void ConnectivityGlobalPlugin::update(CC3DXMLElement *_xmlData, bool _fullInitFlag) {
if (potts->getDisplayUnitsFlag()) {
Unit energyUnit = potts->getEnergyUnit();
CC3DXMLElement * unitsElem = _xmlData->getFirstElement("Units");
if (!unitsElem) { //add Units element
unitsElem = _xmlData->attachElement("Units");
}
if (unitsElem->getFirstElement("PenaltyUnit")) {
unitsElem->getFirstElement("PenaltyUnit")->updateElementValue(energyUnit.toString());
}
else {
CC3DXMLElement * energyElem = unitsElem->attachElement("PenaltyUnit", energyUnit.toString());
}
}
penaltyVec.clear();
Automaton *automaton = potts->getAutomaton();
ASSERT_OR_THROW("CELL TYPE PLUGIN WAS NOT PROPERLY INITIALIZED YET. MAKE SURE THIS IS THE FIRST PLUGIN THAT YOU SET", automaton)
set<unsigned char> cellTypesSet;
map<unsigned char, double> typeIdConnectivityPenaltyMap;
if (_xmlData->getFirstElement("DoNotPrecheckConnectivity")) {
doNotPrecheckConnectivity = true;
}
if (_xmlData->getFirstElement("FastAlgorithm")) {
fast_algorithm = true;
changeEnergyFcnPtr = &ConnectivityGlobalPlugin::changeEnergyFast;
}
CC3DXMLElementList penaltyVecXML = _xmlData->getElements("Penalty");
CC3DXMLElementList connectivityOnVecXML = _xmlData->getElements("ConnectivityOn");
ASSERT_OR_THROW("You cannot use Penalty and ConnectivityOn tags together. Stick to one convention", !(connectivityOnVecXML.size() && penaltyVecXML.size()));
// previous ASSERT_OR_THROW will encure that only one of the subsequent for loops be executed
for (int i = 0; i < penaltyVecXML.size(); ++i) {
typeIdConnectivityPenaltyMap.insert(make_pair(automaton->getTypeId(penaltyVecXML[i]->getAttribute("Type")), penaltyVecXML[i]->getDouble()));
//inserting all the types to the set (duplicate are automatically eleminated) to figure out max value of type Id
cellTypesSet.insert(automaton->getTypeId(penaltyVecXML[i]->getAttribute("Type")));
}
for (int i = 0; i < connectivityOnVecXML.size(); ++i) {
typeIdConnectivityPenaltyMap.insert(make_pair(automaton->getTypeId(connectivityOnVecXML[i]->getAttribute("Type")), 1.0));
//inserting all the types to the set (duplicate are automatically eleminated) to figure out max value of type Id
cellTypesSet.insert(automaton->getTypeId(connectivityOnVecXML[i]->getAttribute("Type")));
}
//Now that we know all the types used in the simulation we will find size of the penaltyVec
vector<unsigned char> cellTypesVector(cellTypesSet.begin(), cellTypesSet.end());//coping set to the vector
int size = 0;
if (cellTypesVector.size()) {
size = *max_element(cellTypesVector.begin(), cellTypesVector.end());
}
maxTypeId = size;
size += 1;//if max element is e.g. 5 then size has to be 6 for an array to be properly allocated
int index;
penaltyVec.assign(size, 0.0);
//inserting connectivity penalty values to penaltyVec;
for (map<unsigned char, double>::iterator mitr = typeIdConnectivityPenaltyMap.begin(); mitr != typeIdConnectivityPenaltyMap.end(); ++mitr) {
penaltyVec[mitr->first] = fabs(mitr->second);
}
cerr << "size=" << size << endl;
for (int i = 0; i < size; ++i) {
cerr << "penaltyVec[" << i << "]=" << penaltyVec[i] << endl;
}
//Here I initialize max neighbor index for direct acces to the list of neighbors
boundaryStrategy = BoundaryStrategy::getInstance();
maxNeighborIndex = 0;
maxNeighborIndex = boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(1);
cerr << "ConnectivityGlobal maxNeighborIndex=" << maxNeighborIndex << endl;
WatchableField3D<CellG *> *cellFieldG = (WatchableField3D<CellG *> *)potts->getCellFieldG();
