Use Github Co-pilot to add Docstrings and Type Hints #316
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Warning Rate limit exceeded@jan-janssen has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait 14 minutes and 52 seconds before requesting another review. How to resolve this issue?After the wait time has elapsed, a review can be triggered using the We recommend that you space out your commits to avoid hitting the rate limit. How do rate limits work?CodeRabbit enforces hourly rate limits for each developer per organization. Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout. Please see our FAQ for further information. WalkthroughThe recent updates significantly enhance the codebase by improving documentation and type annotations across various modules. Comprehensive docstrings have been added to functions and classes, clarifying their purposes and usage. Type hints were introduced for better type safety, particularly in testing, scientific calculations, and structure optimization, making the code more maintainable and user-friendly. Changes
Sequence Diagram(s)sequenceDiagram
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participant Tests
User->>CodeBase: Run Tests
CodeBase->>Tests: Execute unittest
Tests->>CodeBase: Return test results
CodeBase->>User: Show test results
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Actionable comments posted: 18
Outside diff range, codebase verification and nitpick comments (1)
atomistics/workflows/quasiharmonic.py (1)
Line range hint
749-768: Fix undefined nameThermal.The name
Thermalis not defined in theget_thermal_propertiesmethod. Ensure thatThermalis imported or defined appropriately.
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (24)
- .vscode/settings.json (1 hunks)
- atomistics/calculators/ase.py (8 hunks)
- atomistics/calculators/hessian.py (7 hunks)
- atomistics/calculators/interface.py (1 hunks)
- atomistics/calculators/qe.py (6 hunks)
- atomistics/shared/output.py (1 hunks)
- atomistics/shared/thermal_expansion.py (1 hunks)
- atomistics/shared/tqdm_iterator.py (1 hunks)
- atomistics/workflows/elastic/elastic_moduli.py (5 hunks)
- atomistics/workflows/elastic/helper.py (5 hunks)
- atomistics/workflows/elastic/symmetry.py (5 hunks)
- atomistics/workflows/elastic/workflow.py (3 hunks)
- atomistics/workflows/evcurve/debye.py (10 hunks)
- atomistics/workflows/evcurve/fit.py (17 hunks)
- atomistics/workflows/evcurve/helper.py (10 hunks)
- atomistics/workflows/evcurve/thermo.py (21 hunks)
- atomistics/workflows/evcurve/workflow.py (4 hunks)
- atomistics/workflows/interface.py (1 hunks)
- atomistics/workflows/langevin.py (5 hunks)
- atomistics/workflows/molecular_dynamics.py (1 hunks)
- atomistics/workflows/phonons/helper.py (16 hunks)
- atomistics/workflows/phonons/workflow.py (10 hunks)
- atomistics/workflows/quasiharmonic.py (15 hunks)
- atomistics/workflows/structure_optimization.py (1 hunks)
Files skipped from review due to trivial changes (7)
- .vscode/settings.json
- atomistics/calculators/interface.py
- atomistics/shared/thermal_expansion.py
- atomistics/shared/tqdm_iterator.py
- atomistics/workflows/interface.py
- atomistics/workflows/molecular_dynamics.py
- atomistics/workflows/structure_optimization.py
Additional context used
Ruff
atomistics/workflows/elastic/helper.py
147-147: Undefined name
List(F821)
147-147: Undefined name
List(F821)
147-147: Undefined name
Optional(F821)
atomistics/workflows/langevin.py
155-155: Undefined name
Dict(F821)
155-155: Undefined name
Dict(F821)
188-188: Undefined name
Dict(F821)
188-188: Undefined name
Dict(F821)
atomistics/calculators/hessian.py
209-209: Undefined name
Union(F821)
atomistics/workflows/evcurve/helper.py
108-108: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
351-351: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
atomistics/workflows/evcurve/debye.py
354-354: Undefined name
Dict(F821)
354-354: Undefined name
List(F821)
atomistics/workflows/evcurve/thermo.py
19-19: Undefined name
Optional(F821)
20-20: Undefined name
Optional(F821)
21-21: Undefined name
Optional(F821)
22-22: Undefined name
Optional(F821)
23-23: Undefined name
Optional(F821)
24-24: Undefined name
Optional(F821)
444-444: Undefined name
plt(F821)
494-494: Undefined name
DebyeModel(F821)
atomistics/workflows/elastic/elastic_moduli.py
304-304: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
314-314: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
324-324: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
334-334: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
344-344: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
356-356: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
369-369: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
382-382: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
395-395: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
408-408: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
421-421: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
434-434: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
446-446: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
458-458: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
471-471: Use of
functools.lru_cacheorfunctools.cacheon methods can lead to memory leaks(B019)
atomistics/calculators/ase.py
198-198: Do not perform function call
OutputStatic.keysin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
212-212: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
267-267: Undefined name
Calculator(F821)
273-273: Do not use mutable data structures for argument defaults
Replace with
None; initialize within function(B006)
369-369: Do not perform function call
OutputThermalExpansion.keysin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
427-427: Do not perform function call
np.arrayin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
428-428: Do not perform function call
OutputMolecularDynamics.keysin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
495-495: Loop control variable
inot used within loop bodyRename unused
ito_i(B007)
501-501: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
atomistics/workflows/phonons/helper.py
450-450: Undefined name
matplotlib(F821)
452-452: Undefined name
matplotlib(F821)
533-533: Undefined name
matplotlib(F821)
537-537: Undefined name
matplotlib(F821)
atomistics/workflows/quasiharmonic.py
250-250: Loop control variable
tnot used within loop bodyRename unused
tto_t(B007)
252-252: Loop control variable
wnot used within loop bodyRename unused
wto_w(B007)
749-749: Undefined name
Thermal(F821)
Additional comments not posted (106)
atomistics/workflows/elastic/workflow.py (3)
21-30: Docstring addition looks good.The docstring clearly describes the purpose of each argument and their default values.
44-47: Docstring addition looks good.The docstring clearly describes the return value of the method.
62-70: Docstring addition looks good.The docstring clearly describes the parameters and the return value of the method.
atomistics/shared/output.py (2)
11-17: Docstring and type hint addition look good.The docstring clearly describes the return value of the method, and the type hint improves type clarity.
21-29: Docstring and type hint addition look good.The docstring clearly describes the parameters and the return value of the method, and the type hint improves type clarity.
atomistics/workflows/evcurve/workflow.py (4)
29-40: Docstring addition looks good.The docstring clearly describes the purpose of each argument and their default values.
63-66: Docstring addition looks good.The docstring clearly describes the return value of the method.
82-91: Docstring addition looks good.The docstring clearly describes the parameters and the return value of the method.
110-123: Docstring addition looks good.The docstring clearly describes the parameters and the return value of the method.
atomistics/workflows/elastic/helper.py (4)
23-35: Docstring and Type Hints ApprovedThe added type hints and expanded docstring for
generate_structures_helperimprove clarity and maintainability.
108-121: Docstring and Type Hints ApprovedThe added type hints and expanded docstring for
analyse_structures_helperimprove clarity and maintainability.
187-196: Docstring and Type Hints ApprovedThe added type hints and expanded docstring for
_subjob_nameimprove clarity and maintainability.
202-214: Docstring and Type Hints ApprovedThe added type hints and expanded docstring for
_fit_elastic_matriximprove clarity and maintainability.atomistics/workflows/langevin.py (4)
18-28: Docstring and Type Hints ApprovedThe added type hints and expanded docstring for
langevin_delta_vimprove clarity and maintainability.
48-57: Docstring and Type Hints ApprovedThe added type hints and expanded docstring for
convert_to_accelerationimprove clarity and maintainability.
64-74: Docstring and Type Hints ApprovedThe added type hints and expanded docstring for
get_initial_velocitiesimprove clarity and maintainability.
87-98: Docstring and Type Hints ApprovedThe added type hints and expanded docstring for
get_first_half_stepimprove clarity and maintainability.atomistics/calculators/hessian.py (6)
10-22: Docstring ApprovedThe expanded docstring for
check_force_constantsimproves clarity and maintainability.
53-62: Docstring ApprovedThe expanded docstring for
get_displacementimproves clarity and maintainability.
71-82: Docstring and Type Hints ApprovedThe added type hints and expanded docstring for
calc_forces_transformedimprove clarity and maintainability.
94-105: Docstring ApprovedThe expanded docstring for
get_forcesimproves clarity and maintainability.
121-133: Docstring ApprovedThe expanded docstring for
get_energy_potimproves clarity and maintainability.
153-163: Docstring ApprovedThe expanded docstring for
get_stiffness_tensorimproves clarity and maintainability.atomistics/workflows/phonons/workflow.py (11)
46-60: Docstring and type hints added to__init__method.The added type hints and detailed docstring improve the clarity and maintainability of the code.
72-77: Docstring added togenerate_structuresmethod.The added docstring accurately describes the method's functionality and return type.
92-99: Docstring added toanalyse_structuresmethod.The added docstring accurately describes the method's functionality, arguments, and return type.
115-137: Docstring and type hints added toget_thermal_propertiesmethod.The added type hints and detailed docstring improve the clarity and maintainability of the code.
154-160: Docstring and return type hint added toget_dynamical_matrixmethod.The added return type hint and detailed docstring improve the clarity and maintainability of the code.
