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
"type_map": [
"H",
"C"
],
"mass_map": [
1,
12
],The basics related keys specify the basic information about the system. {dargs:argument}type_map <run_jdata/type_map> gives the atom types, i.e. "H" and "C". {dargs:argument}mass_map <run_jdata/mass_map> gives the standard atom weights, i.e. "1" and "12".
The data related keys in param.json are given as follows
"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"
]
],The data related keys specify the init data for training initial DP models and structures used for model_devi calculations. {dargs:argument}init_data_prefix <run_jdata/init_data_prefix> and {dargs:argument}init_data_sys <run_jdata/init_data_sys> specify the location of the init data. {dargs:argument}sys_configs_prefix <run_jdata/sys_configs_prefix> and {dargs:argument}sys_configs <run_jdata/sys_configs> specify the location of the structures.
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
"numb_models": 4,
"default_training_param": {
},The training related keys specify the details of training tasks. {dargs:argument}numb_models <run_jdata/numb_models> specifies the number of models to be trained. "default_training_param" specifies the training parameters for deepmd-kit.
Here, 4 DP models will be trained in 00.train. A detailed explanation of training parameters can be found in DeePMD-kit’s documentation (https://docs.deepmodeling.com/projects/deepmd/en/master/).
The exploration related keys in param.json are given as follows
"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"
}
],The exploration related keys specify the details of exploration tasks. {dargs:argument}model_devi_dt <run_jdata[model_devi_engine=lammps]/model_devi_dt> specifies timestep for MD simulation. {dargs:argument}model_devi_skip <run_jdata[model_devi_engine=lammps]/model_devi_skip> specifies the number of structures skipped for saving in each MD. {dargs:argument}model_devi_f_trust_lo <run_jdata[model_devi_engine=lammps]/model_devi_f_trust_lo> and {dargs:argument}model_devi_f_trust_hi <run_jdata[model_devi_engine=lammps]/model_devi_f_trust_hi> specify the lower and upper bound of model_devi of forces for the selection. {dargs:argument}model_devi_clean_traj <run_jdata[model_devi_engine=lammps]/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 {dargs:argument}model_devi_jobs <run_jdata[model_devi_engine=lammps]/model_devi_jobs>, {dargs:argument}sys_idx <run_jdata[model_devi_engine=lammps]/model_devi_jobs/sys_idx> specifies the group of structures used for model_devi calculations, {dargs:argument}temps <run_jdata[model_devi_engine=lammps]/model_devi_jobs/temps> specifies the temperature (K) in MD, {dargs:argument}press <run_jdata[model_devi_engine=lammps]/model_devi_jobs/press> specifies the pressure (Bar) in MD, {dargs:argument}trj_freq <run_jdata[model_devi_engine=lammps]/model_devi_jobs/trj_freq> specifies the frequency of trajectory saved in MD, {dargs:argument}nsteps <run_jdata[model_devi_engine=lammps]/model_devi_jobs/trj_freq> specifies the running steps of MD, {dargs:argument}ensemble <run_jdata[model_devi_engine=lammps]/model_devi_jobs/ensemble> specifies the ensemble used in MD, and "_idx" specifies the index of iteration.
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 {dargs:argument}model_devi_jobs <run_jdata[model_devi_engine=lammps]/model_devi_jobs>. MD simulations are run for 300 and 3000 time steps with the first and second groups of structures in {dargs:argument}sys_configs <run_jdata/sys_configs> in 00 and 01 iterations. We choose to save all structures generated in MD simulations and have set {dargs:argument}trj_freq <run_jdata[model_devi_engine=lammps]/model_devi_jobs/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 {dargs:argument}model_devi_clean_traj <run_jdata[model_devi_engine=lammps]/model_devi_clean_traj> to be an integer.
The labeling related keys in param.json are given as follows
"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"The labeling related keys specify the details of labeling tasks. {dargs:argument}fp_style <run_jdata/fp_style> specifies software for First Principles. {dargs:argument}fp_task_max <run_jdata/fp_task_max> and {dargs:argument}fp_task_min <run_jdata/fp_task_min> specify the minimum and maximum of structures to be calculated in 02.fp of each iteration. {dargs:argument}fp_pp_path <run_jdata[fp_style=vasp]/fp_pp_path> and {dargs:argument}fp_pp_files <run_jdata[fp_style=vasp]/fp_pp_files> specify the location of the psuedo-potential file to be used for 02.fp. {dargs:argument}run_jdata[fp_style=vasp]/fp_incar specifies input file for VASP. INCAR must specify KSPACING and KGAMMA.
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 {dargs:argument}type_map <run_jdata/type_map>.
All the keys of the DP-GEN are explained in detail in the section Parameters.