Example-of-param.json
We have provided different examples of param.json in dpgen/examples/run/. In this section, we give a description of the param.json, taking dpgen/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json as an example. This is a param.json for a gas-phase methane molecule. Here, DeePMD-kit (v2.x), LAMMPS and VASP codes are used for training, exploration and labeling respectively. The basics related keys in param.json are given as follows The basics related keys specify the basic information about the system. The data related keys in param.json are given as follows The data related keys specify the init data for training initial DP models and structures used for model_devi calculations. Here, the init data is provided at “…… /init/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd”. These structures are divided into two groups and provided at “……/init/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR” and “……/init/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR”. The training related keys in param.json are given as follows The training related keys specify the details of training tasks. Here, 4 DP models will be trained in The exploration related keys in param.json are given as follows The exploration related keys specify the details of exploration tasks. Here, MD simulations are performed at the temperature of 100 K and the pressure of 1.0 Bar with an integrator time of 2 fs under the nvt ensemble. Two iterations are set in The labeling related keys in param.json are given as follows The labeling related keys specify the details of labeling tasks. Here, a minimum of 1 and a maximum of 20 structures will be labeled using the VASP code with the INCAR provided at “……/INCAR_methane” and POTCAR provided at “……/methane/POTCAR” in each iteration. Note that the order of elements in POTCAR should correspond to the order in All the keys of the DP-GEN are explained in detail in the section Parameters.basics
"type_map": [
"H",
"C"
],
"mass_map": [
1,
12
],
type_map
gives the atom types, i.e. “H” and “C”. mass_map
gives the standard atom weights, i.e. “1” and “12”.data
"init_data_prefix": "....../init/",
"init_data_sys": [
"CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd"
],
"sys_configs_prefix": "....../init/",
"sys_configs": [
[
"CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR"
],
[
"CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR"
]
],
init_data_prefix
and init_data_sys
specify the location of the init data. sys_configs_prefix
and sys_configs
specify the location of the structures.training
"numb_models": 4,
"default_training_param": {
},
numb_models
specifies the number of models to be trained. “default_training_param” specifies the training parameters for deepmd-kit
.00.train
. A detailed explanation of training parameters can be found in DeePMD-kit’s documentation (https://docs.deepmodeling.com/projects/deepmd/en/master/).exploration
"model_devi_dt": 0.002,
"model_devi_skip": 0,
"model_devi_f_trust_lo": 0.05,
"model_devi_f_trust_hi": 0.15,
"model_devi_clean_traj": true,
"model_devi_jobs": [
{
"sys_idx": [
0
],
"temps": [
100
],
"press": [
1.0
],
"trj_freq": 10,
"nsteps": 300,
"ensemble": "nvt",
"_idx": "00"
},
{
"sys_idx": [
1
],
"temps": [
100
],
"press": [
1.0
],
"trj_freq": 10,
"nsteps": 3000,
"ensemble": "nvt",
"_idx": "01"
}
],
model_devi_dt
specifies timestep for MD simulation. model_devi_skip
specifies the number of structures skipped for saving in each MD. model_devi_f_trust_lo
and model_devi_f_trust_hi
specify the lower and upper bound of model_devi of forces for the selection. model_devi_clean_traj
specifies whether to clean traj folders in MD. If type of model_devi_clean_traj is boolean type then it denote whether to clean traj folders in MD since they are too large. In model_devi_jobs
, sys_idx
specifies the group of structures used for model_devi calculations, temps
specifies the temperature (K) in MD, press
specifies the pressure (Bar) in MD, trj_freq
specifies the frequency of trajectory saved in MD, nsteps
specifies the running steps of MD, ensemble
specifies the ensemble used in MD, and “_idx” specifies the index of iteration.model_devi_jobs
. MD simulations are run for 300 and 3000 time steps with the first and second groups of structures in sys_configs
in 00 and 01 iterations. We choose to save all structures generated in MD simulations and have set trj_freq
as 10, so 30 and 300 structures are saved in 00 and 01 iterations. If the “max_devi_f” of saved structure falls between 0.05 and 0.15, DP-GEN will treat the structure as a candidate. We choose to clean traj folders in MD since they are too large. If you want to save the most recent n iterations of traj folders, you can set model_devi_clean_traj
to be an integer.labeling
"fp_style": "vasp",
"shuffle_poscar": false,
"fp_task_max": 20,
"fp_task_min": 1,
"fp_pp_path": "....../methane/",
"fp_pp_files": [
"POTCAR"
],
"fp_incar": "....../INCAR_methane"
fp_style
specifies software for First Principles. fp_task_max
and fp_task_min
specify the minimum and maximum of structures to be calculated in 02.fp
of each iteration. fp_pp_path
and fp_pp_files
specify the location of the psuedo-potential file to be used for 02.fp. run_jdata[fp_style=vasp]/fp_incar
specifies input file for VASP. INCAR must specify KSPACING and KGAMMA.type_map
.