esys.finley Package

Our most general domain representation. Imports submodules into its namespace

Classes

class esys.finley.FinleyDomain

A concrete class representing a domain. For more details, please consult the C++ documentation.

__init__((object)arg1, (FinleyDomain)arg2) → None
MPIBarrier((FinleyDomain)arg1) → None :

Wait until all processes have reached this point

addPDEToLumpedSystem((FinleyDomain)arg1, (Data)arg2, (Data)arg3, (Data)mat, (Data)D, (bool)d) → None :

adds a PDE onto the lumped stiffness matrix

Parameters:

  • mat (Data)

  • D (Data)

  • d (Data)

  • useHRZ (bool)

addPDEToRHS((FinleyDomain)arg1, (Data)arg2, (Data)rhs, (Data)X, (Data)Y, (Data)y, (Data)y_contact) → None :

adds a PDE onto the stiffness matrix mat and a rhs

Parameters:

  • rhs (Data)

  • X (Data)

  • Y (Data)

  • y (Data)

  • y_contact (Data)

addPDEToSystem((FinleyDomain)arg1, (Operator)arg2, (Data)arg3, (Data)mat, (Data)rhs, (Data)A, (Data)B, (Data)C, (Data)D, (Data)X, (Data)Y, (Data)d, (Data)y, (Data)d_contact, (Data)y_contact) → None :

adds a PDE onto the stiffness matrix mat and a rhs

Parameters:

  • mat (OperatorAdapter)

  • rhs (Data)

  • A (Data)

  • B (Data)

  • C (Data)

  • D (Data)

  • X (Data)

  • Y (Data)

  • d (Data)

  • d_contact (Data)

  • y_contact (Data)

addPDEToTransportProblem((FinleyDomain)arg1, (TransportProblem)arg2, (Data)arg3, (Data)tp, (Data)source, (Data)M, (Data)A, (Data)B, (Data)C, (Data)D, (Data)X, (Data)Y, (Data)d, (Data)y, (Data)d_contact, (Data)y_contact) → None :
Parameters:

  • tp (AbstractTransportProblem)

  • source (Data)

  • M (Data)

  • A (Data)

  • B (Data)

  • C (Data)

  • D (Data)

  • X (Data)

  • Y (Data)

  • d (Data)

  • y (Data)

  • d_contact (Data)

  • y_contact (Data)

dump((FinleyDomain)arg1, (str)fileName) → None :

dumps the mesh to a file with the given name.

getDataShape((FinleyDomain)arg1, (int)functionSpaceCode) → object :
Returns:

a pair (dps, ns) where dps=the number of data points per sample, and ns=the number of samples

Return type:

tuple

getDescription((FinleyDomain)arg1) → str :
Returns:

a description for this domain

Return type:

string

getDim((FinleyDomain)arg1) → int :
Return type:

int

getMPIRank((FinleyDomain)arg1) → int :
Returns:

the rank of this process

Return type:

int

getMPISize((FinleyDomain)arg1) → int :
Returns:

the number of processes used for this Domain

Return type:

int

getNormal((FinleyDomain)arg1) → Data :
Returns:

boundary normals at the quadrature point on the face elements

Return type:

Data

getNumDataPointsGlobal((FinleyDomain)arg1) → int :
Returns:

the number of data points summed across all MPI processes

Return type:

int

getSize((FinleyDomain)arg1) → Data :
Returns:

the element size

Return type:

Data

getSystemMatrixTypeId((FinleyDomain)arg1, (object)options) → int :
Returns:

the identifier of the matrix type to be used for the global stiffness matrix when particular solver options are used.

Return type:

int

Parameters:

options (SolverBuddy)

getTag((FinleyDomain)arg1, (str)name) → int :
Returns:

tag id for name

Return type:

string

getTransportTypeId((FinleyDomain)arg1, (int)solver, (int)preconditioner, (int)package, (bool)symmetry) → int :
Returns:

the identifier of the transport problem type to be used when a particular solver, preconditioner, package and symmetric matrix is used.

