escript
Revision_
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#include <ElementFile.h>
Public Member Functions | |
ElementFile (ElementTypeId etype, escript::JMPI mpiInfo) | |
~ElementFile () | |
void | allocTable (dim_t NE) |
allocates the element table within an element file to hold NE elements More... | |
void | freeTable () |
deallocates the element table within an element file More... | |
void | copyTable (index_t offset, index_t nodeOffset, index_t idOffset, const ElementFile *in) |
void | print (const index_t *nodesId) const |
prints information about this element file to stdout More... | |
void | distributeByRankOfDOF (const int *mpiRankOfDOF, const index_t *nodesId) |
redistributes the elements including overlap by rank More... | |
void | createColoring (dim_t numNodes, const index_t *degreeOfFreedom) |
void | optimizeOrdering () |
reorders the elements so that they are stored close to the nodes More... | |
void | relabelNodes (const index_t *newNode, index_t offset) |
void | markNodes (std::vector< short > &mask, index_t offset) const |
void | gather (const index_t *index, const ElementFile *in) |
void | setTags (int newTag, const escript::Data &mask) |
sets element tags to newTag where mask > 0 More... | |
ElementFile_Jacobians * | borrowJacobians (const NodeFile *nodes, bool reducedOrder) const |
std::pair< index_t, index_t > | getNodeRange () const |
void | updateTagList () |
Public Attributes | |
escript::JMPI | MPIInfo |
dim_t | numElements |
number of elements More... | |
index_t * | Id |
int * | Tag |
Tag[i] is the tag of element i. More... | |
int * | Owner |
Owner[i] contains the rank that owns element i. More... | |
std::vector< int > | tagsInUse |
array of tags which are actually used More... | |
int | numNodes |
number of nodes per element More... | |
index_t * | Nodes |
Nodes[INDEX(k, i, numNodes)] is the k-th node in the i-th element. More... | |
index_t * | Color |
index_t | minColor |
minimum color value More... | |
index_t | maxColor |
maximum color value More... | |
int | numDim |
number of spatial dimensions of the domain More... | |
int | numLocalDim |
dimension of the element e.g. 2 for a line in 2D or 3D More... | |
ElementTypeId | etype |
element type ID More... | |
const char * | ename |
name of element type More... | |
int | numShapes |
number of shape functions More... | |
Private Member Functions | |
void | swapTable (ElementFile *other) |
Private Attributes | |
ElementFile_Jacobians * | jacobians |
jacobians of the shape function used for solution approximation More... | |
ElementFile_Jacobians * | jacobians_reducedQ |
dudley::ElementFile::ElementFile | ( | ElementTypeId | etype, |
escript::JMPI | mpiInfo | ||
) |
References dudley::Dims, ename, dudley::getElementName(), jacobians, jacobians_reducedQ, dudley::localDims, numDim, numLocalDim, numNodes, and numShapes.
Referenced by optimizeOrdering().
dudley::ElementFile::~ElementFile | ( | ) |
References freeTable(), jacobians, and jacobians_reducedQ.
void dudley::ElementFile::allocTable | ( | dim_t | NE | ) |
allocates the element table within an element file to hold NE elements
References Color, freeTable(), Id, INDEX2, maxColor, minColor, Nodes, numElements, numNodes, Owner, and Tag.
Referenced by dudley::DudleyDomain::create2D(), dudley::DudleyDomain::create3D(), distributeByRankOfDOF(), dudley::DudleyDomain::load(), optimizeOrdering(), and dudley::DudleyDomain::readGmsh().
ElementFile_Jacobians * dudley::ElementFile::borrowJacobians | ( | const NodeFile * | nodes, |
bool | reducedOrder | ||
) | const |
References dudley::ElementFile_Jacobians::absD, dudley::Assemble_jacobians_2D(), dudley::Assemble_jacobians_2D_M1D_E1D(), dudley::Assemble_jacobians_3D(), dudley::Assemble_jacobians_3D_M2D_E2D(), dudley::NodeFile::Coordinates, dudley::ElementFile_Jacobians::DSDX, dudley::Nodes, dudley::ElementFile_Jacobians::numDim, dudley::NodeFile::numDim, dudley::ElementFile_Jacobians::numElements, dudley::ElementFile_Jacobians::numQuad, dudley::ElementFile_Jacobians::numShapes, dudley::QuadNums, dudley::ElementFile_Jacobians::quadweight, dudley::ElementFile_Jacobians::status, and dudley::NodeFile::status.
