rad-extract-tb2j#
Script for extracting of template-based Hamiltonian from TB2J results.
If --output_name is not provided, then the result is printed to the console, otherwise it is written to the text file.
Exchange types#
There are several options to control which exchange types are included in the summary:
Isotropic exchange is always included in the output. By default everything is included.
Usage example#
Example is based on the files from examples folder.
There are two modes in which exchange summary can be printed:
With the model of the template
Full Hamiltonian
In the first case the model of the template template is constructed from the Hamiltonian and exchange output is grouped based on the names provided in the template:
rad-extract-tb2j -fm -if exchange.out -tf template.txt -on summary_formed_model.txt
summary with forced symmetry
================================================================================
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╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚════╝ ╚════╝ ╚══════╝╚═════╝
Version: 0.8.3 ▄ ▄
Documentation: rad-tools.org █▀█▀█
Release date: 14 September 2023 █▄█▄█
Git hash: 5b4dc9b04aecb7efebb9cd710c02e0ad7fb68e44 ███ ▄▄
Licence: GNU GPLv3 ████ █ █
████ █
Generated on 20 September 2023 at 2:22:3 ▀▀▀▀▀▀▀▀
Exchange values are extracted from:
/Users/rybakov.ad/Codes/rad-tools/docs/examples/rad-extract-tb2j/exchange.out
Template used for model formation:
/Users/rybakov.ad/Codes/rad-tools/docs/examples/rad-extract-tb2j/template.txt
================================================================================
Primitive unit cell:
x y z
3.89500000 0.00000000 0.00000000
-1.94700000 3.37300000 0.00000000
0.00000000 0.00000000 24.47800000
================================================================================
Atoms:
Index Name a1 (rel) a2 (rel) a3 (rel) x y z
1 Ni1 0.00000285 0.01808479 0.49999183 -0.03520000 0.06100000 12.23880000
2 I1 0.33328319 0.66252594 0.56152872 0.00820000 2.23470000 13.74510000
3 I2 0.66662375 0.32917284 0.43845085 1.95560000 1.11030000 10.73240000
================================================================================
Magnetic moments of magnetic atoms:
Index Name m_x m_y m_z
1 Ni1 -0.00010000 -0.00010000 1.43680000
================================================================================
Notation of Hamiltonian:
(True, True, -1.0)
H = - \sum_{i,j} e_i J_{ij} e_j
Double counting is present.
Spin vectors are normalized to 1.
================================================================================
Spin model:
--------------------------------------------------------------------------------
J1 contains 6 bonds
Isotropic exchange: 0.1219
Full exchange matrix:
0.0834 -0.0790 0.1773
0.0803 0.0817 0.0096
-0.1773 -0.0176 0.2007
Symmetric anisotropic exchange:
-0.0386 0.0007 0.0000
0.0007 -0.0402 -0.0040
0.0000 -0.0040 0.0788
DMI module:
0.1949
|DMI| / |J_iso|:
1.5982
DMI vectors:
0.0136 -0.1773 -0.0796 (Ni1(1) Ni1(1) -1, 0, 0)
-0.0136 0.1773 0.0796 (Ni1(1) Ni1(1) 1, 0, 0)
-0.1449 0.0987 -0.0850 (Ni1(1) Ni1(1) -1, -1, 0)
0.0952 -0.1700 0.0038 (Ni1(1) Ni1(1) 0, -1, 0)
-0.0952 0.1700 -0.0038 (Ni1(1) Ni1(1) 0, 1, 0)
0.1449 -0.0987 0.0850 (Ni1(1) Ni1(1) 1, 1, 0)
--------------------------------------------------------------------------------
J2 contains 6 bonds
Isotropic exchange: 0.0143
Full exchange matrix:
0.0382 -0.0467 0.0018
0.0467 0.0385 -0.0031
-0.0018 0.0018 -0.0338
Symmetric anisotropic exchange:
0.0239 0.0000 -0.0000
0.0000 0.0242 -0.0007
-0.0000 -0.0007 -0.0481
DMI module:
0.0468
|DMI| / |J_iso|:
3.2726
DMI vectors:
-0.0024 -0.0018 -0.0467 (Ni1(1) Ni1(1) -2, -1, 0)
-0.0148 -0.0298 -0.0329 (Ni1(1) Ni1(1) -1, 1, 0)
0.0148 0.0298 0.0329 (Ni1(1) Ni1(1) 1, -1, 0)
0.0024 0.0018 0.0467 (Ni1(1) Ni1(1) 2, 1, 0)
-0.0327 0.0017 -0.0334 (Ni1(1) Ni1(1) -1, -2, 0)
0.0327 -0.0017 0.0334 (Ni1(1) Ni1(1) 1, 2, 0)
--------------------------------------------------------------------------------
J3 contains 6 bonds
Isotropic exchange: -2.3033
Full exchange matrix:
-2.2989 0.0118 0.0356
-0.0111 -2.2992 0.0133
-0.0356 -0.0120 -2.3119
Symmetric anisotropic exchange:
0.0044 0.0003 0.0000
0.0003 0.0041 0.0007
0.0000 0.0007 -0.0086
DMI module:
0.0395
|DMI| / |J_iso|:
0.0171
DMI vectors:
0.0126 -0.0356 0.0114 (Ni1(1) Ni1(1) -2, 0, 0)
-0.0126 0.0356 -0.0114 (Ni1(1) Ni1(1) 2, 0, 0)
-0.0251 0.0289 0.0095 (Ni1(1) Ni1(1) -2, -2, 0)
0.0193 -0.0344 0.0006 (Ni1(1) Ni1(1) 0, -2, 0)
-0.0193 0.0344 -0.0006 (Ni1(1) Ni1(1) 0, 2, 0)
0.0251 -0.0289 -0.0095 (Ni1(1) Ni1(1) 2, 2, 0)
================================================================================
In the second case exchange summary is printed for every bond in the Hamiltonian. Hamiltonian is filtered with the --max-distance, --min-distance and --template-file.
