//**********************************************************************************************************************
vector<string> ChimeraPintailCommand::setParameters(){
try {
CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
CommandParameter pconservation("conservation", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconservation);
CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pquantile);
CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
CommandParameter pwindow("window", "Number", "", "0", "", "", "","","",false,false); parameters.push_back(pwindow);
CommandParameter pincrement("increment", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pincrement);
CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "ChimeraPintailCommand", "setParameters");
exit(1);
}
}
//keyword "cellvars" in OOFEM input file
void
VTKXMLExportModule :: exportCellVarAs(InternalStateType type, int region,
#ifdef __VTK_MODULE
vtkSmartPointer<vtkUnstructuredGrid> &stream,
#else
FILE *stream,
#endif
TimeStep *tStep)
{
Domain *d = emodel->giveDomain(1);
int ielem, nelem = d->giveNumberOfElements();
int pos;
Element *elem;
FloatMatrix mtrx(3, 3);
IntegrationRule *iRule;
GaussPoint *gp;
FloatArray answer, temp;
double gptot;
int ncomponents = 1;
#ifdef __VTK_MODULE
vtkSmartPointer<vtkDoubleArray> cellVarsArray = vtkSmartPointer<vtkDoubleArray>::New();
cellVarsArray->SetName(__InternalStateTypeToString(type));
#endif
switch ( type ) {
case IST_MaterialNumber:
case IST_ElementNumber:
case IST_Pressure:
// if it wasn't for IST_Pressure,
#ifdef __VTK_MODULE
cellVarsArray->SetNumberOfComponents(1);
cellVarsArray->SetNumberOfTuples(nelem);
#else
fprintf( stream, "<DataArray type=\"Float64\" Name=\"%s\" format=\"ascii\">\n", __InternalStateTypeToString(type) );
#endif
for ( ielem = 1; ielem <= nelem; ielem++ ) {
elem = d->giveElement(ielem);
if ( (( region > 0 ) && ( this->smoother->giveElementVirtualRegionNumber(ielem) != region ))
|| this->isElementComposite(elem) || !elem-> isActivated(tStep) ) { // composite cells exported individually
continue;
}
#ifdef __PARALLEL_MODE
if ( elem->giveParallelMode() != Element_local ) {
continue;
}
#endif
if ( type == IST_MaterialNumber ) {
#ifdef __VTK_MODULE
cellVarsArray->SetTuple1(ielem-1, elem->giveMaterial()->giveNumber() ); // Should be integer..
#else
fprintf( stream, "%d ", elem->giveMaterial()->giveNumber() );
#endif
} else if ( type == IST_ElementNumber ) {
#ifdef __VTK_MODULE
cellVarsArray->SetTuple1(ielem-1, elem->giveNumber() ); // Should be integer..
#else
fprintf( stream, "%d ", elem->giveNumber() );
#endif
} else if (type == IST_Pressure) { ///@todo Why this special treatment for pressure? / Mikael
if (elem->giveNumberOfInternalDofManagers() == 1) {
IntArray pmask(1); pmask.at(1) = P_f;
elem->giveInternalDofManager(1)->giveUnknownVector (answer, pmask,EID_ConservationEquation, VM_Total, tStep);
#ifdef __VTK_MODULE
cellVarsArray->SetTuple1(ielem-1, answer.at(1) ); // Should be integer..
