TB2J 0.9.9rc7__py3-none-any.whl → 0.9.9rc8__py3-none-any.whl

TB2J/exchange.py

@@ -566,12 +566,23 @@ class ExchangeNCL(Exchange):
         AijRs: a list of AijR,
         wherer AijR: array of ((nR, n, n, 4,4), dtype=complex)
         """
+        # if method == "trapezoidal":
+        #    integrate = trapezoidal_nonuniform
+        # elif method == "simpson":
+        #    integrate = simpson_nonuniform
+        #
+
+        # 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)]
+                # self.A_ijR[(R, iatom, jatom)] = integrate(self.contour.path, f)
                 self.A_ijR[(R, iatom, jatom)] = self.contour.integrate_values(f)
 
                 if self.orb_decomposition:
+                    # self.A_ijR_orb[(R, iatom, jatom)] = integrate(
+                    #    self.contour.path, AijRs_orb[(R, iatom, jatom)]
+                    # )
                     self.contour.integrate_values(AijRs_orb[(R, iatom, jatom)])
 
     def get_quantities_per_e(self, e):

TB2J/io_exchange/io_exchange.py

@@ -338,12 +338,6 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
             )
         return Jtensor
 
-    def get_J_tensor_dict(self):
-        Jdict = {}
-        for i, j, R in self.ijR_list():
-            Jdict[(i, j, R)] = self.get_J_tensor(i, j, R)
-        return Jdict
-
     def get_full_Jtensor_for_one_R(self, R, iso_only=False):
         """
         Return the full exchange tensor of all i and j for cell R.
@@ -411,7 +405,6 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
         self.write_multibinit(path=os.path.join(path, "Multibinit"))
         self.write_tom_format(path=os.path.join(path, "TomASD"))
         self.write_vampire(path=os.path.join(path, "Vampire"))
-        self.write_matjes(path=os.path.join(path, "Matjes"))
 
         self.plot_all(savefile=os.path.join(path, "JvsR.pdf"))
         # self.write_Jq(kmesh=[9, 9, 9], path=path)
@@ -580,11 +573,6 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
 
         write_uppasd(self, path=path)
 
-    def write_matjes(self, path):
-        from TB2J.io_exchange.io_matjes import write_matjes
-
-        write_matjes(self, path=path)
-
 
 def gen_distance_dict(ind_mag_atoms, atoms, Rlist):
     distance_dict = {}
@@ -600,21 +588,6 @@ def gen_distance_dict(ind_mag_atoms, atoms, Rlist):
     return distance_dict
 
 
-def get_ind_shell(distance_dict, symprec=1e-5):
-    """
-    return a dictionary of shell index for each pair of atoms.
-    The index of shell is the ith shortest distances between all magnetic atom pairs.
-    """
-    shell_dict = {}
-    distances = np.array([x[1] for x in distance_dict.values()])
-    distances_int = np.round(distances / symprec).astype(int)
-    dint = sorted(np.unique(distances_int))
-    dintdict = dict(zip(dint, range(len(dint))))
-    for key, val in enumerate(distances_int):
-        shell_dict[key] = dintdict[val]
-    return shell_dict
-
-
 def test_spin_io():
     import numpy as np
     from ase import Atoms

TB2J/mycfr.py

@@ -64,6 +64,10 @@ class CFR:
         # zp = 1j / eigp * kb * self.T
         # Rp = 0.25 * np.diag(eigv)**2 * zp **2
 
+        # print the poles and the weights
+        for i in range(len(self.poles)):
+            print("Pole: ", self.poles[i], "Weight: ", self.weights[i])
+
         # add a point to the poles: 1e10j
         self.path = np.concatenate((self.path, [self.Rinf * 1j]))
         # self.path = np.concatenate((self.path, [0.0]))

