TB2J

https://tb2j.readthedocs.io/en/latest/
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### Install TB2J from source

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/install.rst.txt

Install TB2J by downloading the source code from GitHub and running the setup script. The --user option is useful for permission issues.

```bash
python setup.py install
```

--------------------------------

### Install TB2J with all optional dependencies

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/install.rst.txt

Install TB2J along with all available optional dependencies.

```bash
pip install TB2J[all]
```

--------------------------------

### Install TB2J with Lawaf interface

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/install.rst.txt

Install TB2J with optional dependencies for the Lawaf interface.

```bash
pip install TB2J[lawaf]
```

--------------------------------

### Install TB2J using pip

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/install.rst.txt

Use this command for the standard installation of TB2J via pip.

```bash
pip install TB2J
```

--------------------------------

### Example Usage of TB2J_symmetrize.py

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/symmetry.md.txt

This example demonstrates how to run the `TB2J_symmetrize.py` script to symmetrize exchange parameters. It specifies the input directory, output directory, and the precision for symmetry detection.

```bash
TB2J_symmetrize.py -i TB2J_results -o TB2J_symmetrized -s 1e-4
```

--------------------------------

### Install TB2J-OpenMX Plugin

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/openmx.rst.txt

Install the TB2J-OpenMX plugin using pip. This plugin is required for parsing OpenMX files.

```bash
pip install TB2J-OpenMX
```

--------------------------------

### Install Siesta optional dependencies

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/install.rst.txt

Install sisl and netcdf4, which are optional dependencies for the Siesta interface.

```bash
pip3 install sisl netcdf4
```

--------------------------------

### Install TB2J with Siesta interface

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/install.rst.txt

Install TB2J with optional dependencies for the Siesta interface.

```bash
pip install TB2J[siesta]
```

--------------------------------

### Wannier Center and Spread Example

Source: https://tb2j.readthedocs.io/en/latest/src/wannier.html

Example output from a .wout file showing the calculated Wannier center coordinates and their spreads, used to check localization.

```text
Final State
 WF centre and spread    1  (  1.904992,  1.904992,  1.904992 )     0.50185811
 WF centre and spread    2  (  1.904992,  1.904992,  1.904992 )     0.48650086
 WF centre and spread    3  (  1.904992,  1.904992,  1.904992 )     0.48650086
 WF centre and spread    4  (  1.904992,  1.904992,  1.904992 )     0.50185997
 WF centre and spread    5  (  1.904992,  1.904992,  1.904992 )     0.48650084
 WF centre and spread    6  (  1.904992,  1.904992, -0.000000 )     0.74591265
 WF centre and spread    7  (  1.904992,  1.904992,  0.000000 )     0.96557405
 WF centre and spread    8  (  1.904992,  1.904992, -0.000000 )     0.96557405
 WF centre and spread    9  ( -0.000000,  1.904992,  1.904992 )     0.96557489
 WF centre and spread   10  ( -0.000000,  1.904992,  1.904992 )     0.74589254
 WF centre and spread   11  (  0.000000,  1.904992,  1.904992 )     0.96557379
 WF centre and spread   12  (  1.904992,  0.000000,  1.904992 )     0.96557489
 WF centre and spread   13  (  1.904992, -0.000000,  1.904992 )     0.96557379
 WF centre and spread   14  (  1.904992, -0.000000,  1.904992 )     0.74589254
 Sum of centres and spreads ( 20.954915, 20.954915, 20.954915 )    10.49436382
```

--------------------------------

### Wannier90 Output Files (Spin Up)

Source: https://tb2j.readthedocs.io/en/latest/src/wannier.html

Example of output files generated by Abinit for spin-up calculations when using Wannier90.

```text
abinito_w90_up_hr.dat abinito_w90_up_centres.xyz   abinito_w90_up.wout
```

--------------------------------

### Plot Magnon Density of States with TB2J_magnon_dos.py

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/magnon_band.rst.txt

Example of plotting the magnon density of states using TB2J_magnon_dos.py. This command sets the number of k-mesh points, smearing width, and specifies output file names.

```bash
TB2J_magnon_dos.py --show -s 10 -k 25 25 25 -f magnon_dos.png --show
```

--------------------------------

### Specify 3d Orbitals for Fe (Siesta Input)

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/orbital_contribution.md.txt

Example command for Siesta input to consider only the 3d orbitals of Fe for exchange decomposition.

```bash
siesta2J.py --elements Fe_3d  ....

