Skip to main content
Version: 2024.05

Initializes the input

init_param.json

Initial Training Set Preparation, including relaxation, supercell, scaling, perturbation, and AIMD (DFTB, PWMAT, VASP) settings for configurations in VASP and PWmat formats.

Parameter List​

reserve_work​

Whether to keep the temporary working directory, default value is false.

data_shuffle​

Whether to randomly divide the prepared data into training and validation sets, default value is true. If false, divide training and validation sets in order.

train_valid_ratio​

Sets the ratio for dividing the training and validation sets, default value is 0.8, which divides the training set and validation set into 80% and 20% respectively.

interval​

Used to set the interval for selecting structures from the trajectory when extracting data, that is, to select a configuration every few structures in the trajectory, with a default value of 1.

sys_config_prefix​

Sets the path prefix for initial configurations, optional parameter, used in conjunction with sys_configs/config. It can be an absolute path or a relative path, where the relative path is relative to the current directory.

Example: "sys_config_prefix":"/data/structure", "config":"atom.config", then the actual path of atom.config is /data/structure/atom.config

sys_configs​

Sets the file paths for configurations, relaxation, supercell, scaling lattice, perturbing atomic positions, and AIMD. The complete parameters are shown in the following example.

config​

Sets the file path for configurations. If sys_config_prefix is set, the path is concatenated. Otherwise, the path set in the config is used as the config path.

format​

Sets the file type for configurations, supporting POSCAR format for VASP or atom.config format for PWMAT. If it is a POSCAR file, the value is "vasp/poscar", default value is "pwmat/config".

relax​

Whether to perform relaxation for the config, default value is "true".

relax_input_idx​

Sets the control file used for relaxation, used in conjunction with relax_input, specifying the position of the control file. For example, in the example, the relax_input sets the relax_etot1.input file as the PWMAT control file. Default value is 0, which means using the first file in relax_input as the control file.

super_cell​

Used for supercell settings, optional parameter. If not set, no supercell is applied to the structure. The data format is a list, supporting the following input formats: [1, 1, 2] or [[1,0,0],[0, 2, 0],[0,0,1]] or [1,0,0,0, 2, 0,0,0,1].

scale​

Used for scaling the lattice, optional parameter. If not set, no scaling is applied to the structure. The data format is a list, such as [0.9, 0.95，0.96, 0.97], which represents four perturbations of the lattice with 0.9, 0.95, 0.96, 0.97.

perturb​

Perturbs the atomic positions of the structure, used in conjunction with cell_pert_fraction and atom_pert_distance. The value of perturb is the number of structures generated after perturbation. Optional parameter, if not set, no perturbation is applied.

cell_pert_fraction​

Perturbation of the lattice. Add randomly sampled values from a uniform distribution within the range of [- cell_pert_fraction, cell_pert_fraction] to each of the 9 lattice values, with a default value of 0.03.

atom_pert_distance​

The perturbation of atomic coordinates (Angstrom). For each atom's three coordinate values, add randomly sampled values from a uniform distribution within the range of [-atom_pert_distance, atom_pert_distance]. The default value is 0.01.

aimd​

Whether to perform molecular dynamics simulation for the structure, default value is true.

aimd_input_idx​

Sets the control file used for AIMD, used in conjunction with aimd_input, specifying the position of the control file. For example, in the example, the aimd_input sets the aimd_etot.input file as the PWMAT control file. Default value is 0, which means using the first file in aimd_input as the control file.

dft_style​

Sets which DFT calculation software to use for Relax and AIMD, default value is pwmat, also supports VASP format. If it is VASP format, set it to vasp.

pseudo​

Sets the path to the pseudopotential files of PWmat or VASP, in list format. The path to the pseudopotential file can be an absolute path or a relative path (relative to the current path).

in_skf​

The in_skf parameter is used to set the path to the parent directory of the pseudopotential files for DFTB (Integrated by PWMAT). It should be specified as a string in either absolute or relative format (relative to the current directory).

basis_set_file​

Refer to potential_file.

potential_file​

The potential_file parameter is used to set the path to the BASIS_MOLOPT and POTENTIAL files for CP2K pseudopotentials. For example:

"basis_set_file": "~/datas/systems/cp2k/data/BASIS_MOLOPT",
"potential_file": "~/datas/systems/cp2k/data/POTENTIAL"

relax_input​

Sets the input control file for Relax. If there are multiple relax control files, they are organized in list format. For cases where only a single file is used, it can also be set in dict format.

aimd_input​

Set the input control files for AIMD. If there are multiple AIMD control files, they should be organized in a list format. For cases where only a single file is used, it can also be set in dict format.

input​

Set the path to the input control file. It can be an absolute or relative path (relative to the current directory).

kspacing​

This parameter is an optional parameter for PWMAT, used to set the K points. If the MP_N123 parameter is not set in the etot.input file, it will be set using this parameter. If the MP_N123 is already set in the file, setting this parameter will cause an error. Please ensure that only one of MP_N123 and kspacing is set.

If the etot.input file does not set MP_N123 and kspacing is not set, the default value of kspacing will be 0.5.

Note that MP_N123 and kspacing cannot be set simultaneously.

flag_symm​

This parameter is an optional parameter for PWMAT, used to set the K points. For Relax or SCF calculations, the default value is 0. For AIMD calculations, the default value is 3.

example​

    {
        "reserve_work": true,
        "data_shuffle":true,
        "train_valid_ratio": 0.8,
        "sys_configs":[{
            "config":"atom.config", 
            "relax":true, 
            "relax_input_idx":1, 
            "super_cell":[1, 1, 2], 
            "scale":[0.9,0.95], 
            "perturb":20, 
            "cell_pert_fraction":0.03, 
            "atom_pert_distance":0.01, 
            "aimd":true, 
            "aimd_input_idx":0
        }],

    "dft_style":"PWmat",
    "pseudo" : ["/path/Si.SG15.PBE.UPF"],

    "relax_input":[{
            "input":"relax_etot.input",
            "kspacing":0.5,
            "flag_symm":"0"
        },{
            "input":"relax_etot1.input",
            "kspacing":0.3,
            "flag_symm":"0"
        },{
            "input":"relax_etot2.input",
            "kspacing":0.4,
            "flag_symm":"0",
            "_flag":"1个整数，relax or scf 0 , aimd 3, 磁性体系2"
        }],

    "aimd_input":[{
            "input":"aimd_etot.input",
            "kspacing":0.5,
            "flag_symm":"3"
        },{
            "input":"aimd_etot1.input",
            "kspacing":0.5,
            "flag_symm":"3"
        }]
    }

Purpose of the above parameters​

  1. Perform relaxation on the atom.config.
  2. Apply a supercell transformation with dimensions (1, 1, 2) to the relaxed structure.
  3. Scale the lattice of the supercell structure by factors of 0.9 and 0.95, respectively.
  4. Apply atomic positional perturbations to the scaled structures, generating 20 perturbed structures for each.
  5. Perform AIMD simulations on the 40 perturbed structures.
  6. Automatically extract the AIMD trajectories as PWdata data format for pretraining data.

Supplementary Explanation for relax_input and aimd_input Parameters​

The parameters kspacing and flag_symm are used for setting the K-points in PWMAT. If the MP_N123 parameter is not set in the etot.input file, the program will use these two parameters to set the K-points. Therefore, if you have already set the MP_N123 parameter in the etot.input file, you can simplify the relax_input or aimd_input parameters as follows:

"relax_input": [
  "relax_etot.input",
  "relax_etot1.input",
  "relax_etot2.input"
],

"aimd_input": [
  "aimd_etot.input",
  "aimd_etot1.input"
]

If you are using the same relax or AIMD input for all structures in sys_configs, you can further simplify the parameters as follows:

"relax_input": "relax_etot.input",
"aimd_input": "aimd_etot.input"

In this case, you do not need to specify the relax_input_idx or aimd_input_idx parameters in sys_configs. Your sys_configs can be written as follows:

"sys_configs": [{
  "config": "atom.config",
  "relax": true,
  "super_cell": [1, 1, 2],
  "scale": [0.9, 0.95],
  "perturb": 20,
  "cell_pert_fraction": 0.03,
  "atom_pert_distance": 0.01,
  "aimd": true
}]