Dim3D fieldDim = cellFieldG->getDim();
// max_neighbor_index_local_search is different depending whether we are on hex or cartesian lattice and if this is 2D or 3D simulation
if (boundaryStrategy->getLatticeType() == HEXAGONAL_LATTICE) { // on hex lattice in 2D and 3D nearest neighbors "completely cover" a given pixel
max_neighbor_index_local_search = boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(1);
}
else {
if (fieldDim.x == 1 || fieldDim.y == 1 || fieldDim.z == 1) { //2D simulation
max_neighbor_index_local_search = boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(2);
}
else { //3D
max_neighbor_index_local_search = boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(3);
}
}
}
void AdhesionFlexPlugin::update(CC3DXMLElement *_xmlData, bool _fullInitFlag){
automaton = potts->getAutomaton();
ASSERT_OR_THROW("CELL TYPE PLUGIN WAS NOT PROPERLY INITIALIZED YET. MAKE SURE THIS IS THE FIRST PLUGIN THAT YOU SET", automaton)
set<unsigned char> cellTypesSet;
//scanning Adhesion Molecule names
CC3DXMLElementList adhesionMoleculeNameXMLVec=_xmlData->getElements("AdhesionMolecule");
vector<string> adhesionMoleculeNameVec;
set<string> adhesionMoleculeNameSet;
moleculeNameIndexMap.clear();
for (int i = 0 ; i<adhesionMoleculeNameXMLVec.size(); ++i){
string moleculeName=adhesionMoleculeNameXMLVec[i]->getAttribute("Molecule");
if (! adhesionMoleculeNameSet.insert(moleculeName).second){
ASSERT_OR_THROW(string("Duplicate molecule Name=")+moleculeName+ " specified in AdhesionMolecule section ", false);
}
adhesionMoleculeNameVec.push_back(moleculeName);
moleculeNameIndexMap.insert(make_pair(moleculeName,i));
}
numberOfAdhesionMolecules=moleculeNameIndexMap.size();
if (!sim->getRestartEnabled()){
adhesionMoleculeDensityVecMedium=vector<float>(numberOfAdhesionMolecules,0.0);
}
cerr<<"numberOfAdhesionMolecules="<<numberOfAdhesionMolecules<<endl;
//scannning AdhesionMoleculeDensity section
CC3DXMLElementList adhesionMoleculeDensityXMLVec=_xmlData->getElements("AdhesionMoleculeDensity");
typeToAdhesionMoleculeDensityMap.clear();
std::map<int,std::vector<float> >::iterator mitr;
for (int i = 0 ; i<adhesionMoleculeDensityXMLVec.size(); ++i){
int typeId=automaton->getTypeId(adhesionMoleculeDensityXMLVec[i]->getAttribute("CellType"));
cerr<<"typeId="<<typeId<<endl;
mitr=typeToAdhesionMoleculeDensityMap.find(typeId);
if (mitr==typeToAdhesionMoleculeDensityMap.end()){
typeToAdhesionMoleculeDensityMap.insert(make_pair(typeId,vector<float>(numberOfAdhesionMolecules,0.0)));
cerr<<"typeToAdhesionMoleculeDensityMap[typeId].size()="<<typeToAdhesionMoleculeDensityMap[typeId].size()<<endl;
}
string moleculeName=adhesionMoleculeDensityXMLVec[i]->getAttribute("Molecule");
cerr<<"moleculeName="<<moleculeName<<endl;
if(moleculeNameIndexMap.find(moleculeName)==moleculeNameIndexMap.end()){
ASSERT_OR_THROW(string("Molecule Name=")+moleculeName+" was not declared in the AdhesionMolecule section",false);
}
cerr<<"moleculeNameIndexMap[moleculeName]="<<moleculeNameIndexMap[moleculeName]<<endl;
cerr<<"adhesionMoleculeDensityXMLVec[i]->getAttributeAsDouble(Density)="<<adhesionMoleculeDensityXMLVec[i]->getAttributeAsDouble("Density")<<endl;
cerr<<"typeToAdhesionMoleculeDensityMap[typeId].size()="<<typeToAdhesionMoleculeDensityMap[typeId].size()<<endl;
typeToAdhesionMoleculeDensityMap[typeId][moleculeNameIndexMap[moleculeName]]=adhesionMoleculeDensityXMLVec[i]->getAttributeAsDouble("Density");
cerr<<"AFTER ASSIGNING DENSITY"<<endl;
}