```

--------------------------------

### Plot Magnon Band Structure with TB2J_magnon.py

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/magnon_band.rst.txt

Example of plotting a magnon band structure using TB2J_magnon.py for BCC Fe. Specify q-points, output figure name, and choose to display the plot.

```bash
TB2J_magnon.py --qpath GNPGHN --figfname magnon.png --show
```

--------------------------------

### Specify 3d and 4s Orbitals for Fe (Siesta Input)

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/orbital_contribution.md.txt

Example command for Siesta input to consider both 3d and 4s orbitals of Fe for exchange decomposition.

```bash
siesta2J.py --elements Fe_3d_4s  ....

```

--------------------------------

### Compute MAE using abacus_get_MAE

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/mae.md.txt

Example of using the `abacus_get_MAE` function to compute MAE. This function requires paths to SOC and non-SOC calculation outputs, k-mesh parameters, and angular ranges.

```python
import numpy as np
from TB2J.MAEGreen import abacus_get_MAE

def run():
    # theta, phi: along the xz plane, rotating from z to x. 
    thetas = np.linspace(0, 180, 19) * np.pi / 180
    phis = np.zeros(19)
    abacus_get_MAE(
        path_nosoc= 'soc0/OUT.ABACUS',   
        path_soc= 'soc1/OUT.ABACUS',
        kmesh=[6,6,1],
        gamma=True,
        thetas=thetas, 
        phis=phis,
        nel = 16,
        )

if __name__ == '__main__':
    run()
```

--------------------------------

### Orbital Contributions for BCC Fe (Siesta Input)

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/orbital_contribution.md.txt

Example showing the orbital decomposition of the isotropic exchange interaction for BCC Fe using Siesta input, considering only 3d orbitals. Orbital names are specific to the basis set.

```text
==========================================================================================
Orbitals used in decomposition:
The name of the orbitals for the decomposition:
Fe1 : ('3dxy', '3dyz', '3dz2', '3dxz', '3dx2-y2')

==========================================================================================
Exchange:
    i      j          R        J_iso(meV)          vector          distance(A)
----------------------------------------------------------------------------------------
   Fe1   Fe1   ( -1,   0,   0) 17.6873   (-2.467,  0.000,  0.000)  2.467
J_iso: 17.6873
Orbital contributions:
 [[11.462 -0.     0.297 -0.     0.096]
 [-0.     3.69  -0.    -0.214 -0.   ]
 [-0.163 -0.     3.215 -0.    -3.262]
 [-0.     0.396 -0.    11.451 -0.   ]
 [-0.055  0.    -3.263  0.    -4.248]]

```

--------------------------------

### Configure Spin Dynamics in MULTIBINIT

Source: https://tb2j.readthedocs.io/en/latest/src/multibinit.html

This snippet shows the configuration parameters for spin dynamics in the mb.in file. Adjust parameters like supercell size, temperature range, and time steps for your simulation.

```fortran
prt_model = 0

#--------------------------------------------------------------
#Monte carlo / molecular dynamics
#--------------------------------------------------------------
dynamics =  0    ! disable molecular dynamics

ncell =   28 28 28  ! size of supercell.
#-------------------------------------------------------------
#Spin dynamics
#------------------------------------------------------------
spin_dynamics=1  ! enable spin dynamics
spin_mag_field= 0.0 0.0 0.0   ! external magnetic field
spin_ntime_pre = 10000          ! warming up steps.
spin_ntime =10000             ! number of steps.
spin_nctime=100               ! number of time steps between two nc file write
spin_dt=1e-15 s               ! time step.
spin_init_state = 1           ! FM initial state. May cause some trouble

spin_temperature=0.0

spin_var_temperature=1        ! switch on variable temperature calculation
spin_temperature_start=0      ! starting point of temperature
spin_temperature_end=1300      ! ending point of temperature.
spin_temperature_nstep= 52     ! number of temperature steps.

spin_sia_add = 1              ! add a single ion anistropy (SIA) term?
spin_sia_k1amp = 1e-6         ! amplitude of SIA (in Ha), how large should be used?
spin_sia_k1dir = 0.0 0.0 1.0  ! direction of SIA

spin_calc_thermo_obs = 1      ! calculate thermodynamics related observables

