
+    J = J[:, :, [0, 6, 5, 3, 1, 7, 8, 4, 2]].reshape(len(i), -1, 3, 3)
+    J *= -1
+    J[ii] *= 2
+    J[i0] *= 0
+
+    return J

{TB2J-0.8.2.5.data → TB2J-0.8.2.8.data}/scripts/siesta2J.py

@@ -54,19 +54,9 @@ def run_siesta2J():
         action="store_true",
         default=False,
     )
-    # parser.add_argument(
-    #    '--height',
-    #    help=
-    #    'energy contour, a small number (often between 0.1 to 0.5, default 0.2)',
-    #    type=float,
-    #    default=0.1)
     parser.add_argument(
         "--nz", help="number of integration steps. Default: 50", default=50, type=int
     )
-    # parser.add_argument(
-    #    '--nz2', help='number of steps 2, default: 200', default=200, type=int)
-    # parser.add_argument(
-    #    '--nz3', help='number of steps 3, default: 50', default=50, type=int)
     parser.add_argument(
         "--cutoff",
         help="The minimum of J amplitude to write, (in eV). Default: 1e-5 eV",

{TB2J-0.8.2.5.data → TB2J-0.8.2.8.data}/scripts/wann2J.py

@@ -86,24 +86,6 @@ def run_wann2J():
         default=100,
         type=int,
     )
-    # parser.add_argument(
-    #    '--height',
-    #    help=
-    #    'energy contour, a small number (often between 0.1 to 0.5, default 0.1)',
-    #    type=float,
-    #    default=0.1)
-    # parser.add_argument('--nz1',
-    #                    help='number of steps 1, default: 50',
-    #                    default=50,
-    #                    type=int)
-    # parser.add_argument('--nz2',
-    #                    help='number of steps 2, default: 200',
-    #                    default=200,
-    #                    type=int)
-    # parser.add_argument('--nz3',
-    #                    help='number of steps 3, default: 50',
-    #                    default=50,
-    #                    type=int)
     parser.add_argument(
         "--cutoff",
         help="The minimum of J amplitude to write, (in eV), default is 1e-5 eV",
@@ -196,10 +178,6 @@ def run_wann2J():
         emin=args.emin,
         emax=args.emax,
         nz=args.nz,
-        # height=args.height,
-        # nz1=args.nz1,
-        # nz2=args.nz2,
-        # nz3=args.nz3,
         use_cache=args.use_cache,
         np=args.np,
         description=args.description,

{TB2J-0.8.2.5.dist-info → TB2J-0.8.2.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: TB2J
-Version: 0.8.2.5
+Version: 0.8.2.8
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Home-page: UNKNOWN
 Author: Xu He

