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support spin #286

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bf0e41e
support spin
Mar 11, 2025
aa87afc
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 11, 2025
dbd7d1c
Merge branch 'master' of github.com:deepmodeling/dpgen2 into spin
Mar 13, 2025
e864ffc
Merge branch 'spin' of github.com:pxlxingliang/dpgen2 into spin
Mar 13, 2025
e913707
Merge branch 'master' of github.com:deepmodeling/dpgen2 into spin
May 20, 2025
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8 changes: 8 additions & 0 deletions dpgen2/entrypoint/args.py
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Original file line number Diff line number Diff line change
Expand Up @@ -212,6 +212,7 @@ def lmp_args():
"Each task group is described in :ref:`the task group definition<task_group_sec>` "
)
doc_filters = "A list of configuration filters"
doc_lammps_input_file = "The template input file for LAMMPS simulation. Will pass it to dpdata to parse LAMMPS dump file in spin job."

return [
Argument(
Expand Down Expand Up @@ -259,6 +260,13 @@ def lmp_args():
default=[],
doc=doc_filters,
),
Argument(
"lammps_input_file",
str,
optional=True,
default=None,
doc=doc_lammps_input_file,
),
]


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11 changes: 9 additions & 2 deletions dpgen2/entrypoint/submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,7 @@
CustomizedLmpTemplateTaskGroup,
ExplorationStage,
ExplorationTask,
LmpSpinTaskGroup,
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@coderabbitai coderabbitai bot May 20, 2025

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⚠️ Potential issue

Unused import detected.

The LmpSpinTaskGroup import is not used within this file according to static analysis.

Consider removing this import if it's not needed or add a comment explaining why it's included for future reference.

-    LmpSpinTaskGroup,
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
LmpSpinTaskGroup,
🧰 Tools
🪛 Ruff (0.11.9)

84-84: dpgen2.exploration.task.LmpSpinTaskGroup imported but unused

Remove unused import

(F401)

🤖 Prompt for AI Agents 
In dpgen2/entrypoint/submit.py at line 84, the import LmpSpinTaskGroup is not
used anywhere in the file. Remove this import statement to clean up the code
unless there is a specific reason to keep it, in which case add a comment
explaining its purpose for future maintainers.

LmpTemplateTaskGroup,
NPTTaskGroup,
caly_normalize,
Expand Down Expand Up @@ -318,7 +319,9 @@
conv_style = convergence.pop("type")
report = conv_styles[conv_style](**convergence)
# trajectory render, the format of the output trajs are assumed to be lammps/dump
render = TrajRenderLammps(nopbc=output_nopbc)
render = TrajRenderLammps(

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nopbc=output_nopbc, lammps_input_file=config["explore"]["lammps_input_file"]
)
# selector
selector = ConfSelectorFrames(
render,
Expand Down Expand Up @@ -378,7 +381,11 @@
# report
conv_style = convergence.pop("type")
report = conv_styles[conv_style](**convergence)
render = TrajRenderLammps(nopbc=output_nopbc, use_ele_temp=use_ele_temp)
render = TrajRenderLammps(
nopbc=output_nopbc,
use_ele_temp=use_ele_temp,
lammps_input_file=config["explore"]["lammps_input_file"],
)
# selector
selector = ConfSelectorFrames(
render,
Expand Down
10 changes: 9 additions & 1 deletion dpgen2/exploration/deviation/deviation_manager.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,9 @@ class DeviManager(ABC):
MAX_DEVI_F = "max_devi_f"
MIN_DEVI_F = "min_devi_f"
AVG_DEVI_F = "avg_devi_f"
MAX_DEVI_MF = "max_devi_mf"
MIN_DEVI_MF = "min_devi_mf"
AVG_DEVI_MF = "avg_devi_mf"

def __init__(self) -> None:
super().__init__()
Expand All @@ -32,6 +35,9 @@ def _check_name(self, name: str):
DeviManager.MAX_DEVI_F,
DeviManager.MIN_DEVI_F,
DeviManager.AVG_DEVI_F,
DeviManager.MAX_DEVI_MF,
DeviManager.MIN_DEVI_MF,
DeviManager.AVG_DEVI_MF,
), f"Error: unknown deviation name {name}"

