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Commit 7e2f2a95 authored by Kenneth Leiter's avatar Kenneth Leiter
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ENH: Translate element blocks correctly back to exodus. 

When converting exodus files to xdmf, element block information is written
to xdmf sets. When converting back to exodus, this information was
previously ignored. Now, we check whether we have block information written
as an xdmf set and use it to reproduce element blocks in exodus during
conversion.
parent df2dcfcf
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utils/XdmfExodusWriter.cpp
View file @ 7e2f2a95
......@@ -341,31 +341,13 @@ XdmfExodusWriter::write(const std::string & filePath,
title = title.substr(0, MAX_STR_LENGTH);
}
shared_ptr<XdmfGridCollection> gridCollection =
shared_ptr<XdmfGridCollection>();
shared_ptr<XdmfUnstructuredGrid> currGrid = gridToWrite;
// check if they are temporal collections and use the first grid to
// determine geometry and topology.
if(shared_ptr<XdmfGridCollection> tmpGrid =
shared_dynamic_cast<XdmfGridCollection>(gridToWrite)) {
if(tmpGrid->getType() == XdmfGridCollectionType::Temporal() &&
tmpGrid->getNumberUnstructuredGrids() > 0) {
currGrid = tmpGrid->getUnstructuredGrid(0);
gridCollection = tmpGrid;
}
else {
// only temporal collections are currently supported.
XdmfError::message(XdmfError::FATAL, "Only Temporal Collections are currently supported or no unstructured grids provided in XdmfExodusWriter::write");
}
}
else {
// this is expected to fail when we've already found a grid.
}
// make sure geometry and topology are non null
if(!(currGrid->getGeometry() && currGrid->getTopology()))
XdmfError::message(XdmfError::FATAL, "Current grid's geometry or topology is null in XdmfExodusWriter::write");
XdmfError::message(XdmfError::FATAL,
"Current grid's geometry or topology is null in "
"XdmfExodusWriter::write");
int num_dim = currGrid->getGeometry()->getType()->getDimensions();
int num_nodes = currGrid->getGeometry()->getNumberPoints();
......@@ -374,15 +356,28 @@ XdmfExodusWriter::write(const std::string & filePath,
int num_node_sets = 0;
int num_side_sets = 0;
std::vector<shared_ptr<XdmfSet> > blockSets;
for (unsigned int i=0; i<currGrid->getNumberSets(); ++i) {
if(currGrid->getSet(i)->getType() == XdmfSetType::Cell()) {
num_side_sets++;
// check if we have block information written as a set
if(currGrid->getSet(i)->getName().find("Block") == 0) {
blockSets.push_back(currGrid->getSet(i));
}
}
else if(currGrid->getSet(i)->getType() == XdmfSetType::Node()) {
num_node_sets++;
}
}
//
// we have a single block
//
if(blockSets.size() > 0) {
num_elem_blk = blockSets.size();
}
ex_put_init(exodusHandle,
title.c_str(),
num_dim,
......@@ -415,36 +410,121 @@ XdmfExodusWriter::write(const std::string & filePath,
delete [] y;
delete [] z;
shared_ptr<XdmfTopology> topology = currGrid->getTopology();
// write element block parameters
std::string exodusTopologyType =
xdmfToExodusTopologyType(currGrid->getTopology()->getType());
ex_put_elem_block(exodusHandle,
10,
exodusTopologyType.c_str(),
num_elem,
currGrid->getTopology()->getType()->getNodesPerElement(),
num_side_sets);
// write element connectivity
shared_ptr<XdmfTopology> topology = currGrid->getTopology();
bool releaseTopology = false;
if(!topology->isInitialized()) {
topology->read();
releaseTopology = true;
}
const unsigned int connectivitySize = currGrid->getTopology()->getSize();
int * elem_connectivity = new int[connectivitySize];
for(unsigned int i=0; i<connectivitySize; ++i) {
elem_connectivity[i] = currGrid->getTopology()->getValue<int>(i) + 1;
xdmfToExodusTopologyType(topology->getType());
