atomistics 0.2.4__tar.gz → 0.3.0__tar.gz

atomistics-0.3.0/.gitignore

@@ -0,0 +1,4 @@
+*.pyc
+.DS_Store
+.idea/
+notebooks/.ipynb_checkpoints/

{atomistics-0.2.4/atomistics.egg-info → atomistics-0.3.0}/PKG-INFO

@@ -1,7 +1,10 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: atomistics
-Version: 0.2.4
+Version: 0.3.0
 Summary: Interfaces for atomistic simulation codes and workflows
+Project-URL: Homepage, https://github.com/pyiron/atomistics
+Project-URL: Documentation, https://atomistics.readthedocs.io
+Project-URL: Repository, https://github.com/pyiron/atomistics
 Author-email: Jan Janssen <janssen@mpie.de>
 License: BSD 3-Clause License
         
@@ -32,56 +35,53 @@ License: BSD 3-Clause License
         CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-Project-URL: Homepage, https://github.com/pyiron/atomistics
-Project-URL: Documentation, https://atomistics.readthedocs.io
-Project-URL: Repository, https://github.com/pyiron/atomistics
+License-File: LICENSE
 Keywords: pyiron
 Classifier: Development Status :: 5 - Production/Stable
-Classifier: Topic :: Scientific/Engineering :: Physics
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: <3.13,>=3.9
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: ase<=3.24.0,>=3.23.0
-Requires-Dist: numpy==1.26.4
-Requires-Dist: scipy<=1.15.2,>=1.11.1
+Requires-Dist: ase<=3.26.0,>=3.23.0
+Requires-Dist: numpy<=2.3.3,>=1.26.4
+Requires-Dist: scipy<=1.15.2,>=1.11.2
 Requires-Dist: spglib<=2.6.0,>=2.0.2
-Provides-Extra: phonopy
-Requires-Dist: phonopy<=2.38.0,>=2.20.0; extra == "phonopy"
-Requires-Dist: seekpath<=2.1.0,>=1.9.0; extra == "phonopy"
-Requires-Dist: structuretoolkit<=0.0.31,>=0.0.10; extra == "phonopy"
+Provides-Extra: experimental
+Requires-Dist: lxml<=6.0.2,>=4.9.1; extra == 'experimental'
+Requires-Dist: mendeleev<=1.1.0,>=0.12.0; extra == 'experimental'
+Requires-Dist: pandas<=2.3.2,>=2.0.3; extra == 'experimental'
+Requires-Dist: requests<=2.32.5,>=2.24.0; extra == 'experimental'
 Provides-Extra: gpaw
-Requires-Dist: gpaw<=24.6.0,>=20.1.0; extra == "gpaw"
+Requires-Dist: gpaw<=25.7.0,>=21.6.0; extra == 'gpaw'
 Provides-Extra: lammps
-Requires-Dist: pylammpsmpi<=0.2.31,>=0.2.1; extra == "lammps"
-Requires-Dist: jinja2<=3.1.6,>=2.11.3; extra == "lammps"
-Requires-Dist: pandas<=2.2.3,>=2.0.3; extra == "lammps"
-Requires-Dist: pyiron_lammps<=0.4.0,>=0.3.2; extra == "lammps"
+Requires-Dist: jinja2<=3.1.6,>=2.11.3; extra == 'lammps'
+Requires-Dist: pandas<=2.3.2,>=2.0.3; extra == 'lammps'
+Requires-Dist: pyiron-lammps<=0.4.7,>=0.3.2; extra == 'lammps'
+Requires-Dist: pylammpsmpi<=0.3.3,>=0.2.1; extra == 'lammps'
 Provides-Extra: lammps-phonons
-Requires-Dist: pylammpsmpi<=0.2.31,>=0.2.1; extra == "lammps-phonons"
-Requires-Dist: jinja2<=3.1.6,>=2.11.3; extra == "lammps-phonons"
-Requires-Dist: pandas<=2.2.3,>=2.0.3; extra == "lammps-phonons"
-Requires-Dist: dynaphopy<=1.17.16,>=1.17.5; extra == "lammps-phonons"
-Requires-Dist: pyiron_lammps<=0.4.0,>=0.3.2; extra == "lammps-phonons"
-Provides-Extra: experimental
-Requires-Dist: lxml<=5.3.1,>=4.9.1; extra == "experimental"
-Requires-Dist: mendeleev<=0.19.0,>=0.12.0; extra == "experimental"
-Requires-Dist: pandas<=2.2.3,>=2.0.3; extra == "experimental"
-Requires-Dist: requests<=2.32.3,>=2.24.0; extra == "experimental"
-Provides-Extra: sphinxdft
-Requires-Dist: sphinx-parser==0.0.1; extra == "sphinxdft"
+Requires-Dist: dynaphopy<=1.17.16,>=1.17.11; extra == 'lammps-phonons'
+Requires-Dist: jinja2<=3.1.6,>=2.11.3; extra == 'lammps-phonons'
+Requires-Dist: pandas<=2.3.2,>=2.0.3; extra == 'lammps-phonons'
+Requires-Dist: pyiron-lammps<=0.4.7,>=0.3.2; extra == 'lammps-phonons'
+Requires-Dist: pylammpsmpi<=0.3.3,>=0.2.1; extra == 'lammps-phonons'
+Provides-Extra: phonopy
+Requires-Dist: phonopy<=2.43.2,>=2.20.0; extra == 'phonopy'
+Requires-Dist: seekpath<=2.1.0,>=1.9.0; extra == 'phonopy'
+Requires-Dist: structuretoolkit<=0.0.35,>=0.0.10; extra == 'phonopy'
 Provides-Extra: qe
-Requires-Dist: pwtools==1.3.0; extra == "qe"
+Requires-Dist: pwtools==1.3.0; extra == 'qe'
+Provides-Extra: sphinxdft
+Requires-Dist: sphinx-parser==0.1.0; extra == 'sphinxdft'
 Provides-Extra: tqdm
-Requires-Dist: tqdm==4.67.1; extra == "tqdm"
+Requires-Dist: tqdm==4.67.1; extra == 'tqdm'
 Provides-Extra: vasp
-Requires-Dist: pyiron_vasp==0.2.4; extra == "vasp"
+Requires-Dist: pyiron-vasp==0.2.13; extra == 'vasp'
+Description-Content-Type: text/markdown
 