TB2J/symmetrize_J.py

@@ -9,7 +9,7 @@ from TB2J.versioninfo import print_license
 
 
 class TB2JSymmetrizer:
-    def __init__(self, exc, symprec=1e-8, verbose=True, Jonly=True):
+    def __init__(self, exc, symprec=1e-8, verbose=True, Jonly=False):
         # list of pairs with the index of atoms
         ijRs = exc.ijR_list_index_atom()
         finder = SymmetryPairFinder(atoms=exc.atoms, pairs=ijRs, symprec=symprec)
@@ -25,12 +25,6 @@ class TB2JSymmetrizer:
             )
             print("-" * 30)
             if exc.has_dmi:
-                # raise NotImplementedError(
-                #    "Symmetrization of DMI is not yet implemented."
-                #    )
-                # raise Warning(
-                #        "WARNING: Symmetrization of DMI is not yet implemented."
-                #        )
                 print(
                     "WARNING: Currently only the isotropic exchange is symmetrized. Symmetrization of DMI and anisotropic exchange are not yet implemented."
                 )
@@ -39,7 +33,7 @@ class TB2JSymmetrizer:
             print("Symmetry found:")
             print(finder.spacegroup)
             print("-" * 30)
-        self.pldict = finder.get_symmetry_pair_list_dict()
+        self.pgdict = finder.get_symmetry_pair_group_dict()
         self.exc = exc
         self.new_exc = copy.deepcopy(exc)
         self.Jonly = Jonly
@@ -52,25 +46,21 @@ class TB2JSymmetrizer:
         Symmetrize the exchange parameters J.
         """
         symJdict = {}
-        reduced_symJdict = {}
         # Jdict = self.exc.exchange_Jdict
-        for ishell, pairlist in enumerate(self.pldict.pairlists):
-            ijRs = pairlist.get_all_ijR()
+        # ngroup = self.pgdict
+        for pairgroup in self.pgdict.groups:
+            ijRs = pairgroup.get_all_ijR()
             ijRs_spin = [self.exc.ijR_index_atom_to_spin(*ijR) for ijR in ijRs]
             Js = [self.exc.get_J(*ijR_spin) for ijR_spin in ijRs_spin]
             Javg = np.average(Js)
             for i, j, R in ijRs_spin:
                 symJdict[(R, i, j)] = Javg
-            ijRs_ref = ijRs_spin[0]
-            i, j, R = ijRs_ref
-            reduced_symJdict[(R, i, j)] = Javg
         self.new_exc.exchange_Jdict = symJdict
         if self.Jonly:
             self.new_exc.has_dmi = False
             self.new_exc.dmi_ddict = None
             self.new_exc.has_bilinear = False
             self.new_exc.Jani_dict = None
-            self.new_exc.reduced_exchange_Jdict = reduced_symJdict
             self.has_uniaxial_anisotropy = False
             self.k1 = None
             self.k1dir = None
@@ -134,12 +124,12 @@ def symmetrize_J_cli():
         help="precision for symmetry detection. default is 1e-5 Angstrom",
     )
 
-    # parser.add_argument(
-    #    "--Jonly",
-    #    action="store_true",
-    #    help="symmetrize only the exchange parameters and discard the DMI and anisotropic exchange",
-    #    default=True,
-    # )
+    parser.add_argument(
+        "--Jonly",
+        action="store_true",
+        help="symmetrize only the exchange parameters and discard the DMI and anisotropic exchange",
+        default=False,
+    )
 
     args = parser.parse_args()
     if args.inpath is None:
@@ -149,8 +139,7 @@ def symmetrize_J_cli():
         path=args.inpath,
         output_path=args.outpath,
         symprec=args.symprec,
-        # Jonly=args.Jonly,
-        Jonly=True,
+        Jonly=args.Jonly,
     )
 
 

TB2J/thetaphi.py

@@ -0,0 +1,16 @@
+import numpy as np
+
+
+def theta_phi_even_spaced(n):
+    """
+    Return n evenly spaced theta and phi values in the ranges [0, pi] and [0, 2*pi] respectively.
+    """
+    phis = []
+    thetas = []
+    for i in range(n):
+        phi = 2 * np.pi * i / n
+        phis.append(phi)
+        r = np.sin(np.pi * i / n)
+        theta = np.arccos(1 - 2 * r)
+        thetas.append(theta)
+    return thetas, phis

