@mat3ra/made 2026.8.13-0 → 2026.8.26-0

package/src/py/mat3ra/made/tools/build_components/metadata/build_metadata.py

@@ -1,7 +0,0 @@
-from mat3ra.made.metadata import BaseMetadata
-from pydantic import Field
-
-
-class BuildMetadata(BaseMetadata):
-    configuration: dict = Field(default_factory=dict)
-    build_parameters: dict = Field(default_factory=dict)

package/src/py/mat3ra/made/tools/build_components/metadata/material_build_metadata.py

@@ -1,35 +0,0 @@
-from typing import List, Optional
-
-from mat3ra.made.metadata import BaseMetadata
-from pydantic import Field
-
-from .build_metadata import BuildMetadata
-
-
-class MaterialBuildMetadata(BaseMetadata):
-    # Other metadata fields can be added as needed
-    build: List[BuildMetadata] = Field([])
-
-    def get_latest_build_metadata(self) -> BuildMetadata:
-        if not self.build:
-            raise ValueError("No metadata.build on the material.")
-        return self.build[-1]
-
-    def get_build_metadata_of_type(self, configuration_type: str) -> Optional[BuildMetadata]:
-        """
-        Returns the first build configuration of the specified type.
-        Args:
-            configuration_type (str): The type of configuration to search for.
-        Returns:
-            Optional[dict]: The build configuration if found, otherwise None.
-        """
-        for build_step in reversed(self.build):
-            if build_step.configuration.get("type") == configuration_type:
-                return BuildMetadata(
-                    configuration=build_step.configuration, build_parameters=build_step.build_parameters
-                )
-        return None
-
-    def add_build_metadata_step(self, configuration: dict, build_parameters: Optional[dict] = None) -> None:
-        build_metadata = BuildMetadata(configuration=configuration, build_parameters=build_parameters)
-        self.build.append(build_metadata)

package/src/py/mat3ra/made/tools/build_components/metadata/material_with_build_metadata.py

@@ -1,8 +0,0 @@
-from mat3ra.made.material import Material
-from pydantic import Field
-
-from .material_build_metadata import MaterialBuildMetadata
-
-
-class MaterialWithBuildMetadata(Material):
-    metadata: MaterialBuildMetadata = Field(default_factory=MaterialBuildMetadata)

package/src/py/mat3ra/made/tools/build_components/mixins/__init__.py

@@ -1,2 +0,0 @@
-from .convert_generated_items_ase_atoms_mixin import ConvertGeneratedItemsASEAtomsMixin
-from .convert_generated_items_pymatgen_structure_mixin import ConvertGeneratedItemsPymatgenStructureMixin

package/src/py/mat3ra/made/tools/build_components/mixins/convert_generated_items_ase_atoms_mixin.py

@@ -1,8 +0,0 @@
-from ...convert import from_ase
-from ...third_party import ASEAtoms
-
-
-class ConvertGeneratedItemsASEAtomsMixin:
-    @staticmethod
-    def _convert_generated_item(item: ASEAtoms):
-        return from_ase(item)

package/src/py/mat3ra/made/tools/build_components/mixins/convert_generated_items_pymatgen_structure_mixin.py

@@ -1,8 +0,0 @@
-from ...convert import from_pymatgen
-from ...third_party import PymatgenStructure
-
-
-class ConvertGeneratedItemsPymatgenStructureMixin:
-    @staticmethod
-    def _convert_generated_item(item: PymatgenStructure):
-        return from_pymatgen(item)

package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/enums.py

@@ -1,11 +0,0 @@
-from enum import Enum
-
-from .....build.defective_structures.zero_dimensional.point_defect.atom_placement_method_enum import (
-    AtomPlacementMethodEnum,
-)
-
-
-class AdatomPlacementMethodEnum(Enum):
-    EXACT_COORDINATE = AtomPlacementMethodEnum.EXACT_COORDINATE
-    EQUIDISTANT = AtomPlacementMethodEnum.EQUIDISTANT
-    NEW_CRYSTAL_SITE = AtomPlacementMethodEnum.NEW_CRYSTAL_SITE

package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/__init__.py

@@ -1,6 +0,0 @@
-from .builder import MergeBuilder, MergeBuilderParameters
-
-__all__ = [
-    "MergeBuilder",
-    "MergeBuilderParameters",
-]

