TB2J 0.9.10.1__py3-none-any.whl → 0.9.10.3__py3-none-any.whl

TB2J/Jdownfolder.py

@@ -35,6 +35,7 @@ class JR_model:
 
 class JDownfolder:
     def __init__(self, JR, Rlist, iM, iL, qmesh, iso_only=False):
+        self.nxyz = 1 if iso_only else 3
         self.model = JR_model(JR, Rlist)
         self.Rlist = Rlist
         self.nR = len(Rlist)
@@ -53,15 +54,14 @@ class JDownfolder:
     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)
+        self.iMn = ind_to_indn(self.iM, n=self.nxyz)
+        self.iLn = ind_to_indn(self.iL, n=self.nxyz)
         for iq, q in enumerate(self.qpts):
             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, self.Rlist
 
     def downfold_oneq(self, J):
         JMM = J[np.ix_(self.iMn, self.iMn)]
@@ -79,12 +79,13 @@ class PWFDownfolder:
             MagnonWrapper,
         )
 
-        model = MagnonWrapper(JR, Rlist, atoms)
+        model = MagnonWrapper(JR, Rlist, atoms, align_evecs=not iso_only)
         wann = MagnonDownfolder(model)
         # Downfold the band structure.
         index_basis = []
+        self.nxyz = 1 if iso_only else 3
         for i in iM:
-            index_basis += list(range(i * 3, i * 3 + 3))
+            index_basis += list(range(i * self.nxyz, i * self.nxyz + self.nxyz))
         params = dict(
             method="projected",
             # method="maxprojected",
@@ -93,8 +94,10 @@ class PWFDownfolder:
             selected_basis=index_basis,
             # anchors={(0, 0, 0): (-1, -2, -3, -4)},
             # anchors={(0, 0, 0): ()},
-            # use_proj=True,
-            enhance_Amn=1.4,
+            # weight_func="Gauss",
+            # weight_func_params=(-0.143, 0.04),
+            use_proj=True,
+            enhance_Amn=0.0,
         )
         params.update(kwargs)
         wann.set_parameters(**params)
@@ -176,7 +179,19 @@ class JDownfolder_pickle:
         self.nsite = self.nM + self.nL
 
     def _downfold(self, **kwargs):
-        JR2 = self.exc.get_full_Jtensor_for_Rlist(order="i3j3_2D", asr=True)
+        if self.iso_only:
+            JR2 = self.exc.get_full_Jtensor_for_Rlist(
+                order="ij", asr=True, DMI=False, Jani=False
+            )
+            # magmoms = self.exc.magmoms
+            # magmoms of magnetic atoms (metal + ligand)
+            # mmagmoms = magmoms[self.iM + self.iL]
+            # sqrt_magmoms = np.sqrt(np.abs(mmagmoms))
+            # magmoms_mat = np.outer(sqrt_magmoms, sqrt_magmoms)
+            # JR2 = JR2 / magmoms_mat
+        else:
+            JR2 = self.exc.get_full_Jtensor_for_Rlist(order="i3j3_2D", asr=True)
+
         if self.method.lower() == "lowdin":
             d = JDownfolder(
                 JR2,
@@ -199,6 +214,8 @@ class JDownfolder_pickle:
                 **kwargs,
             )
             Jd, Rlist = d.get_JR()
+            # metal_sqrt_magmoms = np.sqrt(np.abs(self.exc.magmoms[self.iM]))
+            # Jd = Jd * np.outer(metal_sqrt_magmoms, metal_sqrt_magmoms)
         return Jd, Rlist
 
     def _Jd_to_exchange(self, Jd, Rlist):
@@ -217,15 +234,21 @@ class JDownfolder_pickle:
                 for j, jspin in enumerate(self.index_spin):
                     if ispin >= 0 and jspin >= 0:
                         if not (tuple(R) == (0, 0, 0) and ispin == jspin):
-                            # self interaction.
-                            J33 = Jd[
-                                iR, ispin * 3 : ispin * 3 + 3, jspin * 3 : jspin * 3 + 3
-                            ]
-                            J, DMI, Jani = decompose_J_tensor(J33)
-                            self.Jdict[(tuple(R), ispin, jspin)] = J
-                            if not self.iso_only:
-                                self.DMIdict[(tuple(R), ispin, jspin)] = DMI
-                                self.Janidict[(tuple(R), ispin, jspin)] = Jani
+                            if self.iso_only:
+                                J = Jd[iR, ispin, jspin]
+                                self.DMIdict = None
+                                self.Janidict = None
+                                self.Jdict[(tuple(R), ispin, jspin)] = J.real
+                            else:
+                                J33 = Jd[
+                                    iR,
+                                    ispin * 3 : ispin * 3 + 3,
+                                    jspin * 3 : jspin * 3 + 3,
+                                ]
+                                J, DMI, Jani = decompose_J_tensor(J33)
+                                self.Jdict[(tuple(R), ispin, jspin)] = J.real
+                                self.DMIdict[(tuple(R), ispin, jspin)] = DMI.real
+                                self.Janidict[(tuple(R), ispin, jspin)] = Jani.real
 