174-180: Docstring added todynamical_matrix_at_qmethod.The added docstring accurately describes the method's functionality, arguments, and return type.
185-192: Docstring and type hints added towrite_phonopy_force_constantsmethod.The added type hints and detailed docstring improve the clarity and maintainability of the code.
201-206: Docstring added toget_hesse_matrixmethod.The added docstring accurately describes the method's functionality and return type.
215-225: Docstring added toget_band_structuremethod.The added docstring accurately describes the method's functionality, arguments, and return type.
236-245: Docstring added toplot_band_structuremethod.The added docstring accurately describes the method's functionality, arguments, and return type.
265-273: Docstring added toplot_dosmethod.The added docstring accurately describes the method's functionality, arguments, and return type.
atomistics/workflows/evcurve/helper.py (10)
14-33: Docstring and error handling added to_strain_axesfunction.The added docstring and improved error handling enhance the clarity and robustness of the code.
Line range hint
39-68:
Docstring and type hints added toapply_strainfunction.The added type hints and detailed docstring improve the clarity and maintainability of the code.
96-107: Docstring and return type hint added toget_energy_lstfunction.The added return type hint and detailed docstring improve the clarity and maintainability of the code.
111-121: Docstring and return type hint added toget_volume_lstfunction.The added return type hint and detailed docstring improve the clarity and maintainability of the code.
128-140: Docstring and return type hint added tofit_ev_curve_internalfunction.The added return type hint and detailed docstring improve the clarity and maintainability of the code.
152-164: Docstring and return type hint added tofit_ev_curvefunction.The added return type hint and detailed docstring improve the clarity and maintainability of the code.
178-192: Docstring and error handling added toget_strainsfunction.The added docstring and improved error handling enhance the clarity and robustness of the code.
214-230: Docstring and error handling added togenerate_structures_helperfunction.The added docstring and improved error handling enhance the clarity and robustness of the code.
249-264: Docstring added toanalyse_structures_helperfunction.The added docstring accurately describes the function's functionality, arguments, and return type.
278-284: Docstring and type hint added toEnergyVolumeCurvePropertiesclass constructor.The added type hint and detailed docstring improve the clarity and maintainability of the code.
atomistics/calculators/qe.py (5)
19-25: Docstring and type hint added to__init__method.The added type hint and detailed docstring improve the clarity and maintainability of the code.
29-34: Docstring and return type hint added toforcesmethod.The added return type hint and detailed docstring improve the clarity and maintainability of the code.
38-43: Docstring and return type hint added toenergymethod.The added return type hint and detailed docstring improve the clarity and maintainability of the code.
47-52: Docstring and return type hint added tostressmethod.The added return type hint and detailed docstring improve the clarity and maintainability of the code.
56-61: Docstring and return type hint added tovolumemethod.The added return type hint and detailed docstring improve the clarity and maintainability of the code
atomistics/workflows/elastic/symmetry.py (4)
24-32: Docstring forfind_symmetry_group_numberis accurate.The added docstring correctly describes the function's purpose, parameters, and return value.
88-96: Docstring forget_symmetry_family_from_SGNis accurate.The added docstring correctly describes the function's purpose, parameters, and return value.
125-133: Docstring forget_LAG_Strain_Listis accurate.The added docstring correctly describes the function's purpose, parameters, and return value.
367-380: Docstring and return type forsymmetry_analysisare accurate.The added docstring correctly describes the function's purpose, parameters, and return value. The return type hint is also accurate.
atomistics/workflows/evcurve/debye.py (12)
22-34: Docstring for__init__method inDebyeThermalPropertiesis accurate.The added docstring correctly describes the method's purpose, parameters, and default values.
48-53: Docstring forfree_energymethod inDebyeThermalPropertiesis accurate.The added docstring correctly describes the method's purpose and return value.
60-65: Docstring fortemperaturesmethod inDebyeThermalPropertiesis accurate.The added docstring correctly describes the method's purpose and return value.
69-74: Docstring forentropymethod inDebyeThermalPropertiesis accurate.The added docstring correctly describes the method's purpose and return value.
89-94: Docstring forheat_capacitymethod inDebyeThermalPropertiesis accurate.The added docstring correctly describes the method's purpose and return value.
110-115: Docstring forvolumesmethod inDebyeThermalPropertiesis accurate.The added docstring correctly describes the method's purpose and return value.
123-131: Docstring for_debye_kernelmethod inDebyeThermalPropertiesis accurate.The added docstring correctly describes the method's purpose, parameters, and return value.
169-176: Docstring for__init__method inDebyeModelis accurate.The added docstring correctly describes the method's purpose, parameters, and default values.
260-268: Docstring forinterpolatemethod inDebyeModelis accurate.The added docstring correctly describes the method's purpose, parameters, and return value.
275-280: Docstring fordebye_temperaturemethod inDebyeModelis accurate.The added docstring correctly describes the method's purpose and return value.
321-331: Docstring forenergy_vibmethod inDebyeModelis accurate.The added docstring correctly describes the method's purpose, parameters, and return value.
381-397: Docstring forget_thermal_propertiesis accurate.The added docstring correctly describes the function's purpose, parameters, and return value.
atomistics/workflows/evcurve/thermo.py (8)
28-33: Return type hint forcopymethod inThermoBulkis accurate.The added return type hint correctly indicates that the method returns an instance of
ThermoBulk.
54-57: Return type hint fornum_atomsmethod inThermoBulkis accurate.The added return type hint correctly indicates that the method returns an integer.
74-79: Return type hint for_coeffmethod inThermoBulkis accurate.The added return type hint correctly indicates that the method returns a numpy array.
86-89: Return type hint fortemperaturesmethod inThermoBulkis accurate.The added return type hint correctly indicates that the method returns a numpy array.
96-99: Return type hint for_d_tempmethod inThermoBulkis accurate.The added return type hint correctly indicates that the method returns a float.
106-109: Return type hint for_d_volmethod inThermoBulkis accurate.The added return type hint correctly indicates that the method returns a float.
133-136: Return type hint forvolumesmethod inThermoBulkis accurate.The added return type hint correctly indicates that the method returns a numpy array.
160-163: Return type hint forentropymethod inThermoBulkis accurate.The added return type hint correctly indicates that the method returns a numpy array.
atomistics/workflows/evcurve/fit.py (8)
14-26: Docstring and type hints are well-defined.The docstring and type hints for the
birchmurnaghan_energyfunction are clear and provide useful information about the function's purpose, parameters, and return value.
36-48: Docstring and type hints are well-defined.The docstring and type hints for the
vinet_energyfunction are clear and provide useful information about the function's purpose, parameters, and return value.
56-68: Docstring and type hints are well-defined.The docstring and type hints for the
murnaghanfunction are clear and provide useful information about the function's purpose, parameters, and return value.
99-111: Docstring and type hints are well-defined.The docstring and type hints for the
pouriertarantolafunction are clear and provide useful information about the function's purpose, parameters, and return value.
153-162: Docstring and type hints are well-defined.The docstring and type hints for the
interpolate_energyfunction are clear and provide useful information about the function's purpose, parameters, and return value.
476-485: Docstring and type hints are well-defined.The docstring and type hints for the
fitfunction in theEnergyVolumeFitclass are clear and provide useful information about the function's purpose, parameters, and return value.
534-544: Docstring and type hints are well-defined.The docstring and type hints for the
fit_polynomialfunction in theEnergyVolumeFitclass are clear and provide useful information about the function's purpose, parameters, and return value.
667-677: Docstring and type hints are well-defined.The docstring and type hints for the
get_energy_volume_curve_fitfunction are clear and provide useful information about the function's purpose, parameters, and return value.atomistics/workflows/quasiharmonic.py (16)
38-47: Docstring and type hints are well-defined.The docstring and type hints for the
get_free_energy_classicalfunction are clear and provide useful information about the function's purpose, parameters, and return value.
70-92: Docstring and type hints are well-defined.The docstring and type hints for the
get_thermal_propertiesfunction are clear and provide useful information about the function's purpose, parameters, and return value.
183-199: Docstring and type hints are well-defined.The docstring and type hints for the
_get_thermal_properties_quantum_mechanicalfunction are clear and provide useful information about the function's purpose, parameters, and return value.
225-240: Docstring and type hints are well-defined.The docstring and type hints for the
_get_thermal_properties_classicalfunction are clear and provide useful information about the function's purpose, parameters, and return value.
443-452: Docstring and type hints are well-defined.The docstring and type hints for the
__init__method in theQuasiHarmonicThermalPropertiesclass are clear and provide useful information about the method's purpose, parameters, and return value.
460-468: Docstring and type hints are well-defined.The docstring and type hints for the
get_propertymethod in theQuasiHarmonicThermalPropertiesclass are clear and provide useful information about the method's purpose, parameters, and return value.
494-499: Docstring and type hints are well-defined.The docstring and type hints for the
temperaturesmethod in theQuasiHarmonicThermalPropertiesclass are clear and provide useful information about the method's purpose and return value.
503-508: Docstring and type hints are well-defined.The docstring and type hints for the
entropymethod in theQuasiHarmonicThermalPropertiesclass are clear and provide useful information about the method's purpose and return value.
512-517: Docstring and type hints are well-defined.The docstring and type hints for the
heat_capacitymethod in theQuasiHarmonicThermalPropertiesclass are clear and provide useful information about the method's purpose and return value.
