void MVertex::deleteLast()
{
GModel *m = GModel::current();
if(_num == m->getMaxVertexNumber())
m->setMaxVertexNumber(m->getMaxVertexNumber() - 1);
delete this;
}
int main(int argc, char **argv)
{
GmshInitialize(argc, argv);
GmshSetOption("Mesh", "Algorithm", 5.);
GmshSetOption("General", "Terminal", 1.);
GModel *m = new GModel();
m->readMSH("bunny.msh");
m->fillVertexArrays();
std::vector<GEntity*> entities;
m->getEntities(entities);
for(unsigned int i = 0; i < entities.size(); i++){
GEntity *ge = entities[i];
printf("coucou entite %d (dimension %d)\n", ge->tag(), ge->dim());
if(ge->va_triangles)
printf(" j'ai un va de triangles: %d vertex\n", ge->va_triangles->getNumVertices());
if(ge->va_lines)
printf(" j'ai un va de lignes: %d vertex\n", ge->va_lines->getNumVertices());
}
delete m;
GmshFinalize();
}
/***********************************************************************//**
* @brief Test unbinned optimizer
***************************************************************************/
void TestGCTAOptimize::test_unbinned_optimizer(void)
{
// Declare observations
GObservations obs;
GCTAObservation run;
// Load unbinned CTA observation
test_try("Load unbinned CTA observation");
try {
run.load_unbinned(cta_events);
run.response(cta_irf,cta_caldb);
obs.append(run);
test_try_success();
}
catch (std::exception &e) {
test_try_failure(e);
}
// Load models from XML file
obs.models(cta_model_xml);
// Perform LM optimization
double fit_results[] = {83.6331, 0,
22.0145, 0,
5.656246512e-16, 1.91458426e-17,
-2.484100472, -0.02573396361,
300000, 0,
1, 0,
2.993705325, 0.03572658413,
6.490832107e-05, 1.749021094e-06,
-1.833584022, -0.01512223495,
1000000, 0,
1, 0};
test_try("Perform LM optimization");
try {
GOptimizerLM opt;
opt.max_iter(100);
obs.optimize(opt);
test_try_success();
for (int i = 0, j = 0; i < obs.models().size(); ++i) {
GModel* model = obs.models()[i];
for (int k = 0; k < model->size(); ++k) {
GModelPar& par = (*model)[k];
std::string msg = "Verify optimization result for " + par.print();
test_value(par.real_value(), fit_results[j++], 5.0e-5, msg);
test_value(par.real_error(), fit_results[j++], 5.0e-5, msg);
}
}
}
catch (std::exception &e) {
test_try_failure(e);
}
// Exit test
return;
}
/***********************************************************************//**
* @brief Test binned optimizer
***************************************************************************/
void TestGCTAOptimize::test_binned_optimizer(void)
{
// Declare observations
GObservations obs;
GCTAObservation run;
// Load binned CTA observation
test_try("Load binned CTA observation");
try {
run.load_binned(cta_cntmap);
run.response(cta_irf,cta_caldb);
obs.append(run);
test_try_success();
}
catch (std::exception &e) {
test_try_failure(e);
}
// Load models from XML file
obs.models(cta_model_xml);
// Perform LM optimization
double fit_results[] = {83.6331, 0,
22.0145, 0,
5.616410411e-16, 1.904730785e-17,
-2.481781246, -0.02580905077,
300000, 0,
1, 0,
2.933677595, 0.06639644824,
6.550723074e-05, 1.945714239e-06,
-1.833781187, -0.0161464076,
1000000, 0,
1, 0};
test_try("Perform LM optimization");
try {
GOptimizerLM opt;
opt.max_iter(100);
obs.optimize(opt);
test_try_success();
for (int i = 0, j = 0; i < obs.models().size(); ++i) {
GModel* model = obs.models()[i];
for (int k = 0; k < model->size(); ++k) {
GModelPar& par = (*model)[k];
std::string msg = "Verify optimization result for " + par.print();
test_value(par.real_value(), fit_results[j++], 5.0e-5, msg);
test_value(par.real_error(), fit_results[j++], 5.0e-5, msg);
}
}
}
catch (std::exception &e) {
test_try_failure(e);
}
// Exit test
return;
}
void Filler::treat_model(){
GRegion* gr;
GModel* model = GModel::current();
GModel::riter it;
for(it=model->firstRegion();it!=model->lastRegion();it++)
{
gr = *it;
if(gr->getNumMeshElements()>0){
treat_region(gr);
}
}
}
/***********************************************************************//**
* @brief Model function evaluation for gradient computation
*
* @param[in] x Function value.
***************************************************************************/
double GObservation::model_func::eval(double x)
{
// Get non-const model pointer (circumvent const correctness)
GModel* model = const_cast<GModel*>(m_model);
// Set value
(*model)[m_ipar].value(x);
// Compute model value
double value = model->eval(*m_event, *m_parent);
// Return value
return value;
}
void collapseSmallEdges(GModel &gm)
{
return;
// gm.renumberMeshVertices(true);
std::list<GFace*> faces;
for (GModel::fiter fit = gm.firstFace(); fit != gm.lastFace(); fit++){
faces.push_back(*fit);
}
BDS_Mesh *pm = gmsh2BDS(faces);
outputScalarField(pm->triangles, "all.pos", 0);
for (GModel::eiter eit = gm.firstEdge(); eit != gm.lastEdge(); eit++){
}
delete pm;
}
void gcm::Geo2MeshLoader::createMshFile(string fileName, float tetrSize)
{
Engine& engine = Engine::getInstance();
if( engine.getNumberOfWorkers() > 1 )
{
if( engine.getRank() != 0 )
{
MPI::COMM_WORLD.Barrier();
createdFiles[fileName] = true;
return;
}
}
/*
* TODO@ashevtsov: I don't really understand the meaning of all these options, values
* have been guessed to get a mesh with acceptable tetrahedra sizes.
* In future need to undestand GMsh meshing algorithms and set these options correctly.
*/
LOG_DEBUG("loadGeoScriptFile (" << fileName << "): will mesh with H = " << tetrSize);
GmshSetOption("General", "Terminal", 1.0);
GmshSetOption("General", "Verbosity", engine.getGmshVerbosity());
GmshSetOption("Mesh", "CharacteristicLengthMin", tetrSize);
GmshSetOption("Mesh", "CharacteristicLengthMax", tetrSize);
GmshSetOption("Mesh", "Optimize", 1.0);
GModel gmshModel;
gmshModel.setFactory ("Gmsh");
gmshModel.readGEO (fileName);
LOG_INFO("Creating mesh using gmsh library");
gmshModel.mesh (3);
gmshModel.writeMSH (getMshFileName(fileName));
createdFiles[fileName] = true;
if (engine.getNumberOfWorkers() > 1)
MPI::COMM_WORLD.Barrier();
}
MVertex::MVertex(double x, double y, double z, GEntity *ge, int num)
: _visible(1), _order(1), _x(x), _y(y), _z(z), _ge(ge)
{
#if defined(_OPENMP)
#pragma omp critical
#endif
{
// we should make GModel a mandatory argument to the constructor
GModel *m = GModel::current();
if(num){
_num = num;
m->setMaxVertexNumber(std::max(m->getMaxVertexNumber(), _num));
}
else{
m->setMaxVertexNumber(m->getMaxVertexNumber() + 1);
_num = m->getMaxVertexNumber();
}
_index = num;
}
}
int GModel::readMED(const std::string &name)
{
med_idt fid = MEDouvrir((char*)name.c_str(), MED_LECTURE);
if(fid < 0) {
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
med_int v[3], vf[3];
MEDversionDonner(&v[0], &v[1], &v[2]);
MEDversionLire(fid, &vf[0], &vf[1], &vf[2]);
Msg::Info("Reading MED file V%d.%d.%d using MED library V%d.%d.%d",
vf[0], vf[1], vf[2], v[0], v[1], v[2]);
if(vf[0] < 2 || (vf[0] == 2 && vf[1] < 2)){
Msg::Error("Cannot read MED file older than V2.2");
return 0;
}
std::vector<std::string> meshNames;
for(int i = 0; i < MEDnMaa(fid); i++){
char meshName[MED_TAILLE_NOM + 1], meshDesc[MED_TAILLE_DESC + 1];
med_int spaceDim;
med_maillage meshType;
#if (MED_MAJOR_NUM == 3)
med_int meshDim, nStep;
char dtUnit[MED_SNAME_SIZE + 1];
char axisName[3 * MED_SNAME_SIZE + 1], axisUnit[3 * MED_SNAME_SIZE + 1];
med_sorting_type sortingType;
med_axis_type axisType;
if(MEDmeshInfo(fid, i + 1, meshName, &spaceDim, &meshDim, &meshType, meshDesc,
dtUnit, &sortingType, &nStep, &axisType, axisName, axisUnit) < 0){
#else
if(MEDmaaInfo(fid, i + 1, meshName, &spaceDim, &meshType, meshDesc) < 0){
#endif
Msg::Error("Unable to read mesh information");
return 0;
}
meshNames.push_back(meshName);
}
if(MEDfermer(fid) < 0){
Msg::Error("Unable to close file '%s'", (char*)name.c_str());
return 0;
}
int ret = 1;
for(unsigned int i = 0; i < meshNames.size(); i++){
// we use the filename as a kind of "partition" indicator, allowing to
// complete a model part by part (used e.g. in DDM, since MED does not store
// a partition index)
GModel *m = findByName(meshNames[i], name);
if(!m) m = new GModel(meshNames[i]);
ret = m->readMED(name, i);
if(!ret) return 0;
}
return ret;
}
int GModel::readMED(const std::string &name, int meshIndex)
{
med_idt fid = MEDouvrir((char*)name.c_str(), MED_LECTURE);
if(fid < 0){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
int numMeshes = MEDnMaa(fid);
if(meshIndex >= numMeshes){
Msg::Info("Could not find mesh %d in MED file", meshIndex);
return 0;
}
checkPointMaxNumbers();
GModel::setCurrent(this); // make sure we increment max nums in this model
// read mesh info
char meshName[MED_TAILLE_NOM + 1], meshDesc[MED_TAILLE_DESC + 1];
med_int spaceDim, nStep = 1;
med_maillage meshType;
#if (MED_MAJOR_NUM == 3)
med_int meshDim;
char dtUnit[MED_SNAME_SIZE + 1];
char axisName[3 * MED_SNAME_SIZE + 1], axisUnit[3 * MED_SNAME_SIZE + 1];
med_sorting_type sortingType;
med_axis_type axisType;
if(MEDmeshInfo(fid, meshIndex + 1, meshName, &spaceDim, &meshDim, &meshType, meshDesc,
dtUnit, &sortingType, &nStep, &axisType, axisName, axisUnit) < 0){
#else
if(MEDmaaInfo(fid, meshIndex + 1, meshName, &spaceDim, &meshType, meshDesc) < 0){
#endif
Msg::Error("Unable to read mesh information");
return 0;
}
// FIXME: we should support multi-step MED3 meshes (probably by
// storing each mesh as a separate model, with a naming convention
// e.g. meshName_step%d). This way we could also handle multi-mesh
// time sequences in MED3.