 # atomistics
 [![Pipeline](https://github.com/pyiron/atomistics/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/atomistics/actions/workflows/pipeline.yml)
@@ -97,6 +97,7 @@ simulation codes - named `calculators`. The supported simulation codes in alphab
 * [LAMMPS](https://www.lammps.org) - Molecular Dynamics
 * [Quantum Espresso](https://www.quantum-espresso.org) - Integrated suite of Open-Source computer codes for electronic-structure calculations
 * [Siesta](https://siesta-project.org) - Electronic structure calculations and ab initio molecular dynamics
+* [SPHInX](https://sxrepo.mpie.de) - Plane wave DFT with interactive tools, charged defect correction and spin constraints
 
 For majority of these simulation codes the `atomistics` package use the [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/)
 to interface the underlying C/ C++ and Fortran Codes with the Python programming language. Still this approach limits
@@ -125,20 +126,14 @@ equilibrium bulk modulus and its derivative using the [GPAW](https://wiki.fysik.
 
 ```python
 from ase.build import bulk
-from atomistics.calculators import evaluate_with_ase
-from atomistics.workflows import EnergyVolumeCurveWorkflow
-from gpaw import GPAW, PW
+from atomistics.workflows import get_tasks_for_energy_volume_curve
 
-workflow = EnergyVolumeCurveWorkflow(
+task_dict = get_tasks_for_energy_volume_curve(
     structure=bulk("Al", a=4.05, cubic=True),
     num_points=11,
-    fit_type='polynomial',
-    fit_order=3,
     vol_range=0.05,
     axes=['x', 'y', 'z'],
-    strains=None,
 )
-task_dict = workflow.generate_structures()
 print(task_dict)
 ```
 ```
@@ -166,6 +161,9 @@ generated structures. Each structure is labeled by the ratio of compression or e
 `task_dict` is evaluate with the [GPAW](https://wiki.fysik.dtu.dk/gpaw/) simulation code using the
 `evaluate_with_ase()` function:
 ```python
+from atomistics.calculators import evaluate_with_ase
+from gpaw import GPAW, PW
+
 result_dict = evaluate_with_ase(
     task_dict=task_dict,
     ase_calculator=GPAW(
@@ -198,7 +196,14 @@ is able to match the calculation results to the corresponding structure. Finally
 function takes the `result_dict` as an input and fits the Equation of State with the fitting parameters defined in
 the first step:
 ```python
-fit_dict = workflow.analyse_structures(output_dict=result_dict)
+from atomistics.workflows import analyse_results_for_energy_volume_curve
+
+fit_dict = analyse_results_for_energy_volume_curve(
+    output_dict=result_dict, 
+    task_dict=task_dict,
+    fit_type='polynomial',
+    fit_order=3,
+)
 print(fit_dict)
 ```
 ```

{atomistics-0.2.4 → atomistics-0.3.0}/README.md

@@ -12,6 +12,7 @@ simulation codes - named `calculators`. The supported simulation codes in alphab
 * [LAMMPS](https://www.lammps.org) - Molecular Dynamics
 * [Quantum Espresso](https://www.quantum-espresso.org) - Integrated suite of Open-Source computer codes for electronic-structure calculations
 * [Siesta](https://siesta-project.org) - Electronic structure calculations and ab initio molecular dynamics
+* [SPHInX](https://sxrepo.mpie.de) - Plane wave DFT with interactive tools, charged defect correction and spin constraints
 
 For majority of these simulation codes the `atomistics` package use the [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase/)
 to interface the underlying C/ C++ and Fortran Codes with the Python programming language. Still this approach limits
@@ -40,20 +41,14 @@ equilibrium bulk modulus and its derivative using the [GPAW](https://wiki.fysik.
 
