TB2J 0.9.0.1__tar.gz → 0.9.2rc0__tar.gz

{TB2J-0.9.0.1 → tb2j-0.9.2rc0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: TB2J
-Version: 0.9.0.1
+Version: 0.9.2rc0
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com

{TB2J-0.9.0.1 → tb2j-0.9.2rc0}/TB2J/Jdownfolder.py

@@ -17,9 +17,23 @@ def ind_to_indn(ind, n=3):
     return indn
 
 
+class JR_model:
+    def __init__(self, JR, Rlist):
+        self.JR = JR
+        self.Rlist = Rlist
+        self.nR = len(Rlist)
+
+    def get_Jq(self, q):
+        Jq = np.zeros(self.JR[0].shape, dtype=complex)
+        for iR, R in enumerate(self.Rlist):
+            phase = np.exp(2.0j * np.pi * np.dot(q, R))
+            Jq += self.JR[iR] * phase
+        return Jq
+
+
 class JDownfolder:
     def __init__(self, JR, Rlist, iM, iL, qmesh, iso_only=False):
-        self.JR = JR
+        self.model = JR_model(JR, Rlist)
         self.Rlist = Rlist
         self.nR = len(Rlist)
         self.nM = len(iM)
@@ -34,25 +48,18 @@ class JDownfolder:
         self.nLn = self.nL * 3
         self.iso_only = iso_only
 
-    def get_Jq(self, q):
-        Jq = np.zeros(self.JR[0].shape, dtype=complex)
-        for iR, R in enumerate(self.Rlist):
-            phase = np.exp(2.0j * np.pi * np.dot(q, R))
-            Jq += self.JR[iR] * phase
-        return Jq
-
     def get_JR(self):
         JR_downfolded = np.zeros((self.nR, self.nMn, self.nMn), dtype=float)
         Jq_downfolded = np.zeros((self.nqpt, self.nMn, self.nMn), dtype=complex)
         self.iMn = ind_to_indn(self.iM, n=3)
         self.iLn = ind_to_indn(self.iL, n=3)
         for iq, q in enumerate(self.qpts):
-            Jq = self.get_Jq(q)
+            Jq = self.model.get_Jq(q)
             Jq_downfolded[iq] = self.downfold_oneq(Jq)
             for iR, R in enumerate(self.Rlist):
                 phase = np.exp(-2.0j * np.pi * np.dot(q, R))
                 JR_downfolded[iR] += np.real(Jq_downfolded[iq] * phase / self.nqpt)
-        return JR_downfolded
+        return JR_downfolded, self.Rlist
 
     def downfold_oneq(self, J):
         JMM = J[np.ix_(self.iMn, self.iMn)]
@@ -63,17 +70,80 @@ class JDownfolder:
         return Jn
 
 
+class PWFDownfolder:
+    def __init__(self, JR, Rlist, iM, iL, qmesh, atoms=None, iso_only=False, **kwargs):
+        from lawaf.interfaces.magnon.magnon_downfolder import (
+            MagnonWrapper,
+            MagnonDownfolder,
+        )
+
+        model = MagnonWrapper(JR, Rlist, atoms)
+        wann = MagnonDownfolder(model)
+        # Downfold the band structure.
+        index_basis = []
+        for i in iM:
+            index_basis += list(range(i * 3, i * 3 + 3))
+        params = dict(
+            method="projected",
+            # method="maxprojected",
+            kmesh=qmesh,
+            nwann=len(index_basis),
+            selected_basis=index_basis,
+            # anchors={(0, 0, 0): (-1, -2, -3, -4)},
+            # anchors={(0, 0, 0): ()},
+            # use_proj=True,
+            enhance_Amn=2.0,
+        )
+        params.update(kwargs)
+        wann.set_parameters(**params)
+        print("begin downfold")
+        ewf = wann.downfold()
+        ewf.save_hr_pickle("downfolded_JR.pickle")
+
+        # Plot the band structure.
+        wann.plot_band_fitting(
+            # kvectors=np.array([[0, 0, 0], [0.5, 0, 0],
+            #                   [0.5, 0.5, 0], [0, 0, 0],
+            #                   [.5, .5, .5]]),
+            # knames=['$\Gamma$', 'X', 'M', '$\Gamma$', 'R'],
+            cell=model.atoms.cell,
+            supercell_matrix=None,
+            npoints=100,
+            efermi=None,
+            erange=None,
+            fullband_color="blue",
+            downfolded_band_color="green",
+            marker="o",
+            ax=None,
+            savefig="downfold_band.png",
+            show=True,
+        )
+        self.JR_downfolded = ewf.HwannR
+        self.Rlist = ewf.Rlist
+
+    def get_JR(self):
+        return self.JR_downfolded, self.Rlist
+
+
 class JDownfolder_pickle:
     def __init__(
-        self, inpath, metals, ligands, outpath, qmesh=[7, 7, 7], iso_only=False
+        self,
+        inpath,
+        metals,
+        ligands,
+        outpath,
+        qmesh=[7, 7, 7],
+        iso_only=False,
+        method="pwf",
+        **kwargs
     ):
         self.exc = SpinIO.load_pickle(path=inpath, fname="TB2J.pickle")
 
