atomistics 0.2.2__tar.gz → 0.2.4__tar.gz

{atomistics-0.2.2/atomistics.egg-info → atomistics-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: atomistics
-Version: 0.2.2
+Version: 0.2.4
 Summary: Interfaces for atomistic simulation codes and workflows
 Author-email: Jan Janssen <janssen@mpie.de>
 License: BSD 3-Clause License
@@ -51,7 +51,7 @@ 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: spglib<=2.5.0,>=2.0.2
+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"
@@ -60,12 +60,12 @@ Provides-Extra: gpaw
 Requires-Dist: gpaw<=24.6.0,>=20.1.0; extra == "gpaw"
 Provides-Extra: lammps
 Requires-Dist: pylammpsmpi<=0.2.31,>=0.2.1; extra == "lammps"
-Requires-Dist: jinja2<=3.1.5,>=2.11.3; 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"
 Provides-Extra: lammps-phonons
 Requires-Dist: pylammpsmpi<=0.2.31,>=0.2.1; extra == "lammps-phonons"
-Requires-Dist: jinja2<=3.1.5,>=2.11.3; 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"

{atomistics-0.2.2 → atomistics-0.2.4}/atomistics/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-03-05T08:13:01+0100",
+ "date": "2025-03-10T21:45:26+0000",
  "dirty": true,
  "error": null,
- "full-revisionid": "5b518f33f60f904bf2c88dff51b72a07fe99091c",
- "version": "0.2.2"
+ "full-revisionid": "bb2b344b87932e4d5e02a4e7f44a87da5c83202b",
+ "version": "0.2.4"
 }
 '''  # END VERSION_JSON
 

{atomistics-0.2.2 → atomistics-0.2.4}/atomistics/calculators/__init__.py

@@ -6,6 +6,7 @@ from atomistics.calculators.ase import (
     evaluate_with_ase,
     optimize_positions_and_volume_with_ase,
     optimize_positions_with_ase,
+    optimize_volume_with_ase,
 )
 from atomistics.calculators.hessian import evaluate_with_hessian
 
@@ -17,6 +18,7 @@ __all__ = [
     "evaluate_with_ase",
     "optimize_positions_with_ase",
     "optimize_positions_and_volume_with_ase",
+    "optimize_volume_with_ase",
     "evaluate_with_hessian",
 ]
 
@@ -88,3 +90,24 @@ try:
     ]
 except ImportError:
     pass
+
+try:
+    from atomistics.calculators.vasp import (
+        calc_static_with_vasp,
+        evaluate_with_vasp,
+        optimize_cell_with_vasp,
+        optimize_positions_and_volume_with_vasp,
+        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

{atomistics-0.2.2 → atomistics-0.2.4}/atomistics/calculators/ase.py

@@ -5,7 +5,8 @@ from ase import units
 from ase.atoms import Atoms
 from ase.calculators.calculator import Calculator as ASECalculator
 from ase.calculators.calculator import PropertyNotImplementedError
-from ase.constraints import UnitCellFilter
+from ase.constraints import FixAtoms
+from ase.filters import Filter, UnitCellFilter
 from ase.md.langevin import Langevin
 from ase.md.npt import NPT
 from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
@@ -149,6 +150,7 @@ def evaluate_with_ase(
     ase_calculator: ASECalculator,
     ase_optimizer: Optimizer = None,
     ase_optimizer_kwargs: dict = None,
+    filter_class: Filter = UnitCellFilter,
 ) -> dict:
     """
     Evaluate tasks using ASE calculator.
@@ -159,6 +161,7 @@ def evaluate_with_ase(
         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 {}.
+        filter_class (Filter): The ASE filter class to use for filtering during structure optimization.
 
