Support spin in dpgen2. #265
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📝 WalkthroughWalkthroughThe pull request introduces several new classes and modifies existing functions to enhance the functionality related to LAMMPS spin simulations. A new class, Changes
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Actionable comments posted: 26
🧹 Outside diff range and nitpick comments (7)
dpgen2/exploration/render/__init__.py (1)
7-9: LGTM! Consider adding to__all__for explicitness.The addition of the
TrajRenderLammpsSpinimport aligns with the PR objectives of supporting LAMMPS spin rendering. The import style is consistent with existing imports in the file.To improve explicitness and silence the unused import warning, consider adding
TrajRenderLammpsSpinto an__all__list in this file. If an__all__list doesn't exist yet, it might be beneficial to create one.Here's a suggestion for adding or updating the
__all__list:__all__ = [ 'TrajRender', 'TrajRenderLammps', 'TrajRenderLammpsSpin', ]This change would make it clear which classes are intended to be part of the public API of this package.
🧰 Tools
🪛 Ruff
8-8:
.traj_render_lammps_spin.TrajRenderLammpsSpinimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
tests/exploration/test_report_trust_levels_spin.py (2)
1-28: Consider removing unused imports and using isort for import management.There are several imports flagged as unused by the static analysis tool:
os(line 1)textwrap(line 2)collections.Counter(line 5)context.dpgen2(line 15)dpgen2.exploration.deviation.DeviManager(line 18)dpgen2.exploration.report.report_trust_levels_base.ExplorationReportTrustLevels(line 25)If these imports are truly unused, consider removing them to improve code clarity. However, if they are needed for context or future use, you may want to add a comment explaining their purpose.
Additionally, instead of using manual
# isort: offand# isort: oncomments, consider using anisortconfiguration file to manage import order consistently across the project.🧰 Tools
🪛 Ruff
1-1:
osimported but unusedRemove unused import:
os(F401)
2-2:
textwrapimported but unusedRemove unused import:
textwrap(F401)
5-5:
collections.Counterimported but unusedRemove unused import:
collections.Counter(F401)
15-15:
context.dpgen2imported but unusedRemove unused import:
context.dpgen2(F401)
18-18:
dpgen2.exploration.deviation.DeviManagerimported but unusedRemove unused import:
dpgen2.exploration.deviation.DeviManager(F401)
25-25:
dpgen2.exploration.report.report_trust_levels_base.ExplorationReportTrustLevelsimported but unusedRemove unused import:
dpgen2.exploration.report.report_trust_levels_base.ExplorationReportTrustLevels(F401)
36-86: Theselection_testmethod is comprehensive but could be improved.The
selection_testmethod thoroughly tests theExplorationReportTrustLevelsSpinclass with various input data and assertions. It covers important scenarios such as adding deviation data, checking trajectory classifications, and verifying candidate selection.However, there are a few points to consider:
- The commented-out lists (lines 55-60) seem to be leftover debug code. Consider removing them if they're no longer needed.
- The variable
all_cand_selon line 67 is assigned but never used. Either remove it or clarify its purpose with a comment if it's intended for future use.- Consider adding more descriptive assertion messages to make test failures easier to understand.
To address the unused variable, you can either remove line 67 or add a comment explaining its purpose if it's intended for future use.
🧰 Tools
🪛 Ruff
67-67: Local variable
all_cand_selis assigned to but never usedRemove assignment to unused variable
all_cand_sel(F841)
tests/exploration/test_devi_manager_spin.py (1)
112-112: Simplify f-strings without placeholders.There are two instances of f-strings without placeholders that can be simplified:
- Line 112:
f"Error: the number of frames in"- Line 118:
f"Error: the number of frames in"Apply this diff to simplify the f-strings:
- f"Error: the number of frames in", + "Error: the number of frames in",This change should be applied to both lines 112 and 118.
Also applies to: 118-118
🧰 Tools
🪛 Ruff
112-112: f-string without any placeholders
Remove extraneous
fprefix(F541)
dpgen2/exploration/render/traj_render_lammps_spin.py (1)
64-64: Clarify the handling ofconf_filtersparameterThe
conf_filtersparameter is accepted but not used in theget_confsmethod, and it's immediately deleted with a comment indicating lack of support. To avoid confusion, consider updating the method's documentation to reflect thatconf_filtersaren't currently supported or remove the parameter until support is implemented.If future implementation is planned, you might add a TODO comment:
del conf_filters # by far does not support conf filters + # TODO: Implement support for conf_filtersAlternatively, if there's no intention to support it soon, consider removing the parameter:
def get_confs( self, trajs: List[Path], id_selected: List[List[int]], type_map: Optional[List[str]] = None, - conf_filters: Optional["ConfFilters"] = None, ) -> dpdata.MultiSystems:dpgen2/exploration/report/report_trust_levels_spin.py (1)
93-95: Add a docstring to therecordmethodAdding a docstring to the
recordmethod will improve code readability by clearly explaining its purpose, parameters, and behavior.dpgen2/exploration/task/make_task_group_from_config.py (1)
Line range hint
336-360: Improve Documentation String and ConsistencyIn
doc_lmp_spin, the documentation string should be updated for clarity and grammatical accuracy. Please revise it to:"LAMMPS SPIN tasks defined by templates. Users provide LAMMPS templates and revision keys."
