TB2J 0.9.11.1__py3-none-any.whl → 0.9.11.3__py3-none-any.whl

TB2J/magnon/magnon3.py

@@ -31,6 +31,7 @@ class MagnonParameters:
     Q: Optional[List[float]] = None
     uz_file: Optional[str] = None
     n: Optional[List[float]] = None
+    spin_conf_file: Optional[str] = None
     show: bool = False
 
     @classmethod
@@ -57,6 +58,8 @@ class MagnonParameters:
         # Convert path to absolute path if uz_file is relative to it
         if self.uz_file and not Path(self.uz_file).is_absolute():
             self.uz_file = str(Path(self.path) / self.uz_file)
+        if self.spin_conf_file and not Path(self.spin_conf_file).is_absolute():
+            self.spin_conf_file = str(Path(self.path) / self.spin_conf_file)
 
 
 @dataclass
@@ -76,7 +79,7 @@ class Magnon:
     _n: np.ndarray
     pbc: tuple = (True, True, True)
 
-    def set_reference(self, Q, uz, n):
+    def set_reference(self, Q, uz, n, magmoms=None):
         """
         Set reference propagation vector and quantization axis
 
@@ -92,6 +95,8 @@ class Magnon:
         self.set_propagation_vector(Q)
         self._uz = np.array(uz, dtype=float)
         self._n = np.array(n, dtype=float)
+        if magmoms is not None:
+            self.magmom = np.array(magmoms, dtype=float)
 
     def set_propagation_vector(self, Q):
         """Set propagation vector"""
@@ -653,26 +658,40 @@ def plot_magnon_bands_from_TB2J(
     )
 
     # Set reference vectors if provided
-    if any(x is not None for x in [params.Q, params.uz_file, params.n]):
-        Q = [0, 0, 0] if params.Q is None else params.Q
-        n = [0, 0, 1] if params.n is None else params.n
-
-        # Handle quantization axes
-        if params.uz_file is not None:
-            uz = np.loadtxt(params.uz_file)
-            if uz.shape[1] != 3:
-                raise ValueError(
-                    f"Quantization axes file should contain a natom×3 array. Got shape {uz.shape}"
-                )
-            if uz.shape[0] != magnon.nspin:
-                raise ValueError(
-                    f"Number of spins in uz file ({uz.shape[0]}) does not match the system ({magnon.nspin})"
-                )
-        else:
-            # Default: [0, 0, 1] for all spins
-            uz = np.array([[0.0, 0.0, 1.0] for _ in range(magnon.nspin)])
+    Q = [0, 0, 0] if params.Q is None else params.Q
+    n = [0, 0, 1] if params.n is None else params.n
+
+    # Handle quantization axes
+    if params.uz_file is not None:
+        uz = np.loadtxt(params.uz_file)
+        if uz.shape[1] != 3:
+            raise ValueError(
+                f"Quantization axes file should contain a natom×3 array. Got shape {uz.shape}"
+            )
+        if uz.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in uz file ({uz.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        # Default: [0, 0, 1] for all spins
+        # uz = np.array([[0.0, 0.0, 1.0] for _ in range(magnon.nspin)])
+        uz = np.array([[0, 0, 1]], dtype=float)
+
+    print(params)
+    if params.spin_conf_file is not None:
+        magmoms = np.loadtxt(params.spin_conf_file)
+        if magmoms.shape[1] != 3:
+            raise ValueError(
+                f"Spin configuration file should contain a nspin×3 array. Got shape {magmoms.shape}"
+            )
+        if magmoms.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in spin configuration file ({magmoms.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        magmoms = None
 
-        magnon.set_reference(Q, uz, n)
+    magnon.set_reference(Q, uz, n, magmoms)
 
     # Get band structure data
     print(f"\nCalculating bands along path {params.kpath}...")
@@ -737,27 +756,32 @@ def main():
 