Referenced by dudley::Assemble_gradient(), dudley::Assemble_integrate(), and dudley::AssembleParameters::AssembleParameters().
void dudley::ElementFile::copyTable | ( | index_t | offset, |
index_t | nodeOffset, | ||
index_t | idOffset, | ||
const ElementFile * | in | ||
) |
void dudley::ElementFile::createColoring | ( | dim_t | numNodes, |
const index_t * | degreeOfFreedom | ||
) |
Tries to reduce the number of colors used to color elements in this ElementFile
References Color, ESYS_ASSERT, dudley::util::getMinMaxInt(), INDEX2, maxColor, minColor, Nodes, numElements, and numNodes.
Referenced by dudley::DudleyDomain::createColoring().
void dudley::ElementFile::distributeByRankOfDOF | ( | const int * | mpiRankOfDOF, |
const index_t * | nodesId | ||
) |
redistributes the elements including overlap by rank
References allocTable(), Id, INDEX2, MPI_INT, MPIInfo, Nodes, numElements, numNodes, Owner, and Tag.
Referenced by dudley::DudleyDomain::distributeByRankOfDOF().
void dudley::ElementFile::freeTable | ( | ) |
deallocates the element table within an element file
References Color, Id, maxColor, minColor, Nodes, numElements, Owner, Tag, and tagsInUse.
Referenced by allocTable(), and ~ElementFile().
void dudley::ElementFile::gather | ( | const index_t * | index, |
const ElementFile * | in | ||
) |
gathers the elements from the element file in
using index[0:out->elements-1]. index
has to be between 0 and in->numElements-1. A conservative assumption on the colouring is made.
References Color, Id, INDEX2, maxColor, minColor, Nodes, numElements, numNodes, Owner, and Tag.
Referenced by optimizeOrdering().
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inline |
returns the minimum and maximum reference number of nodes describing the elements
References dudley::util::getMinMaxInt(), dudley::Nodes, and dudley::ElementFile_Jacobians::numElements.
Referenced by dudley::DudleyDomain::resolveNodeIds().
void dudley::ElementFile::markNodes | ( | std::vector< short > & | mask, |
index_t | offset | ||
) | const |
References INDEX2, Nodes, numElements, and numNodes.
Referenced by dudley::DudleyDomain::markNodes().
void dudley::ElementFile::optimizeOrdering | ( | ) |
reorders the elements so that they are stored close to the nodes
References allocTable(), ElementFile(), etype, gather(), INDEX2, MPIInfo, Nodes, numElements, numNodes, dudley::util::sortValueAndIndex(), and swapTable().
Referenced by dudley::DudleyDomain::optimizeElementOrdering().
void dudley::ElementFile::print | ( | const index_t * | nodesId | ) | const |
void dudley::ElementFile::relabelNodes | ( | const index_t * | newNode, |
index_t | offset | ||
) |
assigns new node reference numbers to the elements. If k is the old node, the new node is newNode[k-offset].
References INDEX2, Nodes, numElements, and numNodes.
Referenced by dudley::DudleyDomain::relabelElementNodes().
void dudley::ElementFile::setTags | ( | int | newTag, |
const escript::Data & | mask | ||
) |
sets element tags to newTag where mask > 0
References escript::Data::actsExpanded(), escript::Data::getDataPointSize(), escript::Data::getSampleDataRO(), dudley::hasReducedIntegrationOrder(), numElements, numNodes, escript::Data::numSamplesEqual(), Tag, and updateTagList().
Referenced by dudley::DudleyDomain::setTags().
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private |
References Color, Id, maxColor, minColor, Nodes, numElements, Owner, paso::swap(), Tag, and tagsInUse.
Referenced by optimizeOrdering().
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inline |
References dudley::ElementFile_Jacobians::numElements, and dudley::util::setValuesInUse().
Referenced by dudley::DudleyDomain::load(), setTags(), and dudley::DudleyDomain::updateTagList().
index_t* dudley::ElementFile::Color |
assigns each element a color. Elements with the same color don't share a node so they can be processed simultaneously. At any time Color must provide a valid value. In any case one can set Color[e]=e for all e.