Return type:

int

Parameters:

  • solver (int)

  • preconditioner (int)

  • package (int)

  • symmetry (int)

getVTKElementType((FinleyDomain)arg1) → int :
Returns:

returns the VTK code for this element type

Return type:

Data

getX((FinleyDomain)arg1) → Data :
Returns:

locations in the FEM nodes

Return type:

Data

isRootRank((FinleyDomain)arg1) → bool :
Returns:

True if this code is executing on the root rank (rank 0)

Return type:

bool

isValidTagName((FinleyDomain)arg1, (str)name) → bool :
Returns:

True is name corresponds to a tag

Return type:

bool

newOperator((FinleyDomain)arg1, (int)row_blocksize, (FunctionSpace)row_functionspace, (int)column_blocksize, (FunctionSpace)column_functionspace, (int)type) → Operator :

creates a stiffness matrix and initializes it with zeros

Parameters:

  • row_blocksize (int)

  • row_functionspace (FunctionSpace)

  • column_blocksize (int)

  • column_functionspace (FunctionSpace)

  • type (int)

newTransportProblem((FinleyDomain)theta, (int)blocksize, (FunctionSpace)functionspace, (int)type) → TransportProblem :

creates a TransportProblem

Parameters:

  • theta (float)

  • blocksize (int)

  • functionspace (FunctionSpace)

  • type (int)

print_mesh_info((FinleyDomain)arg1[, (bool)full=False]) → None :
Parameters:

full (bool)

setTagMap((FinleyDomain)arg1, (str)name, (int)tag) → None :

Give a tag number a name.

Parameters:

  • name (string) – Name for the tag

  • tag (int) – numeric id

Note:

Tag names must be unique within a domain

setX((FinleyDomain)arg1, (Data)arg) → None :

assigns new location to the domain

Parameters:

arg (Data)

showTagNames((FinleyDomain)arg1) → str :
Returns:

A space separated list of tag names

Return type:

string

write((FinleyDomain)arg1, (str)filename) → None :

Write the current mesh to a file with the given name.

Functions

esys.finley.Brick(n0=1, n1=1, n2=1, order=1, l0=1.0, l1=1.0, l2=1.0, periodic0=False, periodic1=False, periodic2=False, integrationOrder=-1, reducedIntegrationOrder=-1, useElementsOnFace=None, useFullElementOrder=False, optimize=False, diracPoints=[], diracTags=[], comm=None, framework=None)

Creates a rectangular mesh with n0 x n1 x n2 elements over the brick [0,l0] x [0,l1] x [0,l2].

Parameters:

  • n0 – number of elements in direction 0

  • n1 – number of elements in direction 1

  • n2 – number of elements in direction 2

  • order – order of shape functions (1, 2, or -1 for macro elements)

  • l0 – length of side 0

  • l1 – length of side 1

  • l2 – length of side 2

  • periodic0 – periodic boundary conditions in direction 0

  • periodic1 – periodic boundary conditions in direction 1

  • periodic2 – periodic boundary conditions in direction 2

  • integrationOrder – order of quadrature scheme (-1 for automatic)

  • reducedIntegrationOrder – order of reduced quadrature scheme (-1 for automatic)

  • useElementsOnFace – whether to use elements on face

  • useFullElementOrder – whether to use Hex27 elements

  • optimize – enable optimization of node labels

  • diracPoints – Dirac point coordinates

  • diracTags – Dirac point tags

  • comm – MPI communicator (optional, defaults to MPI_COMM_WORLD)

  • framework – solver framework to use (optional SolverFramework instance)

Returns:

Domain object

esys.finley.GetMeshFromFile(filename, **kwargs)

Reads a mesh from a file, determines the reader to use based on the file extension. All cases require a filename and gmsh files require a number of dimensions (it doesn’t hurt to pass this in all the time). Other keyword args come from the underlying reader functions.