 ```python
 from ase.build import bulk
-from atomistics.calculators import evaluate_with_ase
-from atomistics.workflows import EnergyVolumeCurveWorkflow
-from gpaw import GPAW, PW
+from atomistics.workflows import get_tasks_for_energy_volume_curve
 
-workflow = EnergyVolumeCurveWorkflow(
+task_dict = get_tasks_for_energy_volume_curve(
     structure=bulk("Al", a=4.05, cubic=True),
     num_points=11,
-    fit_type='polynomial',
-    fit_order=3,
     vol_range=0.05,
     axes=['x', 'y', 'z'],
-    strains=None,
 )
-task_dict = workflow.generate_structures()
 print(task_dict)
 ```
 ```
@@ -81,6 +76,9 @@ generated structures. Each structure is labeled by the ratio of compression or e
 `task_dict` is evaluate with the [GPAW](https://wiki.fysik.dtu.dk/gpaw/) simulation code using the
 `evaluate_with_ase()` function:
 ```python
+from atomistics.calculators import evaluate_with_ase
+from gpaw import GPAW, PW
+
 result_dict = evaluate_with_ase(
     task_dict=task_dict,
     ase_calculator=GPAW(
@@ -113,7 +111,14 @@ is able to match the calculation results to the corresponding structure. Finally
 function takes the `result_dict` as an input and fits the Equation of State with the fitting parameters defined in
 the first step:
 ```python
-fit_dict = workflow.analyse_structures(output_dict=result_dict)
+from atomistics.workflows import analyse_results_for_energy_volume_curve
+
+fit_dict = analyse_results_for_energy_volume_curve(
+    output_dict=result_dict, 
+    task_dict=task_dict,
+    fit_type='polynomial',
+    fit_order=3,
+)
 print(fit_dict)
 ```
 ```

atomistics-0.3.0/atomistics/__init__.py

@@ -0,0 +1,3 @@
+import atomistics._version
+
+__version__ = atomistics._version.__version__

atomistics-0.3.0/atomistics/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.3.0'
+__version_tuple__ = version_tuple = (0, 3, 0)
+
+__commit_id__ = commit_id = None

{atomistics-0.2.4 → atomistics-0.3.0}/atomistics/calculators/__init__.py

@@ -9,8 +9,9 @@ from atomistics.calculators.ase import (
     optimize_volume_with_ase,
 )
 from atomistics.calculators.hessian import evaluate_with_hessian
+from atomistics.shared.import_warning import raise_warning
 
-__all__ = [
+__all__: list[str] = [
     "calc_molecular_dynamics_langevin_with_ase",
     "calc_molecular_dynamics_npt_with_ase",
     "calc_molecular_dynamics_thermal_expansion_with_ase",
@@ -21,6 +22,35 @@ __all__ = [
     "optimize_volume_with_ase",
     "evaluate_with_hessian",
 ]
+lammps_functions: list[str] = [
+    "calc_molecular_dynamics_thermal_expansion_with_lammpslib",
+    "calc_molecular_dynamics_nph_with_lammpslib",
+    "calc_molecular_dynamics_npt_with_lammpslib",
+    "calc_molecular_dynamics_nvt_with_lammpslib",
+    "calc_molecular_dynamics_langevin_with_lammpslib",
+    "calc_static_with_lammpslib",
+    "evaluate_with_lammpslib",
+    "evaluate_with_lammpslib_library_interface",
+    "get_potential_dataframe",
+    "get_potential_by_name",
+    "optimize_positions_and_volume_with_lammpslib",
+    "optimize_positions_with_lammpslib",
+]
+lammps_phonon_functions: list[str] = ["calc_molecular_dynamics_phonons_with_lammpslib"]
+quantum_espresso_function: list[str] = [
+    "calc_static_with_qe",
+    "evaluate_with_qe",
+    "optimize_positions_and_volume_with_qe",
+]
+sphinx_functions: list[str] = ["evaluate_with_sphinx"]
+vasp_functions: list[str] = [
+    "evaluate_with_vasp",
+    "calc_static_with_vasp",
+    "optimize_positions_and_volume_with_vasp",
+    "optimize_positions_with_vasp",
+    "optimize_cell_with_vasp",
+    "optimize_volume_with_vasp",
+]
 
