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Provide CHNO example (#158)
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Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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3 people committed Jul 26, 2023
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70 changes: 70 additions & 0 deletions examples/chno/dpa_manyi.json
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{
"model": {
"type_map": ["H", "C", "N", "O"] ,
"descriptor": {
"type": "se_atten",
"sel": 20,
"rcut_smth": 0.5,
"rcut": 6.0,
"neuron": [
40,
80,
160
],
"resnet_dt": false,
"axis_neuron": 16,
"attn": 128,
"attn_layer": 3,
"attn_dotr": true,
"attn_mask": false,
"seed": 30289,
"_activation_function": "tanh"
},
"fitting_net": {
"neuron": [
240,
240,
240
],
"resnet_dt": true,
"_coord_norm": true,
"_type_fitting_net": false,
"seed": 11273,
"_activation_function": "tanh"
}
},
"learning_rate": {
"type": "exp",
"start_lr": 0.001,
"decay_steps": 5000,
"stop_lr": 5e-08,
"_decay_rate": 0.95
},
"loss": {
"start_pref_e": 0.02,
"limit_pref_e": 2,
"start_pref_f": 1000,
"limit_pref_f": 1,
"start_pref_v": 0,
"limit_pref_v": 0
},
"training": {
"training_data": {
"systems": [
],
"batch_size": 16,
"_comment": "that's all"
},
"numb_steps": 10000000,
"seed": 922,
"disp_file": "lcurve.out",
"disp_freq": 2000,
"numb_test": 5,
"save_freq": 10000,
"save_ckpt": "model.ckpt",
"disp_training": true,
"time_training": true,
"profiling": false,
"profiling_file": "timeline.json"
}
}
204 changes: 204 additions & 0 deletions examples/chno/input.json
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{
"bohrium_config": {
"username": "__write your bohrium username",
"password": "__write your bohrium password",
"project_id" : "__write your bohrium project ID",
"_comment" : "all"
},

"default_step_config": {
"template_config": {
"image" : "registry.dp.tech/dptech/prod-11881/dpgen2-utils:1.2",
"_comment" : "all"
},
"executor" : {
"type" : "dispatcher",
"image_pull_policy" : "IfNotPresent",
"machine_dict": {
"batch_type": "Bohrium",
"context_type": "Bohrium",
"remote_profile": {
"input_data": {
"job_type": "container",
"platform": "ali",
"scass_type": "c2_m8_cpu"
}
}
}
},
"_comment" : "all"
},

"step_configs":{
"run_train_config" : {
"template_config" : {
"image" : "registry.dp.tech/dptech/deepmd-kit:2.1.5-cuda11.6",
"_comment" : "all"
},
"executor" : {
"type" : "dispatcher",
"retry_on_submission_error": 10,
"image_pull_policy" : "IfNotPresent",
"machine_dict": {
"batch_type": "Bohrium",
"context_type": "Bohrium",
"remote_profile": {
"input_data": {
"job_type": "container",
"platform": "ali",
"scass_type": "c8_m32_1 * NVIDIA V100"
}
}
}
},
"_comment" : "all"
},
"run_explore_config" : {
"template_config" : {
"image" : "registry.dp.tech/dptech/deepmd-kit:2.1.5-cuda11.6",
"_comment" : "all"
},
"continue_on_success_ratio" : 0.80,
"executor" : {
"type" : "dispatcher",
"retry_on_submission_error": 10,
"image_pull_policy" : "IfNotPresent",
"machine_dict": {
"batch_type": "Bohrium",
"context_type": "Bohrium",
"remote_profile": {
"input_data": {
"job_type": "container",
"platform": "ali",
"scass_type": "c8_m32_1 * NVIDIA V100"
}
}
}
},
"template_slice_config":{
"group_size": 20,
"pool_size": 5
},
"_comment" : "all"
},
"run_fp_config" : {
"template_config" : {
"image" : "registry.dp.tech/dptech/prod-11881/manyi-dalibao:1.3",
"_comment" : "all"
},
"continue_on_success_ratio" : 0.80,
"executor" : {
"type" : "dispatcher",
"retry_on_submission_error": 10,
"image_pull_policy" : "IfNotPresent",
"machine_dict": {
"batch_type": "Bohrium",
"context_type": "Bohrium",
"remote_profile": {
"input_data": {
"job_type": "container",
"platform": "ali",
"scass_type": "c16_m64_cpu"
}
}
}
},
"template_slice_config":{
"group_size": 20,
"pool_size": 1
},
"_comment" : "all"
},
"_comment" : "all"
},

