PyCOMPADRE: Compadre Toolkit

Important: Be sure to initialize Kokkos before setting up any objects from this library, by created a scoped KokkosParser object, i.e:

kp = pycompadre.KokkosParser()

When kp goes out of scope, then Kokkos will be finalized.

GMLS type objects are passed to ParticleHelper objects. Be sure to deallocate in reverse order, i.e.:

>> kp = pycompadre.KokkosParser()
>> gmls_obj = GMLS(...)
>> gmls_helper = ParticleHelper(gmls_object)
...
...
>> del gmls_obj
>> del gmls_helper
>> del kp

Project details at: https://github.com/sandialabs/compadre

Implementation details at: https://github.com/sandialabs/compadre/blob/master/pycompadre/pycompadre.cpp

Classes

pycompadre.KokkosParser

class pycompadre.KokkosParser

Class wrapping the functionality of Kokkos::ScopeGuard. Multiple instances can can be instantiated and go out of scope with only one instance initiating Kokkos and the last instance finalizing Kokkos when it goes out of scope.

__init__(*args, **kwargs)

Overloaded function.

__init__(self: pycompadre._pycompadre.KokkosParser, args: list[str], print: bool = False) -> None
__init__(self: pycompadre._pycompadre.KokkosParser, print: bool = False) -> None

static status() → str

pycompadre.GMLS

class pycompadre.GMLS

__init__(*args, **kwargs)

Overloaded function.

__init__(self: pycompadre._pycompadre.GMLS, poly_order: int, dimension: int = 3, dense_solver_type: str = ‘QR’, problem_type: str = ‘STANDARD’, constraint_type: str = ‘NO_CONSTRAINT’, curvature_poly_order: int = 2) -> None
__init__(self: pycompadre._pycompadre.GMLS, reconstruction_space: pycompadre._pycompadre.ReconstructionSpace, sampling_functional: pycompadre._pycompadre.SamplingFunctional, poly_order: int, dimension: int = 3, dense_solver_type: str = ‘QR’, problem_type: str = ‘STANDARD’, constraint_type: str = ‘NO_CONSTRAINT’, curvature_poly_order: int = 2) -> None
__init__(self: pycompadre._pycompadre.GMLS, reconstruction_space: pycompadre._pycompadre.ReconstructionSpace, polynomial_sampling_functional: pycompadre._pycompadre.SamplingFunctional, data_sampling_functional: pycompadre._pycompadre.SamplingFunctional, poly_order: int, dimension: int = 3, dense_solver_type: str = ‘QR’, problem_type: str = ‘STANDARD’, constraint_type: str = ‘NO_CONSTRAINT’, curvature_poly_order: int = 2) -> None

addTargets(*args, **kwargs)

Overloaded function.

addTargets(self: pycompadre._pycompadre.GMLS, arg0: pycompadre._pycompadre.TargetOperation) -> None

Add a target operation.

addTargets(self: pycompadre._pycompadre.GMLS, arg0: list[pycompadre._pycompadre.TargetOperation]) -> None

Add a list of target operations.

containsValidAlphas(self: pycompadre._pycompadre.GMLS) → bool

generateAlphas(self: pycompadre._pycompadre.GMLS, number_of_batches: int = 1, keep_coefficients: bool = False, clear_cache: bool = True) → None

getNN(self: int, arg0: int, arg1: pycompadre._pycompadre.ReconstructionSpace) → int: Heuristic number of neighbors.

getNP(self: int, arg0: int, arg1: pycompadre._pycompadre.ReconstructionSpace) → int: Get size of basis.

getSolutionSet(self: pycompadre._pycompadre.GMLS, validity_check: bool = True) → pycompadre._pycompadre.SolutionSet

getWeightingParameter(self: pycompadre._pycompadre.GMLS, parameter index: int = 0) → int: Get weighting kernel parameter[index].

getWeightingType(self: pycompadre._pycompadre.GMLS) → pycompadre._pycompadre.WeightingFunctionType: Get the weighting type.

setDimensionOfQuadraturePoints(self: pycompadre._pycompadre.GMLS, dim: int) → None

setOrderOfQuadraturePoints(self: pycompadre._pycompadre.GMLS, order: int) → None

setQuadratureType(self: pycompadre._pycompadre.GMLS, quadrature_type: str) → None

setSourceExtraData(self: pycompadre._pycompadre.GMLS, arg0: numpy.ndarray[numpy.float64]) → None

setTargetExtraData(self: pycompadre._pycompadre.GMLS, arg0: numpy.ndarray[numpy.float64]) → None

setWeightingParameter(self: pycompadre._pycompadre.GMLS, parameter value: int, parameter index: int = 0) → None: Set weighting kernel parameter[index] to parameter value.

