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Add RunLmpHDF5 #267

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merged 5 commits into from
Oct 21, 2024
Merged

Add RunLmpHDF5 #267

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899aaba
add RunLmpHDF5
zjgemi Oct 17, 2024
47a551d
fix: pyright and upgrade dflow dependency
zjgemi Oct 18, 2024
b25efde
fix pyright
zjgemi Oct 18, 2024
cae6577
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 18, 2024
5cf58f3
fix pyright
zjgemi Oct 21, 2024
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3 changes: 2 additions & 1 deletion dpgen2/entrypoint/submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -110,6 +110,7 @@
RunCalyModelDevi,
RunDPTrain,
RunLmp,
RunLmpHDF5,
RunRelax,
RunRelaxHDF5,
SelectConfs,
Expand Down Expand Up @@ -187,7 +188,7 @@ def make_concurrent_learning_op(
prep_run_explore_op = PrepRunLmp(
"prep-run-lmp",
PrepLmp,
RunLmp,
RunLmpHDF5 if explore_config["use_hdf5"] else RunLmp, # type: ignore
prep_config=prep_explore_config,
run_config=run_explore_config,
upload_python_packages=upload_python_packages,
Expand Down
18 changes: 10 additions & 8 deletions dpgen2/exploration/render/traj_render_lammps.py
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Expand Up @@ -63,15 +63,17 @@
dd = fname.get_data()
else:
dd = np.loadtxt(fname)
if len(np.shape(dd)) == 1: # In case model-devi.out is 1-dimensional
dd = dd.reshape((1, len(dd)))
if (
len(np.shape(dd)) == 1 # type: ignore
): # In case model-devi.out is 1-dimensional
dd = dd.reshape((1, len(dd))) # type: ignore

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Added line #L69 was not covered by tests

model_devi.add(DeviManager.MAX_DEVI_V, dd[:, 1])
model_devi.add(DeviManager.MIN_DEVI_V, dd[:, 2])
model_devi.add(DeviManager.AVG_DEVI_V, dd[:, 3])
model_devi.add(DeviManager.MAX_DEVI_F, dd[:, 4])
model_devi.add(DeviManager.MIN_DEVI_F, dd[:, 5])
model_devi.add(DeviManager.AVG_DEVI_F, dd[:, 6])
model_devi.add(DeviManager.MAX_DEVI_V, dd[:, 1]) # type: ignore
model_devi.add(DeviManager.MIN_DEVI_V, dd[:, 2]) # type: ignore
model_devi.add(DeviManager.AVG_DEVI_V, dd[:, 3]) # type: ignore
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

def get_ele_temp(self, optional_outputs):
ele_temp = []
Expand Down
1 change: 1 addition & 0 deletions dpgen2/op/__init__.py
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Expand Up @@ -36,6 +36,7 @@
)
from .run_lmp import (
RunLmp,
RunLmpHDF5,
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💡 Codebase verification

Define __all__ in dpgen2/op/__init__.py to include RunLmpHDF5

The __all__ variable is not defined in dpgen2/op/__init__.py. To make RunLmpHDF5 part of the public API and resolve the unused import warning, consider adding an __all__ list that includes RunLmpHDF5 along with other public classes and functions.

Example:

__all__ = [
    "CollectData",
    "CollRunCaly",
    "DiffCSPGen",
    "PrepCalyDPOptim",
    "PrepCalyInput",
    "PrepCalyModelDevi",
    "PrepDPTrain",
    "PrepLmp",
    "PrepRelax",
    "RunCalyDPOptim",
    "RunCalyModelDevi",
    "RunDPTrain",
    "RunLmp",
    "RunLmpHDF5",
    "RunRelax",
    "RunRelaxHDF5",
    "SelectConfs",
]
🔗 Analysis chain

Consider adding RunLmpHDF5 to all if it's part of the public API

The addition of RunLmpHDF5 to the imports is good, as it makes the new functionality available to other parts of the package. However, the static analysis tool has flagged this import as unused within this file.

If RunLmpHDF5 is intended to be part of the public API of this package, consider adding it to the __all__ list (if one exists) to explicitly define what should be imported when using from dpgen2.op import *.