if(nStep > 1)
Msg::Warning("Discarding %d last meshes in multi-step MED mesh", nStep - 1);
setName(meshName);
setFileName(name);
if(meshType == MED_NON_STRUCTURE){
Msg::Info("Reading %d-D unstructured mesh <<%s>>", spaceDim, meshName);
}
else{
Msg::Error("Reading structured MED meshes is not supported");
return 0;
}
med_int vf[3];
MEDversionLire(fid, &vf[0], &vf[1], &vf[2]);
// read nodes
#if (MED_MAJOR_NUM == 3)
med_bool changeOfCoord, geoTransform;
med_int numNodes = MEDmeshnEntity(fid, meshName, MED_NO_DT, MED_NO_IT, MED_NODE,
MED_NO_GEOTYPE, MED_COORDINATE, MED_NO_CMODE,
&changeOfCoord, &geoTransform);
#else
med_int numNodes = MEDnEntMaa(fid, meshName, MED_COOR, MED_NOEUD, MED_NONE,
MED_NOD);
#endif
if(numNodes < 0){
Msg::Error("Could not read number of MED nodes");
return 0;
}
if(numNodes == 0){
Msg::Error("No nodes in MED mesh");
return 0;
}
std::vector<MVertex*> verts(numNodes);
std::vector<med_float> coord(spaceDim * numNodes);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshNodeCoordinateRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_FULL_INTERLACE,
&coord[0]) < 0){
#else
std::vector<char> coordName(spaceDim * MED_TAILLE_PNOM + 1);
std::vector<char> coordUnit(spaceDim * MED_TAILLE_PNOM + 1);
med_repere rep;
if(MEDcoordLire(fid, meshName, spaceDim, &coord[0], MED_FULL_INTERLACE,
MED_ALL, 0, 0, &rep, &coordName[0], &coordUnit[0]) < 0){
#endif
Msg::Error("Could not read MED node coordinates");
return 0;
}
std::vector<med_int> nodeTags(numNodes);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshEntityNumberRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_NODE,
MED_NO_GEOTYPE, &nodeTags[0]) < 0)
#else
if(MEDnumLire(fid, meshName, &nodeTags[0], numNodes, MED_NOEUD, MED_NONE) < 0)
#endif
nodeTags.clear();
for(int i = 0; i < numNodes; i++)
verts[i] = new MVertex(coord[spaceDim * i],
(spaceDim > 1) ? coord[spaceDim * i + 1] : 0.,
(spaceDim > 2) ? coord[spaceDim * i + 2] : 0.,
0, nodeTags.empty() ? 0 : nodeTags[i]);
// read elements (loop over all possible MSH element types)
for(int mshType = 0; mshType < MSH_NUM_TYPE; mshType++){
med_geometrie_element type = msh2medElementType(mshType);
if(type == MED_NONE) continue;
#if (MED_MAJOR_NUM == 3)
med_bool changeOfCoord;
med_bool geoTransform;
med_int numEle = MEDmeshnEntity(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, MED_CONNECTIVITY, MED_NODAL, &changeOfCoord,
&geoTransform);
#else
med_int numEle = MEDnEntMaa(fid, meshName, MED_CONN, MED_MAILLE, type, MED_NOD);
#endif
if(numEle <= 0) continue;
int numNodPerEle = type % 100;
std::vector<med_int> conn(numEle * numNodPerEle);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshElementConnectivityRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, MED_NODAL, MED_FULL_INTERLACE, &conn[0]) < 0){
#else
if(MEDconnLire(fid, meshName, spaceDim, &conn[0], MED_FULL_INTERLACE, 0, MED_ALL,
MED_MAILLE, type, MED_NOD) < 0){
#endif
Msg::Error("Could not read MED elements");
return 0;
}
std::vector<med_int> fam(numEle, 0);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshEntityFamilyNumberRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, &fam[0]) < 0){
#else
if(MEDfamLire(fid, meshName, &fam[0], numEle, MED_MAILLE, type) < 0){
#endif
Msg::Info("No family number for elements: using 0 as default family number");
}
std::vector<med_int> eleTags(numEle);
#if (MED_MAJOR_NUM == 3)
if(MEDmeshEntityNumberRd(fid, meshName, MED_NO_DT, MED_NO_IT, MED_CELL,
type, &eleTags[0]) < 0)
#else
if(MEDnumLire(fid, meshName, &eleTags[0], numEle, MED_MAILLE, type) < 0)
#endif
eleTags.clear();
std::map<int, std::vector<MElement*> > elements;
MElementFactory factory;
for(int j = 0; j < numEle; j++){
std::vector<MVertex*> v(numNodPerEle);
for(int k = 0; k < numNodPerEle; k++)
v[k] = verts[conn[numNodPerEle * j + med2mshNodeIndex(type, k)] - 1];
MElement *e = factory.create(mshType, v, eleTags.empty() ? 0 : eleTags[j]);
if(e) elements[-fam[j]].push_back(e);
}
_storeElementsInEntities(elements);
}
_associateEntityWithMeshVertices();
_storeVerticesInEntities(verts);
// read family info
med_int numFamilies = MEDnFam(fid, meshName);
if(numFamilies < 0){
Msg::Error("Could not read MED families");
return 0;
}
for(int i = 0; i < numFamilies; i++){
#if (MED_MAJOR_NUM == 3)
med_int numAttrib = (vf[0] == 2) ? MEDnFamily23Attribute(fid, meshName, i + 1) : 0;
med_int numGroups = MEDnFamilyGroup(fid, meshName, i + 1);
#else
med_int numAttrib = MEDnAttribut(fid, meshName, i + 1);
med_int numGroups = MEDnGroupe(fid, meshName, i + 1);
#endif
if(numAttrib < 0 || numGroups < 0){
Msg::Error("Could not read MED groups or attributes");
return 0;
}
std::vector<med_int> attribId(numAttrib + 1);
std::vector<med_int> attribVal(numAttrib + 1);
std::vector<char> attribDes(MED_TAILLE_DESC * numAttrib + 1);
std::vector<char> groupNames(MED_TAILLE_LNOM * numGroups + 1);
char familyName[MED_TAILLE_NOM + 1];
med_int familyNum;
#if (MED_MAJOR_NUM == 3)
if(vf[0] == 2){ // MED2 file
if(MEDfamily23Info(fid, meshName, i + 1, familyName, &attribId[0],
&attribVal[0], &attribDes[0], &familyNum,
&groupNames[0]) < 0){
Msg::Error("Could not read info for MED2 family %d", i + 1);
continue;
}
}
else{
if(MEDfamilyInfo(fid, meshName, i + 1, familyName, &familyNum,
&groupNames[0]) < 0){
Msg::Error("Could not read info for MED3 family %d", i + 1);
continue;
}
}
#else
if(MEDfamInfo(fid, meshName, i + 1, familyName, &familyNum, &attribId[0],
&attribVal[0], &attribDes[0], &numAttrib, &groupNames[0],
&numGroups) < 0){
Msg::Error("Could not read info for MED family %d", i + 1);
continue;
}
#endif
// family tags are unique (for all dimensions)
GEntity *ge;
if((ge = getRegionByTag(-familyNum))){}
else if((ge = getFaceByTag(-familyNum))){}
else if((ge = getEdgeByTag(-familyNum))){}
else ge = getVertexByTag(-familyNum);
if(ge){
elementaryNames[std::pair<int, int>(ge->dim(), -familyNum)] = familyName;
if(numGroups > 0){
for(int j = 0; j < numGroups; j++){
char tmp[MED_TAILLE_LNOM + 1];
strncpy(tmp, &groupNames[j * MED_TAILLE_LNOM], MED_TAILLE_LNOM);
tmp[MED_TAILLE_LNOM] = '\0';
// don't use same physical number across dimensions, as e.g. getdp
// does not support this
int pnum = setPhysicalName(tmp, ge->dim(), getMaxPhysicalNumber(-1) + 1);
if(std::find(ge->physicals.begin(), ge->physicals.end(), pnum) ==
ge->physicals.end())
ge->physicals.push_back(pnum);
}
}
}
}
// check if we need to read some post-processing data later
#if (MED_MAJOR_NUM == 3)
bool postpro = (MEDnField(fid) > 0) ? true : false;
#else
bool postpro = (MEDnChamp(fid, 0) > 0) ? true : false;
#endif
if(MEDfermer(fid) < 0){
Msg::Error("Unable to close file '%s'", (char*)name.c_str());
return 0;
}
return postpro ? 2 : 1;
}
template<class T>
static void fillElementsMED(med_int family, std::vector<T*> &elements,
std::vector<med_int> &conn, std::vector<med_int> &fam,
med_geometrie_element &type)
{
if(elements.empty()) return;
type = msh2medElementType(elements[0]->getTypeForMSH());
if(type == MED_NONE){
Msg::Warning("Unsupported element type in MED format");
return;
}
for(unsigned int i = 0; i < elements.size(); i++){
elements[i]->setVolumePositive();
for(int j = 0; j < elements[i]->getNumVertices(); j++)
conn.push_back(elements[i]->getVertex(med2mshNodeIndex(type, j))->getIndex());