{tb2j-0.9.9rc7.dist-info → tb2j-0.9.9rc8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.9rc7
+Version: 0.9.9rc8
 Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
 Author: Xu He
 Author-email: mailhexu@gmail.com

{tb2j-0.9.9rc7.dist-info → tb2j-0.9.9rc8.dist-info}/RECORD

@@ -11,7 +11,7 @@ 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=742vEE8DQJuWBTlq45RQoPy0-_n_TT6BZOb_DoTpDKI,25739
+TB2J/exchange.py,sha256=1kkrrQvmoOaPgT_rKG7wgLy31rWpbFGNYXai1ysd58M,26221
 TB2J/exchangeCL2.py,sha256=P7bklMXVYX_tn9DbjEPqeTir1SeZyfPBIP1fhWUzLmY,11419
 TB2J/exchange_params.py,sha256=AcGYYky27DXSF3yDZWVjksr_3rt6im6qeIzpOwvqssk,7141
 TB2J/exchange_pert.py,sha256=jmFMtQbYa_uczM4VAeS6TijkIHRFIqEzZJswzE9Wfuo,8523
@@ -22,7 +22,7 @@ TB2J/greentest.py,sha256=2ISSfhor9ecSEOi_E6b4Cv26wEIQlwlzca0ru8z44_E,1603
 TB2J/io_merge.py,sha256=E1_GfAB2HGpW-ipaO2lqU9SvaslwkiLxssn4DqJpMT8,6899
 TB2J/kpoints.py,sha256=9L7tBarFBHoIhpuc9zuwA6HdnlgH834SQrPek4yRoWk,3191
 TB2J/myTB.py,sha256=ok_B4my29bOIghMSZfx0Es6G8FaXaIiLP4gPxTdSj00,17659
-TB2J/mycfr.py,sha256=Wgj6PpA-oVuxm8Hh32FVw_vthozVBrDJhRV1hA1ku44,3752
+TB2J/mycfr.py,sha256=ZF1PEE2khlKd_4gPyMkoNXepX3XqwWAL2kDbRJNVX-Y,3908
 TB2J/orbital_magmom.py,sha256=JTwO9ZDgRRQndqR9aFIua4eTvwLMoGsTiY_HaIPMZ2I,889
 TB2J/orbmap.py,sha256=XLQjKMxCy2eADaM5eb2F_zG08V7lzpXJxp5uEtTeVYI,7194
 TB2J/pauli.py,sha256=ESpAhk6LG5ugzuW1YFUTqiDxcg-pQ7wNnzR2FtUnvKM,5295
@@ -31,8 +31,9 @@ TB2J/plot.py,sha256=AnFIFWE2vlmj7Z6f_7-dX_O1stJN-qbuiurPj43dUCM,4104
 TB2J/rotate_atoms.py,sha256=Dwptn-wdDW4zYzjYb95yxTzuZOe9WPuLjh3d3-YcSs0,3277
 TB2J/rotate_siestaDM.py,sha256=eR97rspdrRaK9YTwQwUKfobI0S9UnEcbEZ2f5IgR7Tk,1070
 TB2J/sisl_wrapper.py,sha256=A5x1-tt8efUSPeGY5wM5m6-pJYQFXTCzQHVqD6RBa2g,14792
-TB2J/symmetrize_J.py,sha256=gN6Y8zV4IrO5rPh0SG8KHkekrJjMQzNY4GGe2ZBtwbc,4993
+TB2J/symmetrize_J.py,sha256=IypvLL0JxExq-cmqc4o0nLL8psE7OC9ijj9YMcsqJeA,4487
 TB2J/tensor_rotate.py,sha256=4-DfT_Mg5e40fbd74M5W0D5DqmUq-kVOOLDkkkI834A,8083
+TB2J/thetaphi.py,sha256=Z7N3EOSM7rjHd7b9HxMYLPQO__uR0VwEiV9b471Yudc,399
 TB2J/utest.py,sha256=z_ahi7tpHQF9WlHNQihcQ7qzfezRJQXQt28eB1X_z64,3897
 TB2J/utils.py,sha256=DHkc7BK0KUGesfoAv1OxMgIw_iZzcFXh--3ybsFSd_c,12535
 TB2J/versioninfo.py,sha256=atoCpy6lEcGTCC3xahrxEJjoHgoYVtL41Q_3Ryvp76I,338
@@ -54,8 +55,7 @@ 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=KfGHum7B8E4G_KKfillqw0lErtoyKEuFUUttHLs-mg4,32
-TB2J/io_exchange/io_exchange.py,sha256=7-Xt7_K5FKVrFkFvBrHhJGCRrL2Sw7zY-93GRBBv2GM,21050
-TB2J/io_exchange/io_matjes.py,sha256=klM5Z_t2kk0y_1IoqIILLnhUgjHQmXXmsXiono2LeMU,8594
+TB2J/io_exchange/io_exchange.py,sha256=gaT0fXD3EzPsMgE_VX9gvcf7nEGY3KVYN8xxTAPzxc0,20120
 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