package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/build_parameters.py

@@ -1,18 +0,0 @@
-from typing import Optional
-
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseBuilderParameters
-
-
-class MergeBuilderParameters(BaseBuilderParameters):
-    """
-    Parameters for merging materials.
-
-    Args:
-        material_name: Optional name for the merged material.
-        distance_tolerance: Tolerance for resolving overlapping coordinates.
-        merge_dangerously: If True, allows merging even if lattices are different.
-    """
-
-    material_name: Optional[str] = "New Material"
-    distance_tolerance: float = 0.1
-    merge_dangerously: bool = False

package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/builder.py

@@ -1,93 +0,0 @@
-from typing import Any, Dict, List, Optional, Type
-
-from mat3ra.esse.models.materials_category_components.operations.core.combinations.merge import MergeMethodsEnum
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseSingleBuilder, TypeConfiguration
-
-from ......operations.core.binary import merge
-from ..... import MaterialWithBuildMetadata
-from .....entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from .build_parameters import MergeBuilderParameters
-from .configuration import MergeConfiguration
-
-
-class MergeBuilder(BaseSingleBuilder):
-    """
-    Builder class for merging materials based on parameters.
-    """
-
-    _ConfigurationType: Type[MergeConfiguration] = MergeConfiguration
-    _BuildParametersType: Type[MergeBuilderParameters] = MergeBuilderParameters
-    _DefaultBuildParameters: MergeBuilderParameters = MergeBuilderParameters()
-
-    @property
-    def merge_component_types_conversion_map(self) -> Dict[Type, Type]:
-        return {}
-
-    @property
-    def merge_component_types_conversion_pre_process_map(self) -> Dict[Type, Any]:
-        return {}
-
-    def _merge_component_to_material(
-        self,
-        merge_component_configuration_or_material: Any,
-        configuration: MergeConfiguration,
-        merge_component_build_parameters: Any = None,
-    ) -> Optional[MaterialWithBuildMetadata]:
-        builder = self.merge_component_types_conversion_map.get(type(merge_component_configuration_or_material))
-        pre_process_function = self.merge_component_types_conversion_pre_process_map.get(
-            type(merge_component_configuration_or_material), lambda x, y: x
-        )
-
-        if builder:
-            merge_component_configuration_or_material = pre_process_function(
-                merge_component_configuration_or_material, configuration
-            )
-            return builder(build_parameters=merge_component_build_parameters).get_material(
-                merge_component_configuration_or_material
-            )
-        elif isinstance(merge_component_configuration_or_material, VacuumConfiguration):
-            raise ValueError("Merge with VacuumConfiguration is not supported by design.")
-        else:
-            return merge_component_configuration_or_material
-
-    def _merge_by_method(
-        self,
-        materials: List[MaterialWithBuildMetadata],
-        parameters: MergeBuilderParameters,
-        method: MergeMethodsEnum = MergeMethodsEnum.ADD,
-    ) -> MaterialWithBuildMetadata:
-        if method not in MergeMethodsEnum:
-            raise ValueError(f"Unknown merge method: {method}")
-        return merge(
-            materials=materials,
-            merge_method=method,
-            material_name=parameters.material_name or materials[0].name,
-            distance_tolerance=parameters.distance_tolerance,
-            merge_dangerously=parameters.merge_dangerously,
-        )
-
-    def _generate(self, configuration: TypeConfiguration) -> MaterialWithBuildMetadata:
-        materials = []
-        for component in configuration.merge_components:
-            material = self._merge_component_to_material(component, configuration)
-            if material is not None:
-                materials.append(material)
-
-        if len(materials) == 0:
-            raise ValueError("No valid materials found after processing merge components")
-
-        if len(materials) == 1:
-            return materials[0]
-
-        # Optimization: when there are many materials to merge, combine all non-first
-        # materials into one before merging with the base to avoid N sequential merges.
-        if len(materials) > 2:
-            base = materials[0]
-            combined = materials[1]
-            for m in materials[2:]:
-                combined.basis.add_atoms_from_another_basis(m.basis)
-            materials = [base, combined]
-
-        parameters = self.build_parameters or self._DefaultBuildParameters
-        merge_method = getattr(configuration, "merge_method", None)
-        return self._merge_by_method(materials, parameters, merge_method)

package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/merge/configuration.py