```

--------------------------------

### Running Abinit for Wannier90

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/wannier.rst.txt

Execute Abinit with the specified input files to generate Wannier90 output files.

```bash
abinit < abinit.files > log 2> err
```

--------------------------------

### View Help for TB2J Tools

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/parameters.rst.txt

Use the --help option with any TB2J tool to see a complete list of its parameters. This is useful for understanding tool-specific options.

```bash
wann2J.py --help    # For Wannier90-based calculations
siesta2J.py --help  # For SIESTA-based calculations
abacus2J.py --help  # For ABACUS-based calculations
```

--------------------------------

### Initialize MAE calculation with MAEGreen class

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/mae.md.txt

Demonstrates initializing the `MAEGreen` class for MAE calculations. Supports predefined angle sets or custom angle arrays for exploring magnetization directions.

```python
from TB2J.MAEGreen import MAEGreen

# Use predefined angle sets
mae = MAEGreen(
    tbmodels=model,
    atoms=model.atoms,
    kmesh=[6,6,1],
    angles="xyz",  # x, y, z axes
    # angles="fib",  # Fibonacci sphere sampling
    # angles="miller",  # Miller index directions
    # angles="scan",  # Full angular scan
)

# Custom angle arrays
mae = MAEGreen(
    tbmodels=model,
    atoms=model.atoms,
    kmesh=[6,6,1],
    angles=[thetas, phis],  # Custom theta, phi arrays
)

# Run with both perturbation and eigenvalue methods
mae.run(output_path="my_mae_results", with_eigen=True)
```

--------------------------------

### Specify Magnetic Elements

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/parameters.rst.txt

Define the magnetic elements to be included in the Heisenberg model. Example: Fe and Ni.

```bash
--elements Fe Ni
```

--------------------------------

### Display Help for TB2J_magnon.py

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/magnon_band.rst.txt

Use this command to view the available options and arguments for the TB2J_magnon.py script.

```bash
TB2J_magnon.py --help
```

--------------------------------

### Display abacus2J.py Help Message

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/abacus.md.txt

Use the --help flag to view all available parameters and their descriptions for the abacus2J.py script. This is useful for understanding the script's capabilities and options.

```bash
abacus2J.py --help
```

--------------------------------

### Specify Magnetic Atom Indices

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/parameters.rst.txt

Explicitly select magnetic atoms by their unit cell indices (starting from 1). This overrides element-based selection.

```bash
--index_magnetic_atoms 1 2 4
```

--------------------------------

### Run Spin Dynamics with MULTIBINIT

Source: https://tb2j.readthedocs.io/en/latest/src/multibinit.html

Execute the MULTIBINIT code using mpirun with the specified number of processors and input file. This command initiates the spin dynamics simulation.

```bash
mpirun -np 4 multibinit --F03 < mb.files

```

--------------------------------

### Interface TB2J with sisl

Source: https://tb2j.readthedocs.io/en/latest/src/extend.html

This snippet shows how to read a Hamiltonian using sisl, wrap it with SislWrapper, and pass it to the ExchangeNCL class for TB2J calculations. Ensure sisl is installed and the Hamiltonian file is accessible.

```python
# read hamiltonian using sisl
fdf = sisl.get_sile(fdf_fname)
H = fdf.read_hamiltonian()
# wrap the hamiltonian to SislWrapper
tbmodel = SislWrapper(H, spin=None)
# pass to ExchangeNCL
exchange = ExchangeNCL(
    tbmodels=tbmodel,
    atoms=atoms,
    efermi=0.0,
    magnetic_elements=magnetic_elements,
    kmesh=kmesh,
    emin=emin,
    emax=emax,
    nz=nz,
    exclude_orbs=exclude_orbs,
    Rcut=Rcut,
    ne=ne,
    description=description)
exchange.run()
```

--------------------------------

### Run openmx2J.py Script

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/openmx.rst.txt

Execute the openmx2J.py script to process OpenMX output files. Ensure 'HS.fileout on' is enabled in your DFT calculation. Provide the file prefix, magnetic elements, and k-mesh parameters.

```bash
openmx2J.py -- prefix openmx --elements Fe --kmesh 7 7 7
```

--------------------------------

### Orbital Contributions for Cubic SrMnO3 (Wannier90)

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/orbital_contribution.md.txt