Additionally, consider adding an alias for
"lmp-spin"to maintain consistency with other task types that include aliases.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (14)
- dpgen2/entrypoint/submit.py (3 hunks)
- dpgen2/exploration/deviation/init.py (1 hunks)
- dpgen2/exploration/deviation/deviation_spin.py (1 hunks)
- dpgen2/exploration/render/init.py (1 hunks)
- dpgen2/exploration/render/traj_render_lammps_spin.py (1 hunks)
- dpgen2/exploration/report/init.py (1 hunks)
- dpgen2/exploration/report/report_trust_levels_spin.py (1 hunks)
- dpgen2/exploration/task/init.py (1 hunks)
- dpgen2/exploration/task/lmp_spin_task_group.py (1 hunks)
- dpgen2/exploration/task/make_task_group_from_config.py (4 hunks)
- dpgen2/fp/init.py (2 hunks)
- dpgen2/fp/deltaspin.py (1 hunks)
- tests/exploration/test_devi_manager_spin.py (1 hunks)
- tests/exploration/test_report_trust_levels_spin.py (1 hunks)
🧰 Additional context used
🪛 Ruff
dpgen2/entrypoint/submit.py
85-85:
dpgen2.exploration.task.LmpSpinTaskGroupimported but unusedRemove unused import
(F401)
dpgen2/exploration/deviation/__init__.py
5-5:
.deviation_spin.DeviManagerSpinimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
dpgen2/exploration/deviation/deviation_spin.py
5-5:
typing.Dictimported but unusedRemove unused import:
typing.Dict(F401)
61-61: f-string without any placeholders
Remove extraneous
fprefix(F541)
98-98: f-string without any placeholders
Remove extraneous
fprefix(F541)
dpgen2/exploration/render/__init__.py
8-8:
.traj_render_lammps_spin.TrajRenderLammpsSpinimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
dpgen2/exploration/render/traj_render_lammps_spin.py
8-8:
typing.Tupleimported but unusedRemove unused import
(F401)
9-9:
typing.Unionimported but unusedRemove unused import
(F401)
16-16:
..deviation.DeviManagerimported but unusedRemove unused import:
..deviation.DeviManager(F401)
dpgen2/exploration/report/report_trust_levels_spin.py
1-1:
randomimported but unusedRemove unused import:
random(F401)
3-3:
abc.abstractmethodimported but unusedRemove unused import:
abc.abstractmethod(F401)
175-175: Yoda condition detected
Rewrite as
len(set_accu & set_cand) == 0(SIM300)
176-176: Yoda condition detected
Rewrite as
len(set_accu & set_fail) == 0(SIM300)
177-177: Yoda condition detected
Rewrite as
len(set_cand & set_fail) == 0(SIM300)
243-243: Local variable
max_devi_afis assigned to but never usedRemove assignment to unused variable
max_devi_af(F841)
dpgen2/exploration/task/__init__.py
14-14:
.lmp_spin_task_group.LmpSpinTaskGroupimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
dpgen2/exploration/task/lmp_spin_task_group.py
2-2:
randomimported but unusedRemove unused import:
random(F401)
7-7:
typing.Listimported but unusedRemove unused import:
typing.List(F401)
14-14:
dpgen2.constants.lmp_traj_nameimported but unusedRemove unused import
(F401)
17-17:
dpgen2.constants.plm_output_nameimported but unusedRemove unused import
(F401)
24-24:
.lmp.make_lmp_inputimported but unusedRemove unused import:
.lmp.make_lmp_input(F401)
44-44: Do not use mutable data structures for argument defaults
Replace with
None; initialize within function(B006)
dpgen2/fp/deltaspin.py
6-6:
typing.Dictimported but unusedRemove unused import
(F401)
8-8:
typing.Optionalimported but unusedRemove unused import
(F401)
9-9:
typing.Setimported but unusedRemove unused import
(F401)
11-11:
typing.Unionimported but unusedRemove unused import
(F401)
15-15:
numpyimported but unusedRemove unused import:
numpy(F401)
18-18:
dargs.ArgumentEncoderimported but unusedRemove unused import
(F401)
19-19:
dargs.Variantimported but unusedRemove unused import
(F401)
20-20:
dargs.dargsimported but unusedRemove unused import
(F401)
23-23:
dflow.python.OPimported but unusedRemove unused import
(F401)
24-24:
dflow.python.OPIOimported but unusedRemove unused import
(F401)
25-25:
dflow.python.Artifactimported but unusedRemove unused import
(F401)
26-26:
dflow.python.BigParameterimported but unusedRemove unused import
(F401)
27-27:
dflow.python.FatalErrorimported but unusedRemove unused import
(F401)
28-28:
dflow.python.OPIOSignimported but unusedRemove unused import
(F401)
48-48:
.vasp_input.make_kspacing_kpointsimported but unusedRemove unused import:
.vasp_input.make_kspacing_kpoints(F401)
tests/exploration/test_devi_manager_spin.py
1-1:
osimported but unusedRemove unused import:
os(F401)
4-4:
pathlib.Pathimported but unusedRemove unused import:
pathlib.Path(F401)
11-11:
.context.dpgen2imported but unusedRemove unused import:
.context.dpgen2(F401)
112-112: f-string without any placeholders
Remove extraneous
fprefix(F541)
118-118: f-string without any placeholders
Remove extraneous
fprefix(F541)
tests/exploration/test_report_trust_levels_spin.py
1-1:
osimported but unusedRemove unused import:
os(F401)
2-2:
textwrapimported but unusedRemove unused import:
textwrap(F401)
5-5:
collections.Counterimported but unusedRemove unused import:
collections.Counter(F401)
15-15:
context.dpgen2imported but unusedRemove unused import:
context.dpgen2(F401)
18-18:
dpgen2.exploration.deviation.DeviManagerimported but unusedRemove unused import:
dpgen2.exploration.deviation.DeviManager(F401)
25-25:
dpgen2.exploration.report.report_trust_levels_base.ExplorationReportTrustLevelsimported but unusedRemove unused import:
dpgen2.exploration.report.report_trust_levels_base.ExplorationReportTrustLevels(F401)
67-67: Local variable
all_cand_selis assigned to but never usedRemove assignment to unused variable
all_cand_sel(F841)
🔇 Additional comments (18)
dpgen2/exploration/deviation/__init__.py (1)
4-6: Approve the addition of DeviManagerSpin importThe addition of
DeviManagerSpinimport aligns with the PR objectives to support spin in dpgen2. This is a good addition to enhance the functionality related to spin management.However, the static analysis tool Ruff has flagged an unused import warning. To address this, consider one of the following actions:
If
DeviManagerSpinshould be part of the public API of this package, add it to the__all__list (if one exists) or create an__all__list including this and other public symbols.If
DeviManagerSpinis not needed in this file and is not part of the public API, you may want to remove this import.Let's verify if
DeviManagerSpinis being used elsewhere in the package:This will help determine if the import is necessary for other parts of the package.
✅ Verification successful
Approve the addition of
DeviManagerSpinimportThe addition of
DeviManagerSpinaligns with the PR objectives to support spin in dpgen2. To address the Ruff warning about the unused import, consider addingDeviManagerSpinto the__all__list indpgen2/exploration/deviation/__init__.py. This will explicitly exportDeviManagerSpinas part of the package's public API.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Search for usage of DeviManagerSpin in the package rg "DeviManagerSpin" --type pythonLength of output: 65
Script:
#!/bin/bash # Search for usage of DeviManagerSpin in the package using the correct file type rg "DeviManagerSpin" --type pyLength of output: 5430
🧰 Tools
🪛 Ruff
5-5:
.deviation_spin.DeviManagerSpinimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
dpgen2/exploration/report/__init__.py (3)
13-15: LGTM: New import for spin support added.The import of
ExplorationReportTrustLevelsSpinfrom thereport_trust_levels_spinmodule aligns with the PR objective of adding spin support to dpgen2. This new class will likely be used for handling trust levels associated with spin deviations.