@@ -1,20 +0,0 @@
-from typing import Any, List
-
-from mat3ra.esse.models.materials_category_components.operations.core.combinations.merge import (
-    MergeMethodsEnum,
-    MergeSchema,
-)
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseConfigurationPydantic
-
-
-class MergeConfiguration(MergeSchema, BaseConfigurationPydantic):
-    """
-    Parameters for merging materials.
-
-    Args:
-        merge_components: List of materials or configurations to merge.
-        merge_method: Method to use for merging
-    """
-
-    merge_components: List[Any]
-    merge_method: MergeMethodsEnum

package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/stack/builder.py

@@ -1,83 +0,0 @@
-from typing import Any, Optional, Type
-
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-from mat3ra.made.material import Material
-from mat3ra.made.utils import adjust_material_cell_to_set_gap_along_direction
-
-from ......build_components import MaterialWithBuildMetadata
-from ......operations.core.binary import stack
-from .....entities.core.two_dimensional.vacuum.builder import VacuumBuilder
-from .....entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from .....entities.reusable.base_builder import BaseSingleBuilder, TypeConfiguration
-from .configuration import StackConfiguration
-
-
-class StackNComponentsBuilder(BaseSingleBuilder):
-    _ConfigurationType: Type[StackConfiguration] = StackConfiguration
-    _StackComponentTypes = [MaterialWithBuildMetadata, VacuumConfiguration]
-
-    @property
-    def stack_component_types_conversion_map(self):
-        return {
-            VacuumConfiguration: VacuumBuilder,
-        }
-
-    @property
-    def stack_component_types_conversion_pre_process_map(self):
-        return {
-            VacuumConfiguration: self.vacuum_configuration_set_crystal,
-        }
-
-    def vacuum_configuration_set_crystal(
-        self, vacuum_configuration: VacuumConfiguration, stack_configuration: StackConfiguration
-    ) -> VacuumConfiguration:
-        # NOTE: we assume that the first component in the stack is used to define the vacuum crystal
-        vacuum_prototype_crystal = stack_configuration.stack_components[0]
-        vacuum_configuration.crystal = self._stack_component_to_material(vacuum_prototype_crystal, stack_configuration)
-        return vacuum_configuration
-
-    def _stack_component_to_material(
-        self,
-        stack_component_configuration_or_material: Any,
-        configuration: StackConfiguration,
-        stack_component_build_parameters: Any = None,
-    ) -> Optional[MaterialWithBuildMetadata]:
-        cache = getattr(self, "_stack_component_cache", None)
-        cache_key = id(stack_component_configuration_or_material)
-        if cache is not None and cache_key in cache:
-            return cache[cache_key]
-
-        builder = self.stack_component_types_conversion_map.get(type(stack_component_configuration_or_material))
-        pre_process_function = self.stack_component_types_conversion_pre_process_map.get(
-            type(stack_component_configuration_or_material), lambda x, y: x
-        )
-        if builder:
-            stack_component_configuration_or_material = pre_process_function(
-                stack_component_configuration_or_material, configuration
-            )
-            result = builder(build_parameters=stack_component_build_parameters).get_material(
-                stack_component_configuration_or_material
-            )
-        else:
-            result = stack_component_configuration_or_material
-
-        if cache is not None:
-            cache[cache_key] = result
-        return result
-
-    def _generate(self, configuration: TypeConfiguration) -> Material:
-        self._stack_component_cache: Optional[dict] = {}
-        try:
-            materials = []
-            for index, stack_component_config in enumerate(configuration.stack_components):
-                material = self._stack_component_to_material(stack_component_config, configuration)
-                gap = configuration.get_gap_by_id(index)
-                if gap is not None:
-                    material = adjust_material_cell_to_set_gap_along_direction(material, gap, configuration.direction)
-                materials.append(material)
-            # Filter out None values in case some stack components are V
-            materials = [m for m in materials if m is not None]
-            stacked_material = stack(materials, configuration.direction or AxisEnum.z)
-            return stacked_material
-        finally:
-            self._stack_component_cache = None

package/src/py/mat3ra/made/tools/build_components/operations/core/combinations/stack/configuration.py