521-526: Docstring and type hints are well-defined.The docstring and type hints for the
volumesmethod in theQuasiHarmonicThermalPropertiesclass are clear and provide useful information about the method's purpose and return value.
540-559: Docstring and type hints are well-defined.The docstring and type hints for the
generate_structures_helperfunction are clear and provide useful information about the function's purpose, parameters, and return value.
603-618: Docstring and type hints are well-defined.The docstring and type hints for the
analyse_structures_helperfunction are clear and provide useful information about the function's purpose, parameters, and return value.
648-663: Docstring and type hints are well-defined.The docstring and type hints for the
__init__method in theQuasiHarmonicWorkflowclass are clear and provide useful information about the method's purpose, parameters, and return value.
684-689: Docstring and type hints are well-defined.The docstring and type hints for the
generate_structuresmethod in theQuasiHarmonicWorkflowclass are clear and provide useful information about the method's purpose and return value.
715-727: Docstring and type hints are well-defined.The docstring and type hints for the
analyse_structuresmethod in theQuasiHarmonicWorkflowclass are clear and provide useful information about the method's purpose, parameters, and return value.
485-490: Fix typo in parameter name.The parameter name
thermal_propertyshould be consistent with the rest of the code.- return self.get_property(thermal_property="free_energy") + return self.get_property("free_energy")Likely invalid or redundant comment.
atomistics/workflows/elastic/elastic_moduli.py (3)
243-254: LGTM!The type hint and docstring improve the clarity and usability of the function.
286-292: LGTM!The type hint and docstring improve the clarity and usability of the constructor.
472-478: LGTM!The type hint and docstring improve the clarity and usability of the method.
atomistics/calculators/ase.py (4)
27-34: LGTM!The type hints and docstring improve the clarity and usability of the constructor.
154-166: LGTM!The type hint and docstring improve the clarity and usability of the function.
217-239: LGTM!The type hint and docstring improve the clarity and usability of the function.
241-263: LGTM!The type hint and docstring improve the clarity and usability of the function.
atomistics/workflows/phonons/helper.py (2)
18-51: LGTM!The type hints and docstring improve the clarity and usability of the constructor.
265-284: LGTM!The type hints and docstring improve the clarity and usability of the method.
| ) -> Tuple[np.ndarray, np.ndarray, List[List[Tuple[float, float]]], Optional[float]]: | ||
| """ | ||
| Calculate the elastic matrix and other properties. | ||
|
|
||
| Args: | ||
| output_dict (dict): | ||
| output (tuple): | ||
| output_dict (dict): The dictionary containing the output data. | ||
| Lag_strain_list (list[float]): The list of Lagrangian strains. | ||
| epss (float): The list of strains. | ||
| v0 (float): The volume of the unit cell. | ||
| LC (str): The lattice constant. | ||
| fit_order (int, optional): The order of the polynomial fit. Defaults to 2. | ||
| zero_strain_job_name (str, optional): The name of the zero strain job. Defaults to "s_e_0". | ||
|
|
||
| Returns: | ||
|
|
||
| Tuple[np.ndarray, np.ndarray, List[List[Tuple[float, float]]], Optional[float]]: A tuple containing the elastic matrix, A2 coefficients, strain energy data, and ene0 value. |
There was a problem hiding this comment.
Fix Undefined Names
The type hints List and Optional are used but not imported. Add the necessary imports from the typing module.
+ from typing import List, OptionalCommittable 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[np.ndarray, np.ndarray, List[List[Tuple[float, float]]], Optional[float]]: | |
| """ | |
| Calculate the elastic matrix and other properties. | |
| Args: | |
| output_dict (dict): | |
| output (tuple): | |
| output_dict (dict): The dictionary containing the output data. | |
| Lag_strain_list (list[float]): The list of Lagrangian strains. | |
| epss (float): The list of strains. | |
| v0 (float): The volume of the unit cell. | |
| LC (str): The lattice constant. | |
| fit_order (int, optional): The order of the polynomial fit. Defaults to 2. | |
| zero_strain_job_name (str, optional): The name of the zero strain job. Defaults to "s_e_0". | |
| Returns: | |
| Tuple[np.ndarray, np.ndarray, List[List[Tuple[float, float]]], Optional[float]]: A tuple containing the elastic matrix, A2 coefficients, strain energy data, and ene0 value. | |
| + from typing import List, Optional | |
| ) -> Tuple[np.ndarray, np.ndarray, List[List[Tuple[float, float]]], Optional[float]]: | |
| """ | |
| Calculate the elastic matrix and other properties. | |
| Args: | |
| output_dict (dict): The dictionary containing the output data. | |
| Lag_strain_list (list[float]): The list of Lagrangian strains. | |
| epss (float): The list of strains. | |
| v0 (float): The volume of the unit cell. | |
| LC (str): The lattice constant. | |
| fit_order (int, optional): The order of the polynomial fit. Defaults to 2. | |
| zero_strain_job_name (str, optional): The name of the zero strain job. Defaults to "s_e_0". | |
| Returns: | |
| Tuple[np.ndarray, np.ndarray, List[List[Tuple[float, float]]], Optional[float]]: A tuple containing the elastic matrix, A2 coefficients, strain energy data, and ene0 value. |
Tools
Ruff
147-147: Undefined name
List(F821)
147-147: Undefined name
List(F821)
147-147: Undefined name
Optional(F821)
| def analyse_structures(self, output_dict: Dict[str, Dict[int, Atoms]]): | ||
| """ | ||
| Analyzes the structures generated in the Langevin dynamics simulation. | ||
|
|
||
| Args: | ||
| output_dict (dict): A dictionary containing the output structures. | ||
|
|
||
| Returns: | ||
| tuple: A tuple containing the potential energy and kinetic energy. | ||
| """ |
There was a problem hiding this comment.
Fix Undefined Names
The type hint Dict is used but not imported. Add the necessary import from the typing module.
+ from typing import DictCommittable 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 analyse_structures(self, output_dict: Dict[str, Dict[int, Atoms]]): | |
| """ | |
| Analyzes the structures generated in the Langevin dynamics simulation. | |
| Args: | |
| output_dict (dict): A dictionary containing the output structures. | |
| Returns: | |
| tuple: A tuple containing the potential energy and kinetic energy. | |
| """ | |
| + from typing import Dict | |
| def analyse_structures(self, output_dict: Dict[str, Dict[int, Atoms]]): | |
| """ | |
| Analyzes the structures generated in the Langevin dynamics simulation. | |
| Args: | |
| output_dict (dict): A dictionary containing the output structures. | |
| Returns: | |
| tuple: A tuple containing the potential energy and kinetic energy. | |
| """ |
Tools
Ruff
188-188: Undefined name
Dict(F821)
188-188: Undefined name
Dict(F821)
| def generate_structures(self) -> Dict[str, Dict[int, Atoms]]: | ||
| """ | ||
| Generates the structures for the Langevin dynamics simulation. | ||
|
|
||
| Returns: | ||
| (dict) | ||
| dict: A dictionary containing the generated structures. |
There was a problem hiding this comment.
Fix Undefined Names
The type hint Dict is used but not imported. Add the necessary import from the typing module.
+ from typing import DictCommittable 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 generate_structures(self) -> Dict[str, Dict[int, Atoms]]: | |
| """ | |
| Generates the structures for the Langevin dynamics simulation. | |
| Returns: | |
| (dict) | |
| dict: A dictionary containing the generated structures. | |
| + from typing import Dict | |
| def generate_structures(self) -> Dict[str, Dict[int, Atoms]]: | |
| """ | |
| Generates the structures for the Langevin dynamics simulation. | |
| Returns: | |
| dict: A dictionary containing the generated structures. |
Tools
Ruff
155-155: Undefined name
Dict(F821)
155-155: Undefined name
Dict(F821)
| """ | ||
| Convert the EnergyVolumeCurveProperties object to a dictionary. | ||
|
|
||
| Args: | ||
| output_keys (tuple, optional): The keys to include in the output dictionary. | ||
| Defaults to OutputEnergyVolumeCurve.keys(). | ||
|
|
||
| Returns: | ||
| dict: The converted dictionary. | ||
| """ |
There was a problem hiding this comment.
Docstring added to to_dict method.
The added docstring accurately describes the method's functionality, arguments, and return type.
Remove unnecessary .keys() call.
The .keys() call is redundant and can be removed as suggested by the static analysis tool.
- **{k: getattr(self, k) for k in OutputEnergyVolumeCurve.keys()}
+ **{k: getattr(self, k) for k in OutputEnergyVolumeCurve}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.
| """ | |
| Convert the EnergyVolumeCurveProperties object to a dictionary. | |
| Args: | |
| output_keys (tuple, optional): The keys to include in the output dictionary. | |
| Defaults to OutputEnergyVolumeCurve.keys(). | |
| Returns: | |
| dict: The converted dictionary. | |
| """ | |
| """ | |
| Convert the EnergyVolumeCurveProperties object to a dictionary. | |
| Args: | |
| output_keys (tuple, optional): The keys to include in the output dictionary. | |
| Defaults to OutputEnergyVolumeCurve.keys(). | |
| Returns: | |
| dict: The converted dictionary. | |
| """ |
| ) -> dict[str, Union[float, np.ndarray]]: | ||
| """ | ||
| Evaluate the specified tasks using the Hessian calculator. | ||
|
|
||
| Args: | ||
| structure (Atoms): The current structure. | ||
| tasks (dict[str, dict]): The tasks to evaluate. | ||
| structure_equilibrium (Atoms): The equilibrium structure. | ||
| force_constants (np.ndarray): The force constants array. | ||
| bulk_modulus (float, optional): The bulk modulus. Defaults to 0.0. | ||
| shear_modulus (float, optional): The shear modulus. Defaults to 0.0. | ||
|
|
||
| Returns: | ||
| dict[str, Union[float, np.ndarray]]: The results of the evaluated tasks. | ||
|
|
||
| Raises: | ||
| ValueError: If the specified tasks are not supported. | ||
| """ |
There was a problem hiding this comment.