13-20: Summary: Spin support added to exploration report system.The changes in this file successfully integrate spin support into the exploration report system by:
- Importing the new
ExplorationReportTrustLevelsSpinclass.- Adding the new class to the
conv_stylesdictionary with the key"fixed-levels-max-select-spin".These modifications align well with the PR objectives and provide a foundation for handling spin-related trust levels in dpgen2. The implementation appears correct and consistent with the existing structure of the file.
20-20: LGTM: New entry added toconv_stylesdictionary.The addition of
"fixed-levels-max-select-spin": ExplorationReportTrustLevelsSpinto theconv_stylesdictionary makes the new spin-related class available for use in the exploration report system. This change is consistent with the PR's goal of enhancing spin functionality in dpgen2.To ensure the new class is properly implemented, let's verify its existence and basic structure:
dpgen2/exploration/task/__init__.py (1)
13-15: LGTM! Consider addressing the unused import warning.The addition of
LmpSpinTaskGroupaligns with the PR objectives of adding LAMMPS spin support. However, the static analysis tool Ruff has flagged this import as potentially unused.To address this, consider one of the following options:
- Add
LmpSpinTaskGroupto the__all__list if it should be part of the public API.- Use the import within this file if appropriate.
- If the import is needed for type checking, you can add a
# noqa: F401comment to suppress the warning.Let's verify if
LmpSpinTaskGroupis being used elsewhere in the package:This will help determine if the import is necessary for other parts of the package.
🧰 Tools
🪛 Ruff
14-14:
.lmp_spin_task_group.LmpSpinTaskGroupimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
dpgen2/fp/__init__.py (2)
16-19: LGTM: New imports for deltaspin support.The new import statements for
PrepDeltaSpinandRunDeltaSpinfrom the.deltaspinmodule are correctly added and align with the PR objectives of supporting spin in dpgen2.
57-61:⚠️ Potential issueVerify the correct inputs class for deltaspin.
The new entry for "deltaspin" in the
fp_stylesdictionary is mostly correct, but there's a potential issue:
- The "inputs" key is set to
VaspInputs, which seems inconsistent with the deltaspin module.This could lead to errors or unexpected behavior when using the deltaspin functionality.
Consider creating and using a
DeltaSpinInputsclass instead:"deltaspin": { - "inputs": VaspInputs, + "inputs": DeltaSpinInputs, # This class needs to be created "prep": PrepDeltaSpin, "run": RunDeltaSpin, },Make sure to import
DeltaSpinInputsfrom the appropriate module (likely.deltaspin) at the top of the file.To ensure this change doesn't introduce any regressions, please run the following verification script:
tests/exploration/test_report_trust_levels_spin.py (3)
31-33: Test class definition looks good.The test class
TestTrajsExplorationReportSpinis well-defined and follows good naming conventions for test classes. Thetest_exploration_report_trust_levels_spinmethod appropriately callsselection_testandargs_test, which will be defined later in the class.
87-103: Theargs_testmethod effectively tests argument handling.The
args_testmethod does a good job of testing the argument handling ofExplorationReportTrustLevelsSpin. It checks the normalization of input arguments and verifies that the constructor can be called with the normalized data.To further improve this test:
- Consider adding edge cases or invalid inputs to ensure robust error handling.
- You might want to test that the normalized values are actually used by the
ExplorationReportTrustLevelsSpininstance, not just that they can be passed to the constructor.
1-103: Overall, the test file is well-structured and aligns with the PR objectives.This new test file for
ExplorationReportTrustLevelsSpinis a valuable addition that supports the PR's goal of enhancing spin management in dpgen2. The tests cover both the selection logic and argument handling of the new class, which is crucial for ensuring its correct functionality.The test methods are comprehensive and well-thought-out, providing good coverage of the class's behavior. They align well with the PR's objective of introducing support for spin-related features, particularly in the context of LAMMPS simulations.
To further improve the file:
- Address the unused imports and variables as suggested in previous comments.
- Consider expanding the tests to cover more edge cases and error scenarios.
- Add more descriptive assertion messages to make test failures easier to debug.
These improvements will enhance the robustness of the tests and make the code more maintainable in the long run.
🧰 Tools
🪛 Ruff
1-1:
osimported but unusedRemove unused import:
os(F401)
2-2:
textwrapimported but unusedRemove unused import:
textwrap(F401)
5-5:
collections.Counterimported but unusedRemove unused import:
collections.Counter(F401)
15-15:
context.dpgen2imported but unusedRemove unused import:
context.dpgen2(F401)
18-18:
dpgen2.exploration.deviation.DeviManagerimported but unusedRemove unused import:
dpgen2.exploration.deviation.DeviManager(F401)
25-25:
dpgen2.exploration.report.report_trust_levels_base.ExplorationReportTrustLevelsimported but unusedRemove unused import:
dpgen2.exploration.report.report_trust_levels_base.ExplorationReportTrustLevels(F401)
67-67: Local variable
all_cand_selis assigned to but never usedRemove assignment to unused variable
all_cand_sel(F841)
tests/exploration/test_devi_manager_spin.py (5)
22-48: LGTM: Comprehensive test for basic DeviManagerSpin functionality.The
test_successmethod effectively covers the main functionality of theDeviManagerSpinclass:
- Adding deviations for different types (MAX_DEVI_AF and MAX_DEVI_MF).
- Checking the number of trajectories.
- Retrieving and verifying the stored deviations.
- Testing the
clearmethod.- Verifying the behavior for unset deviation types (MAX_DEVI_V).
The assertions are thorough and check for correct behavior in various scenarios.
50-59: LGTM: Proper error handling for invalid deviation names.The
test_add_invalid_namemethod effectively tests the error handling of theDeviManagerSpinclass when an invalid deviation name is provided:
- It attempts to add a deviation with an invalid name "foo".
- It uses
assertRaisesRegexto check for both the exception type (AssertionError) and the specific error message.This test ensures that the
DeviManagerSpinclass properly validates input names before processing them.
61-78: LGTM: Thorough testing of invalid deviation inputs.The
test_add_invalid_deviationmethod effectively tests the error handling of theDeviManagerSpinclass for invalid deviation inputs:
- It checks for an invalid shape by attempting to add a 2D array instead of a 1D array.
- It checks for an invalid type by attempting to add a string instead of a numpy array.
- Both tests use
assertRaisesRegexto verify the exception type and the specific error message.This comprehensive testing ensures that the
DeviManagerSpinclass properly validates both the shape and type of input deviations before processing them.
80-115: LGTM: Comprehensive testing of edge cases and data integrity.The
test_devi_manager_spin_check_datamethod effectively tests various edge cases and error conditions for theDeviManagerSpinclass:
- It checks for inconsistent numbers of trajectories between different deviation types.
- It verifies the behavior when attempting to retrieve a non-existent deviation type.