#else
fprintf( stream, "%f ", answer.at(1) );
#endif
}
}
}
#ifdef __VTK_MODULE
stream->GetCellData()->SetActiveScalars(__InternalStateTypeToString(type));
stream->GetCellData()->SetScalars(cellVarsArray);
#endif
break;
case IST_MaterialOrientation_x:
case IST_MaterialOrientation_y:
case IST_MaterialOrientation_z:
#ifdef __VTK_MODULE
cellVarsArray->SetNumberOfComponents(3);
cellVarsArray->SetNumberOfTuples(nelem);
ncomponents = 3;
#else
fprintf( stream, "<DataArray type=\"Float64\" Name=\"%s\" NumberOfComponents=\"3\" format=\"ascii\">\n", __InternalStateTypeToString(type) );
#endif
if ( type == IST_MaterialOrientation_x ) {
pos = 1;
}
if ( type == IST_MaterialOrientation_y ) {
pos = 2;
}
if ( type == IST_MaterialOrientation_z ) {
pos = 3;
}
for ( ielem = 1; ielem <= nelem; ielem++ ) {
///@todo Should no elements be skipped here? / Mikael
if ( !d->giveElement(ielem)->giveLocalCoordinateSystem(mtrx) ) {
mtrx.resize(3, 3);
mtrx.zero();
}
#ifdef __VTK_MODULE
cellVarsArray->SetTuple3(ielem-1, mtrx.at(1, pos), mtrx.at(2,pos), mtrx.at(3,pos) );
#else
fprintf( stream, "%f %f %f ", mtrx.at(1, pos), mtrx.at(2, pos), mtrx.at(3, pos) );
#endif
}
#ifdef __VTK_MODULE
stream->GetCellData()->SetActiveVectors(__InternalStateTypeToString(type));
stream->GetCellData()->SetVectors(cellVarsArray);
#endif
break;
default:
bool reshape = false;
InternalStateValueType vt = giveInternalStateValueType(type);
if ( vt == ISVT_SCALAR ) {
ncomponents = 1;
} else if ( vt == ISVT_VECTOR ) {
ncomponents = 3;
} else {
ncomponents = 9;
reshape = true;
}
#ifdef __VTK_MODULE
cellVarsArray->SetNumberOfComponents(ncomponents);
cellVarsArray->SetNumberOfTuples(nelem);
#else
fprintf( stream, "<DataArray type=\"Float64\" Name=\"%s\" NumberOfComponents=\"%d\" format=\"ascii\">\n", __InternalStateTypeToString(type), ncomponents );
#endif
IntArray redIndx;
for ( ielem = 1; ielem <= nelem; ielem++ ) {
elem = d->giveElement(ielem);
if ( (( region > 0 ) && ( this->smoother->giveElementVirtualRegionNumber(ielem) != region ))
|| this->isElementComposite(elem) || !elem-> isActivated(tStep) ) { // composite cells exported individually
continue;
}
#ifdef __PARALLEL_MODE
if ( elem->giveParallelMode() != Element_local ) {
continue;
}
#endif
gptot = 0;
answer.resize(0);
iRule = elem->giveDefaultIntegrationRulePtr();
if (iRule) {
MaterialMode mmode = _Unknown;
for (int i = 0; i < iRule->getNumberOfIntegrationPoints(); ++i) {
gp = iRule->getIntegrationPoint(i);
mmode = gp->giveMaterialMode();
elem->giveIPValue(temp, gp, type, tStep);
gptot += gp->giveWeight();
answer.add(gp->giveWeight(), temp);
}
answer.times(1./gptot);
elem->giveMaterial()->giveIntVarCompFullIndx(redIndx, type, mmode);
}
// Reshape the Voigt vectors to include all components (duplicated if necessary, VTK insists on 9 components for tensors.)
if ( reshape && answer.giveSize() != 9) { // If it has 9 components, then it is assumed to be proper already.
FloatArray tmp = answer;
this->makeFullForm(answer, tmp, vt, redIndx);
} else if ( vt == ISVT_VECTOR && answer.giveSize() < 3) {
answer.setValues(3,
answer.giveSize() > 1 ? answer.at(1) : 0.0,
answer.giveSize() > 2 ? answer.at(2) : 0.0,
0.0);
} else if ( ncomponents != answer.giveSize() ) { // Trying to gracefully handle bad cases, just output zeros.
answer.resize(ncomponents);
answer.zero();
}
for (int i = 1; i <= ncomponents; ++i) {
#ifdef __VTK_MODULE
cellVarsArray->SetComponent(ielem-1, i-1, answer.at(i));
#else
fprintf( stream, "%e ", answer.at(i) );
#endif
}
#ifndef __VTK_MODULE
fprintf( stream, "\n" );
#endif
}
#ifdef __VTK_MODULE
if (ncomponents == 1) {
stream->GetCellData()->SetActiveScalars(__InternalStateTypeToString(type));
stream->GetCellData()->SetScalars(cellVarsArray);
} else if (ncomponents == 3) {
stream->GetCellData()->SetActiveVectors(__InternalStateTypeToString(type));
stream->GetCellData()->SetVectors(cellVarsArray);
} else {
stream->GetCellData()->SetActiveTensors(__InternalStateTypeToString(type));
stream->GetCellData()->SetTensors(cellVarsArray);
}
#endif
}
#ifndef __VTK_MODULE
fprintf(stream, "</DataArray>\n");
#endif
}