         io = SpinIO(
             atoms=self.atoms,

TB2J/exchange.py

@@ -202,7 +202,6 @@ class Exchange(ExchangeParams):
                         include_only=self.include_orbs[syms[iatom]],
                     )
                 else:
-                    # print(f"orbs: {orbs}")
                     mmat, reduced_orbs = map_orbs_matrix(
                         orbs, spinor=not (self._is_collinear), include_only=None
                     )

TB2J/exchangeCL2.py

@@ -186,15 +186,17 @@ class ExchangeCL2(ExchangeCL):
             jspin = self.ispin(jatom)
             keyspin = (R, ispin, jspin)
             is_nonself = not (R == (0, 0, 0) and iatom == jatom)
-            Jij = np.imag(val) / np.sign(np.dot(self.spinat[iatom], self.spinat[jatom]))
             Jorbij = np.imag(self.Jorb[key]) / np.sign(
                 np.dot(self.spinat[iatom], self.spinat[jatom])
             )
+
+            Jij = np.imag(val) / np.sign(np.dot(self.spinat[iatom], self.spinat[jatom]))
+
             if is_nonself:
                 self.exchange_Jdict[keyspin] = Jij
-                self.Jiso_orb[keyspin] = self.simplify_orbital_contributions(
-                    Jorbij, iatom, jatom
-                )
+                Jsimp = self.simplify_orbital_contributions(Jorbij, iatom, jatom)
+                self.Jiso_orb[keyspin] = Jsimp
+                self.exchange_Jdict[keyspin] = np.sum(Jsimp)
 
     def get_rho_e(self, rho_up, rho_dn):
         # self.rho_up_list.append(-1.0 / np.pi * np.imag(rho_up[(0,0,0)]))

TB2J/io_exchange/io_exchange.py

@@ -399,6 +399,26 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
                 )
         return Jmat
 
+    def get_full_Jtensor_for_one_R_ij(self, R, Jiso=True, Jani=True, DMI=True):
+        """
+        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.
+        """
+        if Jani or DMI:
+            raise ValueError(
+                "Jani and DMI are not supported for this method. Use get_full_Jtensor_for_one_R_ij33 instead."
+            )
+        n = self.nspin
+        Jmat = np.zeros((n, n), dtype=float)
+        for i in range(self.nspin):
+            for j in range(self.nspin):
+                J = self.get_Jiso(i, j, R)
+                if J is not None:
+                    Jmat[i, j] = J
+        return Jmat
+
     def get_full_Jtensor_for_Rlist(
         self, asr=False, Jiso=True, Jani=True, DMI=True, order="i3j3"
     ):
@@ -439,11 +459,28 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
             if asr:
                 iR0 = np.argmin(np.linalg.norm(self.Rlist, axis=1))
                 assert np.linalg.norm(self.Rlist[iR0]) == 0
+                sum_JR = np.sum(np.sum(Jmat, axis=0))
                 for i in range(n3):
-                    sum_JRi = np.sum(np.sum(Jmat, axis=0)[i])
-                    Jmat[iR0][i, i] -= sum_JRi
+                    Jmat[iR0][i, i] -= sum_JRi[i]
+        elif order == "ij":
+            Jmat = np.zeros((nR, n, n), dtype=float)
+            for iR, R in enumerate(self.Rlist):
+                Jmat[iR] = self.get_full_Jtensor_for_one_R_ij(
+                    R, Jiso=Jiso, Jani=Jani, DMI=DMI
+                )
+            if asr:
+                iR0 = np.argmin(np.linalg.norm(self.Rlist, axis=1))
+                assert np.linalg.norm(self.Rlist[iR0]) == 0
+                # check if Jmat has NaN values
+                # sum_JR = np.sum(np.sum(Jmat, axis=0), axis=0)
+                # sum over axis 0 and 1
+                sum_JR = np.sum(Jmat, axis=(0, 1))
+                for i in range(n):
+                    Jmat[iR0][i, i] -= sum_JR[i]
         else:
-            raise ValueError("order must be either 'i3j3' or 'ij33', or 'i3j3_2D'.")
+            raise ValueError(
+                "order must be either 'i3j3' or 'ij33', or 'i3j3_2D', or 'ij'."
+            )
         return Jmat
 