@@ -1,24 +0,0 @@
-from typing import Any, List
-
-from mat3ra.code.array_with_ids import ArrayWithIds
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-from mat3ra.esse.models.materials_category_components.operations.core.combinations.stack import StackSchema
-
-from .....entities.reusable.base_builder import BaseConfigurationPydantic
-
-
-class StackConfiguration(StackSchema, BaseConfigurationPydantic):
-    type: str = "StackConfiguration"
-
-    stack_components: List[Any]  # Configuration objects only, no Materials
-    gaps: ArrayWithIds = ArrayWithIds.from_values([])
-    direction: AxisEnum = AxisEnum.z
-
-    def __init__(self, **data):
-        gaps = data.get("gaps", [])
-        if not isinstance(gaps, ArrayWithIds):
-            data["gaps"] = ArrayWithIds.from_values(gaps)
-        super().__init__(**data)
-
-    def get_gap_by_id(self, gap_id: int) -> float:
-        return self.gaps.get_element_value_by_index(gap_id)

package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/__init__.py

@@ -1,15 +0,0 @@
-from .functions import (
-    AtomicMassDependentFunctionHolder,
-    FunctionHolder,
-    MaxwellBoltzmannDisplacementHolder,
-    PerturbationFunctionHolder,
-    SineWavePerturbationFunctionHolder,
-)
-
-__all__ = [
-    "AtomicMassDependentFunctionHolder",
-    "FunctionHolder",
-    "MaxwellBoltzmannDisplacementHolder",
-    "PerturbationFunctionHolder",
-    "SineWavePerturbationFunctionHolder",
-]

package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/build_parameters.py

@@ -1,5 +0,0 @@
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseBuilderParameters
-
-
-class PerturbationBuildParameters(BaseBuilderParameters):
-    center_material: bool = True

package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/builders/base.py

@@ -1,33 +0,0 @@
-from typing import Any, Type
-
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseSingleBuilder
-
-from .......modify import translate_to_z_level, wrap_to_unit_cell
-from .......operations.core.unary import perturb
-from ...... import MaterialWithBuildMetadata
-from ..build_parameters import PerturbationBuildParameters
-from ..configuration import PerturbationConfiguration
-
-
-class PerturbationBuilder(BaseSingleBuilder):
-    _ConfigurationType: Type[PerturbationConfiguration] = PerturbationConfiguration
-    _BuildParametersType: Type[PerturbationBuildParameters] = PerturbationBuildParameters
-    _DefaultBuildParameters: PerturbationBuildParameters = PerturbationBuildParameters()
-    _PostProcessParametersType: Any = None
-
-    def _generate(self, configuration: PerturbationConfiguration) -> MaterialWithBuildMetadata:
-        new_material = translate_to_z_level(configuration.material, "center").clone()
-        new_material = perturb(
-            new_material,
-            configuration.perturbation_function_holder,
-            configuration.use_cartesian_coordinates,
-        )
-        new_material = wrap_to_unit_cell(new_material)
-        return new_material
-
-    def _update_material_name(
-        self, material: MaterialWithBuildMetadata, configuration: PerturbationConfiguration
-    ) -> MaterialWithBuildMetadata:
-        perturbation_details = f"Perturbation: {configuration.perturbation_function_holder.function_str}"
-        material.name = f"{material.name} ({perturbation_details})"
-        return material

package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/builders/isometric.py

@@ -1,25 +0,0 @@
-from .......operations.core.unary import edit_cell
-from ...... import MaterialWithBuildMetadata
-from ..configuration import PerturbationConfiguration
-from .base import PerturbationBuilder
-
-
-class IsometricPerturbationBuilder(PerturbationBuilder):
-    def _generate(self, configuration: PerturbationConfiguration) -> MaterialWithBuildMetadata:
-        new_material = configuration.material.clone()
-        renormalized_coordinates = [
-            configuration.perturbation_function_holder.normalize_coordinates(coord)
-            for coord in new_material.basis.coordinates.values
-        ]
-        new_material.set_coordinates(renormalized_coordinates)
-
-        configuration.material = new_material
-
-        new_material = super()._generate(configuration)
-
-        new_lattice_vectors = [
-            configuration.perturbation_function_holder.normalize_coordinates(vector)
-            for vector in new_material.lattice.vector_arrays
-        ]
-        renormalized_material = edit_cell(new_material, new_lattice_vectors)
-        return renormalized_material

