TB2J 0.9.0__py3-none-any.whl → 0.9.0.2__py3-none-any.whl

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/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/MAE.py

@@ -0,0 +1,188 @@
+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.model.occupations import Occupations
+#from TB2J.abacus.abacus_wrapper import AbacusSplitSOCParser
+from HamiltonIO.abacus.abacus_wrapper import AbacusSplitSOCParser
+from HamiltonIO.siesta import SislParser, SiestaHamiltonian
+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)
+        nangles = len(thetas)
+        for i in tqdm.trange(nangles):
+            theta = thetas[i]
+            phi = phis[i]
+            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()
+    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:5.3f}, {psi:5.3f}, {e:10.9f}\n")
+    return es
+
+
+def siesta_get_MAE(fdf_fname, kmesh, thetas, phis, gamma=True, outfile="MAE.txt"):
+    """ """
+    model= SislParser(fdf_fname=fdf_fname, read_H_soc=True).get_model()
+    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")
+                f.write(f"{theta:5.3f}, {psi:5.3f}, {e:10.9f}\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/__init__.py

@@ -1 +1 @@
-__version__ = "0.9.0"
+__version__ = "0.9.0.1"