     Returns:
         dict: Dictionary containing the results of the evaluated tasks.
@@ -180,8 +183,17 @@ def evaluate_with_ase(
                 ase_calculator=ase_calculator,
                 ase_optimizer=ase_optimizer,
                 ase_optimizer_kwargs=ase_optimizer_kwargs,
+                filter_class=filter_class,
             )
         )
+    elif "optimize_volume" in tasks:
+        results["structure_with_optimized_volume"] = optimize_volume_with_ase(
+            structure=structure,
+            ase_calculator=ase_calculator,
+            ase_optimizer=ase_optimizer,
+            ase_optimizer_kwargs=ase_optimizer_kwargs,
+            filter_class=filter_class,
+        )
     elif "calc_energy" in tasks or "calc_forces" in tasks or "calc_stress" in tasks:
         return calc_static_with_ase(
             structure=structure,
@@ -287,6 +299,7 @@ def optimize_positions_and_volume_with_ase(
     ase_calculator: ASECalculator,
     ase_optimizer: Optimizer,
     ase_optimizer_kwargs: dict,
+    filter_class: Filter = UnitCellFilter,
 ) -> Atoms:
     """
     Optimize the atomic positions and cell volume of the structure using ASE optimizer.
@@ -296,13 +309,51 @@ def optimize_positions_and_volume_with_ase(
         ase_calculator (ASECalculator): The ASE calculator object.
         ase_optimizer (Optimizer): The ASE optimizer object.
         ase_optimizer_kwargs (dict): Keyword arguments for the ASE optimizer.
+        filter_class (Filter): The ASE filter class to use for filtering during structure optimization.
+
+    Returns:
+        Atoms: The optimized structure.
+    """
+    structure_optimized = structure.copy()
+    structure_optimized.calc = ase_calculator
+    ase_optimizer_obj = ase_optimizer(filter_class(structure_optimized))
+    ase_optimizer_obj.run(**ase_optimizer_kwargs)
+    return structure_optimized
+
+
+def optimize_volume_with_ase(
+    structure: Atoms,
+    ase_calculator: ASECalculator,
+    ase_optimizer: Optimizer,
+    ase_optimizer_kwargs: dict,
+    filter_class: Filter = UnitCellFilter,
+    hydrostatic_strain: bool = True,
+) -> Atoms:
+    """
+    Optimize the 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.
+        filter_class (Filter): The ASE filter class to use for filtering during structure optimization.
+        hydrostatic_strain (bool): Constrain the cell by only allowing hydrostatic deformation.
 
     Returns:
         Atoms: The optimized structure.
     """
     structure_optimized = structure.copy()
     structure_optimized.calc = ase_calculator
-    ase_optimizer_obj = ase_optimizer(UnitCellFilter(structure_optimized))
+    structure_optimized.set_constraint(
+        FixAtoms(np.ones(len(structure_optimized), dtype=bool))
+    )
+    ase_optimizer_obj = ase_optimizer(
+        filter_class(
+            atoms=structure_optimized,
+            hydrostatic_strain=hydrostatic_strain,
+        )
+    )
     ase_optimizer_obj.run(**ase_optimizer_kwargs)
     return structure_optimized
 

{atomistics-0.2.2 → atomistics-0.2.4}/atomistics/calculators/interface.py

@@ -19,6 +19,8 @@ class TaskEnum(StrEnum):
     calc_stress = "calc_stress"
     optimize_positions = "optimize_positions"
     optimize_positions_and_volume = "optimize_positions_and_volume"
+    optimize_volume = "optimize_volume"
+    optimize_cell = "optimize_cell"
     calc_molecular_dynamics_thermal_expansion = (
         "calc_molecular_dynamics_thermal_expansion"
     )
@@ -28,8 +30,10 @@ class TaskOutputEnum(Enum):
     energy = "calc_energy"
     forces = "calc_forces"
     stress = "calc_stress"
+    structure_with_optimized_cell = "optimize_cell"
     structure_with_optimized_positions = "optimize_positions"
     structure_with_optimized_positions_and_volume = "optimize_positions_and_volume"
+    structure_with_optimized_volume = "optimize_volume"
     volume_over_temperature = "calc_molecular_dynamics_thermal_expansion"
 
 

{atomistics-0.2.2 → atomistics-0.2.4}/atomistics/calculators/vasp.py

@@ -155,6 +155,86 @@ def optimize_positions_and_volume_with_vasp(
     return structure_copy
 
