Update ruff linter (#398)

* Update ruff linter

* add keys again

* fix

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix tests

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: ruff
         name: ruff lint
-        args: ["--select", "I", "--fix"]
+        args: ["--fix"]
         files: ^atomistics/
       - id: ruff-format
         name: ruff format

atomistics/calculators/__init__.py

@@ -10,14 +10,14 @@
 from atomistics.calculators.hessian import evaluate_with_hessian
 
 __all__ = [
-    calc_molecular_dynamics_langevin_with_ase,
-    calc_molecular_dynamics_npt_with_ase,
-    calc_molecular_dynamics_thermal_expansion_with_ase,
-    calc_static_with_ase,
-    evaluate_with_ase,
-    optimize_positions_with_ase,
-    optimize_positions_and_volume_with_ase,
-    evaluate_with_hessian,
+    "calc_molecular_dynamics_langevin_with_ase",
+    "calc_molecular_dynamics_npt_with_ase",
+    "calc_molecular_dynamics_thermal_expansion_with_ase",
+    "calc_static_with_ase",
+    "evaluate_with_ase",
+    "optimize_positions_with_ase",
+    "optimize_positions_and_volume_with_ase",
+    "evaluate_with_hessian",
 ]
 
 
@@ -29,9 +29,9 @@
     )
 
     __all__ += [
-        calc_static_with_qe,
-        evaluate_with_qe,
-        optimize_positions_and_volume_with_qe,
+        "calc_static_with_qe",
+        "evaluate_with_qe",
+        "optimize_positions_and_volume_with_qe",
     ]
 except ImportError:
     pass
@@ -53,18 +53,18 @@
     )
 
     __all__ += [
-        calc_molecular_dynamics_thermal_expansion_with_lammps,
-        calc_molecular_dynamics_nph_with_lammps,
-        calc_molecular_dynamics_npt_with_lammps,
-        calc_molecular_dynamics_nvt_with_lammps,
-        calc_molecular_dynamics_langevin_with_lammps,
-        calc_static_with_lammps,
-        evaluate_with_lammps,
-        evaluate_with_lammps_library,
-        get_potential_dataframe,
-        get_potential_by_name,
-        optimize_positions_and_volume_with_lammps,
-        optimize_positions_with_lammps,
+        "calc_molecular_dynamics_thermal_expansion_with_lammps",
+        "calc_molecular_dynamics_nph_with_lammps",
+        "calc_molecular_dynamics_npt_with_lammps",
+        "calc_molecular_dynamics_nvt_with_lammps",
+        "calc_molecular_dynamics_langevin_with_lammps",
+        "calc_static_with_lammps",
+        "evaluate_with_lammps",
+        "evaluate_with_lammps_library",
+        "get_potential_dataframe",
+        "get_potential_by_name",
+        "optimize_positions_and_volume_with_lammps",
+        "optimize_positions_with_lammps",
     ]
 except ImportError:
     pass
@@ -74,6 +74,6 @@
         calc_molecular_dynamics_phonons_with_lammps,
     )
 
-    __all__ += [calc_molecular_dynamics_phonons_with_lammps]
+    __all__ += ["calc_molecular_dynamics_phonons_with_lammps"]
 except ImportError:
     pass

atomistics/calculators/ase.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-from typing import List
-
 import numpy as np
 from ase import units
 from ase.atoms import Atoms
@@ -24,7 +22,7 @@
 from atomistics.shared.tqdm_iterator import get_tqdm_iterator
 
 
-class ASEExecutor(object):
+class ASEExecutor:
     def __init__(self, ase_structure: Atoms, ase_calculator: ASECalculator) -> None:
         """
         Initialize the ASEExecutor.
@@ -147,10 +145,10 @@ def volume(self) -> float:
 @as_task_dict_evaluator
 def evaluate_with_ase(
     structure: Atoms,
-    tasks: List[str],
+    tasks: list[str],
     ase_calculator: ASECalculator,
     ase_optimizer: Optimizer = None,
-    ase_optimizer_kwargs: dict = {},
+    ase_optimizer_kwargs: dict = None,
 ) -> dict:
     """
     Evaluate tasks using ASE calculator.
@@ -165,6 +163,8 @@ def evaluate_with_ase(
     Returns:
         dict: Dictionary containing the results of the evaluated tasks.
     """
+    if ase_optimizer_kwargs is None:
+        ase_optimizer_kwargs = {}
     results = {}
     if "optimize_positions" in tasks:
         results["structure_with_optimized_positions"] = optimize_positions_with_ase(
@@ -215,54 +215,6 @@ def calc_static_with_ase(
     )
 