setWeightingPower(self: pycompadre._pycompadre.GMLS, parameter value: int, parameter index: int = 0) → None: Set weighting kernel parameter[index] to parameter value. [DEPRECATED]

setWeightingType(*args, **kwargs)

Overloaded function.

setWeightingType(self: pycompadre._pycompadre.GMLS, arg0: str) -> None

Set the weighting type with a string.

setWeightingType(self: pycompadre._pycompadre.GMLS, arg0: pycompadre._pycompadre.WeightingFunctionType) -> None

Set the weighting type with a WeightingFunctionType.

pycompadre.ParticleHelper

class pycompadre.ParticleHelper

Class to manage calling PointCloudSearch, moving data to/from Numpy arrays in Kokkos::Views, and applying GMLS solutions to multidimensional data arrays

__init__(*args, **kwargs)

Overloaded function.

__init__(self: pycompadre._pycompadre.ParticleHelper) -> None

Requires follow-on call to setGMLSObject(gmls_obj) before use
__init__(self: pycompadre._pycompadre.ParticleHelper, gmls_instance: Compadre::GMLS) -> None

applyStencil(self: pycompadre._pycompadre.ParticleHelper, input_data: numpy.ndarray[numpy.float64], target_operation: pycompadre._pycompadre.TargetOperation = <TargetOperation.ScalarPointEvaluation: 0>, sampling_functional: pycompadre._pycompadre.SamplingFunctional = <pycompadre._pycompadre.SamplingFunctional object at 0x7fb94dcb84b0>, evaluation_site_local_index: int = 0) → numpy.ndarray[numpy.float64]

applyStencilAllTargetsAllAdditionalEvaluationSites(self: pycompadre._pycompadre.ParticleHelper, input_data: numpy.ndarray[numpy.float64], target_operation: pycompadre._pycompadre.TargetOperation = <TargetOperation.ScalarPointEvaluation: 0>, sampling_functional: pycompadre._pycompadre.SamplingFunctional = <pycompadre._pycompadre.SamplingFunctional object at 0x7fb94dcb8230>) → numpy.ndarray[numpy.float64]

applyStencilSingleTarget(self: pycompadre._pycompadre.ParticleHelper, input_data: numpy.ndarray[numpy.float64], target_operation: pycompadre._pycompadre.TargetOperation = <TargetOperation.ScalarPointEvaluation: 0>, sampling_functional: pycompadre._pycompadre.SamplingFunctional = <pycompadre._pycompadre.SamplingFunctional object at 0x7fb94dca3e30>, evaluation_site_local_index: int = 0) → float

generateKDTree(self: pycompadre._pycompadre.ParticleHelper, arg0: numpy.ndarray[numpy.float64]) → None

generateNeighborListsFromKNNSearchAndSet(self: pycompadre._pycompadre.ParticleHelper, target_sites: numpy.ndarray[numpy.float64], poly_order: int, dimension: int = 3, epsilon_multiplier: float = 1.6, max_search_radius: float = 0.0, scale_k_neighbor_radius: bool = True, scale_num_neighbors: bool = False) → None

getAdditionalEvaluationIndices(self: pycompadre._pycompadre.ParticleHelper) → Compadre::NeighborLists<Kokkos::View<int*> >

getGMLSObject(self: pycompadre._pycompadre.ParticleHelper) → Compadre::GMLS

getNeighborLists(self: pycompadre._pycompadre.ParticleHelper) → Compadre::NeighborLists<Kokkos::View<int*> >

getPolynomialCoefficients(self: pycompadre._pycompadre.ParticleHelper, input_data: numpy.ndarray[numpy.float64]) → numpy.ndarray[numpy.float64]

getReferenceOutwardNormalDirection(self: pycompadre._pycompadre.ParticleHelper) → numpy.ndarray[numpy.float64]

getSourceSites(self: pycompadre._pycompadre.ParticleHelper) → numpy.ndarray[numpy.float64]

getTangentBundle(self: pycompadre._pycompadre.ParticleHelper) → numpy.ndarray[numpy.float64]

getTargetSites(self: pycompadre._pycompadre.ParticleHelper) → numpy.ndarray[numpy.float64]

getWindowSizes(self: pycompadre._pycompadre.ParticleHelper) → numpy.ndarray[numpy.float64]

setAdditionalEvaluationSitesData(self: pycompadre._pycompadre.ParticleHelper, additional_evaluation_sites_neighbor_lists: numpy.ndarray[numpy.int32], additional_evaluation_sites_coordinates: numpy.ndarray[numpy.float64]) → None

setGMLSObject(self: pycompadre._pycompadre.ParticleHelper, gmls_object: Compadre::GMLS) → None

setNeighbors(self: pycompadre._pycompadre.ParticleHelper, neighbor_lists: numpy.ndarray[numpy.int32]) → None: Sets neighbor lists from 2D array where first column is number of neighbors for corresponding row’s target site.