fam.push_back(family);
}
}
static void writeElementsMED(med_idt &fid, char *meshName, std::vector<med_int> &conn,
std::vector<med_int> &fam, med_geometrie_element type)
{
if(fam.empty()) return;
#if (MED_MAJOR_NUM == 3)
if(MEDmeshElementWr(fid, meshName, MED_NO_DT, MED_NO_IT, 0., MED_CELL, type,
MED_NODAL, MED_FULL_INTERLACE, (med_int)fam.size(),
&conn[0], MED_FALSE, 0, MED_FALSE, 0, MED_TRUE, &fam[0]) < 0)
#else
if(MEDelementsEcr(fid, meshName, (med_int)3, &conn[0], MED_FULL_INTERLACE,
0, MED_FAUX, 0, MED_FAUX, &fam[0], (med_int)fam.size(),
MED_MAILLE, type, MED_NOD) < 0)
#endif
Msg::Error("Could not write MED elements");
}
int GModel::writeMED(const std::string &name, bool saveAll, double scalingFactor)
{
med_idt fid = MEDouvrir((char*)name.c_str(), MED_CREATION);
if(fid < 0){
Msg::Error("Unable to open file '%s'", name.c_str());
return 0;
}
// write header
if(MEDfichDesEcr(fid, (char*)"MED file generated by Gmsh") < 0){
Msg::Error("Unable to write MED descriptor");
return 0;
}
char *meshName = (char*)getName().c_str();
// Gmsh always writes 3D unstructured meshes
#if (MED_MAJOR_NUM == 3)
char dtUnit[MED_SNAME_SIZE + 1] = "";
char axisName[3 * MED_SNAME_SIZE + 1] = "";
char axisUnit[3 * MED_SNAME_SIZE + 1] = "";
if(MEDmeshCr(fid, meshName, 3, 3, MED_UNSTRUCTURED_MESH, "Mesh created with Gmsh",
dtUnit, MED_SORT_DTIT, MED_CARTESIAN, axisName, axisUnit) < 0){
#else
if(MEDmaaCr(fid, meshName, 3, MED_NON_STRUCTURE,
(char*)"Mesh created with Gmsh") < 0){
#endif
Msg::Error("Could not create MED mesh");
return 0;
}
// if there are no physicals we save all the elements
if(noPhysicalGroups()) saveAll = true;
// index the vertices we save in a continuous sequence (MED
// connectivity is given in terms of vertex indices)
indexMeshVertices(saveAll);
// get a vector containing all the geometrical entities in the
// model (the ordering of the entities must be the same as the one
// used during the indexing of the vertices)
std::vector<GEntity*> entities;
getEntities(entities);
std::map<GEntity*, int> families;
// write the families
{
// always create a "0" family, with no groups or attributes
#if (MED_MAJOR_NUM == 3)
if(MEDfamilyCr(fid, meshName, "F_0", 0, 0, "") < 0)
#else
if(MEDfamCr(fid, meshName, (char*)"F_0", 0, 0, 0, 0, 0, 0, 0) < 0)
#endif
Msg::Error("Could not create MED family 0");
// create one family per elementary entity, with one group per
// physical entity and no attributes
for(unsigned int i = 0; i < entities.size(); i++){
if(saveAll || entities[i]->physicals.size()){
int num = - ((int)families.size() + 1);
families[entities[i]] = num;
std::ostringstream fs;
fs << entities[i]->dim() << "D_" << entities[i]->tag();
std::string familyName = "F_" + fs.str();
std::string groupName;
for(unsigned j = 0; j < entities[i]->physicals.size(); j++){
std::string tmp = getPhysicalName
(entities[i]->dim(), entities[i]->physicals[j]);
if(tmp.empty()){ // create unique name
std::ostringstream gs;
gs << entities[i]->dim() << "D_" << entities[i]->physicals[j];
groupName += "G_" + gs.str();
}
else
groupName += tmp;
groupName.resize((j + 1) * MED_TAILLE_LNOM, ' ');
}
#if (MED_MAJOR_NUM == 3)
if(MEDfamilyCr(fid, meshName, familyName.c_str(),
(med_int)num, (med_int)entities[i]->physicals.size(),
groupName.c_str()) < 0)
#else
if(MEDfamCr(fid, meshName, (char*)familyName.c_str(),
(med_int)num, 0, 0, 0, 0, (char*)groupName.c_str(),
(med_int)entities[i]->physicals.size()) < 0)
#endif
Msg::Error("Could not create MED family %d", num);
}
}
}
// write the nodes
{
std::vector<med_float> coord;
std::vector<med_int> fam;
for(unsigned int i = 0; i < entities.size(); i++){
for(unsigned int j = 0; j < entities[i]->mesh_vertices.size(); j++){
MVertex *v = entities[i]->mesh_vertices[j];
if(v->getIndex() >= 0){
coord.push_back(v->x() * scalingFactor);
coord.push_back(v->y() * scalingFactor);
coord.push_back(v->z() * scalingFactor);
fam.push_back(0); // we never create node families
}
}
}
if(fam.empty()){
Msg::Error("No nodes to write in MED mesh");
return 0;
}
#if (MED_MAJOR_NUM == 3)
if(MEDmeshNodeWr(fid, meshName, MED_NO_DT, MED_NO_IT, 0., MED_FULL_INTERLACE,
(med_int)fam.size(), &coord[0], MED_FALSE, "", MED_FALSE, 0,
MED_TRUE, &fam[0]) < 0)
#else
char coordName[3 * MED_TAILLE_PNOM + 1] =
"x y z ";
char coordUnit[3 * MED_TAILLE_PNOM + 1] =
"unknown unknown unknown ";
if(MEDnoeudsEcr(fid, meshName, (med_int)3, &coord[0], MED_FULL_INTERLACE,
MED_CART, coordName, coordUnit, 0, MED_FAUX, 0, MED_FAUX,
&fam[0], (med_int)fam.size()) < 0)
#endif
Msg::Error("Could not write nodes");
}
// write the elements
{
{ // points
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(viter it = firstVertex(); it != lastVertex(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->points, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // lines
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(eiter it = firstEdge(); it != lastEdge(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->lines, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // triangles
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(fiter it = firstFace(); it != lastFace(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->triangles, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // quads
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(fiter it = firstFace(); it != lastFace(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->quadrangles, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // tets
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(riter it = firstRegion(); it != lastRegion(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->tetrahedra, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // hexas
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(riter it = firstRegion(); it != lastRegion(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->hexahedra, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // prisms
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(riter it = firstRegion(); it != lastRegion(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->prisms, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
{ // pyramids
med_geometrie_element typ = MED_NONE;
std::vector<med_int> conn, fam;
for(riter it = firstRegion(); it != lastRegion(); it++)
if(saveAll || (*it)->physicals.size())
fillElementsMED(families[*it], (*it)->pyramids, conn, fam, typ);
writeElementsMED(fid, meshName, conn, fam, typ);
}
}
if(MEDfermer(fid) < 0){
Msg::Error("Unable to close file '%s'", (char*)name.c_str());
return 0;
}
return 1;
}
#else
int GModel::readMED(const std::string &name)
{
Msg::Error("Gmsh must be compiled with MED support to read '%s'",
name.c_str());
return 0;
}
/***********************************************************************//**
* @brief Run maximum likelihood analysis
*
* The following analysis steps are performed:
* 1. Read the parameters (and write them into logger)
* 2. Load observation
* 3. Setup models for optimizing
* 4. Optimize model (and write result into logger)
***************************************************************************/
void ctlike::run(void)
{
// Switch screen logging on in debug mode
if (logDebug()) {
log.cout(true);
}
// Get parameters
get_parameters();
// Write parameters into logger