     # Command line arguments (used if no config file is provided)
     parser.add_argument(
+        "-p",
         "--path",
         default="TB2J_results",
         help="Path to TB2J results directory (default: TB2J_results)",
     )
     parser.add_argument(
+        "-k",
         "--kpath",
         default=None,
         help="k-path specification (default: auto-detected from type of cell)",
     )
     parser.add_argument(
+        "-n",
         "--npoints",
         type=int,
         default=300,
         help="Number of k-points along the path (default: 300)",
     )
     parser.add_argument(
+        "-o",
         "--output",
         default="magnon_bands.png",
         help="Output file name (default: magnon_bands.png)",
     )
     parser.add_argument(
+        "-j",
         "--Jiso",
         action="store_true",
         default=True,
@@ -770,18 +794,21 @@ def main():
         help="Exclude isotropic exchange interactions",
     )
     parser.add_argument(
+        "-a",
         "--Jani",
         action="store_true",
         default=False,
         help="Include anisotropic exchange interactions (default: False)",
     )
     parser.add_argument(
+        "-d",
         "--DMI",
         action="store_true",
         default=False,
         help="Include Dzyaloshinskii-Moriya interactions (default: False)",
     )
     parser.add_argument(
+        "-q",
         "--Q",
         nargs=3,
         type=float,
@@ -789,11 +816,19 @@ def main():
         help="Propagation vector [Qx, Qy, Qz] (default: [0, 0, 0])",
     )
     parser.add_argument(
+        "-u",
         "--uz-file",
         type=str,
-        help="Path to file containing quantization axes for each spin (natom×3 array)",
+        help="Path to file containing quantization axes for each spin (nspin×3 array)",
+    )
+    parser.add_argument(
+        "-c",
+        "--spin-conf-file",
+        type=str,
+        help="Path to file containing magnetic moments for each spin (nspin×3 array)",
     )
     parser.add_argument(
+        "-v",
         "--n",
         nargs=3,
         type=float,
@@ -802,6 +837,7 @@ def main():
     )
 
     parser.add_argument(
+        "-s",
         "--show",
         action="store_true",
         default=False,
@@ -833,6 +869,7 @@ def main():
             DMI=args.DMI,
             Q=args.Q if args.Q is not None else None,
             uz_file=args.uz_file,
+            spin_conf_file=args.spin_conf_file,
             n=args.n if args.n is not None else None,
             show=args.show,
         )

TB2J/magnon/plot_magnon_dos_cli.py

@@ -4,6 +4,8 @@
 import argparse
 from pathlib import Path
 
+import numpy as np
+
 from TB2J.magnon.magnon3 import Magnon
 from TB2J.magnon.magnon_dos import plot_magnon_dos
 
@@ -13,6 +15,7 @@ def main():
         description="Calculate and plot magnon DOS from TB2J results"
     )
     parser.add_argument(
+        "-p",
         "--path",
         default="TB2J_results",
         help="Path to TB2J results directory (default: TB2J_results)",
@@ -51,26 +54,135 @@ def main():
         help="Number of energy points (default: 401)",
     )
     parser.add_argument(
+        "-o",
         "--output",
         default="magnon_dos.png",
         help="Output filename for plot (default: magnon_dos.png)",
     )
     parser.add_argument(
-        "-show",
+        "-s",
+        "--show",
         action="store_true",
         dest="show",
         help="Show plot window",
     )
 
+    # Exchange interaction options (same as in magnon bands)
+    parser.add_argument(
+        "-j",
+        "--Jiso",
+        action="store_true",
+        default=True,
+        help="Include isotropic exchange interactions (default: True)",
+    )
+    parser.add_argument(
+        "--no-Jiso",
+        action="store_false",
+        dest="Jiso",
+        help="Exclude isotropic exchange interactions",
+    )
+    parser.add_argument(
+        "-a",
+        "--Jani",
+        action="store_true",
+        default=False,
+        help="Include anisotropic exchange interactions (default: False)",
+    )
+    parser.add_argument(
+        "-d",
+        "--DMI",
+        action="store_true",
+        default=False,
+        help="Include Dzyaloshinskii-Moriya interactions (default: False)",
+    )
+
+    # Reference vector options (same as in magnon bands)
+    parser.add_argument(
+        "-q",
+        "--Q",
+        nargs=3,
+        type=float,
+        metavar=("Qx", "Qy", "Qz"),
+        help="Propagation vector [Qx, Qy, Qz] (default: [0, 0, 0])",
+    )
+    parser.add_argument(
+        "-u",
+        "--uz-file",
+        type=str,
+        help="Path to file containing quantization axes for each spin (nspin×3 array)",
+    )
+    parser.add_argument(
+        "-c",
+        "--spin-conf-file",
+        type=str,
+        help="Path to file containing magnetic moments for each spin (nspin×3 array)",
+    )
+    parser.add_argument(
+        "-v",
+        "--n",
+        nargs=3,
+        type=float,
+        metavar=("nx", "ny", "nz"),
+        help="Normal vector for rotation [nx, ny, nz] (default: [0, 0, 1])",
+    )
+
     args = parser.parse_args()
 