@@ -80,19 +80,19 @@ 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-0.9.9rc7.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
-tb2j-0.9.9rc7.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
-tb2j-0.9.9rc7.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
-tb2j-0.9.9rc7.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
-tb2j-0.9.9rc7.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
-tb2j-0.9.9rc7.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
-tb2j-0.9.9rc7.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
-tb2j-0.9.9rc7.data/scripts/abacus2J.py,sha256=0HLXoJhAkiZ-ZM1cs26lncccxE8-TzC8JiDTba1h1uM,4163
-tb2j-0.9.9rc7.data/scripts/siesta2J.py,sha256=gp31LioqpPkDmMY0y_5gXIjOBPNnf080P37pRo0yjw8,4886
-tb2j-0.9.9rc7.data/scripts/wann2J.py,sha256=pTFDf6h72I_LN_NX5UivyCoJPgwvyAyHW175nSAJvLo,2987
-tb2j-0.9.9rc7.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-tb2j-0.9.9rc7.dist-info/METADATA,sha256=H5g8ApE237zxKx8_mx0Fr1fUCz2m97VkgDY5LBFYzlg,1660
-tb2j-0.9.9rc7.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-tb2j-0.9.9rc7.dist-info/entry_points.txt,sha256=Hdz1WC9waUzyFVmowKnbbZ6j-J4adHh_Ko6JpxGYAtE,131
-tb2j-0.9.9rc7.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
-tb2j-0.9.9rc7.dist-info/RECORD,,
+tb2j-0.9.9rc8.data/scripts/TB2J_downfold.py,sha256=i4BVqnpDdgrX_amookVWeLGefGBn-qeAutWiwuY9SfQ,2099
+tb2j-0.9.9rc8.data/scripts/TB2J_eigen.py,sha256=Qs9v2hnMm2Tpfoa4h53muUKty2dZjwx8948MBoQooNg,1128
+tb2j-0.9.9rc8.data/scripts/TB2J_magnon.py,sha256=q7UwAmorRcFNk4tfE7gl_ny05l6p7pbD9Wm_LkIpKEw,3101
+tb2j-0.9.9rc8.data/scripts/TB2J_magnon_dos.py,sha256=TMXQvD2dIbO5FZ4tUMmxJgCgH2O2hDAPUNfEKO4z-x4,110
+tb2j-0.9.9rc8.data/scripts/TB2J_merge.py,sha256=y834SF4rIRn1L1ptkhczvavQpC-8Px6DTmDOOSaq_DE,1854
+tb2j-0.9.9rc8.data/scripts/TB2J_rotate.py,sha256=zgiDFuYZNmzKK0rwDmTaYD2OpRlmKA_VGeBx83w2Xwc,873
+tb2j-0.9.9rc8.data/scripts/TB2J_rotateDM.py,sha256=kCvF7gotuqAX1VnJ06cwfVm7RrhrdtiV5v7d9P2Pn_E,567
+tb2j-0.9.9rc8.data/scripts/abacus2J.py,sha256=0HLXoJhAkiZ-ZM1cs26lncccxE8-TzC8JiDTba1h1uM,4163
+tb2j-0.9.9rc8.data/scripts/siesta2J.py,sha256=gp31LioqpPkDmMY0y_5gXIjOBPNnf080P37pRo0yjw8,4886
+tb2j-0.9.9rc8.data/scripts/wann2J.py,sha256=pTFDf6h72I_LN_NX5UivyCoJPgwvyAyHW175nSAJvLo,2987
+tb2j-0.9.9rc8.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
+tb2j-0.9.9rc8.dist-info/METADATA,sha256=4DDVWc-iAm87VSn60YFm-O15MZY-OpcT0ay_lw_0580,1660
+tb2j-0.9.9rc8.dist-info/WHEEL,sha256=DK49LOLCYiurdXXOXwGJm6U4DkHkg4lcxjhqwRa0CP4,91
+tb2j-0.9.9rc8.dist-info/entry_points.txt,sha256=Hdz1WC9waUzyFVmowKnbbZ6j-J4adHh_Ko6JpxGYAtE,131
+tb2j-0.9.9rc8.dist-info/top_level.txt,sha256=whYa5ByLYhl5XnTPBHSWr-IGD6VWmr5Ql2bye2qwV_s,5
+tb2j-0.9.9rc8.dist-info/RECORD,,