//scanning BindingFormula section
CC3DXMLElement * bindingFormulaXMLElem=_xmlData->getFirstElement("BindingFormula");
formulaString=bindingFormulaXMLElem->getFirstElement("Formula")->getText(); //formula string
CC3DXMLElement * variablesSectionXMLElem=bindingFormulaXMLElem->getFirstElement("Variables");
//cerr<<"formulaString="<<formulaString<<endl;
//here we can add options depending on variables input - for now it is har-coded to accept only matrix of bindingParameters
bindingParameters.clear() ; //have to clear binding parameters
CC3DXMLElement * adhesionInteractionMatrixXMLElem = variablesSectionXMLElem->getFirstElement("AdhesionInteractionMatrix");
CC3DXMLElementList bindingParameterXMLVec = adhesionInteractionMatrixXMLElem->getElements("BindingParameter");
for (int i = 0 ; i<bindingParameterXMLVec.size(); ++i){
setBindingParameter(bindingParameterXMLVec[i]->getAttribute("Molecule1") , bindingParameterXMLVec[i]->getAttribute("Molecule2"), bindingParameterXMLVec[i]->getDouble());
}
//vectorized variables for convenient parallel access
unsigned int maxNumberOfWorkNodes=pUtils->getMaxNumberOfWorkNodesPotts();
molecule1Vec.assign(maxNumberOfWorkNodes,0.0);
molecule2Vec.assign(maxNumberOfWorkNodes,0.0);
pVec.assign(maxNumberOfWorkNodes,mu::Parser());
for (int i = 0 ; i< maxNumberOfWorkNodes ; ++i){
pVec[i].DefineVar("Molecule1",&molecule1Vec[i]);
pVec[i].DefineVar("Molecule2",&molecule2Vec[i]);
pVec[i].SetExpr(formulaString);
}
// p=mu::Parser(); //using new parser
// //setting up muParser
// p.DefineVar("Molecule1", &molecule1);
// p.DefineVar("Molecule2", &molecule2);
// p.SetExpr(formulaString);
//scanning NeighborOrder or Depth
//Here I initialize max neighbor index for direct acces to the list of neighbors
boundaryStrategy=BoundaryStrategy::getInstance();
maxNeighborIndex=0;
if(_xmlData->getFirstElement("Depth")){
maxNeighborIndex=boundaryStrategy->getMaxNeighborIndexFromDepth(_xmlData->getFirstElement("Depth")->getDouble());
//cerr<<"got here will do depth"<<endl;
}else{
//cerr<<"got here will do neighbor order"<<endl;
if(_xmlData->getFirstElement("NeighborOrder")){
maxNeighborIndex=boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(_xmlData->getFirstElement("NeighborOrder")->getUInt());
cerr<<"maxNeighborIndex="<<maxNeighborIndex<<endl;
}else{
maxNeighborIndex=boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(1);
}
}
cerr<<"sizeBindingArray="<<moleculeNameIndexMap.size()<<endl;
//initializing binding parameter array
int sizeBindingArray=moleculeNameIndexMap.size();
int indexBindingArray ;
bindingParameterArray.clear();
bindingParameterArray.assign(sizeBindingArray,vector<double>(sizeBindingArray,0.0));
bindingParameters_t::iterator bmitr;
for(int i = 0 ; i < sizeBindingArray ; ++i)
for(int j = 0 ; j < sizeBindingArray ; ++j){
indexBindingArray= getIndex(i,j);
bmitr=bindingParameters.find(indexBindingArray);
if(bmitr!=bindingParameters.end()){
bindingParameterArray[i][j] = bmitr->second;
}
}
for(int i = 0 ; i < sizeBindingArray ; ++i)
for(int j = 0 ; j < sizeBindingArray ; ++j){
cerr<<"bindingParameterArray["<<i<<"]["<<j<<"]="<<bindingParameterArray[i][j]<<endl;
}
}
void BoundaryPixelTrackerPlugin::update(CC3DXMLElement *_xmlData, bool _fullInitFlag) {
//Here I initialize max neighbor index for direct acces to the list of neighbors
boundaryStrategy = BoundaryStrategy::getInstance();
maxNeighborIndex = 0;
if (!_xmlData) { //this happens if plugin is loaded directly as a dependency from another plugin
