TB2J 0.9.12.10__py3-none-any.whl → 0.9.12.13__py3-none-any.whl

TB2J/.gitignore

@@ -0,0 +1,5 @@
+*.o
+*.x
+*.mod
+exchanges.sublime-project
+exchanges.sublime-workspace

TB2J/io_exchange/io_espins.py

@@ -0,0 +1,276 @@
+import os
+
+import numpy as np
+
+
+def _get_shell_index(cls, key):
+    """Determine shell index based on distance grouping.
+
+    Parameters
+    ----------
+    cls : SpinIO
+        SpinIO instance
+    key : tuple
+        (R, i, j) key for exchange parameter
+
+    Returns
+    -------
+    int
+        Shell index (1 for nearest neighbors, 2 for next nearest, etc.)
+    """
+    if not hasattr(cls, "_distance_shells"):
+        # Calculate all distances and group into shells
+        distances = []
+        for k in cls.exchange_Jdict:
+            if cls.distance_dict and k in cls.distance_dict:
+                distances.append(cls.distance_dict[k][1])
+
+        if distances:
+            # Sort distances and group by rounding to nearest 0.01 Å
+            sorted_distances = sorted(set(round(d * 100) for d in distances))
+            cls._distance_shells = {}
+            for shell_idx, dist_int in enumerate(sorted_distances, 1):
+                cls._distance_shells[dist_int / 100] = shell_idx
+        else:
+            cls._distance_shells = {}
+
+    if cls.distance_dict and key in cls.distance_dict:
+        distance = cls.distance_dict[key][1]
+        rounded_dist = round(distance * 100)
+        return cls._distance_shells.get(rounded_dist / 100, 1)
+
+    return 1
+
+
+def write_espins(cls, path="TB2J_results/ESPInS"):
+    """Write ESPInS format input files.
+
+    Parameters
+    ----------
+    cls : SpinIO
+        SpinIO instance containing exchange parameters
+    path : str
+        Output directory path
+    """
+    if not os.path.exists(path):
+        os.makedirs(path)
+
+    write_espins_input(cls, os.path.join(path, "espins.in"))
+
+
+def write_espins_input(cls, fname):
+    """Write the main ESPInS input file.
+
+    Parameters
+    ----------
+    cls : SpinIO
+        SpinIO instance
+    fname : str
+        Output filename
+    """
+    with open(fname, "w") as myfile:
+        # Write unit cell
+        myfile.write("! ESPInS input file generated by TB2J\n")
+        # myfile.write("! Compatible with ESPInS version > 1.0 \n")
+        myfile.write("! The unit cell in angstrom\n")
+        myfile.write("Begin Unit_Cell_Cart\n")
+        cell = cls.atoms.get_cell()
+        for i in range(3):
+            myfile.write("     " + " ".join(f"{x:12.8f}" for x in cell[i]) + "\n")
+        myfile.write("End Unit_Cell_Cart\n\n")
+
+        # Write atomic positions
+        myfile.write("! Atomic positions in reduced coordinates\n")
+        myfile.write("Begin Atoms_Frac\n")
+        scaled_positions = cls.atoms.get_scaled_positions()
+        symbols = cls.atoms.get_chemical_symbols()
+
+        for i, (symbol, pos) in enumerate(zip(symbols, scaled_positions)):
+            if cls.index_spin[i] >= 0:  # Only magnetic atoms
+                myfile.write(
+                    f"  {symbol:<8} {pos[0]:10.7f} {pos[1]:10.7f} {pos[2]:10.7f}    1.00\n"
+                )
+        myfile.write("End Atoms_Frac\n\n\n")
+
+        # Write temperature settings (default values)
+        myfile.write("tem_start          =   1\n")
+        myfile.write("tem_end            =   30\n")
+        myfile.write("tems_num           =   30\n")
+        # myfile.write("!! tems_mode          = man\n")
+        # myfile.write("!! tems               = 5.00 10.00 15.00 20.00\n\n")
+
+        # Write Monte Carlo parameters (default values)
+        myfile.write("! Pt                 = .True.\n")