Referenced by allocTable(), dudley::Assemble_LumpedSystem(), dudley::Assemble_PDE_Points(), dudley::Assemble_PDE_Single_2D(), dudley::Assemble_PDE_Single_3D(), dudley::Assemble_PDE_System_2D(), dudley::Assemble_PDE_System_3D(), createColoring(), dudley::DudleyDomain::dump(), freeTable(), gather(), dudley::IndexList_insertElements(), dudley::IndexList_insertElementsWithRowRangeNoMainDiagonal(), weipa::FinleyElements::initFromDudley(), dudley::DudleyDomain::load(), print(), dudley::DudleyDomain::printElementInfo(), dudley::DudleyDomain::readGmsh(), and swapTable().
const char* dudley::ElementFile::ename |
name of element type
Referenced by ElementFile(), print(), dudley::DudleyDomain::printElementInfo(), and dudley::DudleyDomain::writeElementInfo().
ElementTypeId dudley::ElementFile::etype |
element type ID
Referenced by dudley::DudleyDomain::dump(), weipa::FinleyElements::initFromDudley(), optimizeOrdering(), and dudley::DudleyDomain::printElementInfo().
index_t* dudley::ElementFile::Id |
Id[i] is the id number of node i. This number is used when elements are resorted. In the entire code the term 'element id' refers to i and not to Id[i] unless explicitly stated otherwise.
Referenced by allocTable(), dudley::DudleyDomain::borrowSampleReferenceIDs(), copyTable(), dudley::DudleyDomain::create2D(), dudley::DudleyDomain::create3D(), distributeByRankOfDOF(), dudley::DudleyDomain::dump(), freeTable(), gather(), weipa::FinleyElements::initFromDudley(), dudley::DudleyDomain::load(), print(), dudley::DudleyDomain::printElementInfo(), dudley::DudleyDomain::readGmsh(), swapTable(), and dudley::DudleyDomain::writeElementInfo().
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private |
jacobians of the shape function used for solution approximation
Referenced by ElementFile(), and ~ElementFile().
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private |
jacobians of the shape function used for solution approximation for reduced integration order
Referenced by ElementFile(), and ~ElementFile().
index_t dudley::ElementFile::maxColor |
maximum color value
Referenced by allocTable(), createColoring(), freeTable(), gather(), dudley::DudleyDomain::load(), print(), dudley::DudleyDomain::readGmsh(), and swapTable().
index_t dudley::ElementFile::minColor |
minimum color value
Referenced by allocTable(), dudley::Assemble_LumpedSystem(), dudley::Assemble_PDE_Points(), dudley::Assemble_PDE_Single_2D(), dudley::Assemble_PDE_Single_3D(), dudley::Assemble_PDE_System_2D(), dudley::Assemble_PDE_System_3D(), createColoring(), freeTable(), gather(), dudley::IndexList_insertElements(), dudley::IndexList_insertElementsWithRowRangeNoMainDiagonal(), dudley::DudleyDomain::load(), print(), dudley::DudleyDomain::readGmsh(), and swapTable().
escript::JMPI dudley::ElementFile::MPIInfo |
index_t* dudley::ElementFile::Nodes |
Nodes[INDEX(k, i, numNodes)] is the k-th node in the i-th element.
Referenced by allocTable(), dudley::Assemble_getNormal(), dudley::Assemble_getSize(), dudley::Assemble_gradient(), dudley::Assemble_interpolate(), dudley::Assemble_LumpedSystem(), dudley::Assemble_PDE_Points(), dudley::Assemble_PDE_Single_2D(), dudley::Assemble_PDE_Single_3D(), dudley::Assemble_PDE_System_2D(), dudley::Assemble_PDE_System_3D(), copyTable(), dudley::DudleyDomain::create2D(), dudley::DudleyDomain::create3D(), createColoring(), distributeByRankOfDOF(), dudley::DudleyDomain::dump(), freeTable(), gather(), dudley::IndexList_insertElements(), dudley::IndexList_insertElementsWithRowRangeNoMainDiagonal(), weipa::FinleyElements::initFromDudley(), dudley::DudleyDomain::load(), markNodes(), optimizeOrdering(), print(), dudley::DudleyDomain::printElementInfo(), dudley::DudleyDomain::readGmsh(), relabelNodes(), swapTable(), and dudley::DudleyDomain::writeElementInfo().