 
-def optimize_positions_with_ase(
-    structure: Atoms,
-    ase_calculator: ASECalculator,
-    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_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 calc_molecular_dynamics_langevin_with_ase(
     structure: Atoms,
     ase_calculator: ASECalculator,
@@ -271,7 +223,7 @@ def calc_molecular_dynamics_langevin_with_ase(
     timestep: float = 1.0,
     temperature: float = 100.0,
     friction: float = 0.002,
-    output_keys: List[str] = OutputMolecularDynamics.keys(),
+    output_keys: list[str] = OutputMolecularDynamics.keys(),
 ) -> dict:
     """
     Perform molecular dynamics simulation using the Langevin algorithm with ASE.
@@ -367,7 +319,7 @@ def calc_molecular_dynamics_thermal_expansion_with_ase(
     ttime: float = 100 * units.fs,
     pfactor: float = 2e6 * units.GPa * (units.fs**2),
     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(),
+    output_keys: list[str] = OutputThermalExpansion.keys(),
 ) -> dict:
     """
     Calculate thermal expansion using molecular dynamics simulation with ASE.
@@ -426,7 +378,7 @@ def calc_molecular_dynamics_npt_with_ase(
     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(),
+    output_keys: list[str] = OutputMolecularDynamics.keys(),
 ) -> dict:
     """
     Perform NPT molecular dynamics simulation using ASE.
@@ -477,7 +429,7 @@ def _calc_molecular_dynamics_with_ase(
     temperature: float,
     run: int,
     thermo: int,
-    output_keys: List[str],
+    output_keys: list[str],
 ) -> dict:
     """
     Perform molecular dynamics simulation using ASE.
@@ -497,7 +449,7 @@ def _calc_molecular_dynamics_with_ase(
     structure.calc = ase_calculator
     MaxwellBoltzmannDistribution(atoms=structure, temperature_K=temperature)
     cache = {q: [] for q in output_keys}
-    for i in range(int(run / thermo)):
+    for _i in range(int(run / thermo)):
         dyn.run(thermo)
         ase_instance = ASEExecutor(
             ase_structure=structure, ase_calculator=ase_calculator

atomistics/calculators/hessian.py

@@ -1,4 +1,4 @@
-from typing import Tuple, Union
+from typing import Union
 
 import numpy as np
 from ase.atoms import Atoms
@@ -68,7 +68,7 @@ def get_displacement(structure_equilibrium: Atoms, structure: Atoms) -> np.ndarr
 
 def calc_forces_transformed(
     force_constants: np.ndarray, structure_equilibrium: Atoms, structure: Atoms
-) -> Tuple[np.ndarray, np.ndarray]:
+) -> tuple[np.ndarray, np.ndarray]:
     """
     Calculate the transformed forces and displacements.
 

atomistics/calculators/lammps/__init__.py

@@ -21,23 +21,23 @@
     )
 
     __all__ = [
-        calc_molecular_dynamics_phonons_with_lammps,
+        "calc_molecular_dynamics_phonons_with_lammps",
     ]
 except ImportError:
     __all__ = []
 
 
 __all__ += [
-    calc_molecular_dynamics_thermal_expansion_with_lammps,
-    calc_molecular_dynamics_nph_with_lammps,
-    calc_molecular_dynamics_npt_with_lammps,
-    calc_molecular_dynamics_nvt_with_lammps,
-    calc_molecular_dynamics_langevin_with_lammps,
-    calc_static_with_lammps,
-    evaluate_with_lammps,
-    evaluate_with_lammps_library,
-    optimize_positions_and_volume_with_lammps,
-    optimize_positions_with_lammps,
-    get_potential_dataframe,
-    get_potential_by_name,
+    "calc_molecular_dynamics_thermal_expansion_with_lammps",
+    "calc_molecular_dynamics_nph_with_lammps",
+    "calc_molecular_dynamics_npt_with_lammps",
+    "calc_molecular_dynamics_nvt_with_lammps",
+    "calc_molecular_dynamics_langevin_with_lammps",
+    "calc_static_with_lammps",
+    "evaluate_with_lammps",
+    "evaluate_with_lammps_library",
+    "optimize_positions_and_volume_with_lammps",
+    "optimize_positions_with_lammps",
+    "get_potential_dataframe",
+    "get_potential_by_name",
 ]