- It tests for inconsistent numbers of frames between trajectories.
These tests are crucial for ensuring data integrity and proper error handling in the
DeviManagerSpinclass.🧰 Tools
🪛 Ruff
112-112: f-string without any placeholders
Remove extraneous
fprefix(F541)
1-121: Overall: Well-structured and comprehensive test suite for DeviManagerSpin.This test file provides excellent coverage for the
DeviManagerSpinclass:
- It tests basic functionality, including adding, retrieving, and clearing deviations.
- It verifies error handling for invalid inputs (names, shapes, and types).
- It checks edge cases and data integrity, such as inconsistent trajectory and frame counts.
The test methods are well-organized and use appropriate assertions. With the suggested minor improvements (removing unused imports and simplifying f-strings), this test file will be in excellent shape.
🧰 Tools
🪛 Ruff
1-1:
osimported but unusedRemove unused import:
os(F401)
4-4:
pathlib.Pathimported but unusedRemove unused import:
pathlib.Path(F401)
11-11:
.context.dpgen2imported but unusedRemove unused import:
.context.dpgen2(F401)
112-112: f-string without any placeholders
Remove extraneous
fprefix(F541)
118-118: f-string without any placeholders
Remove extraneous
fprefix(F541)
dpgen2/entrypoint/submit.py (1)
382-385: LGTM! New spin support added.The changes introduce support for spin-related functionality in the trajectory rendering process. This aligns well with the PR objective of adding LAMMPS spin rendering support within the DeepSPIN framework. The implementation correctly uses the new
TrajRenderLammpsSpinclass when "spin" is present in theconv_style, falling back to the existingTrajRenderLammpsclass otherwise.dpgen2/exploration/task/make_task_group_from_config.py (2)
22-24: Import Statement forLmpSpinTaskGroupAdded CorrectlyThe import statement appropriately includes
LmpSpinTaskGroupfrom thedpgen2.exploration.task.lmp_spin_task_groupmodule.
696-704: Handling forlmp-spinTask Type Implemented CorrectlyThe implementation for the
lmp-spintask type within themake_lmp_task_group_from_configfunction is consistent with existing task types and appears to be correctly integrated.
| import os | ||
| import unittest | ||
| from pathlib import ( | ||
| Path, | ||
| ) | ||
|
|
||
| import numpy as np | ||
|
|
||
| # isort: off | ||
| from .context import ( | ||
| dpgen2, | ||
| ) | ||
| from dpgen2.exploration.deviation import ( | ||
| DeviManager, | ||
| DeviManagerSpin, | ||
| ) | ||
|
|
||
| # isort: on |
There was a problem hiding this comment.
Remove unused imports to improve code cleanliness.
The following imports are not used in the file and can be removed:
os(line 1)Pathfrompathlib(lines 3-5)dpgen2from.context(lines 10-12)
Apply this diff to remove the unused imports:
-import os
import unittest
-from pathlib import (
- Path,
-)
import numpy as np
# isort: off
from .context import (
- dpgen2,
)
from dpgen2.exploration.deviation import (
DeviManager,
DeviManagerSpin,
)
# isort: on📝 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.
| import os | |
| import unittest | |
| from pathlib import ( | |
| Path, | |
| ) | |
| import numpy as np | |
| # isort: off | |
| from .context import ( | |
| dpgen2, | |
| ) | |
| from dpgen2.exploration.deviation import ( | |
| DeviManager, | |
| DeviManagerSpin, | |
| ) | |
| # isort: on | |
| import unittest | |
| import numpy as np | |
| # isort: off | |
| from .context import ( | |
| ) | |
| from dpgen2.exploration.deviation import ( | |
| DeviManager, | |
| DeviManagerSpin, | |
| ) | |
| # isort: on |
🧰 Tools
🪛 Ruff
1-1:
osimported but unusedRemove unused import:
os(F401)
4-4:
pathlib.Pathimported but unusedRemove unused import:
pathlib.Path(F401)
11-11:
.context.dpgen2imported but unusedRemove unused import:
.context.dpgen2(F401)
| @@ -81,6 +82,7 @@ | |||
| CustomizedLmpTemplateTaskGroup, | |||
| ExplorationStage, | |||
| ExplorationTask, | |||
| LmpSpinTaskGroup, | |||
There was a problem hiding this comment.
💡 Codebase verification
Remove Unused Import LmpSpinTaskGroup
The LmpSpinTaskGroup is imported in dpgen2/entrypoint/submit.py but is not used within this file. Please remove this import to keep the codebase clean and maintainable.
🔗 Analysis chain
Consider removing unused import.
The LmpSpinTaskGroup is imported but not used in this file. Consider removing this import to keep the codebase clean.
To verify if this import is used elsewhere in the codebase, we can run the following script:
If the script doesn't return any results, it's safe to remove the import. Would you like me to remove this unused import?
Update Shell Script to Verify Usage of LmpSpinTaskGroup
The previous script encountered an error because python is not a recognized file type in rg. Please run the updated script below to check if LmpSpinTaskGroup is used elsewhere in the codebase.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if LmpSpinTaskGroup is used in other files
# Search for LmpSpinTaskGroup usage in Python files
rg --type python "LmpSpinTaskGroup" -g '!dpgen2/entrypoint/submit.py'
Length of output: 100
Script:
#!/bin/bash
# Description: Check if LmpSpinTaskGroup is used in other Python files
# Search for LmpSpinTaskGroup usage in Python files, excluding submit.py
rg --type py "LmpSpinTaskGroup" -g '!dpgen2/entrypoint/submit.py'
Length of output: 461
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🪛 Ruff
85-85:
dpgen2.exploration.task.LmpSpinTaskGroupimported but unusedRemove unused import
(F401)
| ntraj = len(trajs) | ||
| traj_fmt = "lammps/dump" | ||
| ms = dpdata.MultiSystems(type_map=type_map) | ||
| for ii in range(ntraj): | ||
| if len(id_selected[ii]) > 0: |
There was a problem hiding this comment.
Ensure trajs and id_selected have matching lengths
In the get_confs method, there's an assumption that trajs and id_selected are lists of the same length, as they are accessed using the same index ii. To prevent potential IndexError exceptions, ensure that both lists are of equal length or handle cases where they might differ.
You might add a validation check at the beginning of the method:
ntraj = len(trajs)
+ if ntraj != len(id_selected):
+ raise ValueError("The lengths of 'trajs' and 'id_selected' must match.")Alternatively, you could iterate using zip to pair elements directly:
for traj, ids in zip(trajs, id_selected):
if len(ids) > 0:
ss = dpdata.System(traj, fmt=traj_fmt, type_map=type_map)
ss.nopbc = self.nopbc
ss = ss.sub_system(ids)
ms.append(ss)This approach inherently handles lists of unequal lengths by stopping at the shortest list's end.
| import numpy as np | ||
|
|
||
| from ..deviation import ( | ||
| DeviManager, |
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Remove unused import DeviManager
The DeviManager import from ..deviation is not utilized in the code. It's best practice to remove such unused imports to reduce clutter and potential confusion.