const int nodesPerElement = topology->getType()->getNodesPerElement();
if(blockSets.size() > 0) {
std::vector<int> elem_blk_ids;
std::vector<int> num_elem_this_blk;
std::vector<char*> elem_type;
std::vector<int> num_nodes_per_elem(blockSets.size(), nodesPerElement);
std::vector<int> num_attr(blockSets.size(), 0);
for(unsigned int i=0; i<blockSets.size(); ++i) {
elem_blk_ids.push_back(10 + i);
num_elem_this_blk.push_back(blockSets[i]->getSize());
char * cellTypeCStr = new char[exodusTopologyType.size() + 1];
strcpy(cellTypeCStr, exodusTopologyType.c_str());
elem_type.push_back(cellTypeCStr);
}
const int define_maps = 0;
ex_put_concat_elem_block(exodusHandle,
&(elem_blk_ids[0]),
&(elem_type[0]),
&(num_elem_this_blk[0]),
&(num_nodes_per_elem[0]),
&(num_attr[0]),
define_maps);
// write element connectivity
bool releaseTopology = false;
if(!topology->isInitialized()) {
topology->read();
releaseTopology = true;
}
for(unsigned int i=0; i<blockSets.size(); ++i) {
shared_ptr<XdmfSet> & set = blockSets[i];
bool releaseSet = false;
if(!set->isInitialized()) {
set->read();
releaseSet = true;
}
const unsigned int connectivitySize = set->getSize() * nodesPerElement;
int * elem_connectivity = new int[connectivitySize];
int offset = 0;
for(unsigned int j=0; j<set->getSize(); ++j) {
const int elementId = set->getValue<int>(j);
const int topologyOffset = elementId * nodesPerElement;
for(int k=0; k<nodesPerElement; ++k) {
elem_connectivity[offset] =
topology->getValue<int>(topologyOffset + k) + 1;
++offset;
}
}
if(releaseSet) {
set->release();
}
convertXdmfToExodusTopology(elem_connectivity,
topology->getType(),
num_elem);
ex_put_elem_conn(exodusHandle, 10 + i, elem_connectivity);
delete [] elem_connectivity;
}
if(releaseTopology) {
topology->release();
}
for(unsigned int i=0; i<blockSets.size(); ++i) {
delete [] elem_type[i];
}
}
if(releaseTopology) {
topology->release();
else {
ex_put_elem_block(exodusHandle,
10,
exodusTopologyType.c_str(),
num_elem,
nodesPerElement,
num_side_sets);
// write element connectivity
bool releaseTopology = false;
if(!topology->isInitialized()) {
topology->read();
releaseTopology = true;
}
const unsigned int connectivitySize = topology->getSize();
int * elem_connectivity = new int[connectivitySize];
for(unsigned int i=0; i<connectivitySize; ++i) {
elem_connectivity[i] = topology->getValue<int>(i) + 1;
}
if(releaseTopology) {
topology->release();
}
convertXdmfToExodusTopology(elem_connectivity,
topology->getType(),
num_elem);
ex_put_elem_conn(exodusHandle, 10, elem_connectivity);
delete [] elem_connectivity;
}
convertXdmfToExodusTopology(elem_connectivity,
currGrid->getTopology()->getType(),
num_elem);
ex_put_elem_conn(exodusHandle, 10, elem_connectivity);
delete [] elem_connectivity;
// write attributes
int numGlobalAttributes = 0;
......@@ -514,58 +594,88 @@ XdmfExodusWriter::write(const std::string & filePath,
delete [] nodalNames;
delete [] elementNames;
int numGrids = 1;
if(gridCollection) {
numGrids = gridCollection->getNumberUnstructuredGrids();
}
double * globalAttributeVals = new double[numGlobalAttributes];
int globalIndex = 0;
int globalComponentIndex = 0;
int nodalIndex = 0;
int nodalComponentIndex = 0;
int elementIndex = 0;
int elementComponentIndex = 0;
for(unsigned int j=0; j<currGrid->getNumberAttributes(); ++j) {
shared_ptr<XdmfAttribute> currAttribute = currGrid->getAttribute(j);
bool releaseAttribute = false;
if(!currAttribute->isInitialized()) {
currAttribute->read();
releaseAttribute = true;
}
if(currAttribute->getCenter() == XdmfAttributeCenter::Grid()) {
for(int k=0; k<globalComponents[globalComponentIndex]; ++k) {
currAttribute->getValues(k, globalAttributeVals + globalIndex, 1);
globalIndex++;
}