+        myfile.write("! Pt_steps_swap      = 40\n\n")
+
+        myfile.write("steps_warmup      =       100000\n")
+        myfile.write("steps_mc          =       100000\n")
+        myfile.write("steps_measure     =           2\n\n")
+
+        myfile.write("initial_sconfig   =        ferro\n")
+        myfile.write("mcarlo_mode       =       random\n\n")
+
+        myfile.write("supercell_size    =      10     10     1\n\n")
+
+        # Write Hamiltonian settings
+        myfile.write(" ## Hamiltonian\n")
+        myfile.write("Ham_bij           = .False.\n")
+        myfile.write("Ham_jij_matrix    = .True.\n")
+        myfile.write("! We don't have single ion anisotropy, put it to .False.\n")
+        myfile.write("Ham_singleion_matrix    = .False.\n\n\n")
+
+        # Write single ion anisotropy matrix if available
+        # if cls.has_uniaxial_anistropy:
+        #    myfile.write("! Don't put this block\n")
+        #    myfile.write("!Begin SingleIon_Matrix\n")
+        #    # Placeholder for single ion anisotropy
+        #    myfile.write("@Axx=0.000 , Axy=-1.65e-07 , Axz=6e-08 , Ayx=-1.65e-07 , Ayy=7.73e-05 , Ayz=-1.5e-05 , Azx=6e-08 , Azz= 6.8e-05\n")
+        #    myfile.write("!End SingleIon_Matrix\n\n")
+
+        # Write exchange parameters
+        myfile.write(
+            """! f1 is the fractional coordinate of atom i, and f2 is of atom j (rj+Rj). Then jij in eV, sh is index of shell, t1 is index of i, t2 is index of j (counting from 1).  \n
+            !The convention of the Hamiltonian is H = - sum_<ij> Jij Si Sj, and i, j are ordererd so that there is no double counting (ij and ji). To convert from TB2J exchange.out (which has both ij and ji), multiply Jij by 2.  \n 
+            \n"""
+        )
+
+        if cls.has_exchange:
+            myfile.write("Begin Jij_parameters\n")
+
+            # Create a list of unique exchange parameters sorted by distance
+            exchange_list = []
+            # written_keys = set()
+
+            for key, jval in cls.exchange_Jdict.items():
+                R, i, j = key
+
+                # Skip if this is the symmetric counterpart of an already written pair
+                # symmetric_key = (tuple(-np.array(R)), j, i)
+                # if symmetric_key in written_keys:
+                #    continue
+
+                # Get distance for sorting
+                distance = (
+                    cls.distance_dict[key][1]
+                    if cls.distance_dict and key in cls.distance_dict
+                    else 0.0
+                )
+
+                exchange_list.append((distance, key, jval))
+                # written_keys.add(key)
+
+            # Sort by distance
+            exchange_list.sort(key=lambda x: x[0])
+
+            for distance, key, jval in exchange_list:
+                R, i, j = key
+                iatom = cls.iatom(i)
+                jatom = cls.iatom(j)
+
+                # Get fractional coordinates
+                pos_i = cls.atoms.get_scaled_positions()[iatom]
+                pos_j = cls.atoms.get_scaled_positions()[jatom]
+
+                # Calculate fractional coordinates for j+R
+                pos_jR = pos_j + R
+                # Determine shell index based on distance
+                shell = _get_shell_index(cls, key)
+
+                myfile.write(
+                    f"  f1=    {pos_i[0]:10.6f},    {pos_i[1]:10.6f},    {pos_i[2]:10.6f}:f2=    {pos_jR[0]:10.6f},    {pos_jR[1]:10.6f},    {pos_jR[2]:10.6f}:jij=  {jval*2:10.8f}!:sh=  {shell}!:t1=  {i+1}:t2=  {j+1}\n"
+                )
+
+            myfile.write("End Jij_parameters\n\n")
+
+        # Write exchange matrix if available
+        if cls.has_exchange:
+            myfile.write(