Fix Undefined Names
The type hint Union is used but not imported. Add the necessary import from the typing module.
+ from typing import UnionCommittable 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.
| ) -> dict[str, Union[float, np.ndarray]]: | |
| """ | |
| Evaluate the specified tasks using the Hessian calculator. | |
| Args: | |
| structure (Atoms): The current structure. | |
| tasks (dict[str, dict]): The tasks to evaluate. | |
| structure_equilibrium (Atoms): The equilibrium structure. | |
| force_constants (np.ndarray): The force constants array. | |
| bulk_modulus (float, optional): The bulk modulus. Defaults to 0.0. | |
| shear_modulus (float, optional): The shear modulus. Defaults to 0.0. | |
| Returns: | |
| dict[str, Union[float, np.ndarray]]: The results of the evaluated tasks. | |
| Raises: | |
| ValueError: If the specified tasks are not supported. | |
| """ | |
| + from typing import Union | |
| ) -> dict[str, Union[float, np.ndarray]]: | |
| """ | |
| Evaluate the specified tasks using the Hessian calculator. | |
| Args: | |
| structure (Atoms): The current structure. | |
| tasks (dict[str, dict]): The tasks to evaluate. | |
| structure_equilibrium (Atoms): The equilibrium structure. | |
| force_constants (np.ndarray): The force constants array. | |
| bulk_modulus (float, optional): The bulk modulus. Defaults to 0.0. | |
| shear_modulus (float, optional): The shear modulus. Defaults to 0.0. | |
| Returns: | |
| dict[str, Union[float, np.ndarray]]: The results of the evaluated tasks. | |
| Raises: | |
| ValueError: If the specified tasks are not supported. | |
| """ |
Tools
Ruff
209-209: Undefined name
Union(F821)
atomistics/calculators/ase.py
Outdated
| def _calc_molecular_dynamics_with_ase( | ||
| dyn, | ||
| structure: Atoms, | ||
| ase_calculator: ASECalculator, | ||
| temperature: float, | ||
| run: int, | ||
| thermo: int, | ||
| output_keys: List[str], | ||
| ) -> dict: | ||
| """ | ||
| Perform molecular dynamics simulation using ASE. | ||
|
|
||
| Args: | ||
| dyn: The ASE dynamics object. | ||
| structure (Atoms): The atomic structure to simulate. | ||
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | ||
| temperature (float): The desired temperature in Kelvin. | ||
| run (int): The number of MD steps to perform. | ||
| thermo (int): The interval at which to print thermodynamic properties. | ||
| output_keys (List[str]): The keys of the properties to include in the output dictionary. | ||
|
|
||
| Returns: | ||
| dict: A dictionary containing the calculated properties at each MD step. | ||
| """ | ||
| structure.calc = ase_calculator | ||
| MaxwellBoltzmannDistribution(atoms=structure, temperature_K=temperature) | ||
| cache = {q: [] for q in output_keys} | ||
| for i in range(int(run / thermo)): | ||
| dyn.run(thermo) | ||
| ase_instance = ASEExecutor( | ||
| ase_structure=structure, ase_calculator=ase_calculator | ||
| ) | ||
| calc_dict = OutputMolecularDynamics( | ||
| **{k: getattr(ase_instance, k) for k in OutputMolecularDynamics.keys()} | ||
| ).get(output_keys=output_keys) | ||
| for k, v in calc_dict.items(): | ||
| cache[k].append(v) | ||
| return {q: np.array(cache[q]) for q in output_keys} |
There was a problem hiding this comment.
Rename unused loop control variable i.
The loop control variable i is not used within the loop body. Rename it to _.
- for i in range(int(run / thermo)):
+ for _ in range(int(run / thermo)):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 _calc_molecular_dynamics_with_ase( | |
| dyn, | |
| structure: Atoms, | |
| ase_calculator: ASECalculator, | |
| temperature: float, | |
| run: int, | |
| thermo: int, | |
| output_keys: List[str], | |
| ) -> dict: | |
| """ | |
| Perform molecular dynamics simulation using ASE. | |
| Args: | |
| dyn: The ASE dynamics object. | |
| structure (Atoms): The atomic structure to simulate. | |
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | |
| temperature (float): The desired temperature in Kelvin. | |
| run (int): The number of MD steps to perform. | |
| thermo (int): The interval at which to print thermodynamic properties. | |
| output_keys (List[str]): The keys of the properties to include in the output dictionary. | |
| Returns: | |
| dict: A dictionary containing the calculated properties at each MD step. | |
| """ | |
| structure.calc = ase_calculator | |
| MaxwellBoltzmannDistribution(atoms=structure, temperature_K=temperature) | |
| cache = {q: [] for q in output_keys} | |
| for i in range(int(run / thermo)): | |
| dyn.run(thermo) | |
| ase_instance = ASEExecutor( | |
| ase_structure=structure, ase_calculator=ase_calculator | |
| ) | |
| calc_dict = OutputMolecularDynamics( | |
| **{k: getattr(ase_instance, k) for k in OutputMolecularDynamics.keys()} | |
| ).get(output_keys=output_keys) | |
| for k, v in calc_dict.items(): | |
| cache[k].append(v) | |
| return {q: np.array(cache[q]) for q in output_keys} | |
| def _calc_molecular_dynamics_with_ase( | |
| dyn, | |
| structure: Atoms, | |
| ase_calculator: ASECalculator, | |
| temperature: float, | |
| run: int, | |
| thermo: int, | |
| output_keys: List[str], | |
| ) -> dict: | |
| """ | |
| Perform molecular dynamics simulation using ASE. | |
| Args: | |
| dyn: The ASE dynamics object. | |
| structure (Atoms): The atomic structure to simulate. | |
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | |
| temperature (float): The desired temperature in Kelvin. | |
| run (int): The number of MD steps to perform. | |
| thermo (int): The interval at which to print thermodynamic properties. | |
| output_keys (List[str]): The keys of the properties to include in the output dictionary. | |
| Returns: | |
| dict: A dictionary containing the calculated properties at each MD step. | |
| """ | |
| structure.calc = ase_calculator | |
| MaxwellBoltzmannDistribution(atoms=structure, temperature_K=temperature) | |
| cache = {q: [] for q in output_keys} | |
| for _ in range(int(run / thermo)): | |
| dyn.run(thermo) | |
| ase_instance = ASEExecutor( | |
| ase_structure=structure, ase_calculator=ase_calculator | |
| ) | |
| calc_dict = OutputMolecularDynamics( | |
| **{k: getattr(ase_instance, k) for k in OutputMolecularDynamics.keys()} | |
| ).get(output_keys=output_keys) | |
| for k, v in calc_dict.items(): | |
| cache[k].append(v) | |
| return {q: np.array(cache[q]) for q in output_keys} |
Tools
Ruff
495-495: Loop control variable
inot used within loop bodyRename unused
ito_i(B007)
501-501: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
| output_keys: List[str] = OutputThermalExpansion.keys(), | ||
| ) -> dict: | ||
| """ | ||
| Calculate thermal expansion using molecular dynamics simulation with ASE. | ||
|
|
||
| Args: | ||
| structure (Atoms): The atomic structure to simulate. | ||
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | ||
| temperature_start (float, optional): The starting temperature in Kelvin. Defaults to 15.0. | ||
| temperature_stop (float, optional): The stopping temperature in Kelvin. Defaults to 1500.0. | ||
| temperature_step (float, optional): The temperature step size in Kelvin. Defaults to 5.0. | ||
| run (int, optional): The number of MD steps to perform. Defaults to 100. | ||
| thermo (int, optional): The interval at which to print thermodynamic properties. Defaults to 100. | ||
| timestep (float, optional): The time step size in fs. Defaults to 1 * units.fs. | ||
| ttime (float, optional): The total time for the simulation in fs. Defaults to 100 * units.fs. | ||
| pfactor (float, optional): The pressure factor in GPa * fs^2. Defaults to 2e6 * units.GPa * (units.fs**2). | ||
| externalstress (np.ndarray, optional): The external stress tensor in bar. Defaults to np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar. | ||
| output_keys (List[str], optional): The keys of the properties to include in the output dictionary. Defaults to OutputThermalExpansion.keys(). | ||
|
|
||
| Returns: | ||
| dict: A dictionary containing the calculated thermal expansion properties. | ||
| """ |
There was a problem hiding this comment.
Fix default argument for output_keys.
Do not perform function call OutputThermalExpansion.keys in argument defaults; instead, perform the call within the function.