setReferenceOutwardNormalDirection(self: pycompadre._pycompadre.ParticleHelper, reference_normal_directions: numpy.ndarray[numpy.float64], use_to_orient_surface: bool = True) → None

setTangentBundle(self: pycompadre._pycompadre.ParticleHelper, tangent_bundle: numpy.ndarray[numpy.float64]) → None

setTargetSites(self: pycompadre._pycompadre.ParticleHelper, target_coordinates: numpy.ndarray[numpy.float64]) → None

setWindowSizes(self: pycompadre._pycompadre.ParticleHelper, window_sizes: numpy.ndarray[numpy.float64]) → None

pycompadre.ReconstructionSpace

class pycompadre.ReconstructionSpace

Members:

ScalarTaylorPolynomial

VectorTaylorPolynomial

VectorOfScalarClonesTaylorPolynomial

DivergenceFreeVectorTaylorPolynomial

BernsteinPolynomial

property name

pycompadre.TargetOperation

class pycompadre.TargetOperation

Members:

ScalarPointEvaluation

VectorPointEvaluation

LaplacianOfScalarPointEvaluation

VectorLaplacianPointEvaluation

GradientOfScalarPointEvaluation

GradientOfVectorPointEvaluation

DivergenceOfVectorPointEvaluation

CurlOfVectorPointEvaluation

CurlCurlOfVectorPointEvaluation

PartialXOfScalarPointEvaluation

PartialYOfScalarPointEvaluation

PartialZOfScalarPointEvaluation

ChainedStaggeredLaplacianOfScalarPointEvaluation

GaussianCurvaturePointEvaluation

CellAverageEvaluation

CellIntegralEvaluation

FaceNormalAverageEvaluation

FaceNormalIntegralEvaluation

EdgeTangentAverageEvaluation

EdgeTangentIntegralEvaluation

property name

pycompadre.WeightingFunctionType

class pycompadre.WeightingFunctionType

Members:

Power

Gaussian

CubicSpline

CardinalCubicBSpline

Cosine

Sigmoid

property name

pycompadre.NeighborLists

class pycompadre.NeighborLists

computeMaxNumNeighbors(self: pycompadre._pycompadre.NeighborLists) → None: Compute maximum number of neighbors over all neighborhoods.

computeMinNumNeighbors(self: pycompadre._pycompadre.NeighborLists) → None: Compute minimum number of neighbors over all neighborhoods.

getMaxNumNeighbors(self: pycompadre._pycompadre.NeighborLists) → int: Get maximum number of neighbors over all neighborhoods.

getMinNumNeighbors(self: pycompadre._pycompadre.NeighborLists) → int: Get minimum number of neighbors over all neighborhoods.

getNeighbor(self: pycompadre._pycompadre.NeighborLists, target index: int, local neighbor number: int) → int: Get neighbor index from target index and local neighbor number.

getNumberOfNeighbors(self: pycompadre._pycompadre.NeighborLists, target index: int) → int: Get number of neighbors for target.

getNumberOfTargets(self: pycompadre._pycompadre.NeighborLists) → int: Number of targets.

getTotalNeighborsOverAllLists(self: pycompadre._pycompadre.NeighborLists) → int: Get total storage size of all neighbor lists combined.

pycompadre.Quadrature

class pycompadre.Quadrature

__init__(self: pycompadre._pycompadre.Quadrature, order_of_quadrature_points: int, dimension_of_quadrature_points: int, quadrature_type: str = 'LINE') → None

getDimensionOfQuadraturePoints(self: pycompadre._pycompadre.Quadrature) → int

getNumberOfQuadraturePoints(self: pycompadre._pycompadre.Quadrature) → int

getOrderOfQuadraturePoints(self: pycompadre._pycompadre.Quadrature) → int

getQuadratureType(self: pycompadre._pycompadre.Quadrature) → pycompadre._pycompadre.QuadratureType

getSites(self: pycompadre._pycompadre.Quadrature) → numpy.ndarray[numpy.float64]

getWeights(self: pycompadre._pycompadre.Quadrature) → numpy.ndarray[numpy.float64]

validQuadrature(self: pycompadre._pycompadre.Quadrature) → bool: Has quadrature been generated.

pycompadre.Kokkos

Namespace with a subset of Kokkos functionality. KokkosParser class should be preferred.

pycompadre.Kokkos.finalize() → None

pycompadre.Kokkos.initialize(arg0: list) → None

pycompadre.Kokkos.is_initialized() → bool

pycompadre.Kokkos.status() → str