package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/configuration.py

@@ -1,24 +0,0 @@
-from typing import Union
-
-from mat3ra.made.material import Material
-from mat3ra.made.tools.build_components.entities.reusable.base_builder import BaseConfigurationPydantic
-
-from ..... import MaterialWithBuildMetadata
-from .functions import FunctionHolder, PerturbationFunctionHolder, SineWavePerturbationFunctionHolder
-
-
-class PerturbationConfiguration(BaseConfigurationPydantic):
-    """
-    Configuration for a geometrical perturbation.
-
-    Args:
-        material (Material): The Material object.
-        perturbation_function_holder (PerturbationFunctionHolder): The perturbation function holder.
-        use_cartesian_coordinates (bool): Whether to use cartesian coordinates
-    """
-
-    material: Union[Material, MaterialWithBuildMetadata]
-    perturbation_function_holder: Union[
-        SineWavePerturbationFunctionHolder, PerturbationFunctionHolder, FunctionHolder
-    ] = SineWavePerturbationFunctionHolder()
-    use_cartesian_coordinates: bool = True

package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/__init__.py

@@ -1,13 +0,0 @@
-from .atomic_mass_dependent_function_holder import AtomicMassDependentFunctionHolder
-from .function_holder import FunctionHolder
-from .maxwell_boltzmann import MaxwellBoltzmannDisplacementHolder
-from .perturbation_function_holder import PerturbationFunctionHolder
-from .sine_wave_perturbation_function_holder import SineWavePerturbationFunctionHolder
-
-__all__ = [
-    "AtomicMassDependentFunctionHolder",
-    "FunctionHolder",
-    "MaxwellBoltzmannDisplacementHolder",
-    "PerturbationFunctionHolder",
-    "SineWavePerturbationFunctionHolder",
-]

package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/atomic_mass_dependent_function_holder.py

@@ -1,32 +0,0 @@
-from typing import Any, List, Optional, Union
-
-import sympy as sp
-from mat3ra.periodic_table.helpers import get_atomic_mass_from_element
-
-from .function_holder import FunctionHolder
-
-
-class AtomicMassDependentFunctionHolder(FunctionHolder):
-    variables: List[str] = ["x", "y", "z", "m"]
-
-    def __init__(
-        self,
-        function: Union[sp.Expr, str] = sp.Symbol("f"),
-        variables: Optional[List[str]] = None,
-        **data: Any,
-    ):
-        if variables is None:
-            expr = self._to_expr(function)
-            vs = sorted(expr.free_symbols, key=lambda s: s.name)
-            variables = [str(v) for v in vs] or ["x", "y", "z", "m"]
-
-        super().__init__(function=function, variables=variables, **data)
-
-    @staticmethod
-    def get_atomic_mass(coordinate: List[float], material) -> float:
-        if material is None:
-            raise ValueError("Material is required to extract atomic mass")
-
-        atom_id = material.basis.coordinates.get_element_id_by_value(coordinate)
-        element = material.basis.elements.get_element_value_by_index(atom_id)
-        return get_atomic_mass_from_element(element)