 
+def optimize_volume_with_vasp(
+    structure: Atoms,
+    working_directory: str,
+    executable_function: callable,
+    prec: str = "Accurate",
+    algo: str = "Fast",
+    lreal: bool = False,
+    lwave: bool = False,
+    lorbit: int = 0,
+    isif: int = 7,
+    ibrion: int = 2,
+    nsw: int = 100,
+    kpts: Optional[list[int, int, int]] = None,
+    **kwargs,
+) -> Atoms:
+    if kpts is None:
+        kpts = [4, 4, 4]
+    write_input(
+        working_directory=working_directory,
+        atoms=structure,
+        prec=prec,
+        algo=algo,
+        lreal=lreal,
+        lwave=lwave,
+        lorbit=lorbit,
+        kpts=kpts,
+        isif=isif,
+        ibrion=ibrion,
+        nsw=nsw,
+        **kwargs,
+    )
+    executable_function(working_directory)
+    output_dict = parse_vasp_output(
+        working_directory=working_directory, structure=structure
+    )
+    structure_copy = structure.copy()
+    structure_copy.set_cell(output_dict["generic"]["cells"][-1], scale_atoms=True)
+    return structure_copy
+
+
+def optimize_cell_with_vasp(
+    structure: Atoms,
+    working_directory: str,
+    executable_function: callable,
+    prec: str = "Accurate",
+    algo: str = "Fast",
+    lreal: bool = False,
+    lwave: bool = False,
+    lorbit: int = 0,
+    isif: int = 5,
+    ibrion: int = 2,
+    nsw: int = 100,
+    kpts: Optional[list[int, int, int]] = None,
+    **kwargs,
+) -> Atoms:
+    if kpts is None:
+        kpts = [4, 4, 4]
+    write_input(
+        working_directory=working_directory,
+        atoms=structure,
+        prec=prec,
+        algo=algo,
+        lreal=lreal,
+        lwave=lwave,
+        lorbit=lorbit,
+        kpts=kpts,
+        isif=isif,
+        ibrion=ibrion,
+        nsw=nsw,
+        **kwargs,
+    )
+    executable_function(working_directory)
+    output_dict = parse_vasp_output(
+        working_directory=working_directory, structure=structure
+    )
+    structure_copy = structure.copy()
+    structure_copy.set_cell(output_dict["generic"]["cells"][-1], scale_atoms=True)
+    return structure_copy
+
+
 @as_task_dict_evaluator
 def evaluate_with_vasp(
     structure: Atoms,
@@ -172,7 +252,20 @@ def evaluate_with_vasp(
     if kpts is None:
         kpts = [4, 4, 4]
     results = {}
-    if "optimize_positions_and_volume" in tasks:
+    if "optimize_cell" in tasks:
+        results["structure_with_optimized_cell"] = optimize_cell_with_vasp(
+            structure=structure,
+            working_directory=working_directory,
+            executable_function=executable_function,
+            prec=prec,
+            algo=algo,
+            lreal=lreal,
+            lwave=lwave,
+            lorbit=lorbit,
+            kpts=kpts,
+            **kwargs,
+        )
+    elif "optimize_positions_and_volume" in tasks:
         results["structure_with_optimized_positions_and_volume"] = (
             optimize_positions_and_volume_with_vasp(
                 structure=structure,
@@ -200,6 +293,19 @@ def evaluate_with_vasp(
             kpts=kpts,
             **kwargs,
         )
+    elif "optimize_volume" in tasks:
+        results["structure_with_optimized_volume"] = optimize_volume_with_vasp(
+            structure=structure,
+            working_directory=working_directory,
+            executable_function=executable_function,
+            prec=prec,
+            algo=algo,
+            lreal=lreal,
+            lwave=lwave,
+            lorbit=lorbit,
+            kpts=kpts,
+            **kwargs,
+        )
     elif "calc_energy" in tasks or "calc_forces" in tasks or "calc_stress" in tasks:
         return calc_static_with_vasp(
             structure=structure,

{atomistics-0.2.2 → atomistics-0.2.4}/atomistics/workflows/__init__.py

@@ -5,8 +5,10 @@ from atomistics.workflows.molecular_dynamics import (
     calc_molecular_dynamics_thermal_expansion,
 )
 from atomistics.workflows.structure_optimization import (
+    optimize_cell,
     optimize_positions,
     optimize_positions_and_volume,
+    optimize_volume,
 )
 
