Abacustest

https://pypi.org/project/abacustest/
Admin
Abacustest is a Python package designed to handle pre-processing and post-processing for ABACUS...
Tokens:6,862
Snippets:78
Trust Score:10
Update:5 months ago
Show doc for...
Tokens:
Raw
### Install abacustest from source

Source: https://pypi.org/project/abacustest

Clone the repository and install abacustest locally using pip.

```bash
git clone https://github.com/pxlxingliang/abacus-test.git
cd abacus-test
pip install .
```

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

### Prepare ABACUS Input Files for Parameter Testing

Source: https://pypi.org/project/abacustest

Configure this to generate multiple ABACUS input files for parameter testing. Specify example templates, input parameter combinations, and k-point parameter combinations. Sub-folders will be created for mixed inputs.

```json
{
  "prepare": {
    "example_template": ["example1", "example2"],
    "mix_input": {"ecutwfc": [50, 60, 70], 
    "kspacing": [0.1, 0.12]},
    "mix_kpt": [2, [3, 3, 3], [4, 4, 4, 1, 1, 1]]
  }
}

```

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

### Install abacustest via pip

Source: https://pypi.org/project/abacustest

Use this command to install the abacustest package directly from PyPI.

```bash
pip install abacustest
```

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

### Dispatcher Configuration for Remote Jobs

Source: https://pypi.org/project/abacustest

Example configuration for the 'dispatcher' key, used for submitting jobs to remote platforms like supercomputers.

```json
    "dispatcher": {
        "machine_dict": 
        {
          "remote_root": "/home/username/work_path",
          "remote_profile": {
            "hostname": "xxx.xx.xxx.xxx",
            "username": "Username",         
            "password": "password",
            "port": 22
          }
        },
        "resources_dict": {
            "number_node": 1,
            "cpu_per_node": 8,
            "gpu_per_node": 1,
            "queue_name": "Normal"
        }
            }

```

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

### Born Effective Charge Tensor Example Output

Source: https://pypi.org/project/abacustest

This is an example of the output format for the Born effective charge tensor, showing the charge response of lattice ions under an electric field. The rows and columns represent displacement and polarization directions, respectively.

```text
Born effective charge tensor for:
.:atom0_Ti:
        X       Y       Z
X  7.2792  0.0023 -0.0046
Y  0.0000  7.2835 -0.0020
Z  0.0000  0.0021  7.2830
```

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

### Uploading Local Packages with Configuration

Source: https://pypi.org/project/abacustest

Shows how to use the 'upload_packages' key in the configuration file to upload local Python packages to the remote platform.

```json
{
    ...
    "upload_packages": ["my_package1","/home/user/my_package2"],
    ...
}

```

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

### Download Pseudopotentials and Orbitals

Source: https://pypi.org/project/abacustest

Use this command to download recommended pseudopotentials and orbitals for a specific version. This creates version-specific directories for these files.

```bash
abacustest model inputs --download-pporb apns-v1
```

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

### Prepare ABACUS input files

Source: https://pypi.org/project/abacustest

Use the 'prepare' command with a JSON parameter file to generate ABACUS input files. The -s flag specifies the output directory.

```bash
abacustest prepare -p param.json -s abacustest
```

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

### Prepare Band Structure Calculation Input

Source: https://pypi.org/project/abacustest

Use this command to automatically prepare input files for band structure calculations. It generates SCF and NSCF input files and a KPT.nscf file with a high symmetry k-path. Use '-h' for more parameters.

```bash
abacustest model band prepare -j 000000
```

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

### Prepare Vacancy Calculation with ABACUS Input Directory

Source: https://pypi.org/project/abacustest

Use this command to prepare input files for vacancy formation energy calculations when using a pre-prepared ABACUS input directory. Specify the input directory, number of vacancies, and simulation cell.

```bash
abacustest model vacancy prepare -j 000000 -i 1 -s 1 1 1
```

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

### Configure Data Collection Parameters

Source: https://pypi.org/project/abacustest

Prepare a param.json file to specify which key values to extract from job outputs. The 'PARAM' key holds a list of desired metrics, which can be predefined keys or custom-defined evaluations.

```json
{
"PARAM":
        ["natom","kpt","ibzk","nelec","nbands","force","stress",
        "scf_steps","total_time","force_time","stress_time","energy_per_atom","band_gap",
        {"SELF_DEFINED_NAME": "An eval string to get the value"}]
}

