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Ericwang6Ericwang6
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move dp1.x-gmx examples to deprecated and add dp2.x-gmx examples
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examples/run/dp1.x-gromacs-gaussian/param.json renamed to examples/run/deprecated/dp1.x-gromacs-gaussian/param.json

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‎examples/run/dp2.x-gromacs-gaussian/machine.json‎

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{
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"deepmd_version" : "2.0",
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"train": [
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{
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"machine": {
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"batch": "slurm",
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"work_path": "/work/path"
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},
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"resources": {
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"numb_node": 1,
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"numb_gpu": 1,
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"partition": "all",
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"time_limit": "120:0:0",
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"task_per_node": 8,
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"exclude_list": [],
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"module_list": [],
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"source_list": ["/path/to/dp-2.0.env"]
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},
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"command": "dp"
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}
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],
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"model_devi": [
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{
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"machine": {
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"batch": "slurm",
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"work_path": "/work/path"
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},
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"resources": {
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"numb_node": 1,
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"numb_gpu": 1,
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"partition": "all",
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"time_limit": "120:0:0",
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"task_per_node": 8,
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"source_list": [
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"/path/to/gromacs-dp/env"
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],
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"module_list": [],
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"exclude_list": [],
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"envs": {
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"GMX_DEEPMD_INPUT_JSON": "input.json"
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}
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},
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"command": "gmx_mpi",
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"group_size": 1
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}
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],
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"fp": [
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{
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"machine": {
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"batch": "slurm",
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"work_path": "/work/path"
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},
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"resources": {
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"numb_node": 1,
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"numb_gpu": 0,
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"time_limit": "120:0:0",
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"task_per_node": 28,
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"partition": "cpu",
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"exclude_list": [],
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"source_list": [
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"/path/to/gaussian/bashrc"
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],
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"module_list": []
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},
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"command": "g16 < input",
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"group_size": 20
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}
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]
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}

‎examples/run/dp2.x-gromacs-gaussian/param.json‎

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{
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"type_map": ["H", "C", "N", "O", "F", "S", "Cl"],
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"mass_map": [2, 12, 14, 16, 17, 32, 35],
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"init_data_prefix": "/path/to/init/data",
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"init_data_sys": ["data.init"],
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"init_multi_systems": true,
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"sys_configs_prefix": "/path/to/model/devi/data",
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"sys_configs": [
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["model_devi/CHEMBL3402749_500"],
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["model_devi/CHEMBL3402741_400"],
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["model_devi/CHEMBL3402748_5300"],
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["model_devi/CHEMBL3402743_42"],
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["model_devi/CHEMBL3402761_1"],
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["model_devi/CHEMBL3402756_2.7"],
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["model_devi/CHEMBL3402750_400"],
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["model_devi/CHEMBL3402764_90"],
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["model_devi/CHEMBL3402758_10"],
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["model_devi/CHEMBL3402754_40"],
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["model_devi/CHEMBL3402747_3400"],
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["model_devi/CHEMBL3402762_1"],
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["model_devi/CHEMBL3402744_300"],
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["model_devi/CHEMBL3402752_30000"],
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["model_devi/CHEMBL3402742_23"],
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["model_devi/CHEMBL3402759_5.7"],
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["model_devi/CHEMBL3402745_200"],
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["model_devi/CHEMBL3402757_6.5"],
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["model_devi/CHEMBL3402755_4200"],
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["model_devi/CHEMBL3402751_2100"],
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["model_devi/CHEMBL3402753_200"],
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["model_devi/CHEMBL3402763_90"],
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["model_devi/CHEMBL3402765_11-charged-pKa-8.1"],
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["model_devi/CHEMBL3402760_1"]
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],
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"sys_charges": [
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0,
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1,
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0,
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1,
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0,
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1,
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0,
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1,
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1,
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0,
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0,
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1,
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0,
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0,
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1,
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1,
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0,
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1,
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0,
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0,
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0,
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1,
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1,
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1
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],
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"sys_format": "gromacs/gro",
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"numb_models": 4,
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"training_reuse_iter": 1,
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"training_reuse_old_ratio": 0.3,
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"training_reuse_start_lr": 0.0001,
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"training_reuse_decay_steps": 500,
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"training_reuse_numb_steps": 200000,
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"training_reuse_start_pref_e": 1,
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"training_reuse_start_pref_f": 100,
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"train_param": "input.json",
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"default_training_param": {
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"model": {
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"type_map": ["H", "C", "N", "O", "F", "S", "Cl"],
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"descriptor": {
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"type": "se_e2_a",
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"sel": [40, 48, 48, 48, 48, 48, 48],
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"rcut_smth": 0.50,
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"rcut": 6.00,
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"neuron": [25, 50, 100],
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"resnet_dt": false,
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"axis_neuron": 16,
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"type_one_side": true
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},
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"fitting_net": {
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"neuron": [240, 240, 240],
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"resnet_dt": true,
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"type": "ener"
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}
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},
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"learning_rate": {
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"type": "exp",
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"start_lr": 0.001,
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"decay_steps": 5000
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},
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"loss": {
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"start_pref_e": 0.02,
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"limit_pref_e": 8,
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"start_pref_f": 1000,
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"limit_pref_f": 1,
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"start_pref_v": 0,
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"limit_pref_v": 0
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},
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"training": {
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"numb_steps": 1000000,
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"disp_file": "lcurve.out",
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"disp_freq": 1000,
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"numb_test": 1,
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"save_freq": 1000,
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"save_ckpt": "model.ckpt"
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}
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},
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"model_devi_engine": "gromacs",
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"gromacs_settings": {
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"mdp_filename": "md.mdp",
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"topol_filename": "processed.top",
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"conf_filename": "npt.gro",
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"index_filename": "index.raw",
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"ref_filename": "em.tpr",
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"model_devi_script": "model_devi.py",
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"traj_filename": "deepmd_traj.gro",
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"group_name": "Other"
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},
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"model_devi_dt": 0.001,
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"model_devi_f_trust_lo": 0.20,
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"model_devi_f_trust_hi": 0.60,
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"model_devi_e_trust_lo": 1e10,
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"model_devi_e_trust_hi": 1e10,
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"model_devi_clean_traj": false,
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"model_devi_skip": 0,
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"model_devi_nopbc": true,
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"model_devi_activation_func": [
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["tanh", "tanh"],
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["tanh", "tanh"],
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["tanh", "tanh"],
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["tanh", "tanh"]
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],
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"model_devi_jobs": [
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{
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"_idx": 0,
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"ensemble": "nvt",
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"nsteps": 100,
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"press": [],
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"sys_idx": [ 0, 1, 2, 3, 4, 5, 6, 7,
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8, 9, 10, 11, 12, 13, 14, 15,
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16, 17, 18, 19, 20, 21, 22, 23],
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"temps": [],
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"trj_freq": 1
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}
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],
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"fp_style": "gaussian",
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"shuffle_poscar": false,
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"fp_task_max": 50,
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"fp_task_min": 1,
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"fp_pp_path": "./",
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"fp_pp_files": [],
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"fp_params": {
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"keywords": "force m062x/6-31** nosymm",
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"nproc": 28,
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"multiplicity": 1
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}
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}

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