     # Check if TB2J results exist
     if not Path(args.path).exists():
         raise FileNotFoundError(f"TB2J results not found at {args.path}")
 
-    # Load magnon calculator
+    # Load magnon calculator with exchange interaction options
     print(f"Loading exchange parameters from {args.path}...")
-    magnon = Magnon.from_TB2J_results(path=args.path)
+    magnon = Magnon.from_TB2J_results(
+        path=args.path, Jiso=args.Jiso, Jani=args.Jani, DMI=args.DMI
+    )
+
+    # Set reference vectors if provided (same logic as in magnon bands)
+    Q = [0, 0, 0] if args.Q is None else args.Q
+    n = [0, 0, 1] if args.n is None else args.n
+
+    # Handle quantization axes
+    if args.uz_file is not None:
+        # Make path relative to TB2J results if not absolute
+        uz_file = args.uz_file
+        if not Path(uz_file).is_absolute():
+            uz_file = str(Path(args.path) / uz_file)
+
+        uz = np.loadtxt(uz_file)
+        if uz.shape[1] != 3:
+            raise ValueError(
+                f"Quantization axes file should contain a nspin×3 array. Got shape {uz.shape}"
+            )
+        if uz.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in uz file ({uz.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        # Default: [0, 0, 1] for all spins
+        uz = np.array([[0, 0, 1]], dtype=float)
+
+    # Handle spin configuration
+    if args.spin_conf_file is not None:
+        # Make path relative to TB2J results if not absolute
+        spin_conf_file = args.spin_conf_file
+        if not Path(spin_conf_file).is_absolute():
+            spin_conf_file = str(Path(args.path) / spin_conf_file)
+
+        magmoms = np.loadtxt(spin_conf_file)
+        if magmoms.shape[1] != 3:
+            raise ValueError(
+                f"Spin configuration file should contain a nspin×3 array. Got shape {magmoms.shape}"
+            )
+        if magmoms.shape[0] != magnon.nspin:
+            raise ValueError(
+                f"Number of spins in spin configuration file ({magmoms.shape[0]}) does not match the system ({magnon.nspin})"
+            )
+    else:
+        magmoms = None
+
+    # Set reference configuration
+    magnon.set_reference(Q, uz, n, magmoms)
 
     # Convert window from meV to eV if provided
     window = None

TB2J/scripts/TB2J_eigen.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
+import argparse
+
 from TB2J.plot import write_eigen
 from TB2J.versioninfo import print_license
-import argparse
 
 """
 The script to plot the magnon band structure.

TB2J/scripts/TB2J_magnon.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
+import argparse
+
 from TB2J.plot import plot_magnon_band, write_eigen
 from TB2J.versioninfo import print_license
-import argparse
 
 """
 The script to plot the magnon band structure.

TB2J/scripts/TB2J_magnon_dos.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
 
-from TB2J.plot import plot_magnon_dos, command_line_plot_magnon_dos
+from TB2J.plot import command_line_plot_magnon_dos
 
 command_line_plot_magnon_dos()

TB2J/scripts/TB2J_rotate.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 import argparse
-from TB2J.rotate_atoms import rotate_atom_xyz, rotate_xyz, check_ftype
+
+from TB2J.rotate_atoms import rotate_xyz
 
 
 def main():
@@ -17,7 +18,7 @@ def main():
     parser.add_argument(
         "--noncollinear",
         action="store_true",
-        help="If present, six different configurations will be generated. These are required for non-collinear systems."
+        help="If present, six different configurations will be generated. These are required for non-collinear systems.",
     )
 
     args = parser.parse_args()

TB2J/scripts/TB2J_rotateDM.py

@@ -1,16 +1,16 @@
 #!/usr/bin/env python3
 import argparse
+
 from TB2J.rotate_siestaDM import rotate_DM
 
+
 def main():
     parser = argparse.ArgumentParser(description="")
-    parser.add_argument(
-        "--fdf_fname", help="Name of the *.fdf siesta file."
-    )
+    parser.add_argument("--fdf_fname", help="Name of the *.fdf siesta file.")
     parser.add_argument(
         "--noncollinear",
         action="store_true",
-        help="If present, six different configurations will be generated. These are required for non-collinear systems."
+        help="If present, six different configurations will be generated. These are required for non-collinear systems.",
     )
 
     args = parser.parse_args()

{tb2j-0.9.11.1.dist-info → tb2j-0.9.11.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TB2J
-Version: 0.9.11.1
+Version: 0.9.11.3
 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-0.9.11.1.dist-info → tb2j-0.9.11.3.dist-info}/RECORD

