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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
a2129ad
fix: make MC and MD LAMMPS template runnable
njzjz-bot Aug 29, 2026
f759dc4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 29, 2026
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199 changes: 199 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": 6.0,
"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-08,
"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": 0.2,
"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 ${PRES}
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 all custom ${THERMO_FREQ} traj/*.lammpstrj id type x y z

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
33 changes: 33 additions & 0 deletions tests/test_lammps_mc_md_example.py
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import json
import unittest
from pathlib import Path


class TestLammpsMcMdExample(unittest.TestCase):
def test_template_placeholders_and_dump_command(self):
"""The example must become runnable after applying its revision matrix."""
example = Path(__file__).parents[1] / "examples" / "run" / "dp-lammps-MC+MD"
template = (example / "template" / "lammps.in").read_text()
parameters = json.loads((example / "param.json").read_text())
replacements = parameters["model_devi_jobs"][0]["rev_mat"]["lmp"]

rendered = template
for placeholder, values in replacements.items():
self.assertIn(placeholder, template)
rendered = rendered.replace(placeholder, str(values[0]))

variable_lines = [
line for line in rendered.splitlines() if line.startswith("variable")
]
self.assertFalse(any("${" in line for line in variable_lines))
self.assertNotIn('RANDOM_SEED}"', rendered)

dump_line = next(
line for line in template.splitlines() if line.startswith("dump")
)
self.assertGreaterEqual(len(dump_line.split()), 9)
self.assertIn("traj/*.lammpstrj", dump_line)


if __name__ == "__main__":
unittest.main()