if (logTerse()) {
log_parameters();
log << std::endl;
}
// Set energy dispersion flag for all CTA observations and save old
// values in save_edisp vector
std::vector<bool> save_edisp;
save_edisp.assign(m_obs.size(), false);
for (int i = 0; i < m_obs.size(); ++i) {
GCTAObservation* obs = dynamic_cast<GCTAObservation*>(m_obs[i]);
if (obs != NULL) {
save_edisp[i] = obs->response()->apply_edisp();
obs->response()->apply_edisp(m_apply_edisp);
}
}
// Write observation(s) into logger
if (logTerse()) {
log << std::endl;
if (m_obs.size() > 1) {
log.header1("Observations");
}
else {
log.header1("Observation");
}
log << m_obs << std::endl;
}
// Optimize model parameters using LM optimizer
optimize_lm();
// Store Npred
double npred = m_obs.npred();
// Store models for which TS should be computed
std::vector<std::string> ts_srcs;
GModels models_orig = m_obs.models();
for (int i = 0; i < models_orig.size(); ++i) {
GModel* model = models_orig[i];
if (model->tscalc()) {
ts_srcs.push_back(model->name());
}
}
// Compute TS values if requested
if (!ts_srcs.empty()) {
// Store original maximum likelihood and models
double logL_src = m_logL;
GModels models = m_obs.models();
// Fix spatial parameters if requested
if (m_fix_spat_for_ts) {
// Loop over all models
for (int i = 0; i < models.size(); ++i) {
// Continue only if model is skymodel
GModelSky* sky= dynamic_cast<GModelSky*>(models[i]);
if (sky != NULL) {
// Fix spatial parameters
GModelSpatial* spatial = sky->spatial();
for (int j = 0; j < spatial->size(); j++) {
(*spatial)[j].fix();
} // endfor: looped over spatial parameters
} // endif: there was a sky model
} // endfor: looped over models
} // endif: spatial parameter should be fixed
// Loop over stored models, remove source and refit
for (int i = 0; i < ts_srcs.size(); ++i) {
models.remove(ts_srcs[i]);
m_obs.models(models);
double logL_nosrc = reoptimize_lm();
double ts = 2.0 * (logL_src-logL_nosrc);
models_orig[ts_srcs[i]]->ts(ts);
models = models_orig;
}
// Restore best fit values
m_obs.models(models_orig);
}
// Compute number of observed events in all observations
double num_events = 0.0;
for (int i = 0; i < m_obs.size(); ++i) {
double data = m_obs[i]->events()->number();
if (data >= 0.0) {
num_events += data;
}
}
// Write results into logger
if (logTerse()) {
log << std::endl;
log.header1("Maximum likelihood optimisation results");
log << *m_opt << std::endl;
log << gammalib::parformat("Maximum log likelihood");
log << gammalib::str(m_logL,3) << std::endl;
log << gammalib::parformat("Observed events (Nobs)");
log << gammalib::str(num_events, 3) << std::endl;
log << gammalib::parformat("Predicted events (Npred)");
log << gammalib::str(npred, 3);
log << " (Nobs - Npred = ";
log << gammalib::str(num_events-npred);
log << ")" << std::endl;
log << m_obs.models() << std::endl;
}
// Restore energy dispersion flag for all CTA observations
for (int i = 0; i < m_obs.size(); ++i) {
GCTAObservation* obs = dynamic_cast<GCTAObservation*>(m_obs[i]);
if (obs != NULL) {
obs->response()->apply_edisp(save_edisp[i]);
}
}
// Return
return;
}
PView *GMSH_BubblesPlugin::execute(PView *v)
{
double shrink = (double)BubblesOptions_Number[0].def;
std::string fileName = BubblesOptions_String[0].def;
FILE *fp = Fopen(fileName.c_str(), "w");
if(!fp){
Msg::Error("Could not open output file '%s'", fileName.c_str());
return v;
}
GModel *m = GModel::current();
int p = m->getMaxElementaryNumber(0) + 1;
int l = m->getMaxElementaryNumber(1) + 1;
int s = m->getMaxElementaryNumber(2) + 1;
int ll = s, ps = 1;
SBoundingBox3d bbox = m->bounds();
double lc = norm(SVector3(bbox.max(), bbox.min())) / 100;
fprintf(fp, "lc = %g;\n", lc);
for(GModel::viter vit = m->firstVertex(); vit != m->lastVertex(); vit++)
(*vit)->writeGEO(fp, "lc");
for(GModel::eiter eit = m->firstEdge(); eit != m->lastEdge(); eit++)
(*eit)->writeGEO(fp);
for(GModel::fiter fit = m->firstFace(); fit != m->lastFace(); fit++){
(*fit)->writeGEO(fp);
fprintf(fp, "Delete { Surface {%d}; }\n", (*fit)->tag());
int sbeg = s;
int llbeg = ll;
// compute vertex-to-triangle_barycenter map
std::map<MVertex*, std::vector<SPoint3> > v2t;
for(unsigned int i = 0; i < (*fit)->triangles.size(); i++)
for(int j = 0; j < 3; j++)
v2t[(*fit)->triangles[i]->getVertex(j)].push_back((*fit)->triangles[i]->barycenter());
// add boundary vertices in map to get cells "closer" to the boundary
for(std::map<MVertex*, std::vector<SPoint3> >::iterator it = v2t.begin();
it != v2t.end(); it++){
MVertex *v = it->first;
if(v->onWhat() && v->onWhat()->dim() < 2)
it->second.push_back(SPoint3(it->first->x(), it->first->y(), it->first->z()));
}
for(std::map<MVertex*, std::vector<SPoint3> >::iterator it = v2t.begin();
it != v2t.end(); it++){
if(it->second.size() > 2){
// get barycenter of cell boundary points and order them
SPoint3 bc;
for(unsigned int i = 0; i < it->second.size(); i++)
bc += it->second[i];
bc *= 1. / (double)it->second.size();
compareAngle comp(bc);
std::sort(it->second.begin(), it->second.end(), comp);
// shrink cells
if(shrink){
for(unsigned int i = 0; i < it->second.size(); i++){
double dir[3] = {it->second[i].x() - bc.x(),
it->second[i].y() - bc.y(),
it->second[i].z() - bc.z()};
it->second[i][0] -= shrink * dir[0];
it->second[i][1] -= shrink * dir[1];
it->second[i][2] -= shrink * dir[2];
}
}
// create b-spline bounded surface for each cell
int nump = it->second.size();
for(int i = 0; i < nump; i++){
SPoint3 &b(it->second[i]);
fprintf(fp, "Point(%d) = {%.16g, %.16g, %.16g, lc};\n", p++, b.x(), b.y(), b.z());
}
fprintf(fp, "BSpline(%d) = {", l++);
for(int i = nump - 1; i >= 0; i--)
fprintf(fp, "%d,", p - i - 1);
fprintf(fp, "%d};\n", p - nump);
fprintf(fp, "Line Loop(%d) = {%d};\n", ll++, l - 1);
fprintf(fp, "Plane Surface(%d) = {%d};\n", s++, ll - 1);
}
}
fprintf(fp, "Physical Surface(%d) = {%d:%d};\n", ps++, sbeg, s - 1);
fprintf(fp, "Plane Surface(%d) = {%d, %d:%d};\n", s++, (*fit)->tag(), llbeg, ll - 1);
fprintf(fp, "Physical Surface(%d) = {%d};\n", ps++, s - 1);
}
fclose(fp);
return v;
}
/***********************************************************************//**
* @brief Computes
***************************************************************************/
void cterror::run(void)
{
// If we're in debug mode then all output is also dumped on the screen
if (logDebug()) {
log.cout(true);
}
// Get task parameters
get_parameters();
// Write parameters into logger
if (logTerse()) {
log_parameters();
log << std::endl;
}
// Set energy dispersion flag for all CTA observations and save old
// values in save_edisp vector
std::vector<bool> save_edisp;
save_edisp.assign(m_obs.size(), false);
for (int i = 0; i < m_obs.size(); ++i) {
GCTAObservation* obs = dynamic_cast<GCTAObservation*>(m_obs[i]);
if (obs != NULL) {
save_edisp[i] = obs->response()->apply_edisp();
obs->response()->apply_edisp(m_apply_edisp);
}
}
// Write observation(s) into logger
if (logTerse()) {
log << std::endl;
if (m_obs.size() > 1) {
log.header1("Observations");
}
else {
log.header1("Observation");
}
log << m_obs << std::endl;
}
// Write header
if (logTerse()) {
log << std::endl;
log.header1("Compute best-fit likelihood");
}
// Optimize and save best log-likelihood
m_obs.optimize(m_opt);
m_obs.errors(m_opt);
