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fqgongfqgong
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add input files of enhanced sampling method (#446)
* Add fp_pp_files to forward_files in cp2k * Add hills key to param.json so I can take HILLS file back from remote server when I use plumed. * Add a key--'hills' so I can get the HILLS file from remote server when I use plumed during the exploration. * enhance-sampling * restore * restore * add the template of input files Co-authored-by: fqgong <fqgong@users.noreply.github.com>
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‎examples/run/dp-lammps-enhance_sampling/lmp/input.lammps‎

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variable NSTEPS equal V_NSTEPS
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variable TEMP equal V_TEMP
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variable PRES equal V_PRES
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variable THERMO_FREQ equal 10
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variable DUMP equal 10
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variable TAU_T equal 0.100000
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variable TAU_P equal 0.500000
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#Initialization
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units metal
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dimension 3
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atom_style atomic
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read_data conf.lmp
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mass 1 12.011
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mass 2 1.008
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#Interatomic potentials - DeepMD
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pair_style deepmd
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pair_coeff
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#MD parameters
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timestep 0.0005 #ps
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velocity all create ${TEMP} 1815191 mom yes rot yes dist gaussian
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#Run MD - equil at 300K
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run_style verlet #Velocity verlet
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fix dpgen_plm
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fix 1 all nvt temp ${TEMP} ${TEMP} 0.1 #NH thermostat - 300K with 100 fs frequency
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fix 2 all momentum 1 linear 0 0 0 #Remove total linear momentum of the system at each step
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fix 3 all recenter INIT INIT INIT
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thermo_style custom step temp pe etotal press #Setting printing
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thermo ${THERMO_FREQ} #Ouputing thermodynamic properties
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dump dpgen_dump
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#dump 2 all custom 100 vel.xyz id type vx vy vz
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run ${NSTEPS} #25 ps
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‎examples/run/dp-lammps-enhance_sampling/lmp/input.plumed‎

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UNITS LENGTH=A TIME=0.0005 #Amstroeng, hartree, fs
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#RESTART
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ene: ENERGY
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phi: TORSION ATOMS=5,1,2,8
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METAD ...
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LABEL=metad
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ARG=phi
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PACE=50
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HEIGHT=1.0
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SIGMA=0.1
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FILE=HILLS
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BIASFACTOR=20
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TEMP=V_TEMP
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... METAD
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PRINT STRIDE=V_STRIDE FILE=COLVAR ARG=phi,metad.*,ene
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FLUSH STRIDE=V_STRIDE

‎examples/run/dp-lammps-enhance_sampling/param.json‎

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{
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"type_map": ["C", "H"],
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"mass_map": [12.0, 1.0],
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"_comment": "initial data set for Training and the number of frames in each training batch",
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"init_data_prefix": "someplace/tutorial-dpgen-enhance",
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"init_data_sys": [
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"raw_file"
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],
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"init_batch_size": [
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4
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],
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"_comment": "configurations for starting MD in Exploration and batch sizes when traning snapshots derived from these configs (if they were selected)",
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"sys_configs_prefix": "someplace/tutorial-dpgen-enhance",
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"sys_configs": [
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[
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"configs/POSCAR_[0-9]"
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],
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[
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"configs/POSCAR_0"
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]
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],
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"_comment": " 00.train ",
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"numb_models": 4,
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"training_init_model": true,
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"training_reuse_iter": 1,
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"training_reuse_old_ratio": 0.2,
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"training_reuse_stop_batch": 100000,
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"training_reuse_start_lr": 0.0001,
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"training_reuse_start_pref_e": 0.1,
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"training_reuse_start_pref_f": 200,
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"default_training_param": {
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"model": {
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"type_map": ["C","H"],
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"descriptor": {
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"type": "se_a",
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"sel": [2,6],
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"rcut_smth": 0.5,
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"rcut": 5.0,
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"neuron": [20,40,80],
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"resnet_dt": false,
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"axis_neuron": 6,
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"seed": 0
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},
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"fitting_net": {
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"neuron": [120,120,120],
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"resnet_dt": true,
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"coord_norm": true,
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"type_fitting_net": false,
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"seed": 0
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}
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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": 1,
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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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"learning_rate": {
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"type": "exp",
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"start_lr": 0.001,
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"decay_steps": 500,
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"decay_rate": 0.95
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},
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"training": {
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"systems": [],
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"set_prefix": "set",
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"stop_batch": 200000,
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"batch_size": 1,
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"seed": 1,
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"_comment": "frequencies counted in batch",
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"disp_file": "lcurve.out",
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"disp_freq": 100,
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"numb_test": 10,
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"save_freq": 1000,
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"save_ckpt": "model.ckpt",
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"load_ckpt": "model.ckpt",
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"disp_training": true,
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"time_training": true,
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"profiling": false,
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"profiling_file": "timeline.json"
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}
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},
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"_comment": " 01.model_devi ",
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"model_devi_dt": 0.0005,
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"model_devi_skip": 0,
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"model_devi_f_trust_lo": 0.08,
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"model_devi_f_trust_hi": 0.25,
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"model_devi_clean_traj": false,
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"model_devi_plumed" : true,
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"model_devi_jobs": [
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{ "sys_idx": [0],"traj_freq": 10,"_idx": "00",
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"template":{ "lmp": "lmp/input.lammps", "plm": "lmp/input.plumed" },
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"rev_mat":{ "lmp": {"V_NSTEPS": [20000], "V_TEMP": [300], "V_PRES": [1]},
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"plm": {"V_TEMP": [300], "V_STRIDE": [10]}
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}
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},
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{ "sys_idx": [0],"traj_freq": 10,"_idx": "01",
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"template":{ "lmp": "lmp/input.lammps", "plm": "lmp/input.plumed" },
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"rev_mat":{ "lmp": {"V_NSTEPS": [50000], "V_TEMP": [300], "V_PRES": [1]},
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"plm": {"V_TEMP": [300], "V_STRIDE": [10]}
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}
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},
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{ "sys_idx": [1],"traj_freq": 10,"_idx": "01",
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"template":{ "lmp": "lmp/input.lammps", "plm": "lmp/input.plumed" },
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"rev_mat":{ "lmp": {"V_NSTEPS": [300000], "V_TEMP": [300], "V_PRES": [1]},
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"plm": {"V_TEMP": [300], "V_STRIDE": [10]}
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}
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}
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],
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"_comment": " 02.fp ",
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"fp_style": "vasp",
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"shuffle_poscar": false,
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"fp_task_max": 150,
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"_comment": "the maximum number of stcs to calc.",
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"fp_task_min": 5,
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"fp_pp_path": "./",
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"fp_pp_files": ["POTCAR_C", "POTCAR_H"],
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"fp_incar" : "INCAR",
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"_comment": " that's all "
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}

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