@@ -1,4 +1,3 @@
-TB2J/.gitignore,sha256=0Q9EiAAZLJpONgoHwR1XcEskJykFEKfCc45KGH-C3zI,68
 TB2J/Jdownfolder.py,sha256=U6R8v6ZC-AgMA6wvvFPyacXX_lYJcRu1kzNr7aVB1tg,10827
 TB2J/Jtensor.py,sha256=WRhpp5N92a6lA1jeM1hc7jYUoTOLIdMnIIKpdOyzjR4,3192
 TB2J/MAE.py,sha256=fM8U-Dgp9HcQOEeC_kyZV1oVrygBvcux9BraUXVouvY,10994
@@ -47,7 +46,6 @@ TB2J/interfaces/lawaf_interface.py,sha256=PieLnmppdafOYsgeHznqOou1g9L1sam5jOm3Ka
 TB2J/interfaces/manager.py,sha256=PQMLEfMCT5GnDWSl2nI4JOgRPm_fysyR-6Y6l97xWcw,860
 TB2J/interfaces/siesta_interface.py,sha256=Te9-Au0ZGAt-LfEnG8exUFD4lMj6uZu8RmHjopb0XLU,7595
 TB2J/interfaces/wannier90_interface.py,sha256=qzRgXUBb7t1Aiegrl_RV51BB8csdtVM0EP0Z4pjmTcs,4467
-TB2J/interfaces/abacus/.gitignore,sha256=Iytg6TR3gOh014q9m7ReuCKYmx-Qi-o3SgILYB2WRtU,20
 TB2J/interfaces/abacus/__init__.py,sha256=leas71oCvM_HxrF4gnO5A_VKcJmDAgsI1BUctLU3OBw,177
 TB2J/interfaces/abacus/abacus_api.py,sha256=lNV4LNkLcKw7Zux4MQYM9wnh3eFTlcSqbf4Pb7pqhrk,7243
 TB2J/interfaces/abacus/abacus_wrapper.py,sha256=bQFnvvy-0hruTavH_VspMk1wD32t2UFybEkCgwkwle0,11941
@@ -66,13 +64,13 @@ TB2J/io_exchange/io_uppasd.py,sha256=bI4iPEgnK4TvCZNvb6x2xYXgjW7pEehCqmcizy2pqFU
 TB2J/io_exchange/io_vampire.py,sha256=vOStLmtCiWLp9GPhZpsAmrtaRHg9KSmtOM2Fky6yCQA,5762
 TB2J/magnon/__init__.py,sha256=Q69duroGIIotgW_71ZdHYarSiJLGAu9NPYgEacUk6eI,117
 TB2J/magnon/io_exchange2.py,sha256=EcC3x6H13qq61WBsr__xKzHDtSvy_dMz1tEdUaqSG2I,23265
-TB2J/magnon/magnon3.py,sha256=PFZFiyfYTIBscVu8SzvGxtrXhT-QM66EwIhWOqgSYQE,30219
+TB2J/magnon/magnon3.py,sha256=evCwmmq4Ah8scGVUdEprM7BLRUbWme4M8sF-1wznEoI,31360
 TB2J/magnon/magnon_band.py,sha256=ZLHK1qf2Clu9jlcvBwBCBEi1MrPfy2BWrow8JJ2v5pk,6103
 TB2J/magnon/magnon_dos.py,sha256=uztzsxCmFZpDHl-JziaUb_NNwBeZw9-L2ozd3XNTvxI,8506
 TB2J/magnon/magnon_io.py,sha256=H4bmzCcnh1D3Sb6UBIIKWa6jIrA20dg9lX4wfLXHEjo,1241
 TB2J/magnon/magnon_math.py,sha256=0mVQY5tXe6fHsfijivXf-1-Tk-Ku02Gv7-TdAd8qUpc,1359
 TB2J/magnon/plot.py,sha256=oNavax15jRfW4Sxl6FgwLXSrMntyVz2cgVDbmgkWehw,3193
-TB2J/magnon/plot_magnon_dos_cli.py,sha256=XVozodrIO_w4FBhp-ZcpIZbyGWLdegUFLdvY5zL3XOI,2592
+TB2J/magnon/plot_magnon_dos_cli.py,sha256=y3R2DPTuK5Jw9rdnBooWNczQM-s8s_blCP5Wd2zaIWg,6124
 TB2J/magnon/structure.py,sha256=rKefzXgQlEjVvV-A7E2IogVDWwf5egZr3Wxxu6HuJU4,7685
 TB2J/mathutils/__init__.py,sha256=E70Mx8mLXh3DJGmdN3TLWmGYMcsbvKxmgxUbAI6Mzmo,49