m_best_logL = m_obs.logL();
// Store optimizer for later recovery
GOptimizerLM best_opt = m_opt;
// Write optimised model into logger
if (logTerse()) {
log << m_opt << std::endl;
log << gammalib::parformat("Maximum log likelihood");
log << gammalib::str(m_best_logL,3) << std::endl;
log << m_obs.models() << std::endl;
}
// Continue only if source model exists
if (m_obs.models().contains(m_srcname)) {
// Save best fitting models
GModels models_best = m_obs.models();
// Get pointer on model
GModel* model = models_best[m_srcname];
// Get number of parameters
int npars = model->size();
// Loop over parameters of sky model
for (int i = 0; i < npars; ++i) {
// Skip parameter if it is fixed
if (model->at(i).is_fixed()) {
continue;
}
// Initialise with best fitting models
m_obs.models(models_best);
// Get pointer on model parameter
GModels& current_models = const_cast<GModels&>(m_obs.models());
m_model_par = &(current_models[m_srcname]->at(i));
// Extract current value
m_value = m_model_par->factor_value();
// Compute parameter bracketing
double parmin = std::max(m_model_par->factor_min(),
m_value - 10.0*m_model_par->factor_error());
double parmax = std::min(m_model_par->factor_max(),
m_value + 10.0*m_model_par->factor_error());
// Write header
if (logTerse()) {
log << std::endl;
log.header1("Compute error for source \""+m_srcname+"\""
" parameter \""+m_model_par->name()+"\"");
log << gammalib::parformat("Confidence level");
log << m_confidence*100.0 << "%" << std::endl;
log << gammalib::parformat("Log-likelihood difference");
log << m_dlogL << std::endl;
log << gammalib::parformat("Initial factor range");
log << "[";
log << parmin;
log << ", ";
log << parmax;
log << "]" << std::endl;
}
// Compute lower boundary
double value_lo = error_bisection(parmin, m_value);
// Write lower parameter value
if (logTerse()) {
log << gammalib::parformat("Lower parameter factor");
log << value_lo << std::endl;
}
// Compute upper boundary
double value_hi = error_bisection(m_value, parmax);
// Write upper parameter value
if (logTerse()) {
log << gammalib::parformat("Upper parameter factor");
log << value_hi << std::endl;
}
// Compute errors
double error = 0.5 * (value_hi - value_lo);
double error_neg = m_value - value_lo;
double error_pos = value_hi - m_value;
//double error_max = std::max(value_hi-m_value, m_value-value_lo);
//double error_min = std::min(value_hi-m_value, m_value-value_lo);
// Write errors
if (logTerse()) {
log << gammalib::parformat("Error from curvature");
log << m_model_par->error();
log << " " << m_model_par->unit() << std::endl;
log << gammalib::parformat("Error from profile");
log << std::abs(error*m_model_par->scale());
log << " " << m_model_par->unit() << std::endl;
log << gammalib::parformat("Negative profile error");
log << std::abs(error_neg*m_model_par->scale());
log << " " << m_model_par->unit() << std::endl;
log << gammalib::parformat("Positive profile error");
log << std::abs(error_pos*m_model_par->scale());
log << " " << m_model_par->unit() << std::endl;
}
// Save error result
model->at(i).factor_error(error);
} // endfor: looped over spectral parameters
// Restore best fitting models (now with new errors computed)
m_obs.models(models_best);
} // endif: source model exists
// Recover optimizer
m_opt = best_opt;
// Restore energy dispersion flag for all CTA observations
for (int i = 0; i < m_obs.size(); ++i) {
GCTAObservation* obs = dynamic_cast<GCTAObservation*>(m_obs[i]);
if (obs != NULL) {
obs->response()->apply_edisp(save_edisp[i]);
}
}
// Return
return;
}
PView *GMSH_CVTRemeshPlugin::execute(PView *v)
{
//TODO normalization
GModel* m = GModel::current() ;
std::vector<double> vertices ;
std::vector<unsigned int> faces ;
unsigned int offset = 0 ;
for(GModel::fiter it = m->firstFace(); it != m->lastFace(); ++it) {
(*it)->buildSTLTriangulation() ;
for(unsigned int i = 0; i < (*it)->stl_vertices.size(); ++i) {
GPoint p = (*it)->point((*it)->stl_vertices[i]) ;
vertices.push_back(p.x()) ;
vertices.push_back(p.y()) ;
vertices.push_back(p.z()) ;
}
for(unsigned int i = 0; i < (*it)->stl_triangles.size(); ++i) {
faces.push_back((*it)->stl_triangles[i]+offset) ;
}
offset += (*it)->stl_vertices.size() ;
}
Revoropt::MeshBuilder<3> mesh ;
mesh.swap_vertices(vertices) ;
mesh.swap_faces(faces) ;
double mesh_center[3] ;
double mesh_scale ;
Revoropt::normalize_mesh(&mesh, mesh_center, &mesh_scale) ;
double nradius = (double)CVTRemeshOptions_Number[5].def ;
//normals
std::vector<double> normals(3*mesh.vertices_size()) ;
Revoropt::full_robust_vertex_normals(&mesh,nradius,normals.data()) ;
//lifted vertices
std::vector<double> lifted_vertices(6*mesh.vertices_size(), 0) ;
for(unsigned int vertex = 0; vertex < mesh.vertices_size(); ++vertex) {
std::copy( mesh.vertex(vertex),
mesh.vertex(vertex)+3,
lifted_vertices.data()+6*vertex
) ;
std::copy( normals.data()+3*vertex,
normals.data()+3*vertex+3,
lifted_vertices.data()+6*vertex+3
) ;
}
//setup lifted mesh
Revoropt::ROMeshWrapper<3,6> lifted_mesh(
lifted_vertices.data(),
lifted_vertices.size()/6,
&mesh
) ;
//triangle weight factor
double twfactor = (double)CVTRemeshOptions_Number[3].def ;
//face ratios
std::vector<double> triangle_weights(lifted_mesh.faces_size()) ;
if(twfactor > 0) {
for(unsigned int f = 0; f < lifted_mesh.faces_size(); ++f) {
//vertices of the initial triangle
const unsigned int* fverts = mesh.face(f) ;
//positions
const double* x[3] ;
for(int i=0; i<3; ++i) {
x[i] = lifted_mesh.vertex(fverts[i]) ;
}
//ratio
double ratio = 1 ;
//vectors
typedef Eigen::Matrix<double,3,1> Vector3 ;
Eigen::Map<const Vector3> v0(x[0]) ;
Eigen::Map<const Vector3> v1(x[1]) ;
Eigen::Map<const Vector3> v2(x[2]) ;
//triangle frame
Vector3 U = (v1-v0) ;
const double U_len = U.norm() ;
if(U_len > 0) {
U /= U_len ;
Vector3 H = (v2-v0) ;
H = H - H.dot(U)*U ;
const double H_len = H.norm() ;
if(H_len > 0) {
//we know that the triangle is not flat
H /= H_len ;
//gradient of the barycentric weights in the triangle
Eigen::Matrix<double,3,2> bar_grads ;
bar_grads(2,0) = 0 ;
bar_grads(2,1) = 1/H_len ;
//gradient norms of every normal component
for(int i = 0; i < 2; ++i) {
//reference frame for the vertex
Eigen::Map<const Vector3> vi0(x[(i+1)%3]) ;
Eigen::Map<const Vector3> vi1(x[(i+2)%3]) ;
Eigen::Map<const Vector3> vi2(x[ i ]) ;
Vector3 Ui = (vi1-vi0) ;
Ui /= Ui.norm() ;
Vector3 Hi = (vi2-vi0) ;
Hi = Hi - Hi.dot(Ui)*Ui ;
const double Hi_invlen = 1/Hi.norm() ;
Hi *= Hi_invlen ;
bar_grads(i,0) = Hi.dot(U)*Hi_invlen ;
bar_grads(i,1) = Hi.dot(H)*Hi_invlen ;
}
//gradient of each component of the normal
Eigen::Map<const Vector3> n0(x[0]+3) ;
Eigen::Map<const Vector3> n1(x[1]+3) ;
Eigen::Map<const Vector3> n2(x[2]+3) ;
Eigen::Matrix<double,3,2> n_grads = Eigen::Matrix<double,3,2>::Zero() ;
n_grads = n0*bar_grads.row(0) ;
n_grads += n1*bar_grads.row(1) ;
n_grads += n2*bar_grads.row(2) ;
//maximal gradient norm
double g_max = n_grads.row(0).dot(n_grads.row(0)) ;
double g_other = n_grads.row(1).dot(n_grads.row(1)) ;
g_max = g_max > g_other ? g_max : g_other ;
g_other = n_grads.row(2).dot(n_grads.row(2)) ;
g_max = g_max > g_other ? g_max : g_other ;
if(g_max == g_max) { //prevent nan
ratio += g_max ;
}
}
}
triangle_weights[f] = pow(ratio,twfactor) ;
}
}
//normal factor