maxNeighborIndex = boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(1);
return;
}
if (_xmlData->getFirstElement("Depth")) {
maxNeighborIndex = boundaryStrategy->getMaxNeighborIndexFromDepth(_xmlData->getFirstElement("Depth")->getDouble());
// when user specifies depth , fetching of boundary for neighbor order might not work properly - not a big deal because almost nobody is using the Depth tag
neighborOrder = 0;
//cerr<<"got here will do depth"<<endl;
}
else {
//cerr<<"got here will do neighbor order"<<endl;
if (_xmlData->getFirstElement("NeighborOrder")) {
neighborOrder = _xmlData->getFirstElement("NeighborOrder")->getUInt();
maxNeighborIndex = boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(neighborOrder);
}
else {
neighborOrder = 1;
maxNeighborIndex = boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(1);
}
std::set<int> extraBoundariesNeighborOrderSet;
CC3DXMLElementList extraBoundariesVec = _xmlData->getElements("ExtraBoundary");
for (int i = 0; i < extraBoundariesVec.size(); ++i) {
extraBoundariesNeighborOrderSet.insert(extraBoundariesVec[i]->getAttributeAsInt("NeighborOrder"));
}
extraBoundariesNeighborOrder.assign(extraBoundariesNeighborOrderSet.begin(), extraBoundariesNeighborOrderSet.end());
extraBoundariesMaxNeighborIndex.assign(extraBoundariesNeighborOrder.size(), 0); //allocating memory in the extraBoundariesMaxNeighborIndex vector
for (unsigned int i = 0; i < extraBoundariesNeighborOrder.size(); ++i) {
extraBoundariesMaxNeighborIndex[i] = boundaryStrategy->getMaxNeighborIndexFromNeighborOrder(extraBoundariesNeighborOrder[i]);
}
for (unsigned int i = 0; i < extraBoundariesMaxNeighborIndex.size(); ++i) {
cerr << "i=" << i << " extraBoundariesMaxNeighborIndex[i]=" << extraBoundariesMaxNeighborIndex[i] << endl;
}
}
}
int main(int argc, char* argv[])
{
cerr << "Welcome to CC3D command line edition" << endl;
// If we'd want to redirect cerr & cerr to a file (also see at end)
// std::ofstream logFile("cc3d-out.txt");
// std::streambuf *outbuf = std::cerr.rdbuf(logFile.rdbuf());
// std::streambuf *errbuf = std::cerr.rdbuf(logFile.rdbuf());
try {
// Command line
if (argc < 2)
Syntax(argv[0]);
// Load Plugin Libaries
// Libaries in COMPUCELL3D_PLUGIN_PATH can override the
// DEFAULT_PLUGIN_PATH
char* steppablePath = getenv("COMPUCELL3D_STEPPABLE_PATH");
cerr << "steppablePath=" << steppablePath << endl;
if (steppablePath)
Simulator::steppableManager.loadLibraries(steppablePath);
char* pluginPath = getenv("COMPUCELL3D_PLUGIN_PATH");
cerr << "pluginPath=" << pluginPath << endl;
if (pluginPath)
Simulator::pluginManager.loadLibraries(pluginPath);
#ifdef DEFAULT_PLUGIN_PATH
Simulator::steppableManager.loadLibraries(DEFAULT_PLUGIN_PATH);
// Simulator::pluginManager.loadLibraries(DEFAULT_PLUGIN_PATH);
#endif
BasicPluginManager<Steppable>::infos_t* infosG = &Simulator::steppableManager.getPluginInfos();
if (!infosG->empty()) {
cerr << "Found the following Steppables:" << endl;
BasicPluginManager<Steppable>::infos_t::iterator it;
for (it = infosG->begin(); it != infosG->end(); it++)
cerr << " " << *(*it) << endl;
cerr << endl;
}
BasicPluginManager<Plugin>::infos_t* infos = &Simulator::pluginManager.getPluginInfos();
if (!infos->empty()) {
cerr << "Found the following plugins:" << endl;
BasicPluginManager<Plugin>::infos_t::iterator it;
for (it = infos->begin(); it != infos->end(); it++)
cerr << " " << *(*it) << endl;
cerr << endl;
}
}
catch (const BasicException& e) {
cerr << "ERROR: " << e << endl;
}
XMLParserExpat xmlParser;