     def write_pickle(self, path="TB2J_results", fname="TB2J.pickle"):
@@ -473,6 +510,7 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
 
     def write_all(self, path="TB2J_results"):
         self.write_pickle(path=path)
+        self.atoms.write(os.path.join(path, "structure.vasp"), vasp5=True)
         self.write_txt(path=path)
         if self.Jiso_orb:
             self.write_txt(
@@ -492,11 +530,6 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
 
         write_txt(self, *args, **kwargs)
 
-    # def write_txt_with_orb(self, path):
-    #    from TB2J.io_exchange.io_txt import write_txt
-    #    write_txt_with_orb(
-    #        self, path=path, write_experimental=self.write_experimental)
-
     def write_multibinit(self, path):
         from TB2J.io_exchange.io_multibinit import write_multibinit
 
@@ -541,7 +574,7 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
             Js.append(val * 1e3)
         ax.scatter(ds, Js, marker=marker, color=color, **kwargs)
         ax.axhline(color="gray")
-        ax.set_xlabel("Distance ($\AA$)")
+        ax.set_xlabel(r"Distance ($\AA$)")
         ax.set_ylabel("J (meV)")
         if fname is not None:
             plt.savefig(fname)
@@ -569,7 +602,7 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
         ax.axhline(color="gray")
         ax.legend(loc=1)
         ax.set_ylabel("D (meV)")
-        ax.set_xlabel("Distance ($\AA$)")
+        ax.set_xlabel(r"Distance ($\AA$)")
         if fname is not None:
             plt.savefig(fname)
         if show:
@@ -601,7 +634,7 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
             )
         ax.axhline(color="gray")
         ax.legend(loc=1, ncol=2)
-        ax.set_xlabel("Distance ($\AA$)")
+        ax.set_xlabel(r"Distance ($\AA$)")
         ax.set_ylabel("Jani (meV)")
         if fname is not None:
             plt.savefig(fname)

TB2J/io_exchange/io_txt.py

@@ -1,8 +1,10 @@
-import numpy as np
 import os
-from TB2J.utils import symbol_number
+
+import numpy as np
 from numpy import array_str
 
+from TB2J.utils import symbol_number
+
 
 def write_info_section(cls, myfile):
     myfile.write("=" * 90 + "\n")
@@ -17,7 +19,7 @@ def write_atom_section(cls, myfile):
     write the atom section
     including the cell and the atomic positions.
     """
-    myfile.write("=" * 90 + "\n")
+    myfile.write("\n" + "=" * 90 + "\n")
     myfile.write("Cell (Angstrom):\n")
     cell = cls.atoms.get_cell()
     for c in cell:
@@ -42,7 +44,7 @@ def write_atom_section(cls, myfile):
         )
 
     symnum = symbol_number(cls.atoms)
-    sns = list(symnum.keys())
+    # sns = list(symnum.keys())
     poses = cls.atoms.get_positions()
 
     tchg, tmx, tmy, tmz = 0, 0, 0, 0
@@ -105,7 +107,7 @@ def write_exchange_section(
 ):
     symnum = symbol_number(cls.atoms)
     sns = list(symnum.keys())
-    poses = cls.atoms.get_positions()
+    # poses = cls.atoms.get_positions()
 
     myfile.write("=" * 90 + "\n")
     myfile.write("Exchange: \n")
@@ -183,9 +185,8 @@ def write_exchange_section(
                         DMI2[0], DMI2[1], DMI2[2]
                     )
                 )
-                pass
-            except:
-                pass
+            except Exception as e:
+                myfile.write(f"[Debug!] DMI2 not available: {e}\n")
 
         if cls.Jani_dict is not None:
             J = cls.Jani_dict[ll] * 1e3

{tb2j-0.9.10.1.dist-info → tb2j-0.9.10.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.10.1
+Version: 0.9.10.3
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author-email: Xu He <mailhexu@gmail.com>
 Maintainer-email: Xu He <mailhexu@gmail.com>