         self.iso_only = (self.exc.dmi_ddict is None) or iso_only
-
         self.metals = metals
         self.ligands = ligands
         self.outpath = outpath
+        self.method = method
 
         # read atomic structure
         self.atoms = self.exc.atoms
@@ -83,7 +153,8 @@ class JDownfolder_pickle:
         self.Rcut = None
         self._build_atom_index()
         self._prepare_distance()
-        self._downfold()
+        Jd, Rlist = self._downfold(**kwargs)
+        self._Jd_to_exchange(Jd, Rlist)
 
     def _build_atom_index(self):
         self.magnetic_elements = self.metals
@@ -101,18 +172,33 @@ class JDownfolder_pickle:
         self.nL = len(self.iL)
         self.nsite = self.nM + self.nL
 
-    def _downfold(self):
+    def _downfold(self, **kwargs):
         JR2 = self.exc.get_full_Jtensor_for_Rlist(asr=True)
-        d = JDownfolder(
-            JR2,
-            self.exc.Rlist,
-            iM=self.iM,
-            iL=self.iL,
-            qmesh=self.qmesh,
-            iso_only=self.iso_only,
-        )
-        Jd = d.get_JR()
+        if self.method == "lowdin":
+            d = JDownfolder(
+                JR2,
+                self.exc.Rlist,
+                iM=self.iM,
+                iL=self.iL,
+                qmesh=self.qmesh,
+                iso_only=self.iso_only,
+            )
+            Jd, Rlist = d.get_JR()
+        else:
+            d = PWFDownfolder(
+                JR2,
+                self.exc.Rlist,
+                iM=self.iM,
+                iL=self.iL,
+                qmesh=self.qmesh,
+                atoms=self.atoms,
+                iso_only=self.iso_only,
+                **kwargs
+            )
+            Jd, Rlist = d.get_JR()
+        return Jd, Rlist
 
+    def _Jd_to_exchange(self, Jd, Rlist):
         self._prepare_distance()
         self._prepare_index_spin()
         self.Jdict = {}
@@ -123,7 +209,7 @@ class JDownfolder_pickle:
             self.DMIdict = {}
             self.Janidict = {}
 
-        for iR, R in enumerate(d.Rlist):
+        for iR, R in enumerate(Rlist):
             for i, ispin in enumerate(self.index_spin):
                 for j, jspin in enumerate(self.index_spin):
                     if ispin >= 0 and jspin >= 0:

{TB2J-0.9.0.1 → tb2j-0.9.2rc0}/TB2J/Jtensor.py

@@ -79,7 +79,7 @@ def combine_J_tensor(Jiso=0.0, D=np.zeros(3), Jani=np.zeros((3, 3), dtype=float)
     :param Jani: 3x3 matrix anisotropic exchange
     :returns:  A 3x3 matrix, the exchange paraemter in tensor form.
     """
-    Jtensor = np.zeros((3, 3), dtype=float)
+    Jtensor = np.zeros((3, 3), dtype=complex)
     if Jiso is not None:
         Jtensor += np.eye(3, dtype=float) * Jiso
     if Jani is not None:

