# BayesianOpt4dftu
**Repository Path**: wang-tx_1_0/BayesianOpt4dftu
## Basic Information
- **Project Name**: BayesianOpt4dftu
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No
## Statistics
- **Stars**: 0
- **Forks**: 0
- **Created**: 2026-04-15
- **Last Updated**: 2026-08-31
## Categories & Tags
**Categories**: Uncategorized
**Tags**: None
## README
# BayesianOpt4dftu #
Determine the Hubbard U parameters in DFT+U using the Bayesian Optimization approach.
## Prerequisites
### Python Version
- Requires Python ≥ 3.9 (tested on Python 3.9–3.13)
### Python Dependencies
These will be installed automatically when you install the package via pip:
- [`numpy`](https://numpy.org)
- [`scipy`](https://scipy.org)
- [`pandas`](https://pandas.pydata.org)
- [`matplotlib`](https://matplotlib.org)
- [`ase`](https://wiki.fysik.dtu.dk/ase)
- [`pymatgen`](https://pymatgen.org)
- [`bayesian-optimization`](https://github.com/bayesian-optimization/BayesianOptimization)
- [`jsonschema`](https://github.com/python-jsonschema/jsonschema)
### Other Dependencies
These dependencies need to be installed manually:
- [Vienna Ab initio Simulation Package (VASP)](https://www.vasp.at)
## Installation
To install `BayesianOpt4dftu`, use the following command:
```shell
pip install git+https://github.com/caizefeng/BayesianOpt4dftu.git
```
## Usage
For the demonstration,
let's focus on fitting the Hubbard U values for both elements in indium arsenide (InAs).
The example input and output can be found in the `/examples/2d` directory:
### 1. Edit `input.json`
Navigate to the example directory:
```shell
cd examples/2d
```
Adjust the `input.json` file with the appropriate `vasp_env` settings based on your system specifications and the location of your VASP binary.
### 2. Execute
Run the following command:
```shell
bo_dftu
```
### 3. Results
Upon reaching the threshold or maximum iterations, two output files are generated:
- `u_xxx.txt`/`formatted_u_xxx.txt`: Contains U parameters, band gap, Δgap, Δband, and Δmagnetization (optional) for each iteration.
- `1D_xxx.png` or `2D_xxx.png`: Provides a visual representation of the Gaussian process predicted mean and acquisition function.
This file will be omitted if you set three or more optimizable U parameters.
**Example of BO plots**:
- 1-D Bayesian Optimization for Ge
- 2-D Bayesian Optimization for InAs
Optimal U values are automatically deduced from the predicted mean space interpolation.
Alternatively, you can use the `u_xxx.txt` file to select U values with the highest objective value.
## Configuration
Before running the program, configure the `input.json` file. It contains:
- **`vasp_env`**: Environment settings for VASP.
- **`vasp_run_command`**:
- **Description**: Running command for VASP executable.
- **Example**: `"vasp_run_command": "mpirun -np 64 /path/to/vasp/executable"`
- **`out_file_name`**:
- **Description**: The desired name of the VASP output file.
- **Example**: `"out_file_name": "slurm-vasp.out"`
- **`vasp_pp_path`**:
- **Description**: Path directing to the VASP pseudopotential. It should be the directory containing
the `potpaw_PBE` folder.
- **Example**: `"vasp_pp_path": "/path/to/pseudopotentials/"`
- **`dry_run`**:
- **Description**: Specifies if the run is a dry run (generating files only without actual computation) or not.
- **Default**: `"dry_run": false`
- **`dftu_only`**:
- **Description**: Indicates whether only DFT+U is performed. If set to true, completed baseline calculations should be placed in the `/` directory.
- **Default**: `"dftu_only": false`
- **`get_optimal_band`**:
- **Description**: Indicate if an additional DFT+U using optimal U values is performed after Bayesian optimization.
The results of this calculation will be appended to the end of the log file.
- **Default**: `"get_optimal_band": true`
- **`bo`**: Settings specific to Bayesian Optimization.
