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add arguments for lammps revise_template #1015

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Merged
merged 11 commits into from
Nov 11, 2022
Merged

add arguments for lammps revise_template #1015

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e674c1f
add arguments for lammps revise_template
HuangJiameng Oct 31, 2022
84d9b60
set template and rev_mat as optional
HuangJiameng Oct 31, 2022
1bff4d3
set rev_mat as list
HuangJiameng Oct 31, 2022
03871f3
add sys_rev_mat and sys_rev_mat, fix some settings
HuangJiameng Nov 5, 2022
709d45c
add arg doc for md rev_mat and md template
HuangJiameng Nov 8, 2022
f46e6b7
add check of dp-lammps-enhance_sampling
HuangJiameng Nov 10, 2022
27a3e37
correct param trj_freq
HuangJiameng Nov 10, 2022
fcc49f0
set nsteps as optional
HuangJiameng Nov 10, 2022
d26b2d4
set ensemble as optional
HuangJiameng Nov 10, 2022
17df288
add doc for nsteps and ensemble
HuangJiameng Nov 10, 2022
d2ca359
Update arginfo.py
HuangJiameng Nov 10, 2022
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40 changes: 37 additions & 3 deletions dpgen/generator/arginfo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,8 +101,33 @@ def training_args() -> List[Argument]:


# Exploration
def model_devi_jobs_template_args() -> Argument:
doc_template = 'Give a template for 01.model_devi.'
doc_template_lmp = 'The path to input.lammps template'
doc_template_plm = 'The path to input.plumed template'

args = [
Argument("lmp", str, optional=True, doc=doc_template_lmp),
Argument("plm", str, optional=True, doc=doc_template_plm),
]
return Argument("template", list, args, [], optional=True, repeat=False, doc=doc_template)


def model_devi_jobs_rev_mat_args() -> Argument:
doc_rev_mat = '' # looking forward to update
doc_rev_mat_lmp = '' # looking forward to update
doc_rev_mat_plm = '' # looking forward to update

args = [
Argument("lmp", dict, optional=True, doc=doc_rev_mat_lmp),
Argument("plm", dict, optional=True, doc=doc_rev_mat_plm),
]
return Argument("rev_mat", list, args, [], optional=True, repeat=False, doc=doc_rev_mat)


def model_devi_jobs_args() -> List[Argument]:
# this may be not correct
doc_sys_rev_mat = "" # looking forward to update
doc_sys_idx = 'Systems to be selected as the initial structure of MD and be explored. The index corresponds exactly to the sys_configs.'
doc_temps = 'Temperature (K) in MD.'
doc_press = 'Pressure (Bar) in MD. Required when ensemble is npt.'
Expand All @@ -118,8 +143,11 @@ def model_devi_jobs_args() -> List[Argument]:
doc_model_devi_v_trust_hi = 'Upper bound of virial for the selection. If dict, should be set for each index in sys_idx, respectively. Should be used with DeePMD-kit v2.x.'

args = [
model_devi_jobs_template_args(),
model_devi_jobs_rev_mat_args(),
Argument("sys_rev_mat", list, optional=True, doc=doc_sys_rev_mat),
Argument("sys_idx", list, optional=False, doc=doc_sys_idx),
Argument("temps", list, optional=False, doc=doc_temps),
Argument("temps", list, optional=True, doc=doc_temps),
Argument("press", list, optional=True, doc=doc_press),
Argument("trj_freq", int, optional=False, doc=doc_trj_freq),
Argument("nsteps", int, optional=False, doc=doc_nsteps),
Expand Down Expand Up @@ -160,6 +188,8 @@ def model_devi_lmp_args() -> List[Argument]:
doc_model_devi_clean_traj = 'If type of model_devi_clean_traj is bool type then it denote whether to clean traj folders in MD since they are too large. If it is Int type, then the most recent n iterations of traj folders will be retained, others will be removed.'
doc_model_devi_merge_traj = 'If model_devi_merge_traj is set as True, only all.lammpstrj will be generated, instead of lots of small traj files.'
doc_model_devi_nopbc = 'Assume open boundary condition in MD simulations.'
doc_model_devi_plumed = '' # looking forward to update
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Actually, I'm not sure if this parameter is functional at all. Because to run model_devi with plumed, we use "template", which is a completely independent setting and is not at all affected by this parameter.

doc_model_devi_plumed_path = '' # looking forward to update
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Frankly, I've never used this parameter. I don't even know this parameter. Seems useless.

doc_shuffle_poscar = 'Shuffle atoms of each frame before running simulations. The purpose is to sample the element occupation of alloys.'
doc_use_relative = 'Calculate relative force model deviation.'
doc_epsilon = 'The level parameter for computing the relative force model deviation.'
Expand Down Expand Up @@ -194,10 +224,14 @@ def model_devi_lmp_args() -> List[Argument]:
doc=doc_model_devi_f_avg_relative),
Argument("model_devi_clean_traj", [
bool, int], optional=True, default=True , doc=doc_model_devi_clean_traj),
Argument("model_devi_merge_traj", [
bool], optional=True, default=False , doc=doc_model_devi_merge_traj),
Argument("model_devi_merge_traj",
bool, optional=True, default=False , doc=doc_model_devi_merge_traj),
Argument("model_devi_nopbc", bool, optional=True, default=False,
doc=doc_model_devi_nopbc),
Argument("model_devi_plumed",
bool, optional=True, default=False , doc=doc_model_devi_plumed),
Argument("model_devi_plumed_path",
bool, optional=True, default=False , doc=doc_model_devi_plumed_path),
Argument("shuffle_poscar", bool, optional=True, default=False, doc=doc_shuffle_poscar),
Argument("use_relative", bool, optional=True, default=False, doc=doc_use_relative),
Argument("epsilon", float, optional=True, doc=doc_epsilon),
Expand Down