tb2j-0.9.2rc0/TB2J/MAE.py

@@ -0,0 +1,185 @@
+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.mathutils.rotate_spin import spherical_to_cartesian
+from HamiltonIO.occupations import Occupations
+from TB2J.abacus.abacus_wrapper import AbacusSplitSOCParser
+from HamiltonIO.siesta import SislWrapper
+import tqdm
+
+
+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
+
+
+class MAE:
+    def __init__(self, model, kmesh, gamma=True, width=0.1, nel=None):
+        self.model = model
+        if nel is not None:
+            self.model.nel = nel
+        self.kpts = monkhorst_pack(kmesh, gamma_center=gamma)
+        self.kweights = np.ones(len(self.kpts), dtype=float) / len(self.kpts)
+        self.width = width
+
+    def get_band_energy(self):
+        evals, evecs = self.model.solve_all(self.kpts)
+        occ = get_occupation(evals, self.kweights, self.model.nel, width=self.width)
+        eband = np.sum(evals * occ * self.kweights[:, np.newaxis])
+        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_vs_angles(
+        self,
+        thetas,
+        phis,
+    ):
+        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 tqdm.tqdm(enumerate(zip(thetas, phis))):
+            self.model.set_Hsoc_rotation_angle([theta, phi])
+            e = self.get_band_energy()
+            es.append(e)
+            # es2.append(e2)
+        return es
+
+
+def get_model_energy(model, kmesh, gamma=True):
+    ham = MAE(model, kmesh, gamma=gamma)
+    return ham.get_band_energy()
+
+
+def abacus_get_MAE(
+    path_nosoc, path_soc, kmesh, thetas, psis, gamma=True, outfile="MAE.txt", nel=None
+):
+    """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()
+    model.nel = 16
+    ham = MAE(model, kmesh, gamma=gamma)
+    es = ham.get_band_energy_vs_angles(thetas, psis)
+    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 siesta_get_MAE(fdf_fname, kmesh, thetas, phis, gamma=True, outfile="MAE.txt"):
+    """ """
+    parser = SiestaParser(fdf_fname=fdf_fname, read_H_soc=True)
+    model = parser.parse()
+    ham = MAE(model, kmesh, gamma=gamma)
+    es = ham.get_band_energy_vs_angles(thetas, phis)
+    if outfile:
+        with open(outfile, "w") as f:
+            f.write("#theta, psi, energy\n")
+            for theta, psi, e in zip(thetas, phis, 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 = MAE(model, kmesh, gamma=True)
+    # 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),
+        rotation_axis="y",
+        initial_direction=(0, 0, 1),
+        npoints=11,
+    )
+    # print the table of thetas and es, es2
+    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-0.9.0.1 → tb2j-0.9.2rc0}/TB2J/abacus/abacus_wrapper.py

@@ -7,6 +7,8 @@ from pathlib import Path
 import os
 import numpy as np
 from scipy.linalg import eigh
+from copy import deepcopy
+from TB2J.mathutils.rotate_spin import rotate_Matrix_from_z_to_spherical
 from TB2J.utils import symbol_number_list
 from TB2J.myTB import AbstractTB
 from TB2J.abacus.abacus_api import read_HR_SR
@@ -15,17 +17,55 @@ from TB2J.abacus.stru_api import read_abacus, read_abacus_out
 
 
 class AbacusWrapper(AbstractTB):
-    def __init__(self, HR, SR, Rlist, nbasis, nspin=1):
-        self.R2kfactor = -2j * np.pi
+    def __init__(
+        self, HR, SR, Rlist, nbasis, nspin=1, HR_soc=None, HR_nosoc=None, nel=None
+    ):
+        self.R2kfactor = 2j * np.pi
         self.is_orthogonal = False
+        self.split_soc = False
         self._name = "ABACUS"
-        self.HR = HR
+        self._HR = HR
         self.SR = SR
         self.Rlist = Rlist
         self.nbasis = nbasis
         self.nspin = nspin
         self.norb = nbasis * nspin
+        self.nel = nel
         self._build_Rdict()
+        if HR_soc is not None:
+            self.set_HR_soc(HR_soc=HR_soc, HR_nosoc=HR_nosoc, HR_full=HR)
+        self.soc_rotation_angle = 0.0
+
+    def set_HR_soc(self, HR_soc=None, HR_nosoc=None, HR_full=None):
+        self.split_soc = True
+        self.HR_soc = HR_soc
+        if HR_nosoc is not None:
+            self.HR_nosoc = HR_nosoc
+        if HR_full is not None:
+            self.HR_nosoc = HR_full - HR_soc
+
+    def set_Hsoc_rotation_angle(self, angle):
+        """
+        Set the rotation angle for SOC part of Hamiltonian
+        """
+        self.soc_rotation_angle = angle
+
+    @property
+    def HR(self):
+        if self.split_soc:
+            _HR = np.zeros_like(self.HR_soc)
+            for iR, _ in enumerate(self.Rlist):
+                theta, phi = self.soc_rotation_angle
+                _HR[iR] = self.HR_nosoc[iR] + rotate_Matrix_from_z_to_spherical(
+                    self.HR_soc[iR], theta, phi
+                )
+            return _HR
+        else:
+            return self._HR
+
+    @HR.setter
+    def set_HR(self, HR):
+        self._HR = HR
 
     def _build_Rdict(self):
         if hasattr(self, "Rdict"):
@@ -62,6 +102,8 @@ class AbacusWrapper(AbstractTB):
                 S = self.SR[iR] * phase
                 # Sk += S + S.conjugate().T
                 Sk += S
+                # Hk = (Hk + Hk.conj().T)/2
+                # Sk = (Sk + Sk.conj().T)/2
         elif convention == 1:
             # TODO: implement the first convention (the r convention)
             raise NotImplementedError("convention 1 is not implemented yet.")
@@ -74,6 +116,14 @@ class AbacusWrapper(AbstractTB):
         Hk, Sk = self.gen_ham(k, convention=convention)
         return eigh(Hk, Sk)
 