{tb2j-0.9.9rc7.dist-info → tb2j-0.9.9rc8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: setuptools (78.0.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

TB2J/io_exchange/io_matjes.py

@@ -1,225 +0,0 @@
-import os
-
-import numpy as np
-
-from TB2J.utils import symbol_number
-from ase.units import Bohr, nm
-
-
-def get_ind_shell(distance_dict, symprec=1e-5):
-    """
-    return a dictionary of shell index for each pair of atoms.
-    The index of shell is the ith shortest distances between all magnetic atom pairs.
-    """
-    shell_dict = {}
-    distances = np.array([x[1] for x in distance_dict.values()])
-    distances_int = np.round(distances / symprec).astype(int)
-    dint = sorted(np.unique(distances_int))
-    dintdict = dict(zip(dint, range(len(dint))))
-    for key, val in distance_dict.items():
-        di = np.round(val[1] / symprec).astype(int)
-        shell_dict[key] = dintdict[di]
-    return shell_dict
-
-
-def _write_symmetry(cls, path, fname="symmetry.in", symmetry=True):
-    fname = os.path.join(path, fname)
-    if not symmetry:
-        with open(fname, "w") as myfile:
-            myfile.write("1 \n")
-            myfile.write("\n")
-            myfile.write("! identity operation\n")
-            myfile.write("1.0000000000 0.0000000000 0.0000000000\n")
-            myfile.write("0.0000000000 1.0000000000 0.0000000000\n")
-            myfile.write("0.0000000000 0.0000000000 1.0000000000\n")
-            myfile.write("0.0000000000 0.0000000000 0.0000000000\n")
-    else:
-        raise NotImplementedError("Symmetry not implemented yet")
-
-
-def write_matjes(cls, path="TB2J_results/Matjes", symmetry=False):
-    if not os.path.exists(path):
-        os.makedirs(path)
-    inputfname = os.path.join(path, "input")
-    with open(inputfname, "w") as myfile:
-        _write_lattice_supercell(cls, myfile)
-        _write_atoms(cls, myfile)
-        _write_magnetic_interactions(cls, myfile)
-        #_write_isotropic_exchange(cls, myfile, symmetry=symmetry)
-        _write_magnetic_anisotropy(cls, myfile)
-        # _write_dmi(cls, myfile)
-        _write_exchange_tensor(cls, myfile, symmetry=symmetry)
-        _write_parameters(cls, myfile, symmetry=symmetry)
-    print(f"writting symmetries ")
-    _write_symmetry(cls, path,  fname="symmetries.in", symmetry=False)
-
-def _write_parameters(cls, myfile, symmetry=False):
-    if symmetry:
-        myfile.write("cal_sym T\n")
-        myfile.write("sym_mode 2\n")
-    else:
-        myfile.write("cal_sym F \n")
-        myfile.write("sym_mode 0\n")
-
-def _write_lattice_supercell(cls, myfile):
-    myfile.write("# Lattice and supercell\n")
-    myfile.write(
-        "Periodic_log .T. .T. .T.      # periodic boundary conditions along vector 1, 2 and 3\n"
-    )
-    myfile.write("Nsize 8 8 8                 # size of the supercell\n")
-    try:
-        unitcell = cls.atoms.get_cell().reshape((3, 3))
-    except Exception:
-        unitcell = cls.atoms.get_cell().array.reshape((3, 3))
