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/******************************************************* |
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* |
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* Copyright (c) 2003-2009 by University of Queensland |
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* Earth Systems Science Computational Center (ESSCC) |
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* http://www.uq.edu.au/esscc |
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* |
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* Primary Business: Queensland, Australia |
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* Licensed under the Open Software License version 3.0 |
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* http://www.opensource.org/licenses/osl-3.0.php |
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* |
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*******************************************************/ |
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|
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#include <escriptexport/NodeData.h> |
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|
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extern "C" { |
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#include <finley/Mesh.h> |
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#include <finley/NodeFile.h> |
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} |
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|
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#if USE_NETCDF |
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#include <netcdf.hh> |
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#endif |
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|
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#if USE_SILO |
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#include <silo.h> |
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#endif |
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|
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using namespace std; |
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|
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namespace escriptexport { |
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|
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// |
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// Constructor with name |
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// |
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NodeData::NodeData(const string& meshName) : |
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numDims(0), numNodes(0), name(meshName) |
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{ |
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} |
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|
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// |
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// |
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// |
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NodeData::NodeData(NodeData_ptr fullNodes, IntVec& requiredNodes, |
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const string& meshName) : |
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name(meshName) |
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{ |
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numDims = fullNodes->numDims; |
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nodeDist = fullNodes->nodeDist; |
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|
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// first: find the unique set of required nodes and their IDs while |
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// updating the contents of requiredNodes at the same time |
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// requiredNodes contains node indices (not IDs!) |
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IntVec::iterator it; |
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IndexMap indexMap; // maps old index to new index |
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size_t newIndex = 0; |
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|
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for (it = requiredNodes.begin(); it != requiredNodes.end(); it++) { |
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IndexMap::iterator res = indexMap.find(*it); |
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if (res == indexMap.end()) { |
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nodeID.push_back(fullNodes->nodeID[*it]); |
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nodeTag.push_back(fullNodes->nodeTag[*it]); |
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nodeGDOF.push_back(fullNodes->nodeGDOF[*it]); |
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nodeGNI.push_back(fullNodes->nodeGNI[*it]); |
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nodeGRDFI.push_back(fullNodes->nodeGRDFI[*it]); |
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nodeGRNI.push_back(fullNodes->nodeGRNI[*it]); |
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indexMap[*it] = newIndex; |
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*it = newIndex++; |
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} else { |
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*it = res->second; |
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} |
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} |
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|
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// second: now that we know how many nodes we need use the map to fill |
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// the coordinates |
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numNodes = newIndex; |
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for (int dim=0; dim<numDims; dim++) { |
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const float* origC = fullNodes->coords[dim]; |
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float* c = new float[numNodes]; |
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coords.push_back(c); |
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IndexMap::const_iterator mIt; |
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for (mIt = indexMap.begin(); mIt != indexMap.end(); mIt++) { |
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c[mIt->second] = origC[mIt->first]; |
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} |
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} |
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} |
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|
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// |
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// Copy constructor |
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// |
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NodeData::NodeData(const NodeData& m) |
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{ |
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numDims = m.numDims; |
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numNodes = m.numNodes; |
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nodeID = m.nodeID; |
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nodeTag = m.nodeTag; |
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nodeGDOF = m.nodeGDOF; |
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nodeGNI = m.nodeGNI; |
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nodeGRDFI = m.nodeGRDFI; |
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nodeGRNI = m.nodeGRNI; |
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nodeDist = m.nodeDist; |
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name = m.name; |
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for (int i=0; i<numDims; i++) { |
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float* c = new float[numNodes]; |
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copy(m.coords[i], m.coords[i]+numNodes, c); |
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coords.push_back(c); |
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} |
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} |
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|
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// |
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// |
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// |
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NodeData::~NodeData() |