atomistics/calculators/lammps/calculator.py

@@ -426,8 +426,10 @@ def evaluate_with_lammps_library(
     tasks: list[TaskName],
     potential_dataframe: DataFrame,
     lmp: LammpsASELibrary,
-    lmp_optimizer_kwargs: dict = {},
+    lmp_optimizer_kwargs: dict = None,
 ) -> dict:
+    if lmp_optimizer_kwargs is None:
+        lmp_optimizer_kwargs = {}
     results = {}
     if "optimize_positions_and_volume" in tasks:
         results["structure_with_optimized_positions_and_volume"] = (
@@ -478,8 +480,10 @@ def evaluate_with_lammps(
     log_file=None,
     library=None,
     disable_log_file: bool = True,
-    lmp_optimizer_kwargs={},
+    lmp_optimizer_kwargs=None,
 ) -> dict:
+    if lmp_optimizer_kwargs is None:
+        lmp_optimizer_kwargs = {}
     lmp = LammpsASELibrary(
         working_directory=working_directory,
         cores=cores,

atomistics/calculators/lammps/phonon.py

@@ -1,3 +1,5 @@
+import sys
+
 import dynaphopy.dynamics as dyn
 import numpy as np
 import pandas
@@ -24,27 +26,27 @@ def generate_pylammps_trajectory(
     sampling_interval: int = 1,  # in timesteps
 ):
     lmp.interactive_lib_command("neighbor 0.3 bin")
-    lmp.interactive_lib_command("timestep {}".format(time_step))
+    lmp.interactive_lib_command(f"timestep {time_step}")
 
     # Force reset temperature (overwrites lammps script)
     # This forces NVT simulation
     if temperature is not None:
         lmp.interactive_lib_command(
-            "fix int all nvt temp {0} {0} {1}".format(temperature, thermostat_mass)
+            f"fix int all nvt temp {temperature} {temperature} {thermostat_mass}"
         )
 
     # Check if correct number of atoms
     if lmp._interactive_library.extract_global("natoms", 0) < 2:
         print("Number of atoms in MD should be higher than 1!")
-        exit()
+        sys.exit()
 
     # Check if initial velocities all zero
     if not np.array(lmp._interactive_library.gather_atoms("v", 1, 3)).any():
         t = temperature if temperature is not None else 100
         lmp.interactive_lib_command(
-            "velocity all create {} 3627941 dist gaussian mom yes".format(t)
+            f"velocity all create {t} 3627941 dist gaussian mom yes"
         )
-        lmp.interactive_lib_command("velocity all scale {}".format(t))
+        lmp.interactive_lib_command(f"velocity all scale {t}")
 
     lmp.interactive_lib_command("run 0")
     simulation_cell = lmp.interactive_cells_getter()
@@ -57,7 +59,7 @@ def generate_pylammps_trajectory(
     template = get_correct_arrangement(reference, structure)
     indexing = np.argsort(template)
 
-    lmp.interactive_lib_command("run {}".format(int(relaxation_time / time_step)))
+    lmp.interactive_lib_command(f"run {int(relaxation_time / time_step)}")
 
     if not silent:
         _progress_bar(0, "lammps")
@@ -70,7 +72,7 @@ def generate_pylammps_trajectory(
                 "lammps",
             )
 
-        lmp.interactive_lib_command("run {}".format(sampling_interval))
+        lmp.interactive_lib_command(f"run {sampling_interval}")
         energy.append(lmp.interactive_energy_pot_getter())
         velocity.append(lmp.interactive_velocities_getter()[indexing, :])
 
@@ -103,11 +105,13 @@ def calc_molecular_dynamics_phonons_with_lammps(
     time_step: float = 0.001,  # ps
     relaxation_time: int = 5,  # ps
     silent: bool = True,
-    supercell: list[int] = [2, 2, 2],
+    supercell: list[int] = None,
     memmap: bool = False,
     velocity_only: bool = True,
     temperature: float = 300.0,
 ):
+    if supercell is None:
+        supercell = [2, 2, 2]
     dp_structure = Structure(
         cell=phonopy_unitcell.get_cell(),
         scaled_positions=phonopy_unitcell.get_scaled_positions(),