- output_keys: List[str] = OutputThermalExpansion.keys(),
+ output_keys: List[str] = None,
) -> dict:
if output_keys is None:
output_keys = OutputThermalExpansion.keys()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.
| output_keys: List[str] = OutputThermalExpansion.keys(), | |
| ) -> dict: | |
| """ | |
| Calculate thermal expansion using molecular dynamics simulation with ASE. | |
| Args: | |
| structure (Atoms): The atomic structure to simulate. | |
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | |
| temperature_start (float, optional): The starting temperature in Kelvin. Defaults to 15.0. | |
| temperature_stop (float, optional): The stopping temperature in Kelvin. Defaults to 1500.0. | |
| temperature_step (float, optional): The temperature step size in Kelvin. Defaults to 5.0. | |
| run (int, optional): The number of MD steps to perform. Defaults to 100. | |
| thermo (int, optional): The interval at which to print thermodynamic properties. Defaults to 100. | |
| timestep (float, optional): The time step size in fs. Defaults to 1 * units.fs. | |
| ttime (float, optional): The total time for the simulation in fs. Defaults to 100 * units.fs. | |
| pfactor (float, optional): The pressure factor in GPa * fs^2. Defaults to 2e6 * units.GPa * (units.fs**2). | |
| externalstress (np.ndarray, optional): The external stress tensor in bar. Defaults to np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar. | |
| output_keys (List[str], optional): The keys of the properties to include in the output dictionary. Defaults to OutputThermalExpansion.keys(). | |
| Returns: | |
| dict: A dictionary containing the calculated thermal expansion properties. | |
| """ | |
| output_keys: List[str] = None, | |
| ) -> dict: | |
| if output_keys is None: | |
| output_keys = OutputThermalExpansion.keys() | |
| """ | |
| Calculate thermal expansion using molecular dynamics simulation with ASE. | |
| Args: | |
| structure (Atoms): The atomic structure to simulate. | |
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | |
| temperature_start (float, optional): The starting temperature in Kelvin. Defaults to 15.0. | |
| temperature_stop (float, optional): The stopping temperature in Kelvin. Defaults to 1500.0. | |
| temperature_step (float, optional): The temperature step size in Kelvin. Defaults to 5.0. | |
| run (int, optional): The number of MD steps to perform. Defaults to 100. | |
| thermo (int, optional): The interval at which to print thermodynamic properties. Defaults to 100. | |
| timestep (float, optional): The time step size in fs. Defaults to 1 * units.fs. | |
| ttime (float, optional): The total time for the simulation in fs. Defaults to 100 * units.fs. | |
| pfactor (float, optional): The pressure factor in GPa * fs^2. Defaults to 2e6 * units.GPa * (units.fs**2). | |
| externalstress (np.ndarray, optional): The external stress tensor in bar. Defaults to np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar. | |
| output_keys (List[str], optional): The keys of the properties to include in the output dictionary. Defaults to OutputThermalExpansion.keys(). | |
| Returns: | |
| dict: A dictionary containing the calculated thermal expansion properties. | |
| """ |
Tools
Ruff
369-369: Do not perform function call
OutputThermalExpansion.keysin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
| def calc_molecular_dynamics_npt_with_ase( | ||
| structure: Atoms, | ||
| ase_calculator: ASECalculator, | ||
| run: int = 100, | ||
| thermo: int = 100, | ||
| timestep: float = 1 * units.fs, | ||
| ttime: float = 100 * units.fs, | ||
| pfactor: float = 2e6 * units.GPa * (units.fs**2), | ||
| temperature: float = 300.0, | ||
| externalstress: np.ndarray = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar, | ||
| output_keys: List[str] = OutputMolecularDynamics.keys(), | ||
| ) -> dict: | ||
| """ | ||
| Perform NPT molecular dynamics simulation using ASE. | ||
|
|
||
| Args: | ||
| structure (Atoms): The atomic structure to simulate. | ||
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | ||
| run (int, optional): The number of MD steps to perform. Defaults to 100. | ||
| thermo (int, optional): The interval at which to print thermodynamic properties. Defaults to 100. | ||
| timestep (float, optional): The time step size in fs. Defaults to 1 * units.fs. | ||
| ttime (float, optional): The total time for the simulation in fs. Defaults to 100 * units.fs. | ||
| pfactor (float, optional): The pressure factor in GPa * fs^2. Defaults to 2e6 * units.GPa * (units.fs**2). | ||
| temperature (float, optional): The desired temperature in Kelvin. Defaults to 300.0. | ||
| externalstress (np.ndarray, optional): The external stress tensor in bar. Defaults to np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar. | ||
| output_keys (List[str], optional): The keys of the properties to include in the output dictionary. Defaults to OutputMolecularDynamics.keys(). | ||
|
|
||
| Returns: | ||
| dict: A dictionary containing the calculated properties at each MD step. | ||
| """ |
There was a problem hiding this comment.
Fix default arguments for externalstress and output_keys.
Do not perform function calls in argument defaults; instead, perform the calls within the function.
- externalstress: np.ndarray = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar,
- output_keys: List[str] = OutputMolecularDynamics.keys(),
+ externalstress: np.ndarray = None,
+ output_keys: List[str] = None,
) -> dict:
if externalstress is None:
externalstress = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar
if output_keys is None:
output_keys = OutputMolecularDynamics.keys()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 calc_molecular_dynamics_npt_with_ase( | |
| structure: Atoms, | |
| ase_calculator: ASECalculator, | |
| run: int = 100, | |
| thermo: int = 100, | |
| timestep: float = 1 * units.fs, | |
| ttime: float = 100 * units.fs, | |
| pfactor: float = 2e6 * units.GPa * (units.fs**2), | |
| temperature: float = 300.0, | |
| externalstress: np.ndarray = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar, | |
| output_keys: List[str] = OutputMolecularDynamics.keys(), | |
| ) -> dict: | |
| """ | |
| Perform NPT molecular dynamics simulation using ASE. | |
| Args: | |
| structure (Atoms): The atomic structure to simulate. | |
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | |
| run (int, optional): The number of MD steps to perform. Defaults to 100. | |
| thermo (int, optional): The interval at which to print thermodynamic properties. Defaults to 100. | |
| timestep (float, optional): The time step size in fs. Defaults to 1 * units.fs. | |
| ttime (float, optional): The total time for the simulation in fs. Defaults to 100 * units.fs. | |
| pfactor (float, optional): The pressure factor in GPa * fs^2. Defaults to 2e6 * units.GPa * (units.fs**2). | |
| temperature (float, optional): The desired temperature in Kelvin. Defaults to 300.0. | |
| externalstress (np.ndarray, optional): The external stress tensor in bar. Defaults to np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar. | |
| output_keys (List[str], optional): The keys of the properties to include in the output dictionary. Defaults to OutputMolecularDynamics.keys(). | |
| Returns: | |
| dict: A dictionary containing the calculated properties at each MD step. | |
| """ | |
| def calc_molecular_dynamics_npt_with_ase( | |
| structure: Atoms, | |
| ase_calculator: ASECalculator, | |
| run: int = 100, | |
| thermo: int = 100, | |
| timestep: float = 1 * units.fs, | |
| ttime: float = 100 * units.fs, | |
| pfactor: float = 2e6 * units.GPa * (units.fs**2), | |
| temperature: float = 300.0, | |
| externalstress: np.ndarray = None, | |
| output_keys: List[str] = None, | |
| ) -> dict: | |
| if externalstress is None: | |
| externalstress = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar | |
| if output_keys is None: | |
| output_keys = OutputMolecularDynamics.keys() | |
| """ | |
| Perform NPT molecular dynamics simulation using ASE. | |
| Args: | |
| structure (Atoms): The atomic structure to simulate. | |
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | |
| run (int, optional): The number of MD steps to perform. Defaults to 100. | |
| thermo (int, optional): The interval at which to print thermodynamic properties. Defaults to 100. | |
| timestep (float, optional): The time step size in fs. Defaults to 1 * units.fs. | |
| ttime (float, optional): The total time for the simulation in fs. Defaults to 100 * units.fs. | |
| pfactor (float, optional): The pressure factor in GPa * fs^2. Defaults to 2e6 * units.GPa * (units.fs**2). | |
| temperature (float, optional): The desired temperature in Kelvin. Defaults to 300.0. | |
| externalstress (np.ndarray, optional): The external stress tensor in bar. Defaults to np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar. | |
| output_keys (List[str], optional): The keys of the properties to include in the output dictionary. Defaults to OutputMolecularDynamics.keys(). | |
| Returns: | |
| dict: A dictionary containing the calculated properties at each MD step. | |
| """ |
Tools
Ruff
427-427: Do not perform function call
np.arrayin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
428-428: Do not perform function call
OutputMolecularDynamics.keysin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
| dos_energies: np.ndarray, | ||
| dos_total: np.ndarray, | ||
| *args, | ||
| axis: Optional[matplotlib.axes._subplots.AxesSubplot] = None, | ||
| **kwargs, | ||
| ) -> matplotlib.axes._subplots.AxesSubplot: |
There was a problem hiding this comment.
Fix undefined name matplotlib.
The name matplotlib is undefined. Ensure it is imported or defined.