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{ |
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CoordArray::iterator it; |
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for (it = coords.begin(); it != coords.end(); it++) |
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delete[] *it; |
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} |
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|
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// |
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// |
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// |
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bool NodeData::initFromFinley(const Finley_NodeFile* finleyFile) |
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{ |
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numDims = finleyFile->numDim; |
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numNodes = finleyFile->numNodes; |
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|
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int mpisize = finleyFile->MPIInfo->size; |
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int* iPtr = finleyFile->nodesDistribution->first_component; |
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nodeDist.clear(); |
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nodeDist.insert(nodeDist.end(), mpisize+1, 0); |
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copy(iPtr, iPtr+mpisize+1, nodeDist.begin()); |
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|
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CoordArray::iterator it; |
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for (it = coords.begin(); it != coords.end(); it++) |
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delete[] *it; |
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coords.clear(); |
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nodeID.clear(); |
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nodeTag.clear(); |
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nodeGDOF.clear(); |
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nodeGNI.clear(); |
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nodeGRDFI.clear(); |
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nodeGRNI.clear(); |
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|
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if (numNodes > 0) { |
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for (int i=0; i<numDims; i++) { |
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double* srcPtr = finleyFile->Coordinates + i; |
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float* c = new float[numNodes]; |
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coords.push_back(c); |
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for (int j=0; j<numNodes; j++, srcPtr+=numDims) { |
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*c++ = (float) *srcPtr; |
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} |
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} |
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|
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iPtr = finleyFile->Id; |
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nodeID.insert(nodeID.end(), numNodes, 0); |
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copy(iPtr, iPtr+numNodes, nodeID.begin()); |
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|
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iPtr = finleyFile->Tag; |
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nodeTag.insert(nodeTag.end(), numNodes, 0); |
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copy(iPtr, iPtr+numNodes, nodeTag.begin()); |
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|
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iPtr = finleyFile->globalDegreesOfFreedom; |
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nodeGDOF.insert(nodeGDOF.end(), numNodes, 0); |
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copy(iPtr, iPtr+numNodes, nodeGDOF.begin()); |
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|
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iPtr = finleyFile->globalNodesIndex; |
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nodeGNI.insert(nodeGNI.end(), numNodes, 0); |
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copy(iPtr, iPtr+numNodes, nodeGNI.begin()); |
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|
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iPtr = finleyFile->globalReducedDOFIndex; |
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nodeGRDFI.insert(nodeGRDFI.end(), numNodes, 0); |
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copy(iPtr, iPtr+numNodes, nodeGRDFI.begin()); |
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|
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iPtr = finleyFile->globalReducedNodesIndex; |
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nodeGRNI.insert(nodeGRNI.end(), numNodes, 0); |
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copy(iPtr, iPtr+numNodes, nodeGRNI.begin()); |
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|
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} |
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return true; |
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} |
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|
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// |
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// |
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// |
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bool NodeData::readFromNc(NcFile* ncFile) |
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{ |
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#if USE_NETCDF |
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NcAtt* att; |
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NcVar* var; |
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|
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att = ncFile->get_att("numDim"); |
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numDims = att->as_int(0); |
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att = ncFile->get_att("numNodes"); |
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numNodes = att->as_int(0); |
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att = ncFile->get_att("mpi_size"); |
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int mpisize = att->as_int(0); |
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nodeDist.clear(); |
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nodeDist.insert(nodeDist.end(), mpisize+1, 0); |
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var = ncFile->get_var("Nodes_NodeDistribution"); |
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var->get(&nodeDist[0], mpisize+1); |
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CoordArray::iterator it; |
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for (it = coords.begin(); it != coords.end(); it++) |
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delete[] *it; |
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coords.clear(); |
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nodeID.clear(); |
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nodeTag.clear(); |
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nodeGDOF.clear(); |
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nodeGNI.clear(); |
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nodeGRDFI.clear(); |
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nodeGRNI.clear(); |
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// Only attempt to read further if there are any nodes. |
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// Having no nodes is not an error. |
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if (numNodes > 0) { |
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var = ncFile->get_var("Nodes_Coordinates"); |
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for (int i=0; i<numDims; i++) { |
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float* c = new float[numNodes]; |
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var->set_cur(0, i); |
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var->get(c, numNodes, 1); |
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coords.push_back(c); |
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} |
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nodeID.insert(nodeID.end(), numNodes, 0); |
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var = ncFile->get_var("Nodes_Id"); |