```

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

### Converting ABACUS to QE Input Files with abacustest

Source: https://pypi.org/project/abacustest

Enable conversion of ABACUS input files to Quantum ESPRESSO (QE) format. Configure QE settings such as version, and system parameters like ibrav and ecutwfc.

```json
{
  "prepare": {
    "abacus2qe": true,
    "qe_setting": {
      "version": "7.0",
      "system": {
        "ibrav": 0,
        "ecutwfc": 50
        }
    }
  }
}

```

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

### Prepare Vacancy Calculation with CIF Input

Source: https://pypi.org/project/abacustest

Use this command to prepare input files for vacancy formation energy calculations when providing a CIF structure file. Specify the input file, type, number of vacancies, and simulation cell.

```bash
abacustest model vacancy prepare -j stru.cif --ftype cif -i 1 -s 1 1 1 --lcao
```

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

### Configure Job Submission with param.json

Source: https://pypi.org/project/abacustest

Configure job submission parameters by including authentication details and run configurations within the param.json file.

```json
{
    "config": {
        "bohrium_username": "<your username>",
        "bohrium_password": "<your password>",
        "bohrium_project_id": "<your project id>"
    },
    "run_dft":[...]
}
```

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

### Convert Structure Files to ABACUS STRU Format

Source: https://pypi.org/project/abacustest

Use this configuration to convert structure files (e.g., VASP POSCAR, CIF) into ABACUS STRU format. Specify input file paths, formats, and templates for INPUT and KPT files. Pseudopotential and orbital dictionaries/paths can also be configured.

```json
{
  "prepare":{
    "strus": ["1.vasp", "2.vasp"],
    "stru_format": "poscar",
    "input_template": "INPUT",
    "kpt_template": "KPT",
    "pp_dict": {"H": "H.upf", "O": "O.upf"},
    "orb_dict": {"H": "H.orb", "O": "O.orb"},
    "pp_path": "path/to/pp",
    "orb_path": "path/to/orb"
  }
}

```

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

### Postprocess Vacancy Calculation Results

Source: https://pypi.org/project/abacustest

After vacancy calculations are finished, use this command to postprocess the results. It will print the vacancy formation energy and save it to 'metrics_vacancy.json'. A 'ref_energy.txt' file will also be generated.

```bash
abacustest model vacancy post -j 000000
```

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

### Converting ABACUS to VASP Input Files with abacustest

Source: https://pypi.org/project/abacustest

Enable conversion of ABACUS input files to VASP format. This includes specifying POTCAR paths and VASP INCAR settings like ENCUT and EDIFF.

```json
{
  "prepare": {
    "abacus2vasp": true,
    "potcar": {"H": "H.pot", "O": "O.pot"},
    "vasp_setting": {
      "ENCUT": 500,
      "EDIFF": 1e-5,
      "emax_coef": 1.0
    }
  }
}

```

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

### Batch Convert Structure Files to ABACUS Input

Source: https://pypi.org/project/abacustest

Convert multiple structure files (e.g., CIF) into ABACUS input files. Optionally specify pseudopotential and orbital directories, and choose the output INPUT file type.

```bash
abacustest model inputs -f *.cif --ftype cif
```

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

### Collect Data Keys

Source: https://pypi.org/project/abacustest

Use the `collectdata` command with `--outparam` to list all available keys for a given job type. The output shows module names and corresponding functions to retrieve data.

```bash
collectdata --outparam 1 -t 0
```

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

### abacustest prepare parameter JSON structure

Source: https://pypi.org/project/abacustest

Defines the structure for the 'param.json' file used by 'abacustest prepare'. Only the 'prepare' key is recognized.

```json
{
  "prepare": {
    "example_template": ["example1", "example2"],
    "input_template": "INPUT",
    ...
  }
}
```

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

### Postprocess Band Structure Calculation Results

Source: https://pypi.org/project/abacustest

Execute this command after the band structure calculation is complete. It identifies band data, determines the Fermi level, plots the band structure, and calculates the band gap. For non-metallic systems, it also finds CBM and VBM information.

```bash
abacustest model band post -j 000000
```

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

### Download Job Results with AbacusTest

Source: https://pypi.org/project/abacustest

Download job results using the 'abacustest download' command, specifying the parameter file and either the job ID or UID. The job ID may expire, but the UID is typically more persistent.

```bash
abacustest download -p param.json <ID>
```

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

### Set ABACUS Environment Variables

Source: https://pypi.org/project/abacustest

Set environment variables to specify the paths for pseudopotential and orbital libraries. This avoids the need to repeatedly use --pp or --orb parameters.

```bash
export ABACUS_PP_PATH=/path/to/pp/dir
```

```bash
export ABACUS_ORB_PATH=/path/to/orb/dir
```