Apply this diff to remove the unused import:
from ..deviation import (
- DeviManager,
DeviManagerSpin,
)📝 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.
| DeviManager, | |
| from ..deviation import ( | |
| DeviManagerSpin, | |
| ) |
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16-16:
..deviation.DeviManagerimported but unusedRemove unused import:
..deviation.DeviManager(F401)
| Tuple, | ||
| Union, |
There was a problem hiding this comment.
Remove unused imports Tuple and Union
The imports Tuple (line 8) and Union (line 9) from the typing module are not used in the code. Removing unused imports helps keep the code clean and maintain readability.
Apply this diff to remove the unused imports:
from typing import (
TYPE_CHECKING,
List,
Optional,
- Tuple,
- Union,
)📝 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.
| Tuple, | |
| Union, | |
| from typing import ( | |
| TYPE_CHECKING, | |
| List, | |
| Optional, | |
| ) |
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8-8:
typing.Tupleimported but unusedRemove unused import
(F401)
9-9:
typing.Unionimported but unusedRemove unused import
(F401)
| @@ -0,0 +1,300 @@ | |||
| import random | |||
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Remove unused import 'random'
The random module is imported but not used anywhere in the file. Removing unused imports helps keep the code clean and maintainable.
Apply this diff to remove the unused import:
-import random📝 Committable suggestion
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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.
| import random |
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1-1:
randomimported but unusedRemove unused import:
random(F401)
| from abc import ( | ||
| abstractmethod, | ||
| ) |
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Remove unused import 'abstractmethod' from 'abc' module
The abstractmethod decorator is imported from the abc module but is not utilized in this file. It's best practice to remove unused imports to improve code clarity.
Apply this diff to remove the unused import:
-from abc import (
- abstractmethod,
-)📝 Committable suggestion
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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.
| from abc import ( | |
| abstractmethod, | |
| ) |
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3-3:
abc.abstractmethodimported but unusedRemove unused import:
abc.abstractmethod(F401)
| assert 0 == len(set_accu & set_cand) | ||
| assert 0 == len(set_accu & set_fail) | ||
| assert 0 == len(set_cand & set_fail) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Replace Yoda conditions with standard comparison style
Lines 175 to 177 use Yoda conditions (placing the constant before the variable in comparisons), which is unconventional in Python and can reduce readability. It's recommended to place the variable before the constant in assertions.
Apply this diff to rewrite the assertions:
-assert 0 == len(set_accu & set_cand)
-assert 0 == len(set_accu & set_fail)
-assert 0 == len(set_cand & set_fail)
+assert len(set_accu & set_cand) == 0
+assert len(set_accu & set_fail) == 0
+assert len(set_cand & set_fail) == 0📝 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.
| assert 0 == len(set_accu & set_cand) | |
| assert 0 == len(set_accu & set_fail) | |
| assert 0 == len(set_cand & set_fail) | |
| assert len(set_accu & set_cand) == 0 | |
| assert len(set_accu & set_fail) == 0 | |
| assert len(set_cand & set_fail) == 0 |
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175-175: Yoda condition detected
Rewrite as
len(set_accu & set_cand) == 0(SIM300)
176-176: Yoda condition detected
Rewrite as
len(set_accu & set_fail) == 0(SIM300)
177-177: Yoda condition detected
Rewrite as
len(set_cand & set_fail) == 0(SIM300)
| def lmp_spin_task_group_args(): | ||
| doc_lmp_template_fname = "The file name of lammps input template" | ||
| doc_plm_template_fname = "The file name of plumed input template" | ||
| doc_revisions = "The revisions. Should be a dict providing the key - list of desired values pair. Key is the word to be replaced in the templates, and it may appear in both the lammps and plumed input templates. All values in the value list will be enmerated." | ||
|
|
||
| return [ | ||
| Argument("conf_idx", list, optional=False, doc=doc_conf_idx, alias=["sys_idx"]), | ||
| Argument( | ||
| "n_sample", | ||
| int, | ||
| optional=True, | ||
| default=None, | ||
| doc=doc_n_sample, | ||
| ), | ||
| Argument( | ||
| "lmp_template_fname", | ||
| str, | ||
| optional=False, | ||
| doc=doc_lmp_template_fname, | ||
| alias=["lmp_template", "lmp"], | ||
| ), | ||
| Argument( | ||
| "plm_template_fname", | ||
| str, | ||
| optional=True, | ||
| default=None, | ||
| doc=doc_plm_template_fname, | ||
| alias=["plm_template", "plm"], | ||
| ), | ||
| Argument( | ||
| "revisions", | ||
| dict, | ||
| optional=True, | ||
| default={}, | ||
| doc=doc_revisions, | ||
| ), | ||
| ] | ||
|
|
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🛠️ Refactor suggestion
Refactor to Reduce Code Duplication
The lmp_spin_task_group_args() function is very similar to lmp_template_task_group_args(). To adhere to the DRY (Don't Repeat Yourself) principle, consider refactoring common arguments into a shared function or base class. This will enhance maintainability and reduce redundancy.
Typo in Documentation String
There's a minor typo in the documentation string for doc_revisions: "enmerated" should be "enumerated".
Apply this diff to correct the typo:
- doc_revisions = "The revisions. Should be a dict providing the key - list of desired values pair. Key is the word to be replaced in the templates, and it may appear in both the lammps and plumed input templates. All values in the value list will be enmerated."