 __all__ = [
@@ -14,8 +16,10 @@ __all__ = [
     "EnergyVolumeCurveWorkflow",
     "LangevinWorkflow",
     "calc_molecular_dynamics_thermal_expansion",
+    "optimize_cell",
     "optimize_positions",
     "optimize_positions_and_volume",
+    "optimize_volume",
 ]
 
 

{atomistics-0.2.2 → atomistics-0.2.4}/atomistics/workflows/evcurve/fit.py

@@ -1,121 +1,23 @@
 import numpy as np
 import scipy.constants
 import scipy.optimize
+from ase.eos import (
+    birch,
+    murnaghan,
+    pouriertarantola,
+)
+from ase.eos import (
+    birchmurnaghan as birchmurnaghan_energy,
+)
+from ase.eos import (
+    vinet as vinet_energy,
+)
 
 eV_div_A3_to_GPa = (
     1e21 / scipy.constants.physical_constants["joule-electron volt relationship"][0]
 )
 
 
-# https://gitlab.com/ase/ase/blob/master/ase/eos.py
-def birchmurnaghan_energy(
-    V: np.ndarray, E0: float, B0: float, BP: float, V0: float
-) -> np.ndarray:
-    """
-    BirchMurnaghan equation from PRB 70, 224107
-
-    Args:
-        V (np.ndarray): Array of volumes
-        E0 (float): Energy at equilibrium volume
-        B0 (float): Bulk modulus at equilibrium volume
-        BP (float): Pressure derivative of bulk modulus
-        V0 (float): Equilibrium volume
-
-    Returns:
-        np.ndarray: Array of energies
-    """
-    eta = (V0 / V) ** (1 / 3)
-    return E0 + 9 * B0 * V0 / 16 * (eta**2 - 1) ** 2 * (
-        6 + BP * (eta**2 - 1) - 4 * eta**2
-    )
-
-
-def vinet_energy(
-    V: np.ndarray, E0: float, B0: float, BP: float, V0: float
-) -> np.ndarray:
-    """
-    Vinet equation from PRB 70, 224107
-
-    Args:
-        V (np.ndarray): Array of volumes
-        E0 (float): Energy at equilibrium volume
-        B0 (float): Bulk modulus at equilibrium volume
-        BP (float): Pressure derivative of bulk modulus
-        V0 (float): Equilibrium volume
-
-    Returns:
-        np.ndarray: Array of energies
-    """
-    eta = (V / V0) ** (1 / 3)
-    return E0 + 2 * B0 * V0 / (BP - 1) ** 2 * (
-        2 - (5 + 3 * BP * (eta - 1) - 3 * eta) * np.exp(-3 * (BP - 1) * (eta - 1) / 2)
-    )
-
-
-def murnaghan(V: np.ndarray, E0: float, B0: float, BP: float, V0: float) -> np.ndarray:
-    """
-    Murnaghan equation from PRB 28, 5480 (1983)
-
-    Args:
-        V (np.ndarray): Array of volumes
-        E0 (float): Energy at equilibrium volume
-        B0 (float): Bulk modulus at equilibrium volume
-        BP (float): Pressure derivative of bulk modulus
-        V0 (float): Equilibrium volume
-
-    Returns:
-        np.ndarray: Array of energies
-    """
-    E = E0 + B0 * V / BP * (((V0 / V) ** BP) / (BP - 1) + 1) - V0 * B0 / (BP - 1)
-    return E
-
-
-def birch(V: np.ndarray, E0: float, B0: float, BP: float, V0: float) -> np.ndarray:
-    """
-    Birch equation from Intermetallic compounds: Principles and Practice, Vol. I: Principles
-    Chapter 9 pages 195-210 by M. Mehl. B. Klein, D. Papaconstantopoulos
-
-    Args:
-        V (np.ndarray): Array of volumes
-        E0 (float): Energy at equilibrium volume
-        B0 (float): Bulk modulus at equilibrium volume
-        BP (float): Pressure derivative of bulk modulus
-        V0 (float): Equilibrium volume
-
-    Returns:
-        np.ndarray: Array of energies
-    """
-    E = (
-        E0
-        + 9 / 8 * B0 * V0 * ((V0 / V) ** (2 / 3) - 1) ** 2
-        + 9 / 16 * B0 * V0 * (BP - 4) * ((V0 / V) ** (2 / 3) - 1) ** 3
-    )
-    return E
-
-
-def pouriertarantola(
-    V: np.ndarray, E0: float, B0: float, BP: float, V0: float
-) -> np.ndarray:
-    """
-    Pourier-Tarantola equation from PRB 70, 224107
-
-    Args:
-        V (np.ndarray): Array of volumes
-        E0 (float): Energy at equilibrium volume
-        B0 (float): Bulk modulus at equilibrium volume
-        BP (float): Pressure derivative of bulk modulus
-        V0 (float): Equilibrium volume
-
-    Returns:
-        np.ndarray: Array of energies
-    """
-    eta = (V / V0) ** (1 / 3)
-    squiggle = -3 * np.log(eta)
-
-    E = E0 + B0 * V0 * squiggle**2 / 6 * (3 + squiggle * (BP - 2))
-    return E
-
-
 def fitfunction(
     parameters: tuple[float], vol: np.ndarray, fittype: str = "vinet"
 ) -> np.ndarray:

{atomistics-0.2.2 → atomistics-0.2.4}/atomistics/workflows/structure_optimization.py

@@ -15,6 +15,34 @@ def optimize_positions_and_volume(structure: Atoms) -> dict:
     return {"optimize_positions_and_volume": structure}
 
 
+def optimize_volume(structure: Atoms) -> dict:
+    """
+    Optimize the volume of the given structure.
+
+    Parameters:
+        structure (Atoms): The structure to be optimized.
+
+    Returns:
+        dict: A dictionary containing the optimized structure.
+
+    """
+    return {"optimize_volume": structure}
+
+
+def optimize_cell(structure: Atoms) -> dict:
+    """
+    Optimize the cell of the given structure.
+
+    Parameters:
+        structure (Atoms): The structure to be optimized.
+
+    Returns:
+        dict: A dictionary containing the optimized structure.
+
+    """
+    return {"optimize_cell": structure}
+
+
 def optimize_positions(structure: Atoms) -> dict:
     """
     Optimize the positions of the given structure.

{atomistics-0.2.2 → atomistics-0.2.4/atomistics.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: atomistics
-Version: 0.2.2
+Version: 0.2.4
 Summary: Interfaces for atomistic simulation codes and workflows
 Author-email: Jan Janssen <janssen@mpie.de>
 License: BSD 3-Clause License
@@ -51,7 +51,7 @@ 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: spglib<=2.5.0,>=2.0.2
+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"
@@ -60,12 +60,12 @@ Provides-Extra: gpaw
 Requires-Dist: gpaw<=24.6.0,>=20.1.0; extra == "gpaw"
 Provides-Extra: lammps
 Requires-Dist: pylammpsmpi<=0.2.31,>=0.2.1; extra == "lammps"
-Requires-Dist: jinja2<=3.1.5,>=2.11.3; 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"
 Provides-Extra: lammps-phonons
 Requires-Dist: pylammpsmpi<=0.2.31,>=0.2.1; extra == "lammps-phonons"
-Requires-Dist: jinja2<=3.1.5,>=2.11.3; 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"

{atomistics-0.2.2 → atomistics-0.2.4}/atomistics.egg-info/requires.txt

@@ -1,7 +1,7 @@
 ase<=3.24.0,>=3.23.0
 numpy==1.26.4
 scipy<=1.15.2,>=1.11.1
-spglib<=2.5.0,>=2.0.2
+spglib<=2.6.0,>=2.0.2
 
 [experimental]
 lxml<=5.3.1,>=4.9.1
@@ -14,13 +14,13 @@ gpaw<=24.6.0,>=20.1.0
 
 [lammps]
 pylammpsmpi<=0.2.31,>=0.2.1
-jinja2<=3.1.5,>=2.11.3
+jinja2<=3.1.6,>=2.11.3
 pandas<=2.2.3,>=2.0.3
 pyiron_lammps<=0.4.0,>=0.3.2
 