 TB2J/mathutils/auto_kpath.py,sha256=bDXDyQzRByVpPSOpz7NU7F5hYqS6IX-47lwWoMU89lM,4978
@@ -82,14 +80,15 @@ TB2J/mathutils/kR_convert.py,sha256=p_9XWJVNanTzTK2rI6KRjTkbSq42la6N448-zJOsMwY,
 TB2J/mathutils/lowdin.py,sha256=RYbm9OcnFnjcZFdC5YcNUsI9cOJmoDLsWSSCaP0GqKQ,499
 TB2J/mathutils/rotate_spin.py,sha256=sPTnwJThfohCHIY7EuzBV2K3mIXcJI5y1QBytGmEKR4,8229
 TB2J/scripts/TB2J_downfold.py,sha256=f1CPuka_uOcvwBKDWAaseRZ04Bqyx_Cor5PvU6LyIsU,2600
-TB2J/scripts/TB2J_eigen.py,sha256=Pz2c9ZwWx2io5uW6QFI_XRs-3-HtCwlEi1Dzd2swsAY,1142
-TB2J/scripts/TB2J_magnon.py,sha256=YwjXMvH_dl5CljjkqcpYSlvYUd6sK78PVyMcUkz9jS8,3115
+TB2J/scripts/TB2J_eigen.py,sha256=vgy8Fama3J-bep3Ej8oJlDDNq6LFWay6Hr9uaVkoLzM,1143
+TB2J/scripts/TB2J_magnon.py,sha256=fz9nOv5dMy1e0Dac3eGtiNODvdfTnfLlM7jvYbShiN0,3116
 TB2J/scripts/TB2J_magnon2.py,sha256=mfDrkjK9DpXeKl6jLdACzAD6ArAWBCmC-TPb-vCWpJs,1934
-TB2J/scripts/TB2J_magnon_dos.py,sha256=uuNLuLadwgdzVb4OKfsY_92wRx9y7qdzK6vzH4AK1Ps,124
+TB2J/scripts/TB2J_magnon_dos.py,sha256=xQlI6u31Oyv9Yua73_Qa5cF1cnvg1PNrTy1VXs4dcBk,107
 TB2J/scripts/TB2J_merge.py,sha256=Fw9Y4fVmptWWMtOXA71xi4ebPWhsvb6dCSVOga6GguA,2110
 TB2J/scripts/TB2J_plot_magnon_bands.py,sha256=0HxjN5-gYrlqQsppQs94BCp6aynBGt-QMK-5QiFPgDg,888
-TB2J/scripts/TB2J_rotate.py,sha256=d4CSJB2bmlsGI8eKxHU8dm072_CONQ86i6uZE1ZCkMk,887
-TB2J/scripts/TB2J_rotateDM.py,sha256=zJ2pepVaLHeZdvewAOHbtYukq_Wxf3yzAaUGc6elQoQ,581
+TB2J/scripts/TB2J_rotate.py,sha256=WneOj6NBMDzVlpLXnq9tZqnJqTATfv_zmgl4EltD118,859
+TB2J/scripts/TB2J_rotateDM.py,sha256=lH71mkg0BKDGVLoK7VvmIPkf2mCjyc0V5l9rZZgyfP4,570
+TB2J/scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 TB2J/scripts/abacus2J.py,sha256=3DE3EjRIcI0ydBQoH3WTGpYKYMEVL53hnB8PQ4gojdk,1809
 TB2J/scripts/siesta2J.py,sha256=2CrS-wfVr0W2NaGvY9niNslC0xoX0WgDZFlrmIWUr20,2332
 TB2J/scripts/wann2J.py,sha256=djLBG3t4oEimokMG6TIFHyjp8u8DtnizN9coQXOTN7U,3254
@@ -106,9 +105,9 @@ 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-0.9.11.1.dist-info/licenses/LICENSE,sha256=CbZI-jyRTjiqIcWa244cRSHJdjjtUNqGR4HeJkgEwJw,1332
-tb2j-0.9.11.1.dist-info/METADATA,sha256=ssXsEP9mkpL3viTxoA6YkhpMXr0LrZwNqufo0mn5MmA,4138
-tb2j-0.9.11.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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TB2J/.gitignore

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

TB2J/interfaces/abacus/.gitignore

@@ -1,2 +0,0 @@
-TB2J_results/
-*.png