int dudley::ElementFile::numDim |
number of spatial dimensions of the domain
Referenced by dudley::Assemble_AverageElementData(), dudley::Assemble_CopyElementData(), dudley::Assemble_getNormal(), dudley::Assemble_getSize(), dudley::Assemble_interpolate(), dudley::Assemble_LumpedSystem(), dudley::AssembleParameters::AssembleParameters(), and ElementFile().
dim_t dudley::ElementFile::numElements |
number of elements
Referenced by allocTable(), dudley::Assemble_AverageElementData(), dudley::Assemble_CopyElementData(), dudley::Assemble_getNormal(), dudley::Assemble_getSize(), dudley::Assemble_gradient(), dudley::Assemble_integrate(), dudley::Assemble_interpolate(), dudley::Assemble_LumpedSystem(), dudley::Assemble_PDE(), dudley::Assemble_PDE_Points(), dudley::Assemble_PDE_Single_2D(), dudley::Assemble_PDE_Single_3D(), dudley::Assemble_PDE_System_2D(), dudley::Assemble_PDE_System_3D(), dudley::AssembleParameters::AssembleParameters(), copyTable(), createColoring(), distributeByRankOfDOF(), dudley::DudleyDomain::dump(), freeTable(), gather(), dudley::DudleyDomain::getDataShape(), dudley::IndexList_insertElements(), dudley::IndexList_insertElementsWithRowRangeNoMainDiagonal(), weipa::FinleyElements::initFromDudley(), markNodes(), optimizeOrdering(), print(), dudley::DudleyDomain::printElementInfo(), relabelNodes(), setTags(), swapTable(), and dudley::DudleyDomain::writeElementInfo().
int dudley::ElementFile::numLocalDim |
dimension of the element e.g. 2 for a line in 2D or 3D
Referenced by dudley::Assemble_getNormal(), ElementFile(), and dudley::DudleyDomain::getDataShape().
int dudley::ElementFile::numNodes |
number of nodes per element
Referenced by allocTable(), dudley::Assemble_getNormal(), dudley::Assemble_getSize(), dudley::Assemble_gradient(), dudley::Assemble_interpolate(), dudley::AssembleParameters::AssembleParameters(), copyTable(), dudley::DudleyDomain::create2D(), dudley::DudleyDomain::create3D(), createColoring(), distributeByRankOfDOF(), dudley::DudleyDomain::dump(), ElementFile(), gather(), dudley::IndexList_insertElements(), dudley::IndexList_insertElementsWithRowRangeNoMainDiagonal(), weipa::FinleyElements::initFromDudley(), markNodes(), optimizeOrdering(), print(), dudley::DudleyDomain::printElementInfo(), dudley::DudleyDomain::readGmsh(), relabelNodes(), setTags(), and dudley::DudleyDomain::writeElementInfo().
int dudley::ElementFile::numShapes |
number of shape functions
Referenced by ElementFile(), and dudley::IndexList_insertElements().
int* dudley::ElementFile::Owner |
Owner[i] contains the rank that owns element i.
Referenced by allocTable(), dudley::Assemble_integrate(), copyTable(), dudley::DudleyDomain::create2D(), dudley::DudleyDomain::create3D(), distributeByRankOfDOF(), dudley::DudleyDomain::dump(), freeTable(), gather(), weipa::FinleyElements::initFromDudley(), dudley::DudleyDomain::load(), print(), dudley::DudleyDomain::printElementInfo(), dudley::DudleyDomain::readGmsh(), and swapTable().
int* dudley::ElementFile::Tag |
Tag[i] is the tag of element i.
Referenced by allocTable(), copyTable(), dudley::DudleyDomain::create2D(), dudley::DudleyDomain::create3D(), distributeByRankOfDOF(), dudley::DudleyDomain::dump(), freeTable(), gather(), dudley::DudleyDomain::getTagFromSampleNo(), weipa::FinleyElements::initFromDudley(), dudley::DudleyDomain::load(), print(), dudley::DudleyDomain::printElementInfo(), dudley::DudleyDomain::readGmsh(), setTags(), swapTable(), and dudley::DudleyDomain::writeElementInfo().
std::vector<int> dudley::ElementFile::tagsInUse |
array of tags which are actually used
Referenced by dudley::DudleyDomain::borrowListOfTagsInUse(), freeTable(), dudley::DudleyDomain::getNumberOfTagsInUse(), and swapTable().