double nfactor = (double)CVTRemeshOptions_Number[2].def ; ;
//weight the normal component by the provided factor
for(unsigned int i = 0; i<lifted_mesh.vertices_size(); ++i) {
double* v = lifted_vertices.data() + 6*i ;
v[3]*= nfactor ;
v[4]*= nfactor ;
v[5]*= nfactor ;
}
//number of sites
unsigned int nsites = (unsigned int)CVTRemeshOptions_Number[0].def ;
//lifted sites
std::vector<double> lifted_sites(6*nsites) ;
if(twfactor > 0) {
Revoropt::generate_random_sites< Revoropt::ROMesh<3,6> >(
&lifted_mesh, nsites, lifted_sites.data(), triangle_weights.data()
) ;
} else {
Revoropt::generate_random_sites< Revoropt::ROMesh<3,6> >(
&lifted_mesh, nsites, lifted_sites.data()
) ;
}
//setup the cvt minimizer
Revoropt::CVT::DirectMinimizer< Revoropt::ROMesh<3,6> > cvt ;
cvt.set_sites(lifted_sites.data(), nsites) ;
cvt.set_mesh(&lifted_mesh) ;
if(twfactor > 0) {
cvt.set_triangle_weights(triangle_weights.data()) ;
}
//setup the callback
SolverCallback callback ;
//number of iterations
unsigned int niter = (unsigned int)CVTRemeshOptions_Number[1].def ; ;
unsigned int aniso_niter = std::min<unsigned int>(10,niter) ;
//solver status
int status = 0 ;
//isotropic iterations
if(niter > 10) {
aniso_niter = std::max(aniso_niter,niter*10/100) ;
cvt.set_anisotropy(1) ;
status = cvt.minimize<Revoropt::Solver::AlgLBFGS>(niter-aniso_niter, &callback) ;
}
//anisotropic iterations
if(niter > 0) {
//tangent space anisotropy
double tanisotropy = (double)CVTRemeshOptions_Number[4].def ; ;
//anisotropic iterations
cvt.set_anisotropy(tanisotropy) ;
status = cvt.minimize<Revoropt::Solver::AlgLBFGS>(aniso_niter, &callback) ;
}
//rdt
std::vector<unsigned int> rdt_triangles ;
Revoropt::RDTBuilder< Revoropt::ROMesh<3,6> > build_rdt(rdt_triangles) ;
Revoropt::RVD< Revoropt::ROMesh<3,6> > rvd ;
rvd.set_sites(lifted_sites.data(), nsites) ;
rvd.set_mesh(&lifted_mesh) ;
rvd.compute(build_rdt) ;
GFace* res_face = new discreteFace(m, m->getMaxElementaryNumber(2)+1) ;
m->add(res_face) ;
//scale back and transfer to gmsh
std::vector<MVertex*> m_verts(nsites) ;
for(unsigned int i = 0; i < nsites; ++i) {
m_verts[i] = new MVertex(
lifted_sites[6*i ]*mesh_scale + mesh_center[0],
lifted_sites[6*i+1]*mesh_scale + mesh_center[1],
lifted_sites[6*i+2]*mesh_scale + mesh_center[2]
) ;
res_face->addMeshVertex(m_verts[i]) ;
}
for(unsigned int i = 0; i < rdt_triangles.size()/3; ++i) {
res_face->addTriangle(
new MTriangle(
m_verts[rdt_triangles[3*i ]],
m_verts[rdt_triangles[3*i+1]],
m_verts[rdt_triangles[3*i+2]]
)
) ;
}
res_face->setAllElementsVisible(true) ;
return v ;
}
int main(int argc,char *argv[])
{
if(argc < 6){
printf("Usage: %s file lx ly lz rmax [levels=1] [refcs=1]\n", argv[0]);
printf("where\n");
printf(" 'file' contains a CAD model\n");
printf(" 'lx', 'ly' and 'lz' are the sizes of the elements along the"
" x-, y- and z-axis at the coarsest level\n");
printf(" 'rmax' is the radius of the largest sphere that can be inscribed"
" in the structure\n");
printf(" 'levels' sets the number of levels in the grid\n");
printf(" 'refcs' selects if curved surfaces should be refined\n");
return -1;
}
GmshInitialize();
GmshSetOption("General", "Terminal", 1.);
GmshMergeFile(argv[1]);
double lx = atof(argv[2]), ly = atof(argv[3]), lz = atof(argv[4]);
double rmax = atof(argv[5]);
int levels = (argc > 6) ? atof(argv[6]) : 1;
int refineCurvedSurfaces = (argc > 7) ? atof(argv[7]) : 1;
// minimum distance between points in the cloud at the coarsest
// level
double sampling = std::min(rmax, std::min(lx, std::min(ly, lz)));
// radius of the "tube" created around parts to refine at the
// coarsest level
double rtube = std::max(lx, std::max(ly, lz)) * 2.;
GModel *gm = GModel::current();
std::vector<SPoint3> points;
Msg::Info("Filling coarse point cloud on surfaces");
for (GModel::fiter fit = gm->firstFace(); fit != gm->lastFace(); fit++)
(*fit)->fillPointCloud(sampling, &points);
Msg::Info(" %d points in the surface cloud", (int)points.size());
std::vector<SPoint3> refinePoints;
if(levels > 1){
double s = sampling / pow(2., levels - 1);
Msg::Info("Filling refined point cloud on curves and curved surfaces");
for (GModel::eiter eit = gm->firstEdge(); eit != gm->lastEdge(); eit++)
fillPointCloud(*eit, s, refinePoints);
// FIXME: refine this by computing e.g. "mean" curvature
if(refineCurvedSurfaces){
for (GModel::fiter fit = gm->firstFace(); fit != gm->lastFace(); fit++)
if((*fit)->geomType() != GEntity::Plane)
(*fit)->fillPointCloud(2 * s, &refinePoints);
}
Msg::Info(" %d points in the refined cloud", (int)refinePoints.size());
}
SBoundingBox3d bb;
for(unsigned int i = 0; i < points.size(); i++) bb += points[i];
for(unsigned int i = 0; i < refinePoints.size(); i++) bb += refinePoints[i];
bb.scale(1.21, 1.21, 1.21);
SVector3 range = bb.max() - bb.min();
int NX = range.x() / lx;
int NY = range.y() / ly;
int NZ = range.z() / lz;
if(NX < 2) NX = 2;
if(NY < 2) NY = 2;
if(NZ < 2) NZ = 2;
Msg::Info(" bounding box min: %g %g %g -- max: %g %g %g",
bb.min().x(), bb.min().y(), bb.min().z(),
bb.max().x(), bb.max().y(), bb.max().z());
Msg::Info(" Nx=%d Ny=%d Nz=%d", NX, NY, NZ);
cartesianBox<double> box(bb.min().x(), bb.min().y(), bb.min().z(),
SVector3(range.x(), 0, 0),
SVector3(0, range.y(), 0),
SVector3(0, 0, range.z()),
NX, NY, NZ, levels);
Msg::Info("Inserting active cells in the cartesian grid");
Msg::Info(" level %d", box.getLevel());
for (unsigned int i = 0; i < points.size(); i++)
insertActiveCells(points[i].x(), points[i].y(), points[i].z(), rmax, box);
cartesianBox<double> *parent = &box, *child;
while((child = parent->getChildBox())){
Msg::Info(" level %d", child->getLevel());
for(unsigned int i = 0; i < refinePoints.size(); i++)
insertActiveCells(refinePoints[i].x(), refinePoints[i].y(), refinePoints[i].z(),
rtube / pow(2., (levels - child->getLevel())), *child);
parent = child;
}
// remove child cells that do not entirely fill parent cell or for
// which there is no parent neighbor; then remove parent cells that
// have children
Msg::Info("Removing cells to match X-FEM mesh topology constraints");
removeBadChildCells(&box);
removeParentCellsWithChildren(&box);
// we generate duplicate nodes at this point so we can easily access
// cell values at each level; we will clean up by renumbering after
// filtering
Msg::Info("Initializing nodal values in the cartesian grid");
box.createNodalValues();
Msg::Info("Computing levelset on the cartesian grid");
computeLevelset(gm, box);
Msg::Info("Removing cells outside the structure");
removeOutsideCells(&box);
Msg::Info("Renumbering mesh vertices across levels");
box.renumberNodes();
bool decomposeInSimplex = false;
box.writeMSH("yeah.msh", decomposeInSimplex);
Msg::Info("Done!");
GmshFinalize();
}
void carveHole(GRegion *gr, int num, double distance, std::vector<int> &surfaces)
{
Msg::Info("Carving hole %d from surface %d at distance %g", num, surfaces[0], distance);
GModel *m = gr->model();
// add all points from carving surfaces into kdtree
int numnodes = 0;
for(unsigned int i = 0; i < surfaces.size(); i++){
GFace *gf = m->getFaceByTag(surfaces[i]);
if(!gf){
Msg::Error("Unknown carving surface %d", surfaces[i]);
return;
}
numnodes += gf->mesh_vertices.size();
}
ANNpointArray kdnodes = annAllocPts(numnodes, 3);
int k = 0;
for(unsigned int i = 0; i < surfaces.size(); i++){