-    uc_lengths = np.linalg.norm(unitcell, axis=1) 
-    unitcell /= uc_lengths[:, None]
-    myfile.write(f"alat {uc_lengths[0]/nm}  {uc_lengths[1]/nm} {uc_lengths[2]/nm}              #lattice constant lengths\n")
-    myfile.write(
-        "lattice                         #lattice vector should be orthogonal or expressed in cartesian\n")
-    myfile.write(
-        f"{unitcell[0][0]} {unitcell[0][1]} {unitcell[0][2]}     # a_11 a_12 a_1      first lattice vector in line (does not need to be normalize)\n"
-    )
-    myfile.write(
-        f"{unitcell[1][0]} {unitcell[1][1]} {unitcell[1][2]}      # a_21 a_22 a_23    second lattice vector in line (does not need to be normalize)\n"
-    )
-    myfile.write(
-        f"{unitcell[2][0]} {unitcell[2][1]} {unitcell[2][2]}     # a_31 a_32 a_33                     third lattice vector in line\n"
-    )
-
-
-def get_atoms_info(atoms, spinat, symmetry=False):
-    if symmetry:
-        raise NotImplementedError("Symmetry not implemented yet")
-    else:
-        symnum = symbol_number(atoms)
-        atom_types = list(symnum.keys())
-        magmoms = np.linalg.norm(spinat, axis=1)
-        masses = atoms.get_masses()
-        tags = [i for i in range(len(atom_types))]
-    return atom_types, magmoms, masses, tags
-
-
-def _write_atoms(cls, myfile, symmetry=False):
-    myfile.write("\n")
-    myfile.write("# Atoms\n")
-    atom_types, magmoms, masses, tags = get_atoms_info(
-        cls.atoms, cls.spinat, symmetry=symmetry
-    )
-
-    myfile.write(f"atomtypes  {len(atom_types)}       #Number of types atom\n")
-    for i, atom_type in enumerate(atom_types):
-        m = magmoms[i]
-        mass = masses[i]
-        charge = 0
-        myfile.write(
-            f"{atom_type} {m} {mass} 0.0  F 0 # atom type: (name, mag. moment, mass, charge, displacement, number TB-orb.)\n"
-        )
-
-    myfile.write(
-        f"\natoms {len(cls.atoms)}          positions of the atom in the unit cell\n"
-    )
-    for i, atom in enumerate(cls.atoms):
-        spos = cls.atoms.get_scaled_positions()[i]
-        myfile.write(f"{atom_types[tags[i]]} {spos[0]}, {spos[1]}, {spos[2]}  \n")
-
-
-def _write_magnetic_interactions(cls, myfile, symmetry=False):
-    myfile.write("\nThe Hamiltonian\n")
-    myfile.write("# Magnetic interactions\n")
-
-
-def _write_isotropic_exchange(cls, myfile, symmetry=False):
-    myfile.write("\nmagnetic_J\n")
-    shell_dict = get_ind_shell(cls.distance_dict)
-    if symmetry:
-        Jdict = cls.reduced_exchange_Jdict
-    else:
-        Jdict = cls.exchange_Jdict
-    for key, val in Jdict.items():
-        R, i, j = key
-        ishell = shell_dict[(R, i, j)]
-        myfile.write(
-            f"{i+1} {j+1} {ishell} {val}     # between atoms type {i+1} and {j+1}, shell {R}, amplitude in eV  \n"
-        )
-    myfile.write(
-        "\nc_H_J -1        apply 1/2 in front of the sum of the exchange energy - default is -1\n"
-    )
-
-
-def _write_magnetic_anisotropy(cls, myfile):