- **`resume_checkpoint`**:
- **Description**: Determines whether the Bayesian Optimization resumes from a saved checkpoint, as defined by `u_tmp.txt` and `input_tmp.json`.
- **Default**: `"resume_checkpoint": false`
- **`baseline`**:
- **Description**: Specifies the baseline calculation for Bayesian Optimization. Currently, only `"hse"` and `"gw"` are supported. `"gw"` must be executed separately, meaning it is only supported when `"dftu_only": true`.
- **Default**: `"baseline": "hse"`
- **`which_u`**:
- **Description**: Specifies which element you'd like to optimize the U for.
- Format: For a unary substance, it has to be `[1,]`. For
compounds with over 2 elements, you can set each element to `0` or `1` to switch off/on the optimization for that
element.
- **Example**: For InAs, when optimizing for both In and As, it should be set as `"which_u": [1, 1]`
- **`br`**:
- **Description**: Specifies the band range you'd like to include in your Δband.
- Format: A list of two integers, defining the number of valence bands and conduction bands from the Fermi
level.
- **Default**: `"br": [5, 5]`
- **`kappa`**:
- **Description**: Controls the balance between exploration and exploitation when the acquisition function samples the next points.
A lower value (nearing `0`) indicates a preference for exploitation. A higher value (approaching `10`) indicates a preference for exploration.
- **Default**: `"kappa": 5`
- **`alpha_gap`** and **`alpha_band`**:
- **Description**: Specifies the weight coefficients of Δgap and Δband respectively. So far, there are no constraints on the choice of `alpha`s, meaning they can be arbitrary positive real numbers.
- **Default**: `"alpha_gap": 0.25` and `"alpha_band": 0.75`
- **`alpha_mag`**:
- **Description**: Specifies the weight coefficients of Δmagnetization. `LORBIT` must be set in all `INCAR` files. A `alpha_mag` of `0` will exclude Δmagnetization from the loss function.
- **Default**: `"alpha_mag": 0.0`
- **`mag_axis`**:
- **Description**: Specifies the Cartesian component of the non-collinear magnetic moment used to calculate Δmagnetization. Available options are `"x"`, `"y"`, `"z"`, and `"all"`(all 3 components). This parameter is only applicable to non-collinear calculations and has no effect on collinear calculations (when `LNONCOLLINEAR=.FALSE.` and `LSORBIT=.FALSE.`).
- **Default**: `"mag_axis": "all"`
- **`threshold`**:
- **Description**: Specifies the desired accuracy for the objective function, measured as the difference between values from two consecutive iterations, at which you'd like to stop the BO process.
A `threshold` of `0.0` (and `threshold_opt_u` of `0.0` as well) will disable the convergence assessment, meaning the BO will exit only upon reaching the maximum iterations.
- **Default**: `"threshold": 0.0001`
- **`urange`**:
- **Description**: Specifies the U parameter range for optimization. The unit is eV. Defining different U ranges for separate
elements is currently unsupported.
- **Default**: `"urange": [-10, 10]`
- **`elements`**:
- **Description**: Lists the elements in your system. This is used for plotting the BO results. If it's a
unary substance, it has to be `["ele",]`.
- **Example**: `"elements": ["In", "As"]`
- **`iteration`**:
- **Description**: Sets the maximum iterations that BO will perform.
- **Default**: `"iteration": 50`
- **`report_optimum_interval`**:
- **Description**: Sets the interval (in iterations) at which the optimal Hubbard U values are calculated and logged.
- **Default**: `"report_optimum_interval": 10`
- **`threshold_opt_u`**:
- **Description**: This criterion supplements the original `threshold` parameter and can be used as the sole convergence criterion or in conjunction with `threshold`. Specifies the desired accuracy for the optimal Hubbard U values, measured as the difference between values from two iterations separated by `report_optimum_interval`.
A `threshold_opt_u` of `0.0` will disable this optimal U-based convergence assessment.
- **Default**: `"threshold_opt_u": 0.0`
- **`print_magmom`**:
- **Description**: Specifies whether to print the magnetic moment at each iteration.