"upload_python_packages" : [
"/data/dpgen2-master/dpgen2",
"/data/dpdata-master/dpdata"
],

"inputs": {
"_comment" : "super heavy H atom LOL",
"type_map": ["H", "C", "N", "O"] ,
"mass_map": [4, 12, 14, 16],
"mixed_type": true,
"init_data_prefix": null,
"init_data_sys": "mixtedtype.init.data",
"_comment" : "all"
},

"train":{
"type" : "dp",
"numb_models" : 4,
"init_models_paths":[
"/data/druglike.dpgen2.mixed.8-b/init.models/task.0000/frozen_model.pb",
"/data/druglike.dpgen2.mixed.8-b/init.models/task.0001/frozen_model.pb",
"/data/druglike.dpgen2.mixed.8-b/init.models/task.0002/frozen_model.pb",
"/data/druglike.dpgen2.mixed.8-b/init.models/task.0003/frozen_model.pb"
],
"config" : {
"init_model_policy" : "yes",
"init_model_old_ratio" : 0.98,
"init_model_numb_steps" : 600000,
"init_model_start_lr" : 1e-4,
"init_model_start_pref_e" : 0.25,
"init_model_start_pref_f" : 100,
"_comment" : "all"
},
"template_script" : "dpa_manyi.json",
"_comment" : "all"
},

"explore" : {
"type" : "lmp",
"config" : {
"command": "lmp -var restart 0"
},
"convergence": {
"type": "adaptive-lower",
"conv_tolerance": 0.02,
"_numb_candi_f": 3000,
"rate_candi_f": 0.10,
"level_f_hi": 0.5,
"n_checked_steps": 8,
"_command": "all"
},
"max_numb_iter" : 12,
"fatal_at_max" : false,
"output_nopbc": true,
"configuration_prefix": null,
"configurations": [
{
"type" : "file",
"files" : ["md.data/*N1[56].equ/*"],
"fmt" : "deepmd/npy",
"remove_pbc" : true
}
],
"stages": [
[
{
"type" : "lmp-template",
"sys_idx": [0], "n_sample" : 4000,
"lmp" : "template.lammps", "trj_freq" : 500, "revisions" : {"V_NSTEPS" : [20000], "V_TEMP" : [750], "V_DUMPFREQ": [2000]}
}
]
],
"_comment" : "all"
},
"fp" : {
"type" : "gaussian",
"task_max": 5000,
"run_config" : {
"command": "ulimit -s unlimited && export g16root='/root/Gaussian_16' && source $g16root/g16/bsd/g16.profile && g16 "
},
"inputs_config" : {
"keywords" : "wB97XD/6-31G** nosymm scf(conver=8) force",
"multiplicity" : "auto",
"charge" : 0,
"nproc" : 16,
"_comment" : "all"
},
"_comment" : "all"
}
}
42 changes: 42 additions & 0 deletions examples/chno/template.lammps
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variable NSTEPS equal V_NSTEPS
variable TEMP equal V_TEMP
variable PRES equal 0
variable THERMO_FREQ equal V_DUMPFREQ
variable DUMP equal 10
variable TAU_T equal 0.100000
variable TAU_P equal 0.500000


#Initialization
units metal
dimension 3
atom_style atomic
boundary f f f

read_data conf.lmp
mass 1 4.0
mass 2 12.0
mass 3 14.0
mass 4 16.0

#Interatomic potentials - DeepMD
pair_style deepmd
pair_coeff * *


#MD parameters
timestep 0.001 #ps
velocity all create ${TEMP} 1815191 mom yes rot yes dist gaussian

#Run MD - equil at 300K
run_style verlet #Velocity verlet
fix 1 all nve
fix 2 all temp/csvr ${TEMP} ${TEMP} ${TAU_T} 1305191
#fix 1 all nvt temp ${TEMP} ${TEMP} 0.1 #NH thermostat - 300K with 100 fs frequency
fix 3 all momentum 1 linear 0 0 0 #Remove total linear momentum of the system at each step
fix 4 all recenter INIT INIT INIT
thermo_style custom step temp pe etotal press #Setting printing
thermo ${THERMO_FREQ} #Ouputing thermodynamic properties
dump dpgen_dump
#dump 2 all custom 100 vel.xyz id type vx vy vz
run ${NSTEPS} #25 ps

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