+ import matplotlibCommittable 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.
| dos_energies: np.ndarray, | |
| dos_total: np.ndarray, | |
| *args, | |
| axis: Optional[matplotlib.axes._subplots.AxesSubplot] = None, | |
| **kwargs, | |
| ) -> matplotlib.axes._subplots.AxesSubplot: | |
| + import matplotlib | |
| dos_energies: np.ndarray, | |
| dos_total: np.ndarray, | |
| *args, | |
| axis: Optional[matplotlib.axes._subplots.AxesSubplot] = None, | |
| **kwargs, | |
| ) -> matplotlib.axes._subplots.AxesSubplot: |
Tools
Ruff
450-450: Undefined name
matplotlib(F821)
452-452: Undefined name
matplotlib(F821)
| axis: Optional[matplotlib.axes._subplots.AxesSubplot] = None, | ||
| *args, | ||
| label: Optional[str] = None, | ||
| **kwargs, | ||
| ): | ||
| ) -> matplotlib.axes._subplots.AxesSubplot: |
There was a problem hiding this comment.
Fix undefined name matplotlib.
The name matplotlib is undefined. Ensure it is imported or defined.
+ import matplotlibCommittable 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.
| axis: Optional[matplotlib.axes._subplots.AxesSubplot] = None, | |
| *args, | |
| label: Optional[str] = None, | |
| **kwargs, | |
| ): | |
| ) -> matplotlib.axes._subplots.AxesSubplot: | |
| + import matplotlib | |
| axis: Optional[matplotlib.axes._subplots.AxesSubplot] = None, | |
| *args, | |
| label: Optional[str] = None, | |
| **kwargs, | |
| ) -> matplotlib.axes._subplots.AxesSubplot: |
Tools
Ruff
533-533: Undefined name
matplotlib(F821)
537-537: Undefined name
matplotlib(F821)
# Conflicts: # atomistics/workflows/elastic/helper.py
for more information, see https://pre-commit.ci
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Actionable comments posted: 7
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (2)
- atomistics/calculators/ase.py (7 hunks)
- atomistics/workflows/elastic/helper.py (5 hunks)
Additional context used
Ruff
atomistics/workflows/elastic/helper.py
147-147: Undefined name
Optional(F821)
atomistics/calculators/ase.py
152-152: Do not use mutable data structures for argument defaults
Replace with
None; initialize within function(B006)
198-198: Do not perform function call
OutputStatic.keysin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
212-212: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
273-273: Do not use mutable data structures for argument defaults
Replace with
None; initialize within function(B006)
369-369: Do not perform function call
OutputThermalExpansion.keysin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
427-427: Do not perform function call
np.arrayin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
428-428: Do not perform function call
OutputMolecularDynamics.keysin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
495-495: Loop control variable
inot used within loop bodyRename unused
ito_i(B007)
501-501: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
Additional comments not posted (17)
atomistics/workflows/elastic/helper.py (5)
23-35: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
108-121: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
147-161: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
Tools
Ruff
147-147: Undefined name
Optional(F821)
187-196: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
201-214: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
atomistics/calculators/ase.py (12)
27-34: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
39-44: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
48-53: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
57-62: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
66-71: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
77-82: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
89-94: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
101-106: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
110-115: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
119-124: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
128-133: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
137-142: LGTM!The type annotations and expanded docstrings improve clarity and maintainability.
| @@ -1,4 +1,5 @@ | |||
| from collections import OrderedDict | |||
| from typing import Any, Dict, List, Tuple | |||
There was a problem hiding this comment.
Fix Undefined Name Optional.
The type hint Optional is used but not imported. Add the necessary import from the typing module.
+ from typing import OptionalCommittable 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 typing import Any, Dict, List, Tuple | |
| from typing import Any, Dict, List, Tuple | |
| from typing import Optional |
| output_keys: List[str] = OutputThermalExpansion.keys(), | ||
| ) -> dict: | ||
| """ | ||
| Calculate thermal expansion using molecular dynamics simulation with ASE. | ||
|
|
||
| Args: | ||
| structure (Atoms): The atomic structure to simulate. | ||
| ase_calculator (ASECalculator): The ASE calculator to use for energy and force calculations. | ||
| temperature_start (float, optional): The starting temperature in Kelvin. Defaults to 15.0. | ||
| temperature_stop (float, optional): The stopping temperature in Kelvin. Defaults to 1500.0. | ||
| temperature_step (float, optional): The temperature step size in Kelvin. Defaults to 5.0. | ||
| run (int, optional): The number of MD steps to perform. Defaults to 100. | ||
| thermo (int, optional): The interval at which to print thermodynamic properties. Defaults to 100. | ||
| timestep (float, optional): The time step size in fs. Defaults to 1 * units.fs. | ||
| ttime (float, optional): The total time for the simulation in fs. Defaults to 100 * units.fs. | ||
| pfactor (float, optional): The pressure factor in GPa * fs^2. Defaults to 2e6 * units.GPa * (units.fs**2). | ||
| externalstress (np.ndarray, optional): The external stress tensor in bar. Defaults to np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar. | ||
| output_keys (List[str], optional): The keys of the properties to include in the output dictionary. Defaults to OutputThermalExpansion.keys(). | ||
|
|
||
| Returns: | ||
| dict: A dictionary containing the calculated thermal expansion properties. | ||
| """ |
There was a problem hiding this comment.
Avoid function calls in argument defaults.
Replace the function calls np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar and OutputThermalExpansion.keys() with None and initialize them within the function.
- externalstress: np.ndarray = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar,
- output_keys: List[str] = OutputThermalExpansion.keys(),
+ externalstress: np.ndarray = None,
+ output_keys: List[str] = None,
) -> dict:
if externalstress is None:
externalstress = np.array([0.0,
<details>
<summary>Tools</summary>
<details>
<summary>Ruff</summary><blockquote>
369-369: Do not perform function call `OutputThermalExpansion.keys` in argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable
(B008)
</blockquote></details>
</details>
<!-- This is an auto-generated comment by CodeRabbit -->| output_keys: list[str] = OutputStatic.keys(), | ||
| ) -> dict: | ||
| """ | ||
| Calculate static properties using ASE calculator. | ||
|
|
||
| Args: | ||
| structure (Atoms): The ASE structure object. | ||
| ase_calculator (ASECalculator): The ASE calculator object. | ||
| output_keys (list[str], optional): List of output keys. Defaults to OutputStatic.keys(). | ||
|
|
||
| Returns: | ||
| dict: Dictionary containing the calculated static properties. | ||
| """ |
There was a problem hiding this comment.
Avoid function calls in argument defaults.
Replace the function call OutputStatic.keys() with None and initialize it within the function.
- output_keys: list[str] = OutputStatic.keys(),
+ output_keys: list[str] = None,
) -> dict:
if output_keys is None:
output_keys = OutputStatic.keys()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.
| output_keys: list[str] = OutputStatic.keys(), | |
| ) -> dict: | |
| """ | |
| Calculate static properties using ASE calculator. | |
| Args: | |
| structure (Atoms): The ASE structure object. | |
| ase_calculator (ASECalculator): The ASE calculator object. | |
| output_keys (list[str], optional): List of output keys. Defaults to OutputStatic.keys(). | |
| Returns: | |
| dict: Dictionary containing the calculated static properties. | |
| """ | |
| output_keys: list[str] = None, | |
| ) -> dict: | |
| if output_keys is None: | |
| output_keys = OutputStatic.keys() | |
| """ | |
| Calculate static properties using ASE calculator. | |
| Args: | |
| structure (Atoms): The ASE structure object. | |
| ase_calculator (ASECalculator): The ASE calculator object. | |
| output_keys (list[str], optional): List of output keys. Defaults to OutputStatic.keys(). | |
| Returns: | |
| dict: Dictionary containing the calculated static properties. | |
| """ |
Tools
Ruff
198-198: Do not perform function call
OutputStatic.keysin argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable(B008)
| tasks: List[str], | ||
| ase_calculator: ASECalculator, | ||
| ase_optimizer: Optimizer = None, | ||
| ase_optimizer_kwargs: dict = {}, | ||
| ) -> dict: | ||
| """ | ||
| Evaluate tasks using ASE calculator. | ||
|
|
||
| Args: | ||
| structure (Atoms): The ASE structure object. | ||
| tasks (list[TaskName]): List of tasks to evaluate. | ||
| ase_calculator (ASECalculator): The ASE calculator object. | ||
| ase_optimizer (Optimizer, optional): The ASE optimizer object. Defaults to None. | ||
| ase_optimizer_kwargs (dict, optional): Keyword arguments for the ASE optimizer. Defaults to {}. | ||
|
|
||
| Returns: | ||
| dict: Dictionary containing the results of the evaluated tasks. | ||
| """ |
There was a problem hiding this comment.
Avoid mutable default arguments.
Replace the mutable default argument ase_optimizer_kwargs with None and initialize it within the function.