+                "! Each matrix element is corresponding to the previous block. The J tensor include the isotropic, anisotropic exchange and DMI. \n"
+            )
+            myfile.write("Begin Jij_matrix\n")
+
+            # Create a list of unique exchange parameters sorted by distance
+            exchange_list = []
+            # written_keys = set()
+
+            for key in cls.exchange_Jdict:
+                R, i, j = key
+
+                # Skip if this is the symmetric counterpart of an already written pair
+                # symmetric_key = (tuple(-np.array(R)), j, i)
+                # if symmetric_key in written_keys:
+                #    continue
+
+                # Get distance for sorting
+                distance = (
+                    cls.distance_dict[key][1]
+                    if cls.distance_dict and key in cls.distance_dict
+                    else 0.0
+                )
+
+                exchange_list.append((distance, key))
+                # written_keys.add(key)
+
+            # Sort by distance
+            exchange_list.sort(key=lambda x: x[0])
+
+            for distance, key in exchange_list:
+                R, i, j = key
+                # Get full J tensor
+                J_tensor = cls.get_J_tensor(i, j, R, Jiso=True, Jani=True, DMI=True) * 2
+
+                # Format matrix elements exactly as in the example
+                myfile.write(
+                    f"Jxx={J_tensor[0, 0]:.8f}, Jxy={J_tensor[0, 1]:.8f}, Jxz={J_tensor[0, 2]:.8f}, Jyx={J_tensor[1, 0]:.8f}, Jyy={J_tensor[1, 1]:.8f}, Jyz={J_tensor[1, 2]:.8f}, Jzx={J_tensor[2, 0]:.8f}, Jzy={J_tensor[2, 1]:.8f}, Jzz={J_tensor[2, 2]:.8f}\n"
+                )
+
+            myfile.write("End Jij_matrix\n\n")
+
+        # Write biquadratic exchange if available
+        # if cls.has_biquadratic and cls.biquadratic_Jdict:
+        if False:
+            myfile.write("! Biquadratic, don't put it. \n")
+            myfile.write("Begin Bij_parameters\n")
+
+            # Create a list of unique biquadratic parameters sorted by distance
+            biquadratic_list = []
+            written_keys = set()
+
+            for key, bval in cls.biquadratic_Jdict.items():
+                R, i, j = key
+
+                # Skip if this is the symmetric counterpart of an already written pair
+                symmetric_key = (tuple(-np.array(R)), j, i)
+                if symmetric_key in written_keys:
+                    continue
+
+                # Get distance for sorting
+                distance = (
+                    cls.distance_dict[key][1]
+                    if cls.distance_dict and key in cls.distance_dict
+                    else 0.0
+                )
+
+                biquadratic_list.append((distance, key, bval))
+                written_keys.add(key)
+
+            # Sort by distance
+            biquadratic_list.sort(key=lambda x: x[0])
+
+            for distance, key, bval in biquadratic_list:
+                R, i, j = key
+                iatom = cls.iatom(i)
+                jatom = cls.iatom(j)
+
+                # Get fractional coordinates
+                pos_i = cls.atoms.get_scaled_positions()[iatom]
+                pos_j = cls.atoms.get_scaled_positions()[jatom]
+
+                # Calculate fractional coordinates for j+R
+                pos_jR = pos_j + np.dot(R, np.linalg.inv(cls.atoms.get_cell()))
+
+                myfile.write(
+                    f"  f1=    {pos_i[0]:10.6f},    {pos_i[1]:10.6f},    {pos_i[2]:10.6f}:f2=    {pos_jR[0]:10.6f},    {pos_jR[1]:10.6f},    {pos_jR[2]:10.6f}:bij= {bval:10.6f} !t1=  {i+1}:t2=  {j+1}\n"
+                )
+
+            myfile.write("End Bij_parameters\n")