def add(self, name: str, deviation: np.ndarray) -> None:
Expand Down Expand Up @@ -64,7 +70,9 @@ def get(self, name: str) -> List[Optional[np.ndarray]]:
The name of the deviation. The name is restricted to
(DeviManager.MAX_DEVI_V, DeviManager.MIN_DEVI_V,
DeviManager.AVG_DEVI_V, DeviManager.MAX_DEVI_F,
DeviManager.MIN_DEVI_F, DeviManager.AVG_DEVI_F)
DeviManager.MIN_DEVI_F, DeviManager.AVG_DEVI_F,
DeviManager.MAX_DEVI_MF, DeviManager.MIN_DEVI_MF,
DeviManager.AVG_DEVI_MF)
"""
self._check_name(name)
self._check_data()
Expand Down
3 changes: 3 additions & 0 deletions dpgen2/exploration/deviation/deviation_std.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,9 @@ def _check_data(self) -> None:
DeviManager.MAX_DEVI_F,
DeviManager.MIN_DEVI_F,
DeviManager.AVG_DEVI_F,
DeviManager.MAX_DEVI_MF,
DeviManager.MIN_DEVI_MF,
DeviManager.AVG_DEVI_MF,
)
# check the length of model deviations
frames = {}
Expand Down
20 changes: 19 additions & 1 deletion dpgen2/exploration/render/traj_render_lammps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,9 +42,14 @@
self,
nopbc: bool = False,
use_ele_temp: int = 0,
lammps_input_file: str = None, # type: ignore
):
self.nopbc = nopbc
self.use_ele_temp = use_ele_temp
if lammps_input_file is not None:
self.lammps_input = Path(lammps_input_file).read_text()

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else:
self.lammps_input = None

def get_model_devi(
self,
Expand Down Expand Up @@ -74,6 +79,11 @@
model_devi.add(DeviManager.MAX_DEVI_F, dd[:, 4]) # type: ignore
model_devi.add(DeviManager.MIN_DEVI_F, dd[:, 5]) # type: ignore
model_devi.add(DeviManager.AVG_DEVI_F, dd[:, 6]) # type: ignore
# assume the 7-9 columns are for MF
if dd.shape[1] >= 10: # type: ignore
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@wanghan-iapcm wanghan-iapcm Mar 16, 2025

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It seems to be better to judge from the lammps input if the spin model deviation is expected to be output or not.
you may implement a method like self.has_spin(self.lammps_input).
If the input implies spin model deviation output, then the shape[1] of dd must be 9 otherwise must be 6.

model_devi.add(DeviManager.MAX_DEVI_MF, dd[:, 7]) # type: ignore
model_devi.add(DeviManager.MIN_DEVI_MF, dd[:, 8]) # type: ignore
model_devi.add(DeviManager.AVG_DEVI_MF, dd[:, 9]) # type: ignore

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def get_ele_temp(self, optional_outputs):
ele_temp = []
Expand Down Expand Up @@ -117,13 +127,21 @@

traj_fmt = "lammps/dump"
ms = dpdata.MultiSystems(type_map=type_map)
if self.lammps_input is not None:
lammps_input_file = "lammps_input.in"
Path(lammps_input_file).write_text(self.lammps_input)

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@wanghan-iapcm wanghan-iapcm Mar 16, 2025

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What is the purpose of dumping the lammps input script?

else:
lammps_input_file = None
for ii in range(ntraj):
if len(id_selected[ii]) > 0:
if isinstance(trajs[ii], HDF5Dataset):
traj = StringIO(trajs[ii].get_data()) # type: ignore
else:
traj = trajs[ii]
ss = dpdata.System(traj, fmt=traj_fmt, type_map=type_map)
# for spin job, need to read input file to get the key of the spin data
ss = dpdata.System(
traj, fmt=traj_fmt, type_map=type_map, input_file=lammps_input_file
)
ss.nopbc = self.nopbc
if ele_temp:
self.set_ele_temp(ss, ele_temp[ii])
Expand Down
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