- ase_optimizer_kwargs: dict = {},
+ ase_optimizer_kwargs: dict = None,
) -> dict:
if ase_optimizer_kwargs is None:
ase_optimizer_kwargs = {}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.
| tasks: List[str], | |
| ase_calculator: ASECalculator, | |
| ase_optimizer: Optimizer = None, | |
| ase_optimizer_kwargs: dict = {}, | |
| ) -> dict: | |
| """ | |
| Evaluate tasks using ASE calculator. | |
| Args: | |
| structure (Atoms): The ASE structure object. | |
| tasks (list[TaskName]): List of tasks to evaluate. | |
| ase_calculator (ASECalculator): The ASE calculator object. | |
| ase_optimizer (Optimizer, optional): The ASE optimizer object. Defaults to None. | |
| ase_optimizer_kwargs (dict, optional): Keyword arguments for the ASE optimizer. Defaults to {}. | |
| Returns: | |
| dict: Dictionary containing the results of the evaluated tasks. | |
| """ | |
| tasks: List[str], | |
| ase_calculator: ASECalculator, | |
| ase_optimizer: Optimizer = None, | |
| ase_optimizer_kwargs: dict = None, | |
| ) -> dict: | |
| if ase_optimizer_kwargs is None: | |
| ase_optimizer_kwargs = {} | |
| """ | |
| Evaluate tasks using ASE calculator. | |
| Args: | |
| structure (Atoms): The ASE structure object. | |
| tasks (list[TaskName]): List of tasks to evaluate. | |
| ase_calculator (ASECalculator): The ASE calculator object. | |
| ase_optimizer (Optimizer, optional): The ASE optimizer object. Defaults to None. | |
| ase_optimizer_kwargs (dict, optional): Keyword arguments for the ASE optimizer. Defaults to {}. | |
| Returns: | |
| dict: Dictionary containing the results of the evaluated tasks. | |
| """ |
Tools
Ruff
152-152: Do not use mutable data structures for argument defaults
Replace with
None; initialize within function(B006)
| def optimize_positions_and_volume_with_ase( | ||
| structure: Atoms, | ||
| ase_calculator: ASECalculator, | ||
| ase_optimizer: Optimizer, | ||
| ase_optimizer_kwargs: dict, | ||
| ) -> Atoms: | ||
| """ | ||
| Optimize the atomic positions and cell volume of the structure using ASE optimizer. | ||
|
|
||
| Args: | ||
| structure (Atoms): The ASE structure object. | ||
| ase_calculator (ASECalculator): The ASE calculator object. | ||
| ase_optimizer (Optimizer): The ASE optimizer object. | ||
| ase_optimizer_kwargs (dict): Keyword arguments for the ASE optimizer. | ||
|
|
||
| Returns: | ||
| Atoms: The optimized structure. | ||
| """ | ||
| structure.set_calculator(ase_calculator) | ||
| dyn = ase_optimizer(structure, **ase_optimizer_kwargs) | ||
| dyn.run(fmax=0.05, volume=True) | ||
| return structure |
There was a problem hiding this comment.
Avoid mutable default arguments.
Replace the mutable default argument ase_optimizer_kwargs with None and initialize it within the function.
- ase_optimizer_kwargs: dict = {},
+ ase_optimizer_kwargs: dict = None,
) -> Atoms:
if ase_optimizer_kwargs is None:
ase_optimizer_kwargs = {}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 optimize_positions_and_volume_with_ase( | |
| structure: Atoms, | |
| ase_calculator: ASECalculator, | |
| ase_optimizer: Optimizer, | |
| ase_optimizer_kwargs: dict, | |
| ) -> Atoms: | |
| """ | |
| Optimize the atomic positions and cell volume of the structure using ASE optimizer. | |
| Args: | |
| structure (Atoms): The ASE structure object. | |
| ase_calculator (ASECalculator): The ASE calculator object. | |
| ase_optimizer (Optimizer): The ASE optimizer object. | |
| ase_optimizer_kwargs (dict): Keyword arguments for the ASE optimizer. | |
| Returns: | |
| Atoms: The optimized structure. | |
| """ | |
| structure.set_calculator(ase_calculator) | |
| dyn = ase_optimizer(structure, **ase_optimizer_kwargs) | |
| dyn.run(fmax=0.05, volume=True) | |
| return structure | |
| def optimize_positions_and_volume_with_ase( | |
| structure: Atoms, | |
| ase_calculator: ASECalculator, | |
| ase_optimizer: Optimizer, | |
| ase_optimizer_kwargs: dict = None, | |
| ) -> Atoms: | |
| """ | |
| Optimize the atomic positions and cell volume of the structure using ASE optimizer. | |
| Args: | |
| structure (Atoms): The ASE structure object. | |
| ase_calculator (ASECalculator): The ASE calculator object. | |
| ase_optimizer (Optimizer): The ASE optimizer object. | |
| ase_optimizer_kwargs (dict): Keyword arguments for the ASE optimizer. | |
| Returns: | |
| Atoms: The optimized structure. | |
| """ | |
| if ase_optimizer_kwargs is None: | |
| ase_optimizer_kwargs = {} | |
| structure.set_calculator(ase_calculator) | |
| dyn = ase_optimizer(structure, **ase_optimizer_kwargs) | |
| dyn.run(fmax=0.05, volume=True) | |
| return structure |
| def optimize_positions_with_ase( | ||
| structure: Atoms, | ||
| ase_calculator: ASECalculator, | ||
| run: int = 100, | ||
| thermo: int = 100, | ||
| timestep: float = 1 * units.fs, | ||
| ttime: float = 100 * units.fs, | ||
| pfactor: float = 2e6 * units.GPa * (units.fs**2), | ||
| temperature: float = 100.0, | ||
| externalstress: np.ndarray = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar, | ||
| output_keys=OutputMolecularDynamics.keys(), | ||
| ) -> dict: | ||
| return _calc_molecular_dynamics_with_ase( | ||
| dyn=NPT( | ||
| atoms=structure, | ||
| timestep=timestep, | ||
| temperature=None, | ||
| externalstress=externalstress, | ||
| ttime=ttime, | ||
| pfactor=pfactor, | ||
| temperature_K=temperature, | ||
| mask=None, | ||
| trajectory=None, | ||
| logfile=None, | ||
| loginterval=1, | ||
| append_trajectory=False, | ||
| ), | ||
| structure=structure, | ||
| ase_calculator=ase_calculator, | ||
| temperature=temperature, | ||
| run=run, | ||
| thermo=thermo, | ||
| output_keys=output_keys, | ||
| ) | ||
| ase_optimizer: Optimizer, | ||
| ase_optimizer_kwargs: dict, | ||
| ) -> Atoms: | ||
| """ | ||
| Optimize the atomic positions of the structure using ASE optimizer. | ||
|
|
||
| Args: | ||
| structure (Atoms): The ASE structure object. | ||
| ase_calculator (ASECalculator): The ASE calculator object. | ||
| ase_optimizer (Optimizer): The ASE optimizer object. | ||
| ase_optimizer_kwargs (dict): Keyword arguments for the ASE optimizer. | ||
|
|
||
| Returns: | ||
| Atoms: The optimized structure. | ||
| """ | ||
| structure.set_calculator(ase_calculator) | ||
| dyn = ase_optimizer(structure, **ase_optimizer_kwargs) | ||
| dyn.run(fmax=0.05) | ||
| return structure | ||
|
|
There was a problem hiding this comment.
Avoid mutable default arguments.
Replace the mutable default argument ase_optimizer_kwargs with None and initialize it within the function.
- ase_optimizer_kwargs: dict = {},
+ ase_optimizer_kwargs: dict = None,
) -> Atoms:
if ase_optimizer_kwargs is None:
ase_optimizer_kwargs = {}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 optimize_positions_with_ase( | |
| structure: Atoms, | |
| ase_calculator: ASECalculator, | |
| run: int = 100, | |
| thermo: int = 100, | |
| timestep: float = 1 * units.fs, | |
| ttime: float = 100 * units.fs, | |
| pfactor: float = 2e6 * units.GPa * (units.fs**2), | |
| temperature: float = 100.0, | |
| externalstress: np.ndarray = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]) * units.bar, | |
| output_keys=OutputMolecularDynamics.keys(), | |
| ) -> dict: | |
| return _calc_molecular_dynamics_with_ase( | |
| dyn=NPT( | |
| atoms=structure, | |
| timestep=timestep, | |
| temperature=None, | |
| externalstress=externalstress, | |
| ttime=ttime, | |
| pfactor=pfactor, | |
| temperature_K=temperature, | |
| mask=None, | |
| trajectory=None, | |
| logfile=None, | |
| loginterval=1, | |
| append_trajectory=False, | |
| ), | |
| structure=structure, | |
| ase_calculator=ase_calculator, | |
| temperature=temperature, | |
| run=run, | |
| thermo=thermo, | |
| output_keys=output_keys, | |
| ) | |
| ase_optimizer: Optimizer, | |
| ase_optimizer_kwargs: dict, | |
| ) -> Atoms: | |
| """ | |
| Optimize the atomic positions of the structure using ASE optimizer. | |
| Args: | |
| structure (Atoms): The ASE structure object. | |
| ase_calculator (ASECalculator): The ASE calculator object. | |
| ase_optimizer (Optimizer): The ASE optimizer object. | |
| ase_optimizer_kwargs (dict): Keyword arguments for the ASE optimizer. | |
| Returns: | |
| Atoms: The optimized structure. | |
| """ | |
| structure.set_calculator(ase_calculator) | |
| dyn = ase_optimizer(structure, **ase_optimizer_kwargs) | |
| dyn.run(fmax=0.05) | |
| return structure | |
| def optimize_positions_with_ase( | |
| structure: Atoms, | |
| ase_calculator: ASECalculator, | |
| ase_optimizer: Optimizer, | |
| ase_optimizer_kwargs: dict = None, | |
| ) -> Atoms: | |
| """ | |
| Optimize the atomic positions of the structure using ASE optimizer. | |
| Args: | |
| structure (Atoms): The ASE structure object. | |
| ase_calculator (ASECalculator): The ASE calculator object. | |
| ase_optimizer (Optimizer): The ASE optimizer object. | |
| ase_optimizer_kwargs (dict): Keyword arguments for the ASE optimizer. | |
| Returns: | |
| Atoms: The optimized structure. | |
| """ | |
| if ase_optimizer_kwargs is None: | |
| ase_optimizer_kwargs = {} | |
| structure.set_calculator(ase_calculator) | |
| dyn = ase_optimizer(structure, **ase_optimizer_kwargs) | |
| dyn.run(fmax=0.05) | |
| return structure |
atomistics/calculators/ase.py
Outdated
| timestep: float = 1.0, | ||
| temperature: float = 100.0, | ||
| friction: float = 0.002, | ||
| output_keys=OutputMolecularDynamics.keys(), | ||
| ): | ||
| output_keys: List[str] = ["energy", "forces", "positions"], | ||
| ) -> dict: | ||
| """ | ||
| Perform molecular dynamics simulation using the Langevin algorithm with ASE. | ||
|
|
||
| Parameters: | ||
| - structure (Atoms): The atomic structure to simulate. | ||
| - ase_calculator (Calculator): The ASE calculator to use for energy and force calculations. | ||
| - run (int): The number of MD steps to perform. | ||
| - thermo (int): The interval at which to print thermodynamic properties. | ||
| - timestep (float): The time step size in fs. | ||
| - temperature (float): The desired temperature in Kelvin. | ||
| - friction (float): The friction coefficient for the Langevin thermostat. | ||
| - output_keys (List[str]): The keys of the properties to include in the output dictionary. | ||
|
|
||
| Returns: | ||
| - dict: A dictionary containing the calculated properties at each MD step. | ||
| """ |
There was a problem hiding this comment.