GFace *gf = m->getFaceByTag(surfaces[i]);
for(unsigned int j = 0; j < gf->mesh_vertices.size(); j++){
kdnodes[k][0] = gf->mesh_vertices[j]->x();
kdnodes[k][1] = gf->mesh_vertices[j]->y();
kdnodes[k][2] = gf->mesh_vertices[j]->z();
k++;
}
}
ANNkd_tree *kdtree = new ANNkd_tree(kdnodes, numnodes, 3);
// remove the volume elements that are within 'distance' of the
// carved surface
carveHole(gr->tetrahedra, distance, kdtree);
carveHole(gr->hexahedra, distance, kdtree);
carveHole(gr->prisms, distance, kdtree);
carveHole(gr->pyramids, distance, kdtree);
delete kdtree;
annDeallocPts(kdnodes);
// TODO: remove any interior elements left inside the carved surface
// (could shoot a line from each element's barycenter and count
// intersections o see who's inside)
// generate discrete boundary mesh of the carved hole
GFace *gf = m->getFaceByTag(num);
if(!gf) return;
std::set<MFace, Less_Face> faces;
std::list<GFace*> f = gr->faces();
for(std::list<GFace*>::iterator it = f.begin(); it != f.end(); it++){
addFaces((*it)->triangles, faces);
addFaces((*it)->quadrangles, faces);
}
addFaces(gr->tetrahedra, faces);
addFaces(gr->hexahedra, faces);
addFaces(gr->prisms, faces);
addFaces(gr->pyramids, faces);
std::set<MVertex*> verts;
for(std::set<MFace, Less_Face>::iterator it = faces.begin(); it != faces.end(); it++){
for(int i = 0; i < it->getNumVertices(); i++){
it->getVertex(i)->setEntity(gf);
verts.insert(it->getVertex(i));
}
if(it->getNumVertices() == 3)
gf->triangles.push_back(new MTriangle(it->getVertex(0), it->getVertex(1),
it->getVertex(2)));
else if(it->getNumVertices() == 4)
gf->quadrangles.push_back(new MQuadrangle(it->getVertex(0), it->getVertex(1),
it->getVertex(2), it->getVertex(3)));
}
}
// The function that tests whether a 2D surface is a lateral of a valid QuadToTri
// region and whether there are conflicts. If surface is not part of valid QuadToTri region
// or if there are QuadToTri conflicts, return 0. Note that RemoveDuplicateSurfaces()
// makes this DIFFICULT. Also, the tri_quad_flag determins whether the surface
// should be meshed with triangles or quadrangles:
// tri_quad_values: 0 = no override, 1 = mesh as quads, 2 = mesh as triangles.
// Added 2010-12-09.
int IsValidQuadToTriLateral(GFace *face, int *tri_quad_flag, bool *detectQuadToTriLateral )
{
(*tri_quad_flag) = 0;
(*detectQuadToTriLateral) = false;
GModel *model = face->model();
ExtrudeParams *ep = face->meshAttributes.extrude;
if( !ep || !ep->mesh.ExtrudeMesh || !ep->geo.Mode == EXTRUDED_ENTITY ){
Msg::Error("In IsValidQuadToTriLateral(), face %d is not a structured extrusion.",
face->tag() );
return 0;
}
GEdge *face_source = model->getEdgeByTag( std::abs( ep->geo.Source ) );
if( !face_source ){
Msg::Error("In IsValidQuadToTriLateral(), face %d has no source edge.",
face->tag() );
}
// It seems the member pointers to neighboring regions for extruded lateral faces are not set.
// For now, have to loop through
// ALL the regions to see if the presently considered face belongs to the region and if
// any neighboring region is QUADTRI.
// The following loop will find all the regions that the face bounds, and determine
// whether the face is a lateral of the region (including whether the region is even extruded).
// After that information is determined, function can test for QuadToTri neighbor conflicts.
std::vector<GRegion *> lateral_regions;
std::vector<GRegion *> adjacent_regions;
int numRegions = 0;
int numLateralRegions = 0;
numRegions = GetNeighborRegionsOfFace(face, adjacent_regions);
for( int i_reg = 0; i_reg < numRegions; i_reg++ ){
GRegion *region = adjacent_regions[i_reg];
// is region in the current model's region's or is it deleted?
if( !FindVolume( ( region->tag() ) ) )
continue;
// is the region mesh extruded?
if( !region->meshAttributes.extrude ||
( region->meshAttributes.extrude &&
!region->meshAttributes.extrude->mesh.ExtrudeMesh ) )
continue;
if( region->meshAttributes.extrude->geo.Mode != EXTRUDED_ENTITY )
continue;
// Test whether the face is a lateral
if( IsSurfaceALateralForRegion(region, face) ){
lateral_regions.push_back(region);
numLateralRegions++;
if( region->meshAttributes.extrude->mesh.QuadToTri )
(*detectQuadToTriLateral) = true;
}
}
// MAIN test of whether this is even a quadToTri extrusion lateral
// the only return 0 path that is NOT an error
if( !(*detectQuadToTriLateral) )
return 0;
// now will start conflict checks
if(numRegions > 2){
Msg::Error("In IsValidQuadToTriLateral(), too many regions adjacent to surface %d.",
face->tag() );
return 0;
}
bool detect_conflict = false;
// Set the tri_quad_flag that lets ExtrudeMesh override ep->Recombine;
// tri_quad_values: 0 = no override, 1 = mesh as quads, 2 = mesh as triangles.
// if this face is a free surface:
if( adjacent_regions.size() == 1 ){
if( lateral_regions[0]->meshAttributes.extrude->mesh.QuadToTri == QUADTRI_NOVERTS_1_RECOMB ||
lateral_regions[0]->meshAttributes.extrude->mesh.QuadToTri == QUADTRI_ADDVERTS_1_RECOMB ){
(*tri_quad_flag) = 1;
}
if( lateral_regions[0]->meshAttributes.extrude->mesh.QuadToTri == QUADTRI_NOVERTS_1 ||
lateral_regions[0]->meshAttributes.extrude->mesh.QuadToTri == QUADTRI_ADDVERTS_1 ){
(*tri_quad_flag) = 2;
}
else
(*tri_quad_flag) = 0;
}
else if( adjacent_regions.size() > 1 ){
GRegion *adj_region = NULL;
ExtrudeParams *adj_ep = NULL;
if( lateral_regions[0] == adjacent_regions[0] )
adj_region = adjacent_regions[1];
else
adj_region = adjacent_regions[0];
adj_ep = adj_region->meshAttributes.extrude;
// if Neighbor is Transfinite, go with the default, non-QuadTri recombine for this surface
if( adj_region && adj_region->meshAttributes.method == MESH_TRANSFINITE )
(*tri_quad_flag) = 0;
// if a neighbor
// has no extrusion structure,
// don't even consider QuadToTri Recomb on this face.
else if( adj_region && !(adj_ep && adj_ep->mesh.ExtrudeMesh) )
(*tri_quad_flag) = 2;
// This face is the source face of a second
// neighboring extrusion.
else if( adj_ep && adj_ep->mesh.ExtrudeMesh &&
model->getFaceByTag( std::abs( adj_ep->geo.Source ) ) == face ){
if( lateral_regions[0]->meshAttributes.extrude->mesh.QuadToTri == QUADTRI_NOVERTS_1_RECOMB ||
lateral_regions[0]->meshAttributes.extrude->mesh.QuadToTri == QUADTRI_ADDVERTS_1_RECOMB )
(*tri_quad_flag) = 1;
else if( lateral_regions[0]->meshAttributes.extrude->mesh.QuadToTri == QUADTRI_NOVERTS_1 ||
lateral_regions[0]->meshAttributes.extrude->mesh.QuadToTri == QUADTRI_ADDVERTS_1 )
(*tri_quad_flag) = 2;
else
(*tri_quad_flag) = 0;
}
// if both neighbors are structured but none of the previous apply:
else if( adj_ep && adj_ep->mesh.ExtrudeMesh ){
if( (adj_ep && !adj_ep->mesh.QuadToTri && adj_ep->mesh.Recombine) ||
(ep && !ep->mesh.QuadToTri && ep->mesh.Recombine) )
(*tri_quad_flag) = 1;
else if( (adj_ep && !adj_ep->mesh.QuadToTri && !adj_ep->mesh.Recombine) ||
(ep && !ep->mesh.QuadToTri && !ep->mesh.Recombine) )
(*tri_quad_flag) = 2;
// if both are quadToTri ALWAYS try to recombine
else if( ep->mesh.QuadToTri && adj_ep && adj_ep->mesh.QuadToTri )
(*tri_quad_flag) = 1;
else
(*tri_quad_flag) = 0;
}
// any other adjacent surface, just default to the QuadToTri region's non-QuadToTri
// default recombination method. Any mistakes at this point are not this feature's.