if (argc < 2) {
cerr << "SPECIFY XML FILE" << endl;
exit(0);
}
xmlParser.setFileName(string(argv[1]));
xmlParser.parse();
// Create Simulator
Simulator sim;
//extracting plugin elements from the XML file
CC3DXMLElementList pluginDataList = xmlParser.rootElement->getElements("Plugin");
for (int i = 0; i < pluginDataList.size(); ++i) {
cerr << "Plugin: " << pluginDataList[i]->getAttribute("Name") << endl;
sim.ps.addPluginDataCC3D(pluginDataList[i]);
}
//extracting steppable elements from the XML file
CC3DXMLElementList steppableDataList = xmlParser.rootElement->getElements("Steppable");
for (int i = 0; i < steppableDataList.size(); ++i) {
cerr << "Steppable: " << steppableDataList[i]->getAttribute("Type") << endl;
sim.ps.addSteppableDataCC3D(steppableDataList[i]);
}
// extracting Potts section
CC3DXMLElementList pottsDataList = xmlParser.rootElement->getElements("Potts");
ASSERT_OR_THROW("You must have exactly 1 definition of the Potts section", pottsDataList.size() == 1);
sim.ps.addPottsDataCC3D(pottsDataList[0]);
// extracting Metadata section
CC3DXMLElementList metadataDataList = xmlParser.rootElement->getElements("Metadata");
if (metadataDataList.size() == 1) {
sim.ps.addMetadataDataCC3D(metadataDataList[0]);
}
else {
cerr << "Not using Metadata" << endl;
}
// ASSERT_OR_THROW("You must have exactly 1 definition of the Metadata section",metadataDataList.size()==1);
sim.initializeCC3D();
sim.extraInit(); ///additional initialization after all plugins and steppables have been loaded and preinitialized
// Run simulation
#if defined(_WIN32)
volatile DWORD dwStart;
dwStart = GetTickCount();
#endif
sim.start();
for (unsigned int i = 1; i <= sim.getNumSteps(); i++) {
sim.step(i);
}
sim.finish();
#if defined(_WIN32)
cerr << "SIMULATION TOOK " << GetTickCount() - dwStart << " miliseconds to complete" << endl;
dwStart = GetTickCount();
#endif
return 0;
}
void FiPySolver::update(CC3DXMLElement *_xmlData, bool _fullInitFlag){
//notice, only basic steering is enabled for PDE solvers - changing diffusion constants, do -not-diffuse to types etc...
// Coupling coefficients cannot be changed and also there is no way to allocate extra fields while simulation is running
if(potts->getDisplayUnitsFlag()){
Unit diffConstUnit=powerUnit(potts->getLengthUnit(),2)/potts->getTimeUnit();
Unit decayConstUnit=1/potts->getTimeUnit();
Unit secretionConstUnit=1/potts->getTimeUnit();
CC3DXMLElement * unitsElem=_xmlData->getFirstElement("Units");
if (!unitsElem){ //add Units element
unitsElem=_xmlData->attachElement("Units");
}
if(unitsElem->getFirstElement("DiffusionConstantUnit")){
unitsElem->getFirstElement("DiffusionConstantUnit")->updateElementValue(diffConstUnit.toString());
}else{
unitsElem->attachElement("DiffusionConstantUnit",diffConstUnit.toString());
}
if(unitsElem->getFirstElement("DecayConstantUnit")){
unitsElem->getFirstElement("DecayConstantUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("DecayConstantUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("DeltaXUnit")){
unitsElem->getFirstElement("DeltaXUnit")->updateElementValue(potts->getLengthUnit().toString());
}else{
unitsElem->attachElement("DeltaXUnit",potts->getLengthUnit().toString());
}
if(unitsElem->getFirstElement("DeltaTUnit")){
unitsElem->getFirstElement("DeltaTUnit")->updateElementValue(potts->getTimeUnit().toString());
}else{
unitsElem->attachElement("DeltaTUnit",potts->getTimeUnit().toString());
}
if(unitsElem->getFirstElement("CouplingCoefficientUnit")){