To verify if __all__ is defined in this file and if so, what it contains, you can run the following script:

If __all__ is not defined, consider adding it to explicitly control what's exported:

__all__ = [
    "CollectData",
    "CollRunCaly",
    "DiffCSPGen",
    "PrepCalyDPOptim",
    "PrepCalyInput",
    "PrepCalyModelDevi",
    "PrepDPTrain",
    "PrepLmp",
    "PrepRelax",
    "RunCalyDPOptim",
    "RunCalyModelDevi",
    "RunDPTrain",
    "RunLmp",
    "RunLmpHDF5",
    "RunRelax",
    "RunRelaxHDF5",
    "SelectConfs",
]
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for __all__ definition in __init__.py

# Test: Search for __all__ definition
rg --type python '__all__\s*=' dpgen2/op/__init__.py

# If __all__ is not found, suggest adding it
if [ $? -ne 0 ]; then
    echo "__all__ not found. Consider adding it with RunLmpHDF5 included."
fi

Length of output: 240

Script:

#!/bin/bash
# Description: Check for __all__ definition in __init__.py without specifying file type

# Test: Search for __all__ definition
rg '__all__\s*=' dpgen2/op/__init__.py

# Capture the exit status
if [ $? -ne 0 ]; then
    echo "__all__ not found. Consider adding it with RunLmpHDF5 included."
else
    echo "__all__ is defined."
fi

Length of output: 195

🧰 Tools
🪛 Ruff

39-39: .run_lmp.RunLmpHDF5 imported but unused; consider removing, adding to __all__, or using a redundant alias

(F401)

)
from .run_relax import (
RunRelax,
Expand Down
27 changes: 26 additions & 1 deletion dpgen2/op/run_lmp.py
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Expand Up @@ -14,6 +14,7 @@
Tuple,
)

import numpy as np
from dargs import (
Argument,
ArgumentEncoder,
Expand All @@ -26,6 +27,7 @@
Artifact,
BigParameter,
FatalError,
HDF5Datasets,
OPIOSign,
TransientError,
)
Expand Down Expand Up @@ -200,7 +202,7 @@
ret_dict = {
"log": work_dir / lmp_log_name,
"traj": work_dir / lmp_traj_name,
"model_devi": work_dir / lmp_model_devi_name,
"model_devi": self.get_model_devi(work_dir / lmp_model_devi_name),
}
plm_output = (
{"plm_output": work_dir / plm_output_name}
Expand All @@ -213,13 +215,17 @@

return OPIO(ret_dict)

def get_model_devi(self, model_devi_file):
return model_devi_file

@staticmethod
def lmp_args():
doc_lmp_cmd = "The command of LAMMPS"
doc_teacher_model = "The teacher model in `Knowledge Distillation`"
doc_shuffle_models = "Randomly pick a model from the group of models to drive theexploration MD simulation"
doc_head = "Select a head from multitask"
doc_use_ele_temp = "Whether to use electronic temperature, 0 for no, 1 for frame temperature, and 2 for atomic temperature"
doc_use_hdf5 = "Use HDF5 to store trajs and model_devis"
return [
Argument("command", str, optional=True, default="lmp", doc=doc_lmp_cmd),
Argument(
Expand All @@ -243,6 +249,13 @@
Argument(
"model_frozen_head", str, optional=True, default=None, doc=doc_head
),
Argument(
"use_hdf5",
bool,
optional=True,
default=False,
doc=doc_use_hdf5,
),
Comment on lines +252 to +258
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⚠️ Potential issue

Implement logic for use_hdf5 in the execute method.

The use_hdf5 parameter is added, but the execute method does not currently utilize it to alter the behavior of the class. Consider implementing conditional logic in the execute method to handle cases when use_hdf5 is True, such as processing outputs differently or initializing RunLmpHDF5.

]

@staticmethod
Expand Down Expand Up @@ -374,3 +387,15 @@
for model_devi_file in sorted(model_devi_files):
with open(model_devi_file, "r") as f2:
f.write(f2.read())


class RunLmpHDF5(RunLmp):
@classmethod
def get_output_sign(cls):
output_sign = super().get_output_sign()
output_sign["traj"] = Artifact(HDF5Datasets)
output_sign["model_devi"] = Artifact(HDF5Datasets)
return output_sign

Check warning on line 398 in dpgen2/op/run_lmp.py

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Added lines #L395 - L398 were not covered by tests

def get_model_devi(self, model_devi_file):
return np.loadtxt(model_devi_file)

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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -17,7 +17,7 @@ classifiers = [
dependencies = [
'numpy',
'dpdata>=0.2.20',
'pydflow>=1.8.88',
'pydflow>=1.8.95',
'dargs>=0.3.1',
'scipy',
'lbg',
Expand Down