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

### AbacusTest Configuration File Structure

Source: https://pypi.org/project/abacustest

Defines the main structure of the abacustest configuration file, including job execution details and Bohrium settings.

```json
{
    "bohrium_group_name": "abacustest",
    "save_path":"results",
    "max_parallel": 100,
    "run_dft":[
        {
          "ifrun": true,
          "sub_save_path": "123",
          "image": "registry.dp.tech/dptech/abacus-stable:LTSv3.10",
          "example":["00[0-2]","00[3-5]"],
          "group_size" : 1,
          "bohrium": {
            "scass_type":"c8_m16_cpu",
            "job_type":"container",
            "platform":"ali"
          },
          "command": "mpirun -np 8 abacus > log",
          "extra_files":[]
        }
    ]
}

```

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

### Specify Folder Naming Syntax

Source: https://pypi.org/project/abacustest

Customize the naming format for generated output folders using f-string syntax. Use 'x' to represent the input structure path and apply processing logic within curly braces.

```bash
abacustest model inputs -f *.cif --ftype cif --folder-syntax {x[:-4]}
```

```bash
abacustest model inputs -f *.cif --ftype cif --folder-syntax aa-{x[:-4]}-bb
```

```bash
abacustest model inputs -f */POSCAR --folder-syntax {x[:-7]}
```

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

### Submit a Job with AbacusTest

Source: https://pypi.org/project/abacustest

Submit a computational job using the 'abacustest submit' command with a parameter file. The '&' allows the command to run in the background.

```bash
abacustest submit -p param.json &
```

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

### Convert ABACUS to CP2K Input

Source: https://pypi.org/project/abacustest

Use this parameter to enable the conversion of ABACUS input files to CP2K format. It allows for specifying additional CP2K settings.

```json
{
  "prepare": {
    "abacus2cp2k": true,
    "cp2k_setting": {
      "FORCE_EVAL": {
        "DFT": {
          "SCF": {
            "EPS_SCF": 1e-6
          }
        }
      }
    }
  }
}

```

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

### Set Environment Variables for Bohrium Authentication

Source: https://pypi.org/project/abacustest

Set these environment variables to authenticate your Bohrium account before submitting a job. Alternatively, these can be included in the param.json file.

```bash
export BOHRIUM_USERNAME="your_bohrium_username"
export BOHRIUM_PASSWORD="your_bohrium_password"
export BOHRIUM_PROJECT_ID="your_bohrium_project_id"
```

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

### Postprocess Born Effective Charge Calculation Results

Source: https://pypi.org/project/abacustest

Use this command to postprocess the results of Born effective charge calculations. It prints a summary to the screen and saves it to 'bec_summary.txt'. Detailed metrics are saved in 'metrics.json' and 'metrics_bec.json'.

```bash
abacustest model bec post
```

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

### Perturbing Configurations with abacustest

Source: https://pypi.org/project/abacustest

Configure random structure perturbations for ABACUS calculations. Specify parameters like the number of perturbed structures, cell perturbation fraction, atomic perturbation distance, and magnetic moment rotations/tilts.

```json
{
  "prepare": {
    "example_template": ["example1", "example2"],
    "pert_stru": {
      "pert_number": 10,
      "cell_pert_frac": 0.01,
      "atom_pert_dist": 0.1,
      "mag_rotate_angle": 5,
      "mag_tilt_angle": 10,
      "mag_norm_dist": 0.05
    }
  }
}

```

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

### Collect Data from Multiple Jobs

Source: https://pypi.org/project/abacustest

Execute the 'abacustest collectdata' command to gather specified metrics from multiple job outputs. Results are saved to 'metrics.json' by default, or a custom file using the '-o' option. Use '-t' to specify job type (0 for ABACUS, 1 for QE, 2 for VASP).

```bash
abacustest collectdata -p param.json -j job1 job2 job3
```

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

### Import and Use RESULT Class

Source: https://pypi.org/project/abacustest

Import the `RESULT` class from `abacustest` to access job results within a Python script. Initialize `RESULT` with the job format and path, then access specific data like total energy, force, and stress using dictionary-like syntax. Unsupported keys will return `None`.

```python
from abacustest import RESULT

abacusresult = RESULT(fmt="abacus",path="abacusjob") 
# path is the path to the ABACUS job folder, such as "abacusjob"
# fmt is the format of the job, such as "abacus", "qe", "vasp".

energy = abacusresult["total_energy"] 
force = abacusresult["force"]
stress = abacusresult["stress"]

```
Tokens:
Raw