unitsElem->getFirstElement("CouplingCoefficientUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("CouplingCoefficientUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("SecretionUnit")){
unitsElem->getFirstElement("SecretionUnit")->updateElementValue(secretionConstUnit.toString());
}else{
unitsElem->attachElement("SecretionUnit",secretionConstUnit.toString());
}
if(unitsElem->getFirstElement("SecretionOnContactUnit")){
unitsElem->getFirstElement("SecretionOnContactUnit")->updateElementValue(secretionConstUnit.toString());
}else{
unitsElem->attachElement("SecretionOnContactUnit",secretionConstUnit.toString());
}
if(unitsElem->getFirstElement("ConstantConcentrationUnit")){
unitsElem->getFirstElement("ConstantConcentrationUnit")->updateElementValue(secretionConstUnit.toString());
}else{
unitsElem->attachElement("ConstantConcentrationUnit",secretionConstUnit.toString());
}
if(unitsElem->getFirstElement("DecayConstantUnit")){
unitsElem->getFirstElement("DecayConstantUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("DecayConstantUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("DeltaXUnit")){
unitsElem->getFirstElement("DeltaXUnit")->updateElementValue(potts->getLengthUnit().toString());
}else{
unitsElem->attachElement("DeltaXUnit",potts->getLengthUnit().toString());
}
if(unitsElem->getFirstElement("DeltaTUnit")){
unitsElem->getFirstElement("DeltaTUnit")->updateElementValue(potts->getTimeUnit().toString());
}else{
unitsElem->attachElement("DeltaTUnit",potts->getTimeUnit().toString());
}
if(unitsElem->getFirstElement("CouplingCoefficientUnit")){
unitsElem->getFirstElement("CouplingCoefficientUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("CouplingCoefficientUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("UptakeUnit")){
unitsElem->getFirstElement("UptakeUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("UptakeUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("RelativeUptakeUnit")){
unitsElem->getFirstElement("RelativeUptakeUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("RelativeUptakeUnit",decayConstUnit.toString());
}
if(unitsElem->getFirstElement("MaxUptakeUnit")){
unitsElem->getFirstElement("MaxUptakeUnit")->updateElementValue(decayConstUnit.toString());
}else{
unitsElem->attachElement("MaxUptakeUnit",decayConstUnit.toString());
}
}
diffSecrFieldTuppleVec.clear();
bcSpecVec.clear();
bcSpecFlagVec.clear();
CC3DXMLElementList diffFieldXMLVec=_xmlData->getElements("DiffusionField");
for(unsigned int i = 0 ; i < diffFieldXMLVec.size() ; ++i ){
diffSecrFieldTuppleVec.push_back(DiffusionSecretionFiPyFieldTupple());
DiffusionData & diffData=diffSecrFieldTuppleVec[diffSecrFieldTuppleVec.size()-1].diffData;
SecretionData & secrData=diffSecrFieldTuppleVec[diffSecrFieldTuppleVec.size()-1].secrData;
if(diffFieldXMLVec[i]->findElement("DiffusionData"))
diffData.update(diffFieldXMLVec[i]->getFirstElement("DiffusionData"));
if(diffFieldXMLVec[i]->findElement("SecretionData"))
secrData.update(diffFieldXMLVec[i]->getFirstElement("SecretionData"));
if(diffFieldXMLVec[i]->findElement("ReadFromFile"))
readFromFileFlag=true;
//boundary conditions parsing
bcSpecFlagVec.push_back(false);
bcSpecVec.push_back(BoundaryConditionSpecifier());
if (diffFieldXMLVec[i]->findElement("BoundaryConditions")){
bcSpecFlagVec[bcSpecFlagVec.size()-1]=true;
BoundaryConditionSpecifier & bcSpec = bcSpecVec[bcSpecVec.size()-1];
CC3DXMLElement * bcSpecElem = diffFieldXMLVec[i]->getFirstElement("BoundaryConditions");