 
 try:
@@ -29,14 +59,11 @@ try:
         evaluate_with_qe,
         optimize_positions_and_volume_with_qe,
     )
+except ImportError as e:
+    raise_warning(module_list=quantum_espresso_function, import_error=e)
+else:
+    __all__ += quantum_espresso_function
 
-    __all__ += [
-        "calc_static_with_qe",
-        "evaluate_with_qe",
-        "optimize_positions_and_volume_with_qe",
-    ]
-except ImportError:
-    pass
 
 try:
     from atomistics.calculators.lammps import (
@@ -53,43 +80,31 @@ try:
         optimize_positions_and_volume_with_lammpslib,
         optimize_positions_with_lammpslib,
     )
+except ImportError as e:
+    raise_warning(module_list=lammps_functions, import_error=e)
+else:
+    __all__ += lammps_functions
 
-    __all__ += [
-        "calc_molecular_dynamics_thermal_expansion_with_lammpslib",
-        "calc_molecular_dynamics_nph_with_lammpslib",
-        "calc_molecular_dynamics_npt_with_lammpslib",
-        "calc_molecular_dynamics_nvt_with_lammpslib",
-        "calc_molecular_dynamics_langevin_with_lammpslib",
-        "calc_static_with_lammpslib",
-        "evaluate_with_lammpslib",
-        "evaluate_with_lammpslib_library_interface",
-        "get_potential_dataframe",
-        "get_potential_by_name",
-        "optimize_positions_and_volume_with_lammpslib",
-        "optimize_positions_with_lammpslib",
-    ]
-except ImportError:
-    pass
 
 try:
     from atomistics.calculators.lammps.phonon import (
         calc_molecular_dynamics_phonons_with_lammpslib,
     )
+except ImportError as e:
+    raise_warning(module_list=lammps_phonon_functions, import_error=e)
+else:
+    __all__ += lammps_phonon_functions
 
-    __all__ += ["calc_molecular_dynamics_phonons_with_lammpslib"]
-except ImportError:
-    pass
 
 try:
     from atomistics.calculators.sphinxdft import (
         evaluate_with_sphinx,
     )
+except ImportError as e:
+    raise_warning(module_list=sphinx_functions, import_error=e)
+else:
+    __all__ += sphinx_functions
 
-    __all__ += [
-        "evaluate_with_sphinx",
-    ]
-except ImportError:
-    pass
 
 try:
     from atomistics.calculators.vasp import (
@@ -100,14 +115,7 @@ try:
         optimize_positions_with_vasp,
         optimize_volume_with_vasp,
     )
-
-    __all__ += [
-        "evaluate_with_vasp",
-        "calc_static_with_vasp",
-        "optimize_positions_and_volume_with_vasp",
-        "optimize_positions_with_vasp",
-        "optimize_cell_with_vasp",
-        "optimize_volume_with_vasp",
-    ]
-except ImportError:
-    pass
+except ImportError as e:
+    raise_warning(module_list=vasp_functions, import_error=e)
+else:
+    __all__ += vasp_functions

{atomistics-0.2.4 → atomistics-0.3.0}/atomistics/calculators/ase.py

@@ -146,22 +146,22 @@ class ASEExecutor:
 @as_task_dict_evaluator
 def evaluate_with_ase(
     structure: Atoms,
-    tasks: list[str],
+    tasks: list,
     ase_calculator: ASECalculator,
-    ase_optimizer: Optimizer = None,
+    ase_optimizer: type[Optimizer] = None,
     ase_optimizer_kwargs: dict = None,
-    filter_class: Filter = UnitCellFilter,
+    filter_class: type[Filter] = UnitCellFilter,
 ) -> dict:
     """
     Evaluate tasks using ASE calculator.
 