{TB2J-0.8.2.5.dist-info → TB2J-0.8.2.8.dist-info}/RECORD

@@ -1,24 +1,24 @@
 TB2J/Jdownfolder.py,sha256=Nw2ixvn2Uq-o1wficz6rdaYHjfRN3U_kQCvrNJGNb68,6980
 TB2J/Jtensor.py,sha256=0fhfOcfVQGu75gytEnApKWTJZfg9ksKJ0anJgco5wRQ,3179
-TB2J/Oiju.py,sha256=yQMfxQGnOSLbuTS22upkEFsJ9UAZk7wFaWynvg1NVdA,3595
-TB2J/Oiju_epc.py,sha256=sqjLIuWWT-d0uH2O7-6mobsUYQjHP5GyGlmdYqvkXFk,7332
-TB2J/__init__.py,sha256=0JyzwzYqH09rIndCHr8uL-Jd2dG9GDEMaojcYFCc0kM,24
+TB2J/Oiju.py,sha256=cNGv8N5uH_swGq7cnAt2OyiDfqtjLlLrwseGu0E4iaM,3383
+TB2J/Oiju_epc.py,sha256=oytM3NYW7nWmklrGgNlqwIpI_JYv_hb7ZnR4o9nYNog,6809
+TB2J/__init__.py,sha256=am9nQoXsrjfFlI37cMwyeG0iWxg4QrTRX090gUPnDJ4,24
 TB2J/basis.py,sha256=DFo6_QUwjBwisP6zGxvoO0lpGTMDPAOkiL9giNCjOjA,1558
 TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=aw8LX6wVFCRPhcpkzuI0jGnHisvk4cezvUhkF_6Yx94,2633
 TB2J/cut_cell.py,sha256=kr9WeQhBQLm8QXL2B3NcsSYmSw-OAtJk3f9wksAOZbs,2952
 TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
-TB2J/exchange.py,sha256=jtgjtHfNxTUOXFdUn5gjwOq0KZSj7nPK5OpV9Trcb2w,30380
-TB2J/exchangeCL2.py,sha256=mODZU5KKWb2q5KzZAXoAt90vNjjFeLc8L_LySicWV3w,11350
-TB2J/exchange_pert.py,sha256=52XWeVW7JZ_JRUXEfqRfgia8NE_K1R9a0IrJZoLh8gY,8521
+TB2J/exchange.py,sha256=UmZU5h91BPql3ylNALvzMJWTxkfzObZ1OVMxj2Hmp7A,29570
+TB2J/exchangeCL2.py,sha256=TIr-d2X56AiGe4qEhyXyZhRuwXvQG6clJMwDmjnTOaE,10985
+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
-TB2J/green.py,sha256=aaXFZn8B60kjsvThoBk0fVi5jm5RJBb-LT4E9XCFo2w,13169
+TB2J/green.py,sha256=X-D8UZcIyz6zh_0W9VgUUv5yXPP3KWJ6C03m6CMWE3o,13377
 TB2J/greentest.py,sha256=2ISSfhor9ecSEOi_E6b4Cv26wEIQlwlzca0ru8z44_E,1603
 TB2J/io_merge.py,sha256=2dYrQFHSnb_8fwbQiVod9GyaT-BotawA26eagXWUyMg,15265
 TB2J/kpoints.py,sha256=6XK2KqTncidEq3o9GuO6VEZRPNTRtWeXg9QfcV-9smI,532
-TB2J/manager.py,sha256=x5BerzE7HU70U6bUZZEyqsI1_YYzvSbbnJ6wqTIHRb8,15817
+TB2J/manager.py,sha256=4-4x9jJRHpUEqJuhc5HqpXfh2-Ze5G9Wg8gOtn-AqR4,15372
 TB2J/mathutils.py,sha256=tHA6q3KPDpXLIbZHdDZ2NU5s886VVM_oEG490zQ6Ris,300
 TB2J/myTB.py,sha256=cm9Kkyzi686QyoxrR3lm4rsSnE6Imee3-j2xM78XnGI,17721
 TB2J/orbmap.py,sha256=RCMJkOPGbfPrcZzcc5ia1ZMKBQWxGcyj8W1ve8BJaEw,6669
@@ -53,8 +53,10 @@ TB2J/io_exchange/io_vampire.py,sha256=UllC4twf06_q2vBCnAYFzEDGvS8mSefwQXDquBuyc0
 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/h_matrix.py,sha256=MfHIz6RViKkEB3Mu-WcwNx5uk7A5sjAlbqVG9wYA4xk,2784
 TB2J/spinham/hamiltonian.py,sha256=OfsjlGIgFwpXaohopZcgPamSfjm3X46_zc245eyTr_A,16607
 TB2J/spinham/hamiltonian_terms.py,sha256=7e84tfEjvAfZltUkrSWi1sUEiW_itLKy83lxi5iBpcQ,9714
+TB2J/spinham/obtain_J.py,sha256=sg8tiCRRLEN57Olb3MHIuqkDhAkmu-w87AkM00ylXtA,2401
 TB2J/spinham/plot.py,sha256=tLLNqFAATVrP1kmSVLPKzn686i-CUyqu4qgOcs-okHI,6599
 TB2J/spinham/qsolver.py,sha256=Sr9I3aGfVNYn5wzwPx1QonHe6ZZUXBAujWRa7nTA5u4,4986
 TB2J/spinham/spin_api.py,sha256=oN3AKg1WQl0YzR4f5ealcJOaVoAy8d7HodIwrbXvQeY,2219
@@ -63,17 +65,17 @@ 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-0.8.2.5.data/scripts/TB2J_downfold.py,sha256=F9oImXFysejCMP7eIBjbCX2jdHFOCvDW5beF1sG-UM8,1854
-TB2J-0.8.2.5.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-TB2J-0.8.2.5.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-TB2J-0.8.2.5.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-TB2J-0.8.2.5.data/scripts/TB2J_merge.py,sha256=uZKLM__EyCHwxrQvx3Wd73dOEADp_SqfYC8KQvA-N9g,1622
-TB2J-0.8.2.5.data/scripts/TB2J_rotate.py,sha256=XPacPb7-DaFafBXFdWuNW_eNbjd5XPdNhBRNYhge_cg,634
-TB2J-0.8.2.5.data/scripts/abacus2J.py,sha256=M4B07lvTCDczTPTqvnDh_PERzCARAd09TLKv4aIdSQM,4408
-TB2J-0.8.2.5.data/scripts/siesta2J.py,sha256=Q_kvdgE34JJKVUMgBCSe07kARge0XULJ9B6z8hQFu6M,4706
-TB2J-0.8.2.5.data/scripts/wann2J.py,sha256=0g8Y5RbsYgV7iuoRQEeOnpaBy3oNpRfiw1dy6lWD13E,6520
-TB2J-0.8.2.5.dist-info/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-TB2J-0.8.2.5.dist-info/METADATA,sha256=TzvynzouHOxcwMZApLg3DQSXVHbg1m2UqNoehB6FP1Y,1464
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-TB2J-0.8.2.5.dist-info/RECORD,,
+TB2J-0.8.2.8.data/scripts/TB2J_downfold.py,sha256=F9oImXFysejCMP7eIBjbCX2jdHFOCvDW5beF1sG-UM8,1854
+TB2J-0.8.2.8.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
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+TB2J-0.8.2.8.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
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