- **Default**: `"print_magmom": false`
- **`structure_info`** : Includes geometry information (such as lattice parameter, lattice vectors, atomic position,
etc.) of the target materials.
#### An example of InAs:
- **`lattice_param`** and **`cell`**: Specify the 2nd to 5th rows in your POSCAR.
```json
{
"lattice_param": 6.0584,
"cell": [
[
0.0,
0.5,
0.5
],
[
0.5,
0.0,
0.5
],
[
0.5,
0.5,
0.0
]
]
}
```
- **`atoms`**: Specifies the atomic positions of each atom in your system and the initial magnetic moment if there is
any.
Non-collinear magnetism:
```json
{
"atoms": [
[
"In",
[
0,
0,
0
],
[
0,
0,
1e-06
]
],
[
"As",
[
0.75,
0.75,
0.75
],
[
0,
0,
1e-06
]
]
]
}
```
Collinear magnetism:
```json
{
"atoms": [
[
"In",
[
0,
0,
0
],
1e-06
],
[
"As",
[
0.75,
0.75,
0.75
],
1e-06
]
]
}
```
In this case, there are two atoms in the primitive cell at positions `[0, 0, 0]`
and `[0.75, 0.75, 0.75]`.
The second term under each atom specifies the initial magnetic moment.
For calculations excluding non-collinear magnetization or spin-orbit coupling, this is an integer (or it could be a one-dimensional array with one element).
Otherwise, it's a one-dimensional array with three elements, each representing the initial moment in a specific Cartesian direction.
To avoid omission errors in the `ASE` package, the initial moment should be set to a small, non-zero number if it is intended to be 0.
- **`kgrid_hse`** and **`kgrid_pbe`**:
- **Description**: Set the self-consistent k-point grid for HSE and PBE+U calculations, respectively.
- **Example**: `"kgrid_pbe": [7, 7, 7]` specifies a 7x7x7 k-point grid for PBE+U calculation.
- **`num_kpts`** and **`kpath`**:
- **Description**: Specify the non-self-consistent (non-SC) k-point path for band structure calculations.
`num_kpts` can be either an integer or a string "auto".
- **Example**: `"num_kpts": 50` and `"kpath": "G X W L G K"` set the k-point path to `G-X-W-L-G-K` and the number of k-points per path segment to 50. Important: In this mode, contributions to Δband are weighted to achieve an approximately uniform density of sampling along the path.
`"num_kpts": "auto"` automatically determines the path and number of k-points based on the HSE or GW baseline calculation.
- **`custom_kpoints`**:
- **Description**: Specifies the custom reciprocal coordinates for certain k-points in `kpath`. If it conflicts with common BZ coordinate conventions for certain k-points, this setting takes higher priority.
- **Example**: `"custom_kpoints": null` (the default) or `"custom_kpoints": {"H": [0.5, -0.5, 0.5], "F": [0.5, 0.5, 0]}`
- **`custom_POTCAR_path`**:
- **Description**: Specifies the path to the custom POTCAR file. This file will be copied to all VASP working directories.
- **Example**: `"custom_POTCAR_path": null` (the default) or `"custom_POTCAR_path": "./POTCAR_Pb_sv_Te_sv"`
- **`general_flags`**: General INCAR tags required in all VASP calculations.
- **`scf`**: INCAR tags that will only be added in SCF calculations.
- **`band`**: INCAR tags that will only be added in band structure calculations.
- **`pbe`**: INCAR tags that will only be added when using PBE as exchange-correlation functional.
- **`hse`**: INCAR tags that will only be added when using HSE06 as exchange-correlation functional.
Check the [ASE VASP calculator](https://wiki.fysik.dtu.dk/ase/ase/calculators/vasp.html) documentation for additional tag keys.
(A large portion of them are simply the lowercase versions of the corresponding INCAR tags.)
## Citation
Please cite the following work if you use this code.
[1] M. Yu, S. Yang, C. Wu, N. Marom, Machine learning the Hubbard U parameter in DFT+ U using Bayesian optimization, npj
Computational Materials, 6(1):1–6, 2020.