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var->get(&nodeID[0], numNodes); |
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nodeTag.insert(nodeTag.end(), numNodes, 0); |
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var = ncFile->get_var("Nodes_Tag"); |
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var->get(&nodeTag[0], numNodes); |
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nodeGDOF.insert(nodeGDOF.end(), numNodes, 0); |
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var = ncFile->get_var("Nodes_gDOF"); |
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var->get(&nodeGDOF[0], numNodes); |
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nodeGNI.insert(nodeGNI.end(), numNodes, 0); |
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var = ncFile->get_var("Nodes_gNI"); |
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var->get(&nodeGNI[0], numNodes); |
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nodeGRDFI.insert(nodeGRDFI.end(), numNodes, 0); |
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var = ncFile->get_var("Nodes_grDfI"); |
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var->get(&nodeGRDFI[0], numNodes); |
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nodeGRNI.insert(nodeGRNI.end(), numNodes, 0); |
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var = ncFile->get_var("Nodes_grNI"); |
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var->get(&nodeGRNI[0], numNodes); |
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} |
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return true; |
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#else // !USE_NETCDF |
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return false; |
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#endif |
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} |
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|
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// |
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// |
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// |
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const IntVec& NodeData::getVarDataByName(const string& name) const |
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{ |
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if (name == "Nodes_Id") |
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return nodeID; |
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else if (name == "Nodes_Tag") |
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return nodeTag; |
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else if (name == "Nodes_gDOF") |
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return nodeGDOF; |
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else if (name == "Nodes_gNI") |
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return nodeGNI; |
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else if (name == "Nodes_grDfI") |
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return nodeGRDFI; |
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else if (name == "Nodes_grNI") |
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return nodeGRNI; |
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else |
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throw "Invalid variable name"; |
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} |
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|
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// |
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// |
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// |
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StringVec NodeData::getVarNames() const |
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{ |
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StringVec res; |
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if (numNodes > 0) { |
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res.push_back("Nodes_Id"); |
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res.push_back("Nodes_Tag"); |
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res.push_back("Nodes_gDOF"); |
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res.push_back("Nodes_gNI"); |
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res.push_back("Nodes_grDfI"); |
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res.push_back("Nodes_grNI"); |
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} |
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return res; |
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} |
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|
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// |
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// |
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// |
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bool NodeData::writeToSilo(DBfile* dbfile) |
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{ |
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#if USE_SILO |
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if (numNodes == 0) |
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return true; |
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int ret; |
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if (siloPath != "") { |
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ret = DBSetDir(dbfile, siloPath.c_str()); |
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if (ret != 0) |
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return false; |
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} |
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string siloMeshName = getFullSiloName(); |
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|
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// Write node-centered variables |
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ret = DBPutUcdvar1(dbfile, "Nodes_Id", siloMeshName.c_str(), |
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(float*)&nodeID[0], numNodes, NULL, 0, DB_INT, DB_NODECENT, NULL); |
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|
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if (ret == 0) |
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ret = DBPutUcdvar1(dbfile, "Nodes_Tag", siloMeshName.c_str(), |
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(float*)&nodeTag[0], numNodes, NULL, 0, DB_INT, |
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DB_NODECENT, NULL); |
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if (ret == 0) |
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ret = DBPutUcdvar1(dbfile, "Nodes_gDOF", siloMeshName.c_str(), |
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(float*)&nodeGDOF[0], numNodes, NULL, 0, DB_INT, |
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DB_NODECENT, NULL); |
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if (ret == 0) |
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ret = DBPutUcdvar1(dbfile, "Nodes_gNI", siloMeshName.c_str(), |
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(float*)&nodeGNI[0], numNodes, NULL, 0, DB_INT, |
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DB_NODECENT, NULL); |
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if (ret == 0) |
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ret = DBPutUcdvar1(dbfile, "Nodes_grDfI", siloMeshName.c_str(), |
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(float*)&nodeGRDFI[0], numNodes, NULL, 0, DB_INT, |
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DB_NODECENT, NULL); |
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if (ret == 0) |
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ret = DBPutUcdvar1(dbfile, "Nodes_grNI", siloMeshName.c_str(), |
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(float*)&nodeGRNI[0], numNodes, NULL, 0, DB_INT, |
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DB_NODECENT, NULL); |
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DBSetDir(dbfile, "/"); |
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return (ret == 0); |
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|
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#else // !USE_SILO |
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return false; |
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#endif |
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} |
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|
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} // namespace escriptexport |
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