 [lammps_phonons]
 pylammpsmpi<=0.2.31,>=0.2.1
-jinja2<=3.1.5,>=2.11.3
+jinja2<=3.1.6,>=2.11.3
 pandas<=2.2.3,>=2.0.3
 dynaphopy<=1.17.16,>=1.17.5
 pyiron_lammps<=0.4.0,>=0.3.2

{atomistics-0.2.2 → atomistics-0.2.4}/pyproject.toml

@@ -27,7 +27,7 @@ dependencies = [
     "ase>=3.23.0,<=3.24.0",
     "numpy==1.26.4",
     "scipy>=1.11.1,<=1.15.2",
-    "spglib>=2.0.2,<=2.5.0",
+    "spglib>=2.0.2,<=2.6.0",
 ]
 dynamic = ["version"]
 
@@ -47,13 +47,13 @@ gpaw = [
 ]
 lammps = [
     "pylammpsmpi>=0.2.1,<=0.2.31",
-    "jinja2>=2.11.3,<=3.1.5",
+    "jinja2>=2.11.3,<=3.1.6",
     "pandas>=2.0.3,<=2.2.3",
     "pyiron_lammps>=0.3.2,<=0.4.0",
 ]
 lammps_phonons = [
     "pylammpsmpi>=0.2.1,<=0.2.31",
-    "jinja2>=2.11.3,<=3.1.5",
+    "jinja2>=2.11.3,<=3.1.6",
     "pandas>=2.0.3,<=2.2.3",
     "dynaphopy>=1.17.5,<=1.17.16",
     "pyiron_lammps>=0.3.2,<=0.4.0",

{atomistics-0.2.2 → atomistics-0.2.4}/tests/test_calc_stress_ase_emt.py

@@ -4,7 +4,7 @@ from ase.optimize import LBFGS
 import unittest
 
 from atomistics.calculators import evaluate_with_ase
-from atomistics.workflows import optimize_positions_and_volume
+from atomistics.workflows import optimize_volume
 
 
 class TestStess(unittest.TestCase):
@@ -15,7 +15,7 @@ class TestStess(unittest.TestCase):
             task_dict=task_dict,
             ase_calculator=EMT(),
         )
-        task_dict = optimize_positions_and_volume(structure=structure)
+        task_dict = optimize_volume(structure=structure)
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
             ase_calculator=EMT(),
@@ -23,7 +23,7 @@ class TestStess(unittest.TestCase):
             ase_optimizer_kwargs={"fmax": 0.000001},
         )
         task_dict = {
-            "calc_stress": result_dict["structure_with_optimized_positions_and_volume"]
+            "calc_stress": result_dict["structure_with_optimized_volume"]
         }
         stress_post_dict = evaluate_with_ase(
             task_dict=task_dict,

{atomistics-0.2.2 → atomistics-0.2.4}/tests/test_elastic_ase_emt.py

@@ -1,17 +1,16 @@
 from ase.build import bulk
 from ase.calculators.emt import EMT
 from ase.optimize import LBFGS
-import numpy as np
 import unittest
 
 from atomistics.calculators import evaluate_with_ase
-from atomistics.workflows import ElasticMatrixWorkflow, optimize_positions_and_volume
+from atomistics.workflows import ElasticMatrixWorkflow, optimize_volume
 
 
 class TestElastic(unittest.TestCase):
     def test_calc_elastic(self):
         structure = bulk("Al", cubic=True)
-        task_dict = optimize_positions_and_volume(structure=structure)
+        task_dict = optimize_volume(structure=structure)
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
             ase_calculator=EMT(),
@@ -19,7 +18,7 @@ class TestElastic(unittest.TestCase):
             ase_optimizer_kwargs={"fmax": 0.000001},
         )
         workflow = ElasticMatrixWorkflow(
-            structure=result_dict["structure_with_optimized_positions_and_volume"],
+            structure=result_dict["structure_with_optimized_volume"],
             num_of_point=5,
             eps_range=0.005,
             sqrt_eta=True,