rad-extract-tb2j -if exchange.out -tf template.txt -on summary.txt
summary without forced symmetry
================================================================================
██████╗ █████╗ ██████╗ ████████╗ █████╗ █████╗ ██╗ ██████╗
██╔══██╗██╔══██╗██╔══██╗ ╚══██╔══╝██╔══██╗██╔══██╗██║ ██╔════╝
██████╔╝███████║██║ ██║█████╗ ██║ ██║ ██║██║ ██║██║ ╚═█████╗
██╔══██╗██╔══██║██║ ██║╚════╝ ██║ ██║ ██║██║ ██║██║ ╚══██║
██║ ██║██║ ██║██████╔╝ ██║ ╚█████╔╝╚█████╔╝███████╗██████╔╝
╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚════╝ ╚════╝ ╚══════╝╚═════╝
Version: 0.8.3 ▄ ▄
Documentation: rad-tools.org █▀█▀█
Release date: 14 September 2023 █▄█▄█
Git hash: 5b4dc9b04aecb7efebb9cd710c02e0ad7fb68e44 ███ ▄▄
Licence: GNU GPLv3 ████ █ █
████ █
Generated on 20 September 2023 at 2:22:4 ▀▀▀▀▀▀▀▀
Exchange values are extracted from:
/Users/rybakov.ad/Codes/rad-tools/docs/examples/rad-extract-tb2j/exchange.out
Template used for filtering:
/Users/rybakov.ad/Codes/rad-tools/docs/examples/rad-extract-tb2j/template.txt
================================================================================
Primitive unit cell:
x y z
3.89500000 0.00000000 0.00000000
-1.94700000 3.37300000 0.00000000
0.00000000 0.00000000 24.47800000
================================================================================
Atoms:
Index Name a1 (rel) a2 (rel) a3 (rel) x y z
1 Ni1 0.00000285 0.01808479 0.49999183 -0.03520000 0.06100000 12.23880000
2 I1 0.33328319 0.66252594 0.56152872 0.00820000 2.23470000 13.74510000
3 I2 0.66662375 0.32917284 0.43845085 1.95560000 1.11030000 10.73240000
================================================================================
Magnetic moments of magnetic atoms:
Index Name m_x m_y m_z
1 Ni1 -0.00010000 -0.00010000 1.43680000
================================================================================
Notation of Hamiltonian:
(True, True, -1.0)
H = - \sum_{i,j} e_i J_{ij} e_j
Double counting is present.
Spin vectors are normalized to 1.