+ doc_revisions = "The revisions. Should be a dict providing the key - list of desired values pair. Key is the word to be replaced in the templates, and it may appear in both the lammps and plumed input templates. All values in the value list will be enumerated."📝 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.
| def lmp_spin_task_group_args(): | |
| doc_lmp_template_fname = "The file name of lammps input template" | |
| doc_plm_template_fname = "The file name of plumed input template" | |
| doc_revisions = "The revisions. Should be a dict providing the key - list of desired values pair. Key is the word to be replaced in the templates, and it may appear in both the lammps and plumed input templates. All values in the value list will be enmerated." | |
| return [ | |
| Argument("conf_idx", list, optional=False, doc=doc_conf_idx, alias=["sys_idx"]), | |
| Argument( | |
| "n_sample", | |
| int, | |
| optional=True, | |
| default=None, | |
| doc=doc_n_sample, | |
| ), | |
| Argument( | |
| "lmp_template_fname", | |
| str, | |
| optional=False, | |
| doc=doc_lmp_template_fname, | |
| alias=["lmp_template", "lmp"], | |
| ), | |
| Argument( | |
| "plm_template_fname", | |
| str, | |
| optional=True, | |
| default=None, | |
| doc=doc_plm_template_fname, | |
| alias=["plm_template", "plm"], | |
| ), | |
| Argument( | |
| "revisions", | |
| dict, | |
| optional=True, | |
| default={}, | |
| doc=doc_revisions, | |
| ), | |
| ] | |
| def lmp_spin_task_group_args(): | |
| doc_lmp_template_fname = "The file name of lammps input template" | |
| doc_plm_template_fname = "The file name of plumed input template" | |
| doc_revisions = "The revisions. Should be a dict providing the key - list of desired values pair. Key is the word to be replaced in the templates, and it may appear in both the lammps and plumed input templates. All values in the value list will be enumerated." | |
| return [ | |
| Argument("conf_idx", list, optional=False, doc=doc_conf_idx, alias=["sys_idx"]), | |
| Argument( | |
| "n_sample", | |
| int, | |
| optional=True, | |
| default=None, | |
| doc=doc_n_sample, | |
| ), | |
| Argument( | |
| "lmp_template_fname", | |
| str, | |
| optional=False, | |
| doc=doc_lmp_template_fname, | |
| alias=["lmp_template", "lmp"], | |
| ), | |
| Argument( | |
| "plm_template_fname", | |
| str, | |
| optional=True, | |
| default=None, | |
| doc=doc_plm_template_fname, | |
| alias=["plm_template", "plm"], | |
| ), | |
| Argument( | |
| "revisions", | |
| dict, | |
| optional=True, | |
| default={}, | |
| doc=doc_revisions, | |
| ), | |
| ] |
| Path, | ||
| ) | ||
| from typing import ( | ||
| Dict, |
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Remove Unused Imports from typing Module
The following imports from the typing module are unused and can be removed to clean up the code:
Dicton line 6Optionalon line 8Seton line 9Unionon line 11
Apply this diff to remove the unused imports:
from typing import (
- Dict,
List,
- Optional,
- Set,
Tuple,
- Union,
)Also applies to: 8-8, 9-9, 11-11
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6-6:
typing.Dictimported but unusedRemove unused import
(F401)
There was a problem hiding this comment.
- it seems that the lmp_spin task group is very similar to the lmp_template task group. The difference is lmp_spin removes support for the template and restrict the input file to a certain form with restricted functionality. I suggest derive the lmp-spin from lmp-template and support all the functions in the lmp-template, and makes lmp-spin as a template task group, which provides best flexibility to the users.
- vasp delta spin should added via fpop.
- abacus delta spin support should be added via fpop.
- please provide a full set of example inputs, from which anyone may try the functionality.
There was a problem hiding this comment.
should be named as vasp_deltaspin.py
the module is not covered by UT.
| @@ -644,6 +693,15 @@ def make_lmp_task_group_from_config( | |||
| sh_cmd, | |||
| **config, | |||
| ) | |||
| elif config["type"] == "lmp-spin": | |||
There was a problem hiding this comment.
is it a template task group? if so, should be named as lmp-spin-template
There was a problem hiding this comment.
module name up to revision, see my comment on the name of the task group
| self.MAX_DEVI_AF, | ||
| self.MIN_DEVI_AF, | ||
| self.AVG_DEVI_AF, | ||
| self.MAX_DEVI_MF, | ||
| self.MIN_DEVI_MF, | ||
| self.AVG_DEVI_MF, |
There was a problem hiding this comment.
should be added to devi manager.
what is the difference between DeviManager.XXX_DEVI_F and self.XXX_DEVI_AF? they should be referring to the same thing.
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #265 +/- ##
==========================================
- Coverage 83.72% 82.88% -0.84%
==========================================
Files 104 109 +5
Lines 6015 6357 +342
==========================================
+ Hits 5036 5269 +233
- Misses 979 1088 +109 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 3
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- dpgen2/exploration/render/traj_render_lammps_spin.py (1 hunks)
🧰 Additional context used
🪛 Ruff
dpgen2/exploration/render/traj_render_lammps_spin.py
8-8:
typing.Tupleimported but unusedRemove unused import
(F401)
9-9:
typing.Unionimported but unusedRemove unused import
(F401)
16-16:
..deviation.DeviManagerimported but unusedRemove unused import:
..deviation.DeviManager(F401)
| conf_filters: Optional["ConfFilters"] = None, | ||
| ) -> dpdata.MultiSystems: | ||
| del conf_filters # by far does not support conf filters |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider removing the conf_filters parameter if unsupported
The get_confs method accepts a conf_filters parameter but immediately deletes it since it's not supported:
del conf_filters # by far does not support conf filtersIf conf_filters is not intended for future use, consider removing it from the method signature to avoid confusion. If you plan to support it later, you might leave a TODO comment explaining when it will be implemented.
Apply this diff to remove the unused parameter:
def get_confs(
self,
trajs: List[Path],
id_selected: List[List[int]],
type_map: Optional[List[str]] = None,
- conf_filters: Optional["ConfFilters"] = None,
) -> dpdata.MultiSystems:
- del conf_filters # by far does not support conf filters
ntraj = len(trajs)| dd = np.loadtxt(fname) | ||
| model_devi.add(DeviManagerSpin.MAX_DEVI_AF, dd[:, 4]) | ||
| model_devi.add(DeviManagerSpin.MIN_DEVI_AF, dd[:, 5]) | ||
| model_devi.add(DeviManagerSpin.AVG_DEVI_AF, dd[:, 6]) | ||
| model_devi.add(DeviManagerSpin.MAX_DEVI_MF, dd[:, 7]) | ||
| model_devi.add(DeviManagerSpin.MIN_DEVI_MF, dd[:, 8]) | ||
| model_devi.add(DeviManagerSpin.AVG_DEVI_MF, dd[:, 9]) |
There was a problem hiding this comment.
Add validation for the shape of loaded data
In the _load_one_model_devi method, the code assumes that the data loaded from fname has at least 10 columns:
dd = np.loadtxt(fname)
model_devi.add(DeviManagerSpin.MAX_DEVI_AF, dd[:, 4])
model_devi.add(DeviManagerSpin.MIN_DEVI_AF, dd[:, 5])
model_devi.add(DeviManagerSpin.AVG_DEVI_AF, dd[:, 6])
model_devi.add(DeviManagerSpin.MAX_DEVI_MF, dd[:, 7])
model_devi.add(DeviManagerSpin.MIN_DEVI_MF, dd[:, 8])
model_devi.add(DeviManagerSpin.AVG_DEVI_MF, dd[:, 9])If the loaded data does not have the expected number of columns, this will raise an IndexError. Consider adding a validation step to ensure the data has the correct shape before accessing specific columns.