package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/function_holder.py

@@ -1,80 +0,0 @@
-from typing import Any, Callable, List, Optional, Union
-
-import sympy as sp
-from mat3ra.code.entity import InMemoryEntityPydantic
-from mat3ra.made.utils import AXIS_TO_INDEX_MAP
-from pydantic import field_serializer
-from sympy import parse_expr
-
-
-def default_function() -> sp.Expr:
-    return sp.Symbol("f")
-
-
-class FunctionHolder(InMemoryEntityPydantic):
-    variables: List[str] = ["x"]
-    symbols: List[sp.Symbol] = sp.symbols(variables)
-    function: sp.Expr = sp.Symbol("f")
-    function_numeric: Callable = sp.lambdify(sp.symbols(variables), sp.Symbol("f"), modules=["numpy"])
-    derivatives_numeric: dict = {}
-
-    def __init__(self, function: Union[sp.Expr, str], variables: Optional[List[str]] = None, **data: Any):
-        # normalize string → Expr
-        expr = self._to_expr(function)
-
-        # if no variables list given, infer from free symbols (defaults to x,y,z)
-        if variables is None:
-            vs = sorted(expr.free_symbols, key=lambda s: s.name)
-            variables = [str(v) for v in vs] or ["x", "y", "z"]
-        super().__init__(**data)
-
-        self.variables = variables
-        self.symbols = sp.symbols(variables)
-        self.function = expr
-
-        self.function_numeric = sp.lambdify(self.symbols, self.function, modules=["numpy"])
-        self.derivatives_numeric = {
-            var: sp.lambdify(sp.symbols(variables), sp.diff(self.function, var), modules=["numpy"])
-            for var in self.variables
-        }
-
-    @staticmethod
-    def _to_expr(expr_or_str: Union[sp.Expr, str]) -> sp.Expr:
-        if isinstance(expr_or_str, sp.Expr):
-            return expr_or_str
-        if isinstance(expr_or_str, str):
-            # We can swap in sympy.sympify for slightly laxer parsing,
-            # or configure parse_expr with custom transformations.
-            return parse_expr(expr_or_str, evaluate=True)
-        raise TypeError(f"Expected sympy.Expr or str, got {type(expr_or_str)}")
-
-    @property
-    def function_str(self) -> str:
-        return str(self.function)
-
-    def apply_function(self, coordinate: List[float], **kwargs: Any) -> float:
-        values = [coordinate[AXIS_TO_INDEX_MAP[var]] for var in self.variables]
-        return self.function_numeric(*values)
-
-    def calculate_derivative(self, coordinate: List[float], axis: str) -> float:
-        if axis in self.variables:
-            values = [coordinate[AXIS_TO_INDEX_MAP[var]] for var in self.variables]
-            return self.derivatives_numeric[axis](*values)
-        else:
-            return 0
-
-    @field_serializer("function")
-    def serialize_function(self, value: sp.Expr) -> str:
-        return str(value)
-
-    @field_serializer("symbols")
-    def serialize_symbols(self, value: List[sp.Symbol]) -> List[str]:
-        return [str(symbol) for symbol in value]
-
-    @field_serializer("function_numeric")
-    def serialize_function_numeric(self, value: Callable) -> str:
-        return "lambdified_function"
-
-    @field_serializer("derivatives_numeric")
-    def serialize_derivatives_numeric(self, value: dict) -> dict:
-        return {k: "lambdified_derivative" for k, v in value.items()}

package/src/py/mat3ra/made/tools/build_components/operations/core/modifications/perturb/functions/maxwell_boltzmann.py

@@ -1,39 +0,0 @@
-from typing import Any, List, Optional
-
-import numpy as np
-from pydantic import Field, model_validator
-
-from .atomic_mass_dependent_function_holder import AtomicMassDependentFunctionHolder
-
-DEFAULT_DISORDER_PARAMETER = 1.0
-
-
-class MaxwellBoltzmannDisplacementHolder(AtomicMassDependentFunctionHolder):
-    disorder_parameter: float = Field(
-        default=DEFAULT_DISORDER_PARAMETER,
-        exclude=True,
-        description="Disorder parameter. Can be viewed as effective temperature in eV.",
-    )
-    random_seed: Optional[int] = Field(default=None, exclude=True)
-    random_state: Any = Field(default=None, exclude=True)
-    is_mass_used: bool = Field(default=True, exclude=True)
-
-    @model_validator(mode="after")
-    def setup_random_state(self):
-        if self.random_state is None:
-            self.random_state = np.random.RandomState(self.random_seed) if self.random_seed is not None else np.random
-        return self
-
-    def apply_function(self, coordinate, material=None) -> List[float]:
-        if material is None:
-            raise ValueError("MaxwellBoltzmannDisplacementHolder requires 'material' kwargs")
-
-        if self.is_mass_used:
-            mass = self.get_atomic_mass(coordinate, material)
-            variance = self.disorder_parameter / mass
-        else:
-            variance = self.disorder_parameter
-
-        std_dev = np.sqrt(variance)
-        displacement = self.random_state.normal(0.0, std_dev, size=3)
-        return displacement.tolist()