Example showing the orbital decomposition of the isotropic exchange interaction for cubic SrMnO3 using Wannier90. Orbital names are generic ('orb_1', etc.) as they are not known from the Wannier90 input.

```text
=======================================================================================
Orbitals used in decomposition:
The name of the orbitals for the decomposition:
Mn1 : ['orb_1', 'orb_2', 'orb_3', 'orb_4', 'orb_5']

=======================================================================================
Exchange:
    i      j          R        J_iso(meV)          vector          distance(A)
----------------------------------------------------------------------------------------
   Mn1   Mn1   (  0,   0,   1) -7.1027   ( 0.000,  0.000,  3.810)  3.810
J_iso: -7.1027
Orbital contributions:
 [[ 3.184 -0.    -0.     0.    -0.   ]
 [-0.    -5.06   0.    -0.     0.   ]
 [-0.     0.    -5.06  -0.     0.   ]
 [ 0.    -0.    -0.    -0.121 -0.   ]
 [-0.     0.     0.     0.    -0.047]]

```

--------------------------------

### Configure Spin Dynamics with MULTIBINIT

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/multibinit.rst.txt

This snippet shows the configuration for spin dynamics in MULTIBINIT, including parameters for molecular dynamics, spin dynamics, temperature range, and anisotropy. It's used to set up simulations for calculating thermodynamic observables.

```fortran
prt_model = 0

#--------------------------------------------------------------
#Monte carlo / molecular dynamics
#--------------------------------------------------------------
dynamics =  0    ! disable molecular dynamics

ncell =   28 28 28  ! size of supercell.
#-------------------------------------------------------------
#Spin dynamics
#------------------------------------------------------------
spin_dynamics=1  ! enable spin dynamics
spin_mag_field= 0.0 0.0 0.0   ! external magnetic field
spin_ntime_pre = 10000          ! warming up steps.
spin_ntime =10000             ! number of steps.
spin_nctime=100               ! number of time steps between two nc file write
spin_dt=1e-15 s               ! time step.
spin_init_state = 1           ! FM initial state. May cause some trouble

spin_temperature=0.0

spin_var_temperature=1        ! switch on variable temperature calculation
spin_temperature_start=0      ! starting point of temperature
spin_temperature_end=1300      ! ending point of temperature.
spin_temperature_nstep= 52     ! number of temperature steps.

spin_sia_add = 1              ! add a single ion anistropy (SIA) term?
spin_sia_k1amp = 1e-6         ! amplitude of SIA (in Ha), how large should be used?
spin_sia_k1dir = 0.0 0.0 1.0  ! direction of SIA

spin_calc_thermo_obs = 1      ! calculate thermodynamics related observables
```

--------------------------------

### Create a virtual environment

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/install.rst.txt

Create a new Python virtual environment named TB2J in a specified path.

```bash
python3 -m venv <your path>/TB2J
```

--------------------------------

### Enable Cache for Wavefunctions

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/parameters.rst.txt

Use the --use_cache option to store wavefunctions and the Hamiltonian on disk, reducing memory usage. Useful for large systems. Default is False.

```bash
--use_cache
```

--------------------------------

### Activate a virtual environment

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/install.rst.txt

Activate the created virtual environment to use TB2J and its dependencies within an isolated environment.

```bash
source <your path>/TB2J/bin/activate
```

--------------------------------

### Generate Initial Heisenberg Hamiltonian

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/downfold.md.txt

Generate the initial Heisenberg Hamiltonian including both transitional metal and ligand elements using `wann2J.py`. This is a prerequisite step before downfolding.

```bash
wann2J.py --elements Cr I ....
```

--------------------------------

### Display Help for TB2J_magnon_dos.py

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/magnon_band.rst.txt

Use this command to view the available options and arguments for the TB2J_magnon_dos.py script, which plots magnon density of states.

```bash
TB2J_magnon_dos.py --help
```

--------------------------------

### Abinit Input for Wannier90

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/wannier.rst.txt

Add these lines to the Abinit input file to enable Wannier90 functionality and specify projection methods.

```bash
prtwant 2    # enable wannier90
w90iniprj 2  # use projection to orbitals instead of random.
w90prtunk 0  # use 1 if you want to visualize the WF's later.
```

--------------------------------

### Add Calculation Details to Output

Source: https://tb2j.readthedocs.io/en/latest/src/parameters.html

Use the --description parameter to include essential calculation details like functional, U values, and magnetic state in the XML output.

```bash
--description "LDA+U, U=5eV, FM state"
```