Apply this diff to add data shape validation:
def _load_one_model_devi(self, fname, model_devi):
dd = np.loadtxt(fname)
+ if dd.shape[1] < 10:
+ raise ValueError(f"Expected at least 10 columns in {fname}, but got {dd.shape[1]}")
model_devi.add(DeviManagerSpin.MAX_DEVI_AF, dd[:, 4])
model_devi.add(DeviManagerSpin.MIN_DEVI_AF, dd[:, 5])
model_devi.add(DeviManagerSpin.AVG_DEVI_AF, dd[:, 6])
model_devi.add(DeviManagerSpin.MAX_DEVI_MF, dd[:, 7])
model_devi.add(DeviManagerSpin.MIN_DEVI_MF, dd[:, 8])
model_devi.add(DeviManagerSpin.AVG_DEVI_MF, dd[:, 9])| nopbc: bool = False, | ||
| use_ele_temp: int = 0, | ||
| ): |
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Unused use_ele_temp parameter in __init__ method
The parameter use_ele_temp in the __init__ method is not used within the class. If it's not needed, consider removing it to clean up the code. If you plan to use it in the future, you might want to store it as an instance variable.
Apply this diff to remove the unused parameter:
def __init__(
self,
nopbc: bool = False,
- use_ele_temp: int = 0,
):
self.nopbc = nopbc📝 Committable suggestion
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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.
| nopbc: bool = False, | |
| use_ele_temp: int = 0, | |
| ): | |
| nopbc: bool = False, | |
| ): |
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Actionable comments posted: 3
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (1)
- dpgen2/exploration/render/traj_render_lammps_spin.py (1 hunks)
🧰 Additional context used
🪛 Ruff
dpgen2/exploration/render/traj_render_lammps_spin.py
8-8:
typing.Tupleimported but unusedRemove unused import
(F401)
9-9:
typing.Unionimported but unusedRemove unused import
(F401)
16-16:
..deviation.DeviManagerimported but unusedRemove unused import:
..deviation.DeviManager(F401)
🔇 Additional comments (3)
dpgen2/exploration/render/traj_render_lammps_spin.py (3)
37-47: LGTM: Well-structured method for loading model deviation dataThe
get_model_devimethod is well-implemented. It efficiently initializes aDeviManagerSpininstance and iterates through the provided files to load data using the private_load_one_model_devimethod. This structure promotes code reusability and maintainability.
1-76: Summary: Good implementation of LAMMPS spin support with minor improvements neededThis new file,
traj_render_lammps_spin.py, successfully implements theTrajRenderLammpsSpinclass, which aligns well with the PR objective of supporting spin in dpgen2. The class provides methods for handling LAMMPS spin data, including model deviation calculations and configuration extraction.Key points:
- The implementation supports LAMMPS spin rendering within the DeepSPIN framework, as mentioned in the PR objectives.
- The
get_model_devimethod could potentially be used for reporting trust levels associated with spin deviations, another goal of the PR.- The overall structure and functionality of the class seem well-suited for integrating spin support into the existing dpgen2 framework.
To further improve the code:
- Remove unused imports and parameters as suggested in previous comments.
- Add error handling and data validation in the
_load_one_model_devimethod to enhance robustness.These changes will result in a cleaner, more maintainable implementation that fully supports the PR's objectives for integrating spin functionality into dpgen2.
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8-8:
typing.Tupleimported but unusedRemove unused import
(F401)
9-9:
typing.Unionimported but unusedRemove unused import
(F401)
16-16:
..deviation.DeviManagerimported but unusedRemove unused import:
..deviation.DeviManager(F401)
29-35:⚠️ Potential issueRemove unused parameter in constructor
The
use_ele_tempparameter in the__init__method is not used within the class. If it's not needed, it should be removed to improve code clarity.Apply this diff to remove the unused parameter:
def __init__( self, nopbc: bool = False, - use_ele_temp: int = 0, ): self.nopbc = nopbcLikely invalid or redundant comment.
| def _load_one_model_devi(self, fname, model_devi): | ||
| dd = np.loadtxt(fname) | ||
| model_devi.add(DeviManagerSpin.MAX_DEVI_AF, dd[:, 4]) | ||
| model_devi.add(DeviManagerSpin.MIN_DEVI_AF, dd[:, 5]) | ||
| model_devi.add(DeviManagerSpin.AVG_DEVI_AF, dd[:, 6]) | ||
| model_devi.add(DeviManagerSpin.MAX_DEVI_MF, dd[:, 7]) | ||
| model_devi.add(DeviManagerSpin.MIN_DEVI_MF, dd[:, 8]) | ||
| model_devi.add(DeviManagerSpin.AVG_DEVI_MF, dd[:, 9]) |
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Add error handling and data validation in _load_one_model_devi
The _load_one_model_devi method currently lacks error handling for file loading and doesn't validate the shape of the loaded data. This could lead to unexpected errors if the file is missing, inaccessible, or doesn't have the expected format.
Consider adding error handling and data validation:
- Wrap the
np.loadtxtcall in a try-except block to handle potential file loading errors. - Validate the shape of the loaded data before accessing specific columns.
Here's an example of how you could modify the method:
def _load_one_model_devi(self, fname, model_devi):
try:
dd = np.loadtxt(fname)
if dd.shape[1] < 10:
raise ValueError(f"Expected at least 10 columns in {fname}, but got {dd.shape[1]}")
model_devi.add(DeviManagerSpin.MAX_DEVI_AF, dd[:, 4])
model_devi.add(DeviManagerSpin.MIN_DEVI_AF, dd[:, 5])
model_devi.add(DeviManagerSpin.AVG_DEVI_AF, dd[:, 6])
model_devi.add(DeviManagerSpin.MAX_DEVI_MF, dd[:, 7])
model_devi.add(DeviManagerSpin.MIN_DEVI_MF, dd[:, 8])
model_devi.add(DeviManagerSpin.AVG_DEVI_MF, dd[:, 9])
except Exception as e:
raise RuntimeError(f"Failed to load or process deviation data from {fname}: {e}")This modification will provide more informative error messages and prevent potential index out of bounds errors.