+    def solve_all(self, kpts, convention=2):
+        nk = len(kpts)
+        evals = np.zeros((nk, self.nbasis), dtype=float)
+        evecs = np.zeros((nk, self.nbasis, self.nbasis), dtype=complex)
+        for ik, k in enumerate(kpts):
+            evals[ik], evecs[ik] = self.solve(k, convention=convention)
+        return evals, evecs
+
     def HSE_k(self, kpt, convention=2):
         H, S = self.gen_ham(tuple(kpt), convention=convention)
         evals, evecs = eigh(H, S)
@@ -196,6 +246,20 @@ class AbacusParser:
             raise ValueError(f"EFERMI not found in the {str(fname)}  file.")
         return efermi
 
+    def read_nel(self):
+        """
+        Reading the number of electrons from the scf log file.
+        """
+        fname = str(Path(self.outpath) / "running_scf.log")
+        nel = None
+        with open(fname, "r") as myfile:
+            for line in myfile:
+                if "NELECT" in line:
+                    nel = float(line.split()[2])
+        if nel is None:
+            raise ValueError(f"NELECT not found in the {str(fname)}  file.")
+        return nel
+
     def get_basis(self):
         slist = symbol_number_list(self.atoms)
         if self.spin == "collinear":
@@ -213,6 +277,42 @@ class AbacusParser:
             return basis
 
 
+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_nosoc, SR = self.parser_nosoc.Read_HSR_noncollinear()
+        nbasis2, Rlist2, HR2, SR2 = self.parser_soc.Read_HSR_noncollinear()
+        # print(HR[0])
+        HR_soc = HR2 - HR_nosoc
+        model = AbacusWrapper(
+            HR=None,
+            SR=SR,
+            Rlist=Rlist,
+            nbasis=nbasis,
+            nspin=2,
+            HR_soc=HR_soc,
+            HR_nosoc=HR_nosoc,
+        )
+        model.efermi = self.parser_soc.efermi
+        model.basis = self.parser_nosoc.basis
+        model.atoms = self.parser_nosoc.atoms
+        return model
+
+
 def test_abacus_wrapper_collinear():
     outpath = "/Users/hexu/projects/TB2J_abacus/abacus-tb2j-master/abacus_example/case_Fe/1_no_soc/OUT.Fe"
     parser = AbacusParser(outpath=outpath, spin=None, binary=False)
@@ -221,7 +321,6 @@ def test_abacus_wrapper_collinear():
     # parser.read_HSR_collinear()
     model_up, model_dn = parser.get_models()
     H, S, E, V = model_up.HSE_k([0, 0, 0])
-    # print(H.shape)
     # print(H.diagonal().real)
     # print(model_up.get_HR0().diagonal().real)
     print(parser.efermi)

tb2j-0.9.2rc0/TB2J/abacus/test_density_matrix.py

@@ -0,0 +1,38 @@
+from scipy.linalg import eigh
+import numpy as np
+
+
+def gen_random_hermitean_matrix(n):
+    A = np.random.rand(n, n) + 1j * np.random.rand(n, n)
+    return A + A.conj().T
+
+
+def gen_overlap_matrix(n):
+    A = np.random.rand(n, n) + 1j * np.random.rand(n, n)
+    return np.dot(A, A.conj().T)
+
+
+def fermi_function(x, ef, beta):
+    return 1.0 / (np.exp(beta * (x - ef)) + 1)
+
+
+def test():
+    n = 10
+    A = gen_random_hermitean_matrix(n)
+    S = gen_overlap_matrix(n)
+    beta = 0.1
+    ef = 0
+
+    evals, evecs = eigh(A, S)
+
+    etot = np.sum(evals * fermi_function(evals, ef, beta))
+
+    rho = np.einsum("ib,b,jb->ij", evecs, fermi_function(evals, ef, beta), evecs.conj())
+
+    etot2 = np.trace(np.dot(A, rho))
+
+    print(etot, etot2)
+
+
+if __name__ == "__main__":
+    test()