globalComponentIndex++;
}
else if(currAttribute->getCenter() == XdmfAttributeCenter::Node()) {
for(int k=0; k<nodalComponents[nodalComponentIndex]; ++k) {
double * nodalValues = new double[num_nodes];
currAttribute->getValues(k,
nodalValues,
num_nodes,
nodalComponents[nodalComponentIndex]);
ex_put_nodal_var(exodusHandle,
1,
nodalIndex+1,
num_nodes,
nodalValues);
ex_update(exodusHandle);
delete [] nodalValues;
nodalIndex++;
}
nodalComponentIndex++;
}
else if(currAttribute->getCenter() == XdmfAttributeCenter::Cell()) {
if(blockSets.size() > 0) {
for(unsigned int k=0; k<blockSets.size(); ++k) {
const shared_ptr<XdmfSet> & set = blockSets[k];
const int num_elem_in_blk = set->getSize();
for(int i=0; i<numGrids; ++i) {
double * globalAttributeVals = new double[numGlobalAttributes];
bool releaseSet = false;
if(!set->isInitialized()) {
set->read();
releaseSet = true;
}
int globalIndex = 0;
int globalComponentIndex = 0;
int nodalIndex = 0;
int nodalComponentIndex = 0;
int elementIndex = 0;
int elementComponentIndex = 0;
double * elementValues = new double[num_elem_in_blk];
if(gridCollection) {
currGrid = gridCollection->getUnstructuredGrid(i);
}
// loop over components
for(int l=0; l<elementComponents[elementComponentIndex]; ++l) {
for(int m=0; m<num_elem_in_blk; ++m) {
const int elementId = set->getValue<int>(elementId);
elementValues[m] =
currAttribute->getValue<double>(elementId + l);
}
ex_put_elem_var(exodusHandle,
1,
elementIndex+1,
10+k,
num_elem,
elementValues);
ex_update(exodusHandle);
elementIndex++;
}
elementComponentIndex++;
for(unsigned int j=0; j<currGrid->getNumberAttributes(); ++j) {
shared_ptr<XdmfAttribute> currAttribute = currGrid->getAttribute(j);
bool releaseAttribute = false;
if(!currAttribute->isInitialized()) {
currAttribute->read();
releaseAttribute = true;
}
if(currAttribute->getCenter() == XdmfAttributeCenter::Grid()) {
for(int k=0; k<globalComponents[globalComponentIndex]; ++k) {
currAttribute->getValues(k, globalAttributeVals + globalIndex, 1);
globalIndex++;
}
globalComponentIndex++;
}
else if(currAttribute->getCenter() == XdmfAttributeCenter::Node()) {
for(int k=0; k<nodalComponents[nodalComponentIndex]; ++k) {
double * nodalValues = new double[num_nodes];
currAttribute->getValues(k,
nodalValues,
num_nodes,
nodalComponents[nodalComponentIndex]);
ex_put_nodal_var(exodusHandle,
i+1,
nodalIndex+1,
num_nodes,
nodalValues);
ex_update(exodusHandle);
delete [] nodalValues;
nodalIndex++;
delete [] elementValues;
if(releaseSet) {
set->release();
}
}
nodalComponentIndex++;
}
else if(currAttribute->getCenter() == XdmfAttributeCenter::Cell()) {
else {
for(int k=0; k<elementComponents[elementComponentIndex]; ++k) {
double * elementValues = new double[num_elem];
currAttribute->getValues(k,
......@@ -573,9 +683,10 @@ XdmfExodusWriter::write(const std::string & filePath,
num_elem,
elementComponents[elementComponentIndex]);
ex_put_elem_var(exodusHandle,
i+1,
1,
elementIndex+1,
10, num_elem,
10,
num_elem,
elementValues);
ex_update(exodusHandle);
delete [] elementValues;
......@@ -583,22 +694,21 @@ XdmfExodusWriter::write(const std::string & filePath,
}
elementComponentIndex++;
}
if(releaseAttribute) {
currAttribute->release();
}
}
ex_put_glob_vars(exodusHandle,
i+1,
numGlobalAttributes,
globalAttributeVals);
ex_update(exodusHandle);
delete [] globalAttributeVals;
writeSets(exodusHandle,
currGrid);
if(releaseAttribute) {
currAttribute->release();
}
}
ex_put_glob_vars(exodusHandle,
1,
numGlobalAttributes,
globalAttributeVals);
ex_update(exodusHandle);
delete [] globalAttributeVals;
writeSets(exodusHandle,
currGrid);
// close exodus file
ex_close(exodusHandle);
}
......
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