CC3DXMLElementList planeVec = bcSpecElem->getElements("Plane");
for(unsigned int ip = 0 ; ip < planeVec.size() ; ++ip ){
ASSERT_OR_THROW ("Boundary Condition specification Plane element is missing Axis attribute",planeVec[ip]->findAttribute("Axis"));
string axisName=planeVec[ip]->getAttribute("Axis");
int index=0;
if (axisName=="x" ||axisName=="X" ){
index=0;
}
if (axisName=="y" ||axisName=="Y" ){
index=2;
}
if (axisName=="z" ||axisName=="Z" ){
index=4;
}
if (planeVec[ip]->findElement("Periodic")){
bcSpec.planePositions[index]=BoundaryConditionSpecifier::PERIODIC;
bcSpec.planePositions[index+1]=BoundaryConditionSpecifier::PERIODIC;
}else {
//if (planeVec[ip]->findElement("ConstantValue")){
CC3DXMLElementList cvVec=planeVec[ip]->getElements("ConstantValue");
CC3DXMLElementList cdVec=planeVec[ip]->getElements("ConstantDerivative");
for (unsigned int v = 0 ; v < cvVec.size() ; ++v ){
string planePos=cvVec[v]->getAttribute("PlanePosition");
double value=cvVec[v]->getAttributeAsDouble("Value");
changeToLower(planePos);
if (planePos=="min"){
bcSpec.planePositions[index]=BoundaryConditionSpecifier::CONSTANT_VALUE;
bcSpec.values[index]=value;
}else if (planePos=="max"){
bcSpec.planePositions[index+1]=BoundaryConditionSpecifier::CONSTANT_VALUE;
bcSpec.values[index+1]=value;
}else{
ASSERT_OR_THROW("PlanePosition attribute has to be either max on min",false);
}
}
if (cvVec.size()<=1){
for (unsigned int d = 0 ; d < cdVec.size() ; ++d ){
string planePos=cdVec[d]->getAttribute("PlanePosition");
double value=cdVec[d]->getAttributeAsDouble("Value");
changeToLower(planePos);
if (planePos=="min"){
bcSpec.planePositions[index]=BoundaryConditionSpecifier::CONSTANT_DERIVATIVE;
bcSpec.values[index]=value;
}else if (planePos=="max"){
bcSpec.planePositions[index+1]=BoundaryConditionSpecifier::CONSTANT_DERIVATIVE;
bcSpec.values[index+1]=value;
}else{
ASSERT_OR_THROW("PlanePosition attribute has to be either max on min",false);
}
}
}
}
}
}
}
if(_xmlData->findElement("Serialize")){
serializeFlag=true;
if(_xmlData->getFirstElement("Serialize")->findAttribute("Frequency")){
serializeFrequency=_xmlData->getFirstElement("Serialize")->getAttributeAsUInt("Frequency");
}
cerr<<"serialize Flag="<<serializeFlag<<endl;
}
if(_xmlData->findElement("ReadFromFile")){
readFromFileFlag=true;
cerr<<"readFromFileFlag="<<readFromFileFlag<<endl;
}
for(int i = 0 ; i < diffSecrFieldTuppleVec.size() ; ++i){
diffSecrFieldTuppleVec[i].diffData.setAutomaton(automaton);
diffSecrFieldTuppleVec[i].secrData.setAutomaton(automaton);
diffSecrFieldTuppleVec[i].diffData.initialize(automaton);
diffSecrFieldTuppleVec[i].secrData.initialize(automaton);
}
///assigning member method ptrs to the vector
for(unsigned int i = 0 ; i < diffSecrFieldTuppleVec.size() ; ++i){
diffSecrFieldTuppleVec[i].secrData.secretionFcnPtrVec.assign(diffSecrFieldTuppleVec[i].secrData.secrTypesNameSet.size(),0);
unsigned int j=0;
for(set<string>::iterator sitr=diffSecrFieldTuppleVec[i].secrData.secrTypesNameSet.begin() ; sitr != diffSecrFieldTuppleVec[i].secrData.secrTypesNameSet.end() ; ++sitr){
if((*sitr)=="Secretion"){
diffSecrFieldTuppleVec[i].secrData.secretionFcnPtrVec[j]=&FiPySolver::secreteSingleField;
++j;
}
else if((*sitr)=="SecretionOnContact"){
diffSecrFieldTuppleVec[i].secrData.secretionFcnPtrVec[j]=&FiPySolver::secreteOnContactSingleField;
++j;
}
else if((*sitr)=="ConstantConcentration"){
diffSecrFieldTuppleVec[i].secrData.secretionFcnPtrVec[j]=&FiPySolver::secreteConstantConcentrationSingleField;
++j;
}
}
}
}