--------------------------------

### Run siesta2J.py for Exchange Parameters

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/siesta.rst.txt

Calculates exchange parameters using the siesta2J.py script. It reads Siesta input files and Hamiltonian/overlap matrices to compute J with a specified k-point grid. Ensure k-mesh density is sufficient for convergence.

```bash
siesta2J.py --fdf_fname siesta.fdf --elements Fe --kmesh 7 7 7
```

--------------------------------

### Add Calculation Description to Output

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/parameters.rst.txt

Include essential calculation details such as the exchange-correlation functional, Hubbard U values, and magnetic state in the XML output.

```bash
--description "LDA+U, U=5eV, Ferromagnetic"
```

--------------------------------

### Initialize MAEGreen with predefined angle sets

Source: https://tb2j.readthedocs.io/en/latest/src/mae.html

Initializes the MAEGreen class using predefined angle sets for sampling magnetization directions. Supported presets include 'xyz', 'fib', 'miller', and 'scan'.

```python
from TB2J.MAEGreen import MAEGreen

# Use predefined angle sets
mae = MAEGreen(
    tbmodels=model,
    atoms=model.atoms,
    kmesh=[6,6,1],
    angles="xyz",  # x, y, z axes
    # angles="fib",  # Fibonacci sphere sampling
    # angles="miller",  # Miller index directions
    # angles="scan",  # Full angular scan
)
```

--------------------------------

### Enable Spin-Orbit Coupling Reading for SIESTA

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/parameters.rst.txt

Enable reading of spin-orbit coupling data from SIESTA output by setting --split_soc. Default is False.

```bash
--split_soc
```

--------------------------------

### Display TB2J_eigen.py Usage

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/eigen.rst.txt

This command displays the help message for the TB2J_eigen.py script, outlining its available options and their descriptions.

```bash
TB2J_eigen.py --help
```

--------------------------------

### Initialize MAEGreen with custom angle arrays

Source: https://tb2j.readthedocs.io/en/latest/src/mae.html

Initializes the MAEGreen class with custom theta and phi arrays for defining specific magnetization directions. This allows for fine-grained control over the angular sampling.

```python
from TB2J.MAEGreen import MAEGreen

# Custom angle arrays
mae = MAEGreen(
    tbmodels=model,
    atoms=model.atoms,
    kmesh=[6,6,1],
    angles=[thetas, phis],  # Custom theta, phi arrays
)
```

--------------------------------

### Wannier90 Spin Down File Generation

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/wannier.rst.txt

For Wannier90 versions prior to 3.0, manually run 'wannier90.x' with the spin-down input file to generate the necessary output files due to a known bug.

```bash
wannier90.x abinito_w90_down
```

--------------------------------

### Calculate Exchange Parameters with TB2J

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/wannier.rst.txt

Use this command to calculate exchange parameters. Specify the Fermi energy, k-point mesh, magnetic elements, and prefixes for Wannier90 output files. Ensure the POSCAR or abinit.in file is prepared.

```bash
wann2J.py --posfile abinit.in --efermi 6.15 --kmesh 4 4 4 --elements Mn --prefix_up abinito_w90_up --prefix_down abinito_w90_down  --emin -10.0 --emax 0.0
```

--------------------------------

### Run abacus2J.py for Collinear Calculation

Source: https://tb2j.readthedocs.io/en/latest/src/abacus.html

Execute abacus2J.py to compute exchange parameters. Specify the path to DFT output, suffix, elements, and k-mesh. Note: The kmesh may require adjustment for practical calculations.

```bash
abacus2J.py --path . --suffix Fe --elements Fe  --kmesh 7 7 7

```

--------------------------------

### Step One: Collinear Spin Calculation for MAE

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/mae.md.txt

Input parameters for the first step of MAE calculation, a collinear spin calculation. SOC is enabled but its strength is set to zero to save the Hamiltonian in spinor form.

```text
INPUT_PARAMETERS
# SCF calculation with SOC turned on, but soc_lambda=0. 
calculation                             scf
nspin                                   4
symmetry                                0
noncolin                                1
lspinorb                                1
ecutwfc                                 100
scf_thr                                 1e-06
init_chg                                atomic
out_mul                                 1
out_chg                                 1
out_dos                                 0
out_band                                0
out_wfc_lcao                            1
out_mat_hs2                             1
ks_solver                               scalapack_gvx
scf_nmax                                500
out_bandgap                             0
basis_type                              lcao
gamma_only                              0
smearing_method                         gaussian
smearing_sigma                          0.01
mixing_type                             broyden
mixing_beta                             0.5
soc_lambda                              0.0
ntype                                   1
dft_functional                          PBE
```