esys.finley.GlueFaces((list)meshList[, (float)safetyFactor=0.2[, (float)tolerance=1e-08[, (bool)optimize=True]]]) → Domain :

Detects matching faces in the mesh, removes them from the mesh and joins the elements touched by the face elements.

esys.finley.JoinFaces((list)meshList[, (float)safetyFactor=0.2[, (float)tolerance=1e-08[, (bool)optimize=True]]]) → Domain :

Detects matching faces in the mesh and replaces them by joint elements.

esys.finley.LoadMesh((str)fileName[, (object)comm=None]) → Domain :

Load a mesh from an HDF5 file.

Parameters:

  • fileName (string) – Path to HDF5 file

  • comm – MPI communicator (optional, defaults to MPI_COMM_WORLD)

Return type:

FinleyDomain

esys.finley.Merge((list)meshList) → Domain :

Merges a list of meshes into one mesh.

Return type:

Domain

esys.finley.ReadGmsh(fileName, numDim, integrationOrder=-1, reducedIntegrationOrder=-1, optimize=True, useMacroElements=False, diracPoints=[], diracTags=[], comm=None, framework=None)

Read a gmsh mesh file.

Parameters:

  • fileName – Path to gmsh file

  • numDim – Number of spatial dimensions

  • integrationOrder – Order of quadrature scheme (-1 for automatic)

  • reducedIntegrationOrder – Order of reduced quadrature scheme (-1 for automatic)

  • optimize – Enable optimization of node labels

  • useMacroElements – Enable usage of macro elements instead of second order elements

  • diracPoints – Dirac point coordinates

  • diracTags – Dirac point tags

  • comm – MPI communicator (optional, defaults to MPI_COMM_WORLD)

  • framework – solver framework to use (optional SolverFramework instance)

Returns:

Domain object

esys.finley.ReadMesh(filename, integrationOrder=-1, reducedIntegrationOrder=-1, optimize=True, diracPoints=[], diracTags=[], comm=None, framework=None)

Read a mesh from a file. For MPI parallel runs fan out the mesh to multiple processes.

Parameters:

  • filename – Path to mesh file

  • integrationOrder – Order of quadrature scheme (-1 for automatic)

  • reducedIntegrationOrder – Order of reduced quadrature scheme (-1 for automatic)

  • optimize – Enable optimization of node labels

  • diracPoints – Dirac point coordinates

  • diracTags – Dirac point tags

  • comm – MPI communicator (optional, defaults to MPI_COMM_WORLD)

  • framework – solver framework to use (optional SolverFramework instance)

Returns:

Domain object

esys.finley.Rectangle(n0=1, n1=1, order=1, l0=1.0, l1=1.0, periodic0=False, periodic1=False, integrationOrder=-1, reducedIntegrationOrder=-1, useElementsOnFace=None, useFullElementOrder=False, optimize=False, diracPoints=[], diracTags=[], comm=None, framework=None)

Creates a rectangular mesh with n0 x n1 elements over the rectangle [0,l0] x [0,l1].

Parameters:

  • n0 – number of elements in direction 0

  • n1 – number of elements in direction 1

  • order – order of shape functions (1, 2, or -1 for macro elements)

  • l0 – length of side 0

  • l1 – length of side 1

  • periodic0 – periodic boundary conditions in direction 0

  • periodic1 – periodic boundary conditions in direction 1

  • integrationOrder – order of quadrature scheme (-1 for automatic)

  • reducedIntegrationOrder – order of reduced quadrature scheme (-1 for automatic)

  • useElementsOnFace – whether to use elements on face

  • useFullElementOrder – whether to use Rec9 elements

  • optimize – enable optimization of node labels

  • diracPoints – Dirac point coordinates

  • diracTags – Dirac point tags

  • comm – MPI communicator (optional, defaults to MPI_COMM_WORLD)

  • framework – solver framework to use (optional SolverFramework instance)

Returns:

Domain object

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