TB2J/io_exchange/io_exchange.py

@@ -149,6 +149,7 @@ class SpinIO(object):
         self.has_biquadratic = not (
             biquadratic_Jdict == {} or biquadratic_Jdict is None
         )
+
         self.biquadratic_Jdict = biquadratic_Jdict
 
         if NJT_ddict is not None:
@@ -459,9 +460,10 @@ 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))
+                sum_JR = np.sum(np.sum(Jmat, axis=0), axis=0)
+                print(sum_JR)
                 for i in range(n3):
-                    Jmat[iR0][i, i] -= sum_JRi[i]
+                    Jmat[iR0][i, i] -= sum_JR[i]
         elif order == "ij":
             Jmat = np.zeros((nR, n, n), dtype=float)
             for iR, R in enumerate(self.Rlist):
@@ -521,6 +523,7 @@ 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_espins(path=os.path.join(path, "ESPInS"))
 
         self.plot_all(savefile=os.path.join(path, "JvsR.pdf"))
         # self.write_Jq(kmesh=[9, 9, 9], path=path)
@@ -684,6 +687,11 @@ Generation time: {now.strftime("%y/%m/%d %H:%M:%S")}
 
         write_uppasd(self, path=path)
 
+    def write_espins(self, path):
+        from TB2J.io_exchange.io_espins import write_espins
+
+        write_espins(self, path=path)
+
 
 def gen_distance_dict(ind_mag_atoms, atoms, Rlist):
     distance_dict = {}

TB2J/io_exchange/io_vampire.py

@@ -66,7 +66,7 @@ def write_vampire_unitcell_file(cls, fname):
 
 def write_vampire_mat_file(cls, fname):
     mat_tmpl = """#---------------------------------------------------
-# Material {id} 
+# Material {id}
 #---------------------------------------------------
 material[{id}]:material-name={name}
 material[{id}]:damping-constant={damping}
@@ -75,6 +75,8 @@ material[{id}]:uniaxial-anisotropy-constant={k1}
 material[{id}]:material-element={name}
 material[{id}]:initial-spin-direction = {spinat}
 material[{id}]:uniaxial-anisotropy-direction = {k1dir}
+# The following line is required for vampire 5 and later. 
+material[{id}]:unit-cell-category =  {id}
 #---------------------------------------------------
 """
     with open(fname, "w") as myfile:

TB2J/rotate_atoms.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
 import copy
-from ase.io import read, write
+
 import numpy as np
+from ase.io import read, write
 from TB2J.tensor_rotate import Rzx, Rzy, Rzz
 
 
@@ -15,14 +16,16 @@ def rotate_atom_xyz(atoms, noncollinear=False):
     will be generated.
     """
 
+    yield atoms
     rotation_axes = [(1, 0, 0), (0, 1, 0)]
     if noncollinear:
         rotation_axes += [(1, 1, 0), (1, 0, 1), (0, 1, 1)]
-    
+
     for axis in rotation_axes:
         rotated_atoms = copy.deepcopy(atoms)
         rotated_atoms.rotate(90, axis, rotate_cell=True)
         yield rotated_atoms
+    yield atoms
 
 
 def rotate_atom_spin_one_rotation(atoms, Rotation):
@@ -109,7 +112,7 @@ def rotate_xyz(fname, ftype="xyz", noncollinear=False):
     rotated = rotate_atom_xyz(atoms, noncollinear=noncollinear)
 
     for i, rotated_atoms in enumerate(rotated):
-        write(f"atoms_{i+1}.{ftype}", rotated_atoms)
-    write(f"atoms_0.{ftype}", atoms)
-
-    print(f"The output has been written to the atoms_i.{ftype} files. atoms_0.{ftype} contains the reference structure.")
+        write(f"atoms_{i}.{ftype}", rotated_atoms)
+    print(
+        f"The output has been written to the atoms_i.{ftype} files. atoms_0.{ftype} contains the reference structure."
+    )

TB2J/symmetrize_J.py

@@ -33,7 +33,7 @@ class TB2JSymmetrizer:
             print("Symmetry found:")
             print(finder.spacegroup)
             print("-" * 30)
-        self.pgdict = finder.get_symmetry_pair_group_dict()
+        self.pgdict = finder.get_symmetry_pair_list_dict()
         self.exc = exc
         self.new_exc = copy.deepcopy(exc)
         self.Jonly = Jonly
@@ -48,7 +48,7 @@ class TB2JSymmetrizer:
         symJdict = {}
         # Jdict = self.exc.exchange_Jdict
         # ngroup = self.pgdict
-        for pairgroup in self.pgdict.groups:
+        for pairgroup in self.pgdict.pairlists:
             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]

{tb2j-0.9.12.10.dist-info → tb2j-0.9.12.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.12.10
+Version: 0.9.12.13
 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>
@@ -35,7 +35,7 @@ Requires-Dist: pathos
 Requires-Dist: packaging>=20.0
 Requires-Dist: HamiltonIO>=0.2.4
 Requires-Dist: pre-commit
-Requires-Dist: sympair>0.1.0
+Requires-Dist: sympair>0.1.1
 Requires-Dist: tomli>=2.0.0
 Requires-Dist: tomli-w>=1.0.0
 Requires-Dist: typing_extensions