--------------------------------

### Step One: Collinear Spin Calculation for MAE

Source: https://tb2j.readthedocs.io/en/latest/src/mae.html

This snippet shows the input parameters for the first step of an MAE calculation in ABACUS. It configures a collinear spin calculation with SOC enabled but turned off (soc_lambda=0.0) to save the Hamiltonian in spinor form.

```bash
INPUT_PARAMETERS
# SCF calculation with SOC turned on, but soc_lambda=0. 
calculation                             scf
nspin                                   4
symmetry                                0
noncolin                                1
lspinorb                                1
ecutwfc                                 100
scf_thr                                 1e-06
init_chg                                atomic
out_mul                                 1
out_chg                                 1
out_dos                                 0
out_band                                0
out_wfc_lcao                            1
out_mat_hs2                             1
ks_solver                               scalapack_gvx
scf_nmax                                500
out_bandgap                             0
basis_type                              lcao
gamma_only                              0
smearing_method                         gaussian
smearing_sigma                          0.01
mixing_type                             broyden
mixing_beta                             0.5
soc_lambda                              0.0
ntype                                   1
dft_functional                          PBE


```

--------------------------------

### Specify ABACUS Calculation File Location

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/parameters.rst.txt

Set the path to ABACUS calculation files. Default is the current directory.

```bash
--path /path/to/abacus/output
```

--------------------------------

### Enable Caching for Hamiltonian and Eigenvectors

Source: https://tb2j.readthedocs.io/en/latest/src/ReleaseNotes.html

Introduces the --use_cache option to reduce memory usage by storing the Hamiltonian and eigenvectors on disk. This is useful for large calculations.

```bash
add --use_cache option to reduce the memory usage by storing the Hamiltonian

:   and eigenvectors on disk using memory map.
```

--------------------------------

### Calculate Exchange Parameters with ABACUS (Collinear)

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/abacus.md.txt

Use the abacus2J.py script to compute exchange parameters. Specify the path to DFT calculation results, the output suffix, elements, and the k-point mesh. The script reads atomic structures, Hamiltonian, and overlap matrices.

```bash
abacus2J.py --path . --suffix Fe --elements Fe  --kmesh 7 7 7
```

--------------------------------

### Specify 3d and 4s Orbitals for Siesta Input

Source: https://tb2j.readthedocs.io/en/latest/src/orbital_contribution.html

This command demonstrates how to include both 3d and 4s orbitals in the decomposition analysis for Siesta input.

```bash
siesta2J.py --elements Fe_3d_4s  ....
```

--------------------------------

### TB2J_symmetrize.py Usage Information

Source: https://tb2j.readthedocs.io/en/latest/_sources/src/symmetry.md.txt

This snippet displays the command-line usage and available options for the `TB2J_symmetrize.py` script. It outlines the purpose of the script and its parameters for input/output paths and symmetry precision.

```bash
usage: TB2J_symmetrize.py [-h] [-i INPATH] [-o OUTPATH] [-s SYMPREC]

Symmetrize exchange parameters. Currently, it takes the crystal symmetry into account and not the magnetic moment.
Also, only the isotropic exchange is symmetrized in this version. The symmetrization of the DMI and anisotropic exchange will be implemented in a future version. 

options:
  -h, --help            show this help message and exit
  -i INPATH, --inpath INPATH
                        input path to the exchange parameters
  -o OUTPATH, --outpath OUTPATH
                        output path to the symmetrized exchange parameters
  -s SYMPREC, --symprec SYMPREC
                        precision for symmetry detection. The default value is 1e-5 Angstrom
```

--------------------------------

### TB2J Output Directory Structure

Source: https://tb2j.readthedocs.io/en/latest/src/wannier.html

Overview of the directory structure created by TB2J, containing exchange parameters in various formats and files for spin dynamics simulations.

```text
TB2J_results/
├── exchange.txt
├── Multibinit
│   ├── exchange.xml
│   ├── mb.files
│   └── mb.in
├── TomASD
│   ├── exchange.exch
│   └── exchange.ucf
└── Vampire
    ├── input
    ├── vampire.mat
    └── vampire.UCF
```
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