================================================================================
Spin Hamiltonian:
Atom1 Atom2 ( i, j, k) J_iso Distance
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 0, -1, 0) 0.1354 3.8946
Full exchange matrix:
-0.1153 -0.2164 0.3256
-0.2176 0.3967 0.1959
0.2724 0.1661 0.1247
Symmetric anisotropic exchange:
-0.2507 -0.2170 0.2990
-0.2170 0.2613 0.1810
0.2990 0.1810 -0.0107
DMI module:
0.0305
|DMI| / |J_iso|:
0.2253
DMI vector:
0.0149 -0.0266 0.0006
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 0, 1, 0) 0.1354 3.8946
Full exchange matrix:
-0.1153 -0.2176 0.2724
-0.2164 0.3967 0.1661
0.3256 0.1959 0.1247
Symmetric anisotropic exchange:
-0.2507 -0.2170 0.2990
-0.2170 0.2613 0.1810
0.2990 0.1810 -0.0107
DMI module:
0.0305
|DMI| / |J_iso|:
0.2253
DMI vector:
-0.0149 0.0266 -0.0006
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 1, 0, 0) 0.1261 3.8950
Full exchange matrix:
0.5708 0.1127 -0.2509
-0.1127 -0.4622 -0.3343
0.2509 -0.2957 0.2698
Symmetric anisotropic exchange:
0.4447 0.0000 0.0000
0.0000 -0.5883 -0.3150
0.0000 -0.3150 0.1437
DMI module:
0.2757
|DMI| / |J_iso|:
2.1860
DMI vector:
-0.0193 0.2509 0.1127
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( -1, 0, 0) 0.1261 3.8950
Full exchange matrix:
0.5708 -0.1127 0.2509
0.1127 -0.4622 -0.2957
-0.2509 -0.3343 0.2698
Symmetric anisotropic exchange:
0.4447 0.0000 0.0000
0.0000 -0.5883 -0.3150
0.0000 -0.3150 0.1437
DMI module:
0.2757
|DMI| / |J_iso|:
2.1860
DMI vector:
0.0193 -0.2509 -0.1127
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 1, 1, 0) 0.1043 3.8951
Full exchange matrix:
-0.2054 0.3404 -0.1580
0.0976 0.3106 0.3290
-0.4400 -0.0850 0.2076
Symmetric anisotropic exchange:
-0.3097 0.2190 -0.2990
0.2190 0.2063 0.1220
-0.2990 0.1220 0.1033
DMI module:
0.2783
|DMI| / |J_iso|:
2.6694
DMI vector:
0.2070 -0.1410 0.1214
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( -1, -1, 0) 0.1043 3.8951
Full exchange matrix:
-0.2054 0.0976 -0.4400
0.3404 0.3106 -0.0850
-0.1580 0.3290 0.2076
Symmetric anisotropic exchange:
-0.3097 0.2190 -0.2990
0.2190 0.2063 0.1220
-0.2990 0.1220 0.1033
DMI module:
0.2783
|DMI| / |J_iso|:
2.6694
DMI vector:
-0.2070 0.1410 -0.1214
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 1, -1, 0) 0.0158 6.7458
Full exchange matrix:
0.0411 0.0264 -0.0277
-0.0304 0.0381 0.0128
0.0237 -0.0128 -0.0319
Symmetric anisotropic exchange:
0.0253 -0.0020 -0.0020
-0.0020 0.0223 0.0000
-0.0020 0.0000 -0.0477
DMI module:
0.0404
|DMI| / |J_iso|:
2.5614
DMI vector:
0.0128 0.0257 0.0284
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( -1, 1, 0) 0.0158 6.7458
Full exchange matrix:
0.0411 -0.0304 0.0237
0.0264 0.0381 -0.0128
-0.0277 0.0128 -0.0319
Symmetric anisotropic exchange:
0.0253 -0.0020 -0.0020
-0.0020 0.0223 0.0000
-0.0020 0.0000 -0.0477
DMI module:
0.0404
|DMI| / |J_iso|:
2.5614
DMI vector:
-0.0128 -0.0257 -0.0284
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( -1, -2, 0) 0.0161 6.7460
Full exchange matrix:
0.0368 -0.0287 -0.0015
0.0287 0.0428 -0.0311
0.0015 0.0251 -0.0312
Symmetric anisotropic exchange:
0.0207 0.0000 0.0000
0.0000 0.0267 -0.0030
0.0000 -0.0030 -0.0473
DMI module:
0.0402
|DMI| / |J_iso|:
2.4914
DMI vector:
-0.0281 0.0015 -0.0287
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 1, 2, 0) 0.0161 6.7460
Full exchange matrix:
0.0368 0.0287 0.0015
-0.0287 0.0428 0.0251
-0.0015 -0.0311 -0.0312
Symmetric anisotropic exchange:
0.0207 0.0000 0.0000
0.0000 0.0267 -0.0030
0.0000 -0.0030 -0.0473
DMI module:
0.0402
|DMI| / |J_iso|:
2.4914
DMI vector:
0.0281 -0.0015 0.0287
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 2, 1, 0) 0.0110 6.7467
Full exchange matrix:
0.0367 0.0618 -0.0003
-0.0578 0.0347 0.0041
0.0043 -0.0021 -0.0383
Symmetric anisotropic exchange:
0.0257 0.0020 0.0020
0.0020 0.0237 0.0010
0.0020 0.0010 -0.0493
DMI module:
0.0599
|DMI| / |J_iso|:
5.4312
DMI vector:
0.0031 0.0023 0.0598
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( -2, -1, 0) 0.0110 6.7467
Full exchange matrix:
0.0367 -0.0578 0.0043
0.0618 0.0347 -0.0021