{tb2j-0.9.12.10.dist-info → tb2j-0.9.12.13.dist-info}/RECORD

@@ -1,3 +1,4 @@
+TB2J/.gitignore,sha256=0Q9EiAAZLJpONgoHwR1XcEskJykFEKfCc45KGH-C3zI,68
 TB2J/Jdownfolder.py,sha256=K8WrvU_5daH7eQgB53VymJPFRWZoOMlvQGgIca9GNt0,10885
 TB2J/Jtensor.py,sha256=WRhpp5N92a6lA1jeM1hc7jYUoTOLIdMnIIKpdOyzjR4,3192
 TB2J/MAE.py,sha256=fM8U-Dgp9HcQOEeC_kyZV1oVrygBvcux9BraUXVouvY,10994
@@ -28,10 +29,10 @@ TB2J/orbmap.py,sha256=XLQjKMxCy2eADaM5eb2F_zG08V7lzpXJxp5uEtTeVYI,7194
 TB2J/pauli.py,sha256=ESpAhk6LG5ugzuW1YFUTqiDxcg-pQ7wNnzR2FtUnvKM,5295
 TB2J/pert.py,sha256=RaCJfewl0doht4cjAnzzGKe-uj2le4aqe0iPKFrq9fo,1192
 TB2J/plot.py,sha256=AhZW7ThKYWVZR8L_T2WhvBoqtw1CkrwG1TxgExtvQYI,4079
-TB2J/rotate_atoms.py,sha256=Gl_NDPrzJR0Xi9GP-0N2ZZFZ3hpccoEG-nLE6vr9L0o,3247
+TB2J/rotate_atoms.py,sha256=taVNQh2OISHx-nuktRNOwDCbz2a_iKTIghCIT_ld250,3250
 TB2J/rotate_siestaDM.py,sha256=I4ytO8uFP8_GFyBs9-zMdiMSZS3Y3lj2dSLfNBNI2ZY,1078
 TB2J/sisl_wrapper.py,sha256=A5x1-tt8efUSPeGY5wM5m6-pJYQFXTCzQHVqD6RBa2g,14792
-TB2J/symmetrize_J.py,sha256=pv65f7TXW371kfnByIkg885XFEGg4UmWlzqY7cOUNAk,4474
+TB2J/symmetrize_J.py,sha256=woZfqWe-NSDBpS_LZAgSXjd2Bkmy6JbVHE4URLfKjaQ,4476
 TB2J/tensor_rotate.py,sha256=ZAC52knugXNJHpvpqSrmrHVdCs04b9v5X2F7rXV2zn4,8059
 TB2J/thetaphi.py,sha256=Z7N3EOSM7rjHd7b9HxMYLPQO__uR0VwEiV9b471Yudc,399
 TB2J/utest.py,sha256=z_ahi7tpHQF9WlHNQihcQ7qzfezRJQXQt28eB1X_z64,3897
@@ -56,12 +57,13 @@ 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=LjNmd3VWXQD588ICcytQfR2_DLDyXKuIuFiPcf2tKhg,24698
+TB2J/io_exchange/io_espins.py,sha256=M5VP2z6QY88RtzP06ebqHoQy5ywchojz8gr9Uw9rATk,10615
+TB2J/io_exchange/io_exchange.py,sha256=VUCog9y120d3Zved-lJ-qIb0pazx1IdAs8SHl3B_MfM,24931
 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=jFScdZ5W5_VNSEWYq6WDNKWeshZ0wxFfEzyjfvvU9MA,10601
 TB2J/io_exchange/io_uppasd.py,sha256=qhGhHbp3cZmwuBo1SrEBQulrPjEWPD3yRgVs-juQ7Fs,3268
-TB2J/io_exchange/io_vampire.py,sha256=vOStLmtCiWLp9GPhZpsAmrtaRHg9KSmtOM2Fky6yCQA,5762
+TB2J/io_exchange/io_vampire.py,sha256=nheRskvFdjEnWT8BRZ5ckZjC0dosno_PXB9erKPq_T4,5862
 TB2J/magnon/__init__.py,sha256=Q69duroGIIotgW_71ZdHYarSiJLGAu9NPYgEacUk6eI,117
 TB2J/magnon/io_exchange2.py,sha256=EcC3x6H13qq61WBsr__xKzHDtSvy_dMz1tEdUaqSG2I,23265
 TB2J/magnon/magnon3.py,sha256=ecMCCAZiBCPyEPdNI60h5rV0nRyjFeB40FIX8-o87kE,31801
@@ -105,9 +107,9 @@ 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=XPh0PNgX_fKYQodDOzZj6DKsvgULMQERU8Kjh4U2xZY,4563
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