| from pathlib import ( | ||
| Path, | ||
| ) | ||
| from typing import ( | ||
| TYPE_CHECKING, | ||
| List, | ||
| Optional, | ||
| Tuple, | ||
| Union, | ||
| ) | ||
|
|
||
| import dpdata | ||
| import numpy as np | ||
|
|
||
| from ..deviation import ( | ||
| DeviManager, | ||
| DeviManagerSpin, | ||
| ) | ||
| from .traj_render import ( | ||
| TrajRender, | ||
| ) | ||
|
|
||
| if TYPE_CHECKING: | ||
| from dpgen2.exploration.selector import ( | ||
| ConfFilters, | ||
| ) |
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Remove unused imports
There are several unused imports in this file. To improve code cleanliness and reduce potential confusion, please remove the following unused imports:
Apply this diff to remove the unused imports:
from typing import (
TYPE_CHECKING,
List,
Optional,
- Tuple,
- Union,
)
from ..deviation import (
- DeviManager,
DeviManagerSpin,
)📝 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.
| from pathlib import ( | |
| Path, | |
| ) | |
| from typing import ( | |
| TYPE_CHECKING, | |
| List, | |
| Optional, | |
| Tuple, | |
| Union, | |
| ) | |
| import dpdata | |
| import numpy as np | |
| from ..deviation import ( | |
| DeviManager, | |
| DeviManagerSpin, | |
| ) | |
| from .traj_render import ( | |
| TrajRender, | |
| ) | |
| if TYPE_CHECKING: | |
| from dpgen2.exploration.selector import ( | |
| ConfFilters, | |
| ) | |
| from pathlib import ( | |
| Path, | |
| ) | |
| from typing import ( | |
| TYPE_CHECKING, | |
| List, | |
| Optional, | |
| ) | |
| import dpdata | |
| import numpy as np | |
| from ..deviation import ( | |
| DeviManagerSpin, | |
| ) | |
| from .traj_render import ( | |
| TrajRender, | |
| ) | |
| if TYPE_CHECKING: | |
| from dpgen2.exploration.selector import ( | |
| ConfFilters, | |
| ) |
🧰 Tools
🪛 Ruff
8-8:
typing.Tupleimported but unusedRemove unused import
(F401)
9-9:
typing.Unionimported but unusedRemove unused import
(F401)
16-16:
..deviation.DeviManagerimported but unusedRemove unused import:
..deviation.DeviManager(F401)
| def get_confs( | ||
| self, | ||
| trajs: List[Path], | ||
| id_selected: List[List[int]], | ||
| type_map: Optional[List[str]] = None, | ||
| conf_filters: Optional["ConfFilters"] = None, | ||
| optional_outputs: Optional[List[Path]] = None, | ||
| ) -> dpdata.MultiSystems: | ||
| del conf_filters # by far does not support conf filters | ||
| ntraj = len(trajs) | ||
| traj_fmt = "lammps/dump" | ||
| ms = dpdata.MultiSystems(type_map=type_map) | ||
| for ii in range(ntraj): | ||
| if len(id_selected[ii]) > 0: | ||
| ss = dpdata.System(trajs[ii], fmt=traj_fmt, type_map=type_map) | ||
| ss.nopbc = self.nopbc | ||
| ss = ss.sub_system(id_selected[ii]) | ||
| ms.append(ss) | ||
| return ms |
There was a problem hiding this comment.
Remove unused parameter and LGTM for get_confs method
The get_confs method is well-implemented overall, efficiently processing trajectory files and creating subsystems based on selected IDs. However, there's an unused parameter that should be addressed.
- Remove the unused
conf_filtersparameter:
def get_confs(
self,
trajs: List[Path],
id_selected: List[List[int]],
type_map: Optional[List[str]] = None,
- conf_filters: Optional["ConfFilters"] = None,
optional_outputs: Optional[List[Path]] = None,
) -> dpdata.MultiSystems:
- del conf_filters # by far does not support conf filters-
The rest of the method looks good. It correctly initializes a
MultiSystemsobject, iterates through the trajectories, and creates subsystems based on the selected IDs. -
The use of
dpdata.Systemanddpdata.MultiSystemsseems appropriate for handling the trajectory data. -
The
nopbcattribute is correctly set for each system.
Overall, once the unused parameter is removed, this method will be clean and effective.
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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.
| def get_confs( | |
| self, | |
| trajs: List[Path], | |
| id_selected: List[List[int]], | |
| type_map: Optional[List[str]] = None, | |
| conf_filters: Optional["ConfFilters"] = None, | |
| optional_outputs: Optional[List[Path]] = None, | |
| ) -> dpdata.MultiSystems: | |
| del conf_filters # by far does not support conf filters | |
| ntraj = len(trajs) | |
| traj_fmt = "lammps/dump" | |
| ms = dpdata.MultiSystems(type_map=type_map) | |
| for ii in range(ntraj): | |
| if len(id_selected[ii]) > 0: | |
| ss = dpdata.System(trajs[ii], fmt=traj_fmt, type_map=type_map) | |
| ss.nopbc = self.nopbc | |
| ss = ss.sub_system(id_selected[ii]) | |
| ms.append(ss) | |
| return ms | |
| def get_confs( | |
| self, | |
| trajs: List[Path], | |
| id_selected: List[List[int]], | |
| type_map: Optional[List[str]] = None, | |
| optional_outputs: Optional[List[Path]] = None, | |
| ) -> dpdata.MultiSystems: | |
| ntraj = len(trajs) | |
| traj_fmt = "lammps/dump" | |
| ms = dpdata.MultiSystems(type_map=type_map) | |
| for ii in range(ntraj): | |
| if len(id_selected[ii]) > 0: | |
| ss = dpdata.System(trajs[ii], fmt=traj_fmt, type_map=type_map) | |
| ss.nopbc = self.nopbc | |
| ss = ss.sub_system(id_selected[ii]) | |
| ms.append(ss) | |
| return ms |
| ) | ||
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| class TrajRenderLammpsSpin(TrajRender): |
There was a problem hiding this comment.
Perhaps you can derive TrajRenderLammpsSpin from TrajRenderLammps, overriding only necessary methods, so that it can inherit new features from TrajRenderLammps.
| ) | ||
|
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||
| class LmpSpinTaskGroup(ConfSamplingTaskGroup): |
There was a problem hiding this comment.
What is the difference between LmpSpinTaskGroup and LmpTemplateTaskGroup? Why revise_lmp_input_model is not needed in LmpSpinTaskGroup?
Summary by CodeRabbit
Release Notes
New Features
TrajRenderLammpsSpinfor enhanced trajectory rendering of LAMMPS spin data.DeviManagerSpinfor managing deviations specific to the DeepSPIN model.ExplorationReportTrustLevelsSpinfor reporting trust levels in exploration processes.LmpSpinTaskGroupfor managing LAMMPS SPIN simulation tasks.PrepDeltaSpinandRunDeltaSpinfor DeltaSpin task management.Bug Fixes
Tests
DeviManagerSpinandExplorationReportTrustLevelsSpinto ensure functionality and data integrity.