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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

@Vibsteamer Vibsteamer Mar 9, 2023

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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}"

@njzjz-bot njzjz-bot Aug 10, 2026 •
edited
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[Blocking] The extra quote after the random seed makes LAMMPS fail immediately with Unmatched double quote in command; I reproduced this with LAMMPS 22 Jul 2025. Please change it to:

Suggested change
velocity all create ${TEMP_MD} ${RANDOM_SEED}"
velocity all create ${TEMP_MD} ${RANDOM_SEED}

The MC seed is also hard-coded to 500 and should be parameterized separately. In addition, dumping after rejected swaps produces repeated configurations, so the intended sampling weight should be documented or the frames should be deduplicated.

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