Avoid mutable default arguments.
Replace the mutable default argument output_keys with None and initialize it within the function.
- output_keys: List[str] = ["energy", "forces", "positions"],
+ output_keys: List[str] = None,
) -> dict:
if output_keys is None:
output_keys = ["energy", "forces", "positions"]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.
| timestep: float = 1.0, | |
| temperature: float = 100.0, | |
| friction: float = 0.002, | |
| output_keys=OutputMolecularDynamics.keys(), | |
| ): | |
| output_keys: List[str] = ["energy", "forces", "positions"], | |
| ) -> dict: | |
| """ | |
| Perform molecular dynamics simulation using the Langevin algorithm with ASE. | |
| Parameters: | |
| - structure (Atoms): The atomic structure to simulate. | |
| - ase_calculator (Calculator): The ASE calculator to use for energy and force calculations. | |
| - run (int): The number of MD steps to perform. | |
| - thermo (int): The interval at which to print thermodynamic properties. | |
| - timestep (float): The time step size in fs. | |
| - temperature (float): The desired temperature in Kelvin. | |
| - friction (float): The friction coefficient for the Langevin thermostat. | |
| - output_keys (List[str]): The keys of the properties to include in the output dictionary. | |
| Returns: | |
| - dict: A dictionary containing the calculated properties at each MD step. | |
| """ | |
| timestep: float = 1.0, | |
| temperature: float = 100.0, | |
| friction: float = 0.002, | |
| output_keys: List[str] = None, | |
| ) -> dict: | |
| if output_keys is None: | |
| output_keys = ["energy", "forces", "positions"] | |
| """ | |
| Perform molecular dynamics simulation using the Langevin algorithm with ASE. | |
| Parameters: | |
| - structure (Atoms): The atomic structure to simulate. | |
| - ase_calculator (Calculator): The ASE calculator to use for energy and force calculations. | |
| - run (int): The number of MD steps to perform. | |
| - thermo (int): The interval at which to print thermodynamic properties. | |
| - timestep (float): The time step size in fs. | |
| - temperature (float): The desired temperature in Kelvin. | |
| - friction (float): The friction coefficient for the Langevin thermostat. | |
| - output_keys (List[str]): The keys of the properties to include in the output dictionary. | |
| Returns: | |
| - dict: A dictionary containing the calculated properties at each MD step. | |
| """ |
Tools
Ruff
273-273: Do not use mutable data structures for argument defaults
Replace with
None; initialize within function(B006)
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Files selected for processing (2)
- atomistics/calculators/hessian.py (7 hunks)
- atomistics/workflows/elastic/helper.py (5 hunks)
Files skipped from review as they are similar to previous changes (2)
- atomistics/calculators/hessian.py
- atomistics/workflows/elastic/helper.py
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Files selected for processing (1)
- atomistics/workflows/evcurve/thermo.py (21 hunks)
Additional context used
Ruff
atomistics/workflows/evcurve/thermo.py
19-19: Undefined name
Optional(F821)
20-20: Undefined name
Optional(F821)
21-21: Undefined name
Optional(F821)
22-22: Undefined name
Optional(F821)
23-23: Undefined name
Optional(F821)
24-24: Undefined name
Optional(F821)
Additional comments not posted (23)
atomistics/workflows/evcurve/thermo.py (23)
9-9: LGTM!The class definition has been simplified by removing explicit
objectinheritance. This is a good change as it makes the code cleaner.
28-31: LGTM!The
copymethod has been updated with a return type hint and a docstring. This improves readability and maintainability.
44-44: LGTM!The
_reset_energymethod has been updated with a docstring. This improves readability and maintainability.
54-57: LGTM!The
num_atomsproperty has been updated with a return type hint and a docstring. This improves readability and maintainability.
66-69: LGTM!The
num_atomssetter has been updated with a docstring. This improves readability and maintainability.
74-79: LGTM!The
_coeffproperty has been updated with a return type hint and a docstring. This improves readability and maintainability.
86-89: LGTM!The
temperaturesproperty has been updated with a return type hint and a docstring. This improves readability and maintainability.
96-99: LGTM!The
_d_tempproperty has been updated with a return type hint and a docstring. This improves readability and maintainability.
106-109: LGTM!The
_d_volproperty has been updated with a return type hint and a docstring. This improves readability and maintainability.
116-119: LGTM!The
temperaturessetter has been updated with a docstring. This improves readability and maintainability.
133-136: LGTM!The
volumesproperty has been updated with a return type hint and a docstring. This improves readability and maintainability.
143-146: LGTM!The
volumessetter has been updated with a docstring. This improves readability and maintainability.
160-163: LGTM!The
entropyproperty has been updated with a return type hint and a docstring. This improves readability and maintainability.
172-175: LGTM!The
pressureproperty has been updated with a return type hint and a docstring. This improves readability and maintainability.
184-187: LGTM!The
energiesproperty has been updated with a return type hint and a docstring. This improves readability and maintainability.
194-197: LGTM!The
energiessetter has been updated with a docstring. This improves readability and maintainability.
218-223: LGTM!The
set_temperaturesmethod has been updated with a docstring. This improves readability and maintainability.
233-238: LGTM!The
set_volumesmethod has been updated with a docstring. This improves readability and maintainability.
246-249: LGTM!The
meshgridmethod has been updated with a return type hint and a docstring. This improves readability and maintainability.
255-261: LGTM!The
get_minimum_energy_pathmethod has been updated with a return type hint and a docstring. This improves readability and maintainability.
281-288: LGTM!The
get_free_energymethod has been updated with a return type hint and a docstring. This improves readability and maintainability.
297-304: LGTM!The
interpolate_volumemethod has been updated with a return type hint and a docstring. This improves readability and maintainability.
493-503: LGTM!The
get_thermo_bulk_modelfunction has been updated with a return type hint and a docstring. This improves readability and maintainability.
| self._volumes: Optional[np.ndarray] = None | ||
| self._temperatures: Optional[np.ndarray] = None | ||
| self._energies: Optional[np.ndarray] = None | ||
| self._entropy: Optional[np.ndarray] = None | ||
| self._pressure: Optional[np.ndarray] = None | ||
| self._num_atoms: Optional[int] = None |
There was a problem hiding this comment.
Fix undefined name Optional in __init__ method.
The method __init__ uses Optional which is not imported.
+ from typing import OptionalCommittable 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.
| self._volumes: Optional[np.ndarray] = None | |
| self._temperatures: Optional[np.ndarray] = None | |
| self._energies: Optional[np.ndarray] = None | |
| self._entropy: Optional[np.ndarray] = None | |
| self._pressure: Optional[np.ndarray] = None | |
| self._num_atoms: Optional[int] = None | |
| + from typing import Optional | |
| self._volumes: Optional[np.ndarray] = None | |
| self._temperatures: Optional[np.ndarray] = None | |
| self._energies: Optional[np.ndarray] = None | |
| self._entropy: Optional[np.ndarray] = None | |
| self._pressure: Optional[np.ndarray] = None | |
| self._num_atoms: Optional[int] = None |
Tools
Ruff
19-19: Undefined name
Optional(F821)
20-20: Undefined name
Optional(F821)
21-21: Undefined name
Optional(F821)
22-22: Undefined name
Optional(F821)
23-23: Undefined name
Optional(F821)
24-24: Undefined name
Optional(F821)
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Summary by CodeRabbit
New Features
ThermoBulkclass with refined method signatures and improved usability in thermodynamic calculations.Documentation
Bug Fixes
Refactor