     Args:
         structure (Atoms): The ASE structure object.
-        tasks (list[TaskName]): List of tasks to evaluate.
+        tasks (list): 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 (Type[Optimizer], optional): The ASE optimizer object. Defaults to None.
         ase_optimizer_kwargs (dict, optional): Keyword arguments for the ASE optimizer. Defaults to {}.
-        filter_class (Filter): The ASE filter class to use for filtering during structure optimization.
+        filter_class (Type[Filter]): The ASE filter class to use for filtering during structure optimization.
 
     Returns:
         dict: Dictionary containing the results of the evaluated tasks.
@@ -240,18 +240,18 @@ def calc_molecular_dynamics_langevin_with_ase(
     """
     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.
+    Args:
+        structure (Atoms): The atomic structure to simulate.
+        ase_calculator (ASECalculator): 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.
+        dict: A dictionary containing the calculated properties at each MD step.
     """
     return _calc_molecular_dynamics_with_ase(
         dyn=Langevin(
@@ -272,7 +272,7 @@ def calc_molecular_dynamics_langevin_with_ase(
 def optimize_positions_with_ase(
     structure: Atoms,
     ase_calculator: ASECalculator,
-    ase_optimizer: Optimizer,
+    ase_optimizer: type[Optimizer],
     ase_optimizer_kwargs: dict,
 ) -> Atoms:
     """
@@ -297,9 +297,9 @@ def optimize_positions_with_ase(
 def optimize_positions_and_volume_with_ase(
     structure: Atoms,
     ase_calculator: ASECalculator,
-    ase_optimizer: Optimizer,
+    ase_optimizer: type[Optimizer],
     ase_optimizer_kwargs: dict,
-    filter_class: Filter = UnitCellFilter,
+    filter_class: type[Filter] = UnitCellFilter,
 ) -> Atoms:
     """
     Optimize the atomic positions and cell volume of the structure using ASE optimizer.
@@ -324,9 +324,9 @@ def optimize_positions_and_volume_with_ase(
 def optimize_volume_with_ase(
     structure: Atoms,
     ase_calculator: ASECalculator,
-    ase_optimizer: Optimizer,
+    ase_optimizer: type[Optimizer],
     ase_optimizer_kwargs: dict,
-    filter_class: Filter = UnitCellFilter,
+    filter_class: type[Filter] = UnitCellFilter,
     hydrostatic_strain: bool = True,
 ) -> Atoms:
     """
@@ -387,7 +387,7 @@ def calc_molecular_dynamics_thermal_expansion_with_ase(
         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().
+        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.
@@ -444,7 +444,7 @@ def calc_molecular_dynamics_npt_with_ase(
         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().
+        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.
@@ -486,13 +486,13 @@ def _calc_molecular_dynamics_with_ase(
     Perform molecular dynamics simulation using ASE.
 
     Args:
-        dyn: The ASE dynamics object.
+        dyn (ase.md.MDLogger): 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.
+        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.

{atomistics-0.2.4 → atomistics-0.3.0}/atomistics/calculators/lammps/__init__.py

@@ -14,20 +14,9 @@ from atomistics.calculators.lammps.potential import (
     get_potential_by_name,
     get_potential_dataframe,
 )
+from atomistics.shared.import_warning import raise_warning
 
-try:
-    from atomistics.calculators.lammps.phonon import (
-        calc_molecular_dynamics_phonons_with_lammpslib,
-    )
-
-    __all__ = [
-        "calc_molecular_dynamics_phonons_with_lammpslib",
-    ]
-except ImportError:
-    __all__ = []
-
-
-__all__ += [
+__all__: list[str] = [
     "calc_molecular_dynamics_thermal_expansion_with_lammpslib",
     "calc_molecular_dynamics_nph_with_lammpslib",
     "calc_molecular_dynamics_npt_with_lammpslib",
@@ -41,3 +30,14 @@ __all__ += [
     "get_potential_dataframe",
     "get_potential_by_name",
 ]
+lammps_phonon_functions: list[str] = ["calc_molecular_dynamics_phonons_with_lammpslib"]
+
+
+try:
+    from atomistics.calculators.lammps.phonon import (
+        calc_molecular_dynamics_phonons_with_lammpslib,
+    )
+except ImportError as e:
+    raise_warning(module_list=lammps_phonon_functions, import_error=e)
+else:
+    __all__ += lammps_phonon_functions