-    if cls.k1 is None:
-        return
-    else:
-        myfile.write("\nmagnetic_anisotropy \n")
-        for i, k1 in enumerate(cls.k1):
-            myfile.write(
-                f"{i+1} {cls.k1dir[i][0]} {cls.k1dir[i][1]} {cls.k1dir[i][2]} {k1}     anisotropy of atoms type {i+1}, direction {cls.k1dir[i][0]} {cls.k1dir[i][1]} {cls.k1dir[i][2]} and amplitude in eV\n"
-            )
-        myfile.write("\nc_H_ani 1.0\n")
-
-
-def _write_dmi(cls, myfile):
-    if cls.has_dmi:
-        myfile.write("\nmagnetic_D\n")
-        for key, val in cls.dmi_ddict.items():
-            R, i, j = key
-            myfile.write(
-                f"{i+1} {j+1} {R[0]} {R[1]} {R[2]} {val}         #between atoms type {i+1} and {j+1}, mediated by atom type {R}, shell {R}, amplitude in eV\n"
-            )
-        myfile.write(
-            "\nc_H_D   -1.0             # coefficients to put in from of the sum - default is -1\n"
-        )
-
-
-def _write_exchange_tensor(cls, myfile, symmetry=False):
-    myfile.write(
-        "\nmagnetic_r2_tensor #Exchange tensor elements, middle 9 entries: xx, xy, xz, yx, etc. (in units of eV) and direction in which it should be applied\n"
-    )
-
-    Jtensor = cls.get_J_tensor_dict()
-    shelldict = get_ind_shell(cls.distance_dict)
-    unitcell = cls.atoms.get_cell().array.reshape((3, 3))
-    uc_lengths = np.linalg.norm(unitcell, axis=1) 
-    if Jtensor is not None:
-        for key, val in Jtensor.items():
-            i, j, R = key
-            # distance vector
-            dvec = cls.distance_dict[(R, i, j)][0]/nm/uc_lengths
-            dscalar = np.linalg.norm(dvec)
-            val = np.real(val)
-            ishell = shelldict[(R, i, j)]
-            myfile.write(
-                f"{i+1} {j+1} {ishell} {' '.join([str(x) for x in val.flatten()])}  {dvec[0]} {dvec[1]} {dvec[2]} \n"
-                #f"{i+1} {j+1} {dscalar} {' '.join([str(x) for x in val.flatten()])}  {dvec[0]} {dvec[1]} {dvec[2]} \n"
-            )
-        myfile.write(
-            "\nc_H_Exchten -1         apply 1/2 in front of the sum of the exchange tensor energy - default is -1\n"
-        )
-
-def rattle_atoms_and_cell(atoms, stdev=0.001, cell_stdev=0.001):
-    """
-    Rattle both atomic positions and cell parameters.
-    
-    Parameters:
-    -----------
-    atoms: ASE atoms object
-        The atoms to be rattled
-    stdev: float
-        Standard deviation for atomic displacement in Angstrom
-    cell_stdev: float
-        Standard deviation for cell parameter variation (fractional)
-    
-    Returns:
-    --------
-    None
-        The atoms object is modified in-place
-    """
-    # Rattle atomic positions
-    positions = atoms.get_positions()
-    displacement = np.random.normal(0, stdev, positions.shape)
-    atoms.set_positions(positions + displacement)
-    
-    # Rattle cell parameters
-    cell = atoms.get_cell()
-    cell_noise = np.random.normal(0, cell_stdev, cell.shape)
-    atoms.set_cell(cell * (1 + cell_noise), scale_atoms=True)