{tb2j-0.9.10.1.dist-info → tb2j-0.9.10.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-TB2J/Jdownfolder.py,sha256=ZKF0AVnwaJ4DPKfQ28NsJXhpOZE9_rsusEFtNCm5kls,9675
+TB2J/Jdownfolder.py,sha256=U6R8v6ZC-AgMA6wvvFPyacXX_lYJcRu1kzNr7aVB1tg,10827
 TB2J/Jtensor.py,sha256=WRhpp5N92a6lA1jeM1hc7jYUoTOLIdMnIIKpdOyzjR4,3192
 TB2J/MAE.py,sha256=fM8U-Dgp9HcQOEeC_kyZV1oVrygBvcux9BraUXVouvY,10994
 TB2J/MAEGreen.py,sha256=zVLjQtFDFcRmC8PYm7MOgKnkOuFJEMKr-eoNBABUsMc,15759
@@ -11,8 +11,8 @@ TB2J/citation.py,sha256=gcQeyJZaT1Qrtsl8Y3s4neOH3-vvgmIcCvXeV2o3vj0,2891
 TB2J/contour.py,sha256=zLHQZZ3hhgLkLFPATCraLOJyLJKLC0fba_L_5sRz23o,3246
 TB2J/density_matrix.py,sha256=D5k8Oe21OCiLVORNYbo4TZOFG0slrQSbj91kJ3TMFjs,1514
 TB2J/epc.py,sha256=zLbtqZJhDr8DnnGN6YENcXwrMb3Qxu6KB08mLy9Pw20,3474
-TB2J/exchange.py,sha256=-BEXSQqx374cRbJWjvjyJAZkchzNK1uPUDvTYox3Axs,26982
-TB2J/exchangeCL2.py,sha256=P7bklMXVYX_tn9DbjEPqeTir1SeZyfPBIP1fhWUzLmY,11419
+TB2J/exchange.py,sha256=qDID0faZOWggPLaIC8QY2tOinZaEFU88FNqOJid53-s,26937
+TB2J/exchangeCL2.py,sha256=1b0Lx5dSjgCUYSSng5cqJzo-hmXCD91cbaes9jqsU5s,11474
 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
@@ -56,10 +56,10 @@ 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=KQNCd3G_9Ck-qQX1UMKjfEPHyv5mC3BgRot_ngpACYs,23340
+TB2J/io_exchange/io_exchange.py,sha256=hJ8Z0m46KKjK5aAsM70Fn4dR6vRmSIrR1B_QZz8Wrj8,24686
 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_txt.py,sha256=jFScdZ5W5_VNSEWYq6WDNKWeshZ0wxFfEzyjfvvU9MA,10601
 TB2J/io_exchange/io_uppasd.py,sha256=bI4iPEgnK4TvCZNvb6x2xYXgjW7pEehCqmcizy2pqFU,3301
 TB2J/io_exchange/io_vampire.py,sha256=vOStLmtCiWLp9GPhZpsAmrtaRHg9KSmtOM2Fky6yCQA,5762
 TB2J/magnon/__init__.py,sha256=Q69duroGIIotgW_71ZdHYarSiJLGAu9NPYgEacUk6eI,117
@@ -92,9 +92,9 @@ 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-0.9.10.1.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-tb2j-0.9.10.1.dist-info/METADATA,sha256=aCAWVmSmHiwD7uwDvnlBQocGJaXPpqJAbBtOoJznASc,4138
-tb2j-0.9.10.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-tb2j-0.9.10.1.dist-info/entry_points.txt,sha256=RuFfrRenhXgzZA1ND_4j4D8ylTXl6VbWLyV3fDx6KKw,734
-tb2j-0.9.10.1.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
-tb2j-0.9.10.1.dist-info/RECORD,,
+tb2j-0.9.10.3.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
+tb2j-0.9.10.3.dist-info/METADATA,sha256=tdo-W3OUCQH6J7S4kYa9CUgpzpAO0r6ZOkOQCZr-v0U,4138
+tb2j-0.9.10.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+tb2j-0.9.10.3.dist-info/entry_points.txt,sha256=RuFfrRenhXgzZA1ND_4j4D8ylTXl6VbWLyV3fDx6KKw,734
+tb2j-0.9.10.3.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
+tb2j-0.9.10.3.dist-info/RECORD,,