-0.0003 0.0041 -0.0383
Symmetric anisotropic exchange:
0.0257 0.0020 0.0020
0.0020 0.0237 0.0010
0.0020 0.0010 -0.0493
DMI module:
0.0599
|DMI| / |J_iso|:
5.4312
DMI vector:
-0.0031 -0.0023 -0.0598
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 0, -2, 0) -2.2810 7.7892
Full exchange matrix:
-2.2827 -0.0076 0.0403
-0.0084 -2.2637 0.0236
-0.0083 -0.0036 -2.2967
Symmetric anisotropic exchange:
-0.0017 -0.0080 0.0160
-0.0080 0.0173 0.0100
0.0160 0.0100 -0.0157
DMI module:
0.0278
|DMI| / |J_iso|:
0.0122
DMI vector:
0.0136 -0.0243 0.0004
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 0, 2, 0) -2.2810 7.7892
Full exchange matrix:
-2.2827 -0.0084 -0.0083
-0.0076 -2.2637 -0.0036
0.0403 0.0236 -2.2967
Symmetric anisotropic exchange:
-0.0017 -0.0080 0.0160
-0.0080 0.0173 0.0100
0.0160 0.0100 -0.0157
DMI module:
0.0278
|DMI| / |J_iso|:
0.0122
DMI vector:
-0.0136 0.0243 -0.0004
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 2, 0, 0) -2.3130 7.7900
Full exchange matrix:
-2.2927 -0.0131 -0.0408
0.0131 -2.3297 -0.0325
0.0408 -0.0035 -2.3167
Symmetric anisotropic exchange:
0.0203 0.0000 0.0000
0.0000 -0.0167 -0.0180
0.0000 -0.0180 -0.0037
DMI module:
0.0452
|DMI| / |J_iso|:
0.0196
DMI vector:
-0.0145 0.0408 -0.0131
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( -2, 0, 0) -2.3130 7.7900
Full exchange matrix:
-2.2927 0.0131 0.0408
-0.0131 -2.3297 -0.0035
-0.0408 -0.0325 -2.3167
Symmetric anisotropic exchange:
0.0203 0.0000 0.0000
0.0000 -0.0167 -0.0180
0.0000 -0.0180 -0.0037
DMI module:
0.0452
|DMI| / |J_iso|:
0.0196
DMI vector:
0.0145 -0.0408 0.0131
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( -2, -2, 0) -2.3160 7.7902
Full exchange matrix:
-2.3213 0.0199 -0.0492
-0.0019 -2.3043 -0.0188
0.0172 0.0388 -2.3223
Symmetric anisotropic exchange:
-0.0053 0.0090 -0.0160
0.0090 0.0117 0.0100
-0.0160 0.0100 -0.0063
DMI module:
0.0453
|DMI| / |J_iso|:
0.0196
DMI vector:
-0.0288 0.0332 0.0109
--------------------------------------------------------------------------------
Ni1(1) Ni1(1) ( 2, 2, 0) -2.3160 7.7902
Full exchange matrix:
-2.3213 -0.0019 0.0172
0.0199 -2.3043 0.0388
-0.0492 -0.0188 -2.3223
Symmetric anisotropic exchange:
-0.0053 0.0090 -0.0160
0.0090 0.0117 0.0100
-0.0160 0.0100 -0.0063
DMI module:
0.0453
|DMI| / |J_iso|:
0.0196
DMI vector:
0.0288 -0.0332 -0.0109
================================================================================
Arguments#
-if, --input-filename#
Relative or absolute path to the "exchange.out" file, including the name and extension of the file itself.
required
type: str
-tf, --template-file#
Relative or absolute path to the template file, including the name and extension of the file.
optional
type: str
-on, --output-name#
Name of the output files.
If this parameter is not specified, the result is printed in the standard output stream.
optional
type: str
-d, --decimals#
Decimals after the comma for the exchange values.
default: 4
type: int
Changed in version 0.5.17: Renamed from -acc/--accuracy.
-fm, --form-model#
Whether to form the model from the template.
default: False
type: bool
Changed in version 0.8.0: Renamed from -fs/--force-symmetry.
-noa, --no-anisotropic#
Whether to output anisotropic exchange.
default: False
type: bool
Changed in version 0.8.0: Renamed from -a/--anisotropic.
-nom, --no-matrix#
Whether to output whole matrix exchange.
default: False
type: bool
Changed in version 0.8.0: Renamed from -m/--matrix.
-nodmi#
Whether to output DMI exchange.
default: False
type: bool
Changed in version 0.8.0: Renamed from -dmi.
-v, --verbose#
Verbose output, propagates to the called methods.
default: False
type: bool
-maxd, --max-distance#
(<=) Maximum distance.
All the bonds with the distance between atom 1 and atom 2 greater than maximum distance are excluded from the model.
optional
type: float
Added in version 0.8.0.
-mind, --min-distance#
(>=) Minimum distance.
All the bonds with the distance between atom 1 and atom 2 lower than minimum distance are excluded from the Hamiltonian.
optional
type: float
Added in version 0.8.0.