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Lammps template for MD+MC #1149

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Lammps template for MD+MC #1149

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7b2beda
Lammps template for MD+MC
wujing81 Mar 8, 2023
2ae7756
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 9, 2023
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126 changes: 126 additions & 0 deletions examples/run/dp-lammps-MC+MD/param.json
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{
"type_map": ["Sr", "Pb", "Ti", "O"],
"mass_map": [87.62, 207.2, 47.867, 15.999],
"init_data_prefix": "./data",
"init_data_sys": [
"deepmd"
],

"sys_configs": [
["someplace/POSCAR"]
],

"_comment": " 00.train ",
"numb_models": 4,
"default_training_param": {
"model":{
"type_map":[
"Sr",
"Pb",
"Ti",
"O"
],
"descriptor": {
"type": "se_e2_a",
"sel": "auto",
"rcut_smth": 0.5,
"rcut": 6.00,
"neuron": [25, 50, 100],
"resnet_dt": false,
"axis_neuron": 16,
"seed": 1
},
"fitting_net": {
"neuron": [
240,
240,
240
],
"resnet_dt": true,
"seed": 1
}
},
"learning_rate": {
"type": "exp",
"start_lr": 0.001,
"stop_lr":3.51e-8,
"decay_steps": 2000
},
"loss": {
"type":"ener",
"start_pref_e": 0.02,
"limit_pref_e": 1,
"start_pref_f": 1000,
"limit_pref_f": 1,
"start_pref_v": 0.0,
"limit_pref_v": 0.0
},
"training": {
"set_prefix": "set",
"stop_batch": 400000,
"batch_size": "auto",
"disp_file": "lcurve.out",
"disp_freq": 1000,
"numb_test": 4,
"save_freq": 1000,
"save_ckpt": "model.ckpt",
"disp_training": true,
"time_training": true,
"profiling": false,
"profiling_file": "timeline.json",
"_comment": "that's all"
}
},

"model_devi_dt": 0.002,
"model_devi_skip": 0,
"model_devi_f_trust_lo": 0.1,
"model_devi_f_trust_hi": 0.20,
"model_devi_clean_traj": true,
"model_devi_jobs": [
{"_idx": 0, "ensemble": "npt","sys_idx": [0], "trj_freq": 10,
"rev_mat":{"lmp":{
"${MC_NSTEPS}":[50],
"${MD_NSTEPS}":[1000],
"${PRES}":[0,100],
"${TEMP_MD}":[100,300],
"${TEMP_MC}":[100,300],
"${RANDOM_SEED}":[15196],
"${ELEMENT_TYPE_1}":[1],
"${ELEMENT_TYPE_2}":[2],
"${N_LOOP}":[10]
}
},
"template":{"lmp":"template/lammps.in"}

},
{"_idx": 1, "ensemble": "npt","press": [1,100],"sys_idx": [0], "trj_freq": 10,
"rev_mat":{"lmp":{
"${MC_NSTEPS}":[50],
"${MD_NSTEPS}":[1000],
"${PRES}":[0,100],
"${TEMP_MD}":[100],
"${TEMP_MC}":[100],
"${RANDOM_SEED}":[15196],
"${ELEMENT_TYPE_1}":[1],
"${ELEMENT_TYPE_2}":[2],
"${N_LOOP}":[10]
}
},
"template":{"lmp":"template/lammps.in"}

}
],
"fp_style": "vasp",
"shuffle_poscar": false,
"fp_task_max": 100,
"fp_task_min": 10,
"fp_pp_path": "workplace",
"fp_pp_files": [
"POTCAR_Sr",
"POTCAR_Pb",
"POTCAR_Ti",
"POTCAR_O"
],
"fp_incar": "workplace/INCAR"
}
55 changes: 55 additions & 0 deletions examples/run/dp-lammps-MC+MD/template/lammps.in
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variable MD_NSTEPS equal MD_NSTEPS
variable MC_NSTEPS equal MC_NSTEPS
variable THERMO_FREQ equal 10
variable TEMP_MD equal TEMP_MD
variable TEMP_MC equal TEMP_MC
variable PRES equal press
variable TAU_T equal 0.100000
variable TAU_P equal 0.500000
variable RANDOM_SEED equal RANDOM_SEED
variable ELEMENT_TYPE_1 equal ELEMENT_TYPE_1
variable ELEMENT_TYPE_2 equal ELEMENT_TYPE_2
variable N_LOOP equal N_LOOP

#Initialization
units metal
boundary p p p
atom_style atomic
neighbor 1.0 bin

#read data
read_data conf.lmp
mass 1 87.620000
mass 2 207.200000
mass 3 47.867000
mass 4 15.999000

# read in the potentia
pair_style deepmd ../graph.001.pb ../graph.000.pb ../graph.003.pb ../graph.002.pb out_freq ${THERMO_FREQ} out_file model_devi.out
pair_coeff
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pair_coeff
--> pair coeff * *

to be compatible with the latest version of lammps


# output observables
thermo_style custom step temp pe ke etotal press vol lx ly lz xy xz yz
thermo ${THERMO_FREQ}
dump dpgen_dump

timestep 0.002000

variable loop1 loop ${N_LOOP}
label runloop1

# Monte Carlo followed by short md
fix mc1 all atom/swap 1 1 500 ${TEMP_MC} ke no semi-grand no types ${ELEMENT_TYPE_1} ${ELEMENT_TYPE_2}
run ${MC_NSTEPS}
unfix mc1

velocity all create ${TEMP_MD} ${RANDOM_SEED}"
velocity all zero linear
fix md1 all npt temp ${TEMP_MD} ${TEMP_MD} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}
run ${MD_NSTEPS}
unfix md1

variable idx equal "(v_loop1-1)"
write_data conf.${idx}.lmp
next loop1
jump SELF runloop1