else
(*tri_quad_flag) = 0;
}
// if this executes, there's a mistake here :
else{
detect_conflict = true;
(*tri_quad_flag) = 0;
}
if( detect_conflict )
return 0;
else
return 1;
}
void GMSH_SimplePartitionPlugin::run()
{
#if defined(HAVE_MESH)
int numSlicesX = (int)SimplePartitionOptions_Number[0].def;
int numSlicesY = (int)SimplePartitionOptions_Number[1].def;
int numSlicesZ = (int)SimplePartitionOptions_Number[2].def;
int createTopology = (int)SimplePartitionOptions_Number[3].def;
std::vector<std::string> exprX(1), exprY(1), exprZ(1);
exprX[0] = SimplePartitionOptions_String[0].def;
exprY[0] = SimplePartitionOptions_String[1].def;
exprZ[0] = SimplePartitionOptions_String[2].def;
GModel *m = GModel::current();
if(!m->getNumMeshElements()){
Msg::Error("Plugin(SimplePartition) requires a mesh");
return;
}
if(numSlicesX < 1 || numSlicesY < 1 || numSlicesZ < 1){
Msg::Error("Number of slices should be strictly positive");
return;
}
m->unpartitionMesh();
SBoundingBox3d bbox = m->bounds();
double pminX = bbox.min()[0], pmaxX = bbox.max()[0];
double pminY = bbox.min()[1], pmaxY = bbox.max()[1];
double pminZ = bbox.min()[2], pmaxZ = bbox.max()[2];
std::vector<double> ppX(numSlicesX + 1);
std::vector<double> ppY(numSlicesY + 1);
std::vector<double> ppZ(numSlicesZ + 1);
std::vector<std::string> variables(1, "t");
std::vector<double> values(1), res(1);
{
mathEvaluator f(exprX, variables);
for(int p = 0; p <= numSlicesX; p++) {
double t = values[0] = (double)p / (double)numSlicesX;
if(f.eval(values, res)) t = res[0];
ppX[p] = pminX + t * (pmaxX - pminX);
}
}
bool emptyX = (ppX[0] == ppX[numSlicesX]);
{
mathEvaluator f(exprY, variables);
for(int p = 0; p <= numSlicesY; p++) {
double t = values[0] = (double)p / (double)numSlicesY;
if(f.eval(values, res)) t = res[0];
ppY[p] = pminY + t * (pmaxY - pminY);
}
}
bool emptyY = (ppY[0] == ppY[numSlicesY]);
{
mathEvaluator f(exprZ, variables);
for(int p = 0; p <= numSlicesZ; p++) {
double t = values[0] = (double)p / (double)numSlicesZ;
if(f.eval(values, res)) t = res[0];
ppZ[p] = pminZ + t * (pmaxZ - pminZ);
}
}
bool emptyZ = (ppZ[0] == ppZ[numSlicesZ]);
std::vector<GEntity *> entities;
m->getEntities(entities);
hashmap<MElement *, unsigned int> elmToPartition;
for(std::size_t i = 0; i < entities.size(); i++) {
GEntity *ge = entities[i];
for(std::size_t j = 0; j < ge->getNumMeshElements(); j++) {
MElement *e = ge->getMeshElement(j);
SPoint3 point = e->barycenter();
int part = 0;
for(int kx = 0; kx < numSlicesX; kx++) {
if(part) break;
for(int ky = 0; ky < numSlicesY; ky++) {
if(part) break;
for(int kz = 0; kz < numSlicesZ; kz++) {
if(part) break;
if((emptyX || (kx == 0 && ppX[0] == point[0]) ||
(ppX[kx] < point[0] && point[0] <= ppX[kx + 1])) &&
(emptyY || (ky == 0 && ppY[0] == point[1]) ||
(ppY[ky] < point[1] && point[1] <= ppY[ky + 1])) &&
(emptyZ || (kz == 0 && ppZ[0] == point[2]) ||
(ppZ[kz] < point[2] && point[2] <= ppZ[kz + 1]))){
part = kx * numSlicesY * numSlicesZ + ky * numSlicesZ + kz + 1;
elmToPartition.insert(std::pair<MElement *, unsigned int>(e, part));
e->setPartition(part); // this will be removed
}
}
}
}
}
}
opt_mesh_partition_create_topology(0, GMSH_SET | GMSH_GUI, createTopology);
int ier = PartitionUsingThisSplit(m, numSlicesX * numSlicesY * numSlicesZ,
elmToPartition);
if(!ier) {
opt_mesh_color_carousel(0, GMSH_SET | GMSH_GUI, 3.);
CTX::instance()->mesh.changed = ENT_ALL;
}
#else
Msg::Error("Gmsh must be compiled with Mesh support to partition meshes");
#endif
}
// The function that tests whether a surface is a QuadToTri top surface and whether
// there are conflicts. If surface is not a top for a valid QuadToTri region or if
// there are QuadToTri conflicts, return 0.
// if the surface turns out to be the source of a toroidal loop extrusion (which will then
// NOT have geo.Mode == COPIED_ENTITY), return 2 (this will require special meshing considerations).
// Note that RemoveDuplicateSurfaces() makes this DIFFICULT.
// Also, the type of QuadToTri interface is placed into the
// pointer argument quadToTri. .
// Added 2010-12-09.
int IsValidQuadToTriTop(GFace *face, int *quadToTri, bool *detectQuadToTriTop)
{
(*quadToTri) = NO_QUADTRI;
(*detectQuadToTriTop) = false;
int is_toroidal_quadtri = 0;
GModel *model = face->model();
// First thing is first: determine if this is a toroidal quadtri extrusion. if so, can skip the rest
// It seems the member pointers to neighboring regions for extruded top faces are not set.
// For now, have to loop through
// ALL the regions to see if the presently considered face belongs to the region.
// The following loop will find all the regions that the face bounds, and determine
// whether the face is a top face of the region (including whether the region is even extruded).
// After that information is determined, function can test for QuadToTri neighbor conflicts.
// first determine if this is toroidal quadtotri
is_toroidal_quadtri = IsInToroidalQuadToTri(face);
if( is_toroidal_quadtri )
(*detectQuadToTriTop) = true;
else{
std::vector<GRegion *> top_regions;
std::vector<GRegion *> adjacent_regions;
std::vector<GRegion *> all_regions;
int numRegions = 0;
int numTopRegions = 0;
std::set<GRegion *, GEntityLessThan>::iterator itreg;
for( itreg = model->firstRegion(); itreg != model->lastRegion(); itreg++ )
all_regions.push_back( (*itreg) );
for(unsigned int i_reg = 0; i_reg < all_regions.size(); i_reg++ ){
// save time
if( numRegions >= 2 )
break;
GRegion *region = all_regions[i_reg];
// is region in the current model's regions or is it deleted?
if( !FindVolume( ( region->tag() ) ) )
continue;
// does face belong to region?
std::list<GFace *> region_faces = std::list<GFace *>( region->faces() );
if( std::find( region_faces.begin(), region_faces.end(), face ) !=
region_faces.end() ){
adjacent_regions.push_back(region);
numRegions++;
}
else
continue;
// is region a structured extruded?
if( !(region->meshAttributes.extrude && region->meshAttributes.extrude->mesh.ExtrudeMesh &&
region->meshAttributes.extrude->geo.Mode == EXTRUDED_ENTITY) )
continue;
// Test whether the face is a top for the region
if( IsSurfaceATopForRegion(region, face) ){
top_regions.push_back(region);
numTopRegions++;
if( region->meshAttributes.extrude->mesh.QuadToTri )
(*detectQuadToTriTop) = true;
}
}
// MAIN test of whether this is even a quadToTri extrusion lateral
// the only return 0 path that is NOT an error
if( !(*detectQuadToTriTop) )
return 0;
ExtrudeParams *ep = face->meshAttributes.extrude;
if(!ep && !is_toroidal_quadtri){
Msg::Error("In IsValidQuadToTriTop(), no extrude info for surface %d.",
face->tag() );
return 0;
}
if( ep->geo.Mode != COPIED_ENTITY ){
Msg::Error("In IsValidQuadToTriTop(), surface %d is not copied from source.",
face->tag() );
return 0;
}
if( ep->mesh.QuadToTri == 0){
Msg::Error("In IsValidQuadToTriTop(), surface %d was determined to be the top surface "
"for a QuadToTri extrusion, but does not have QuadToTri parameters set within itself.",
face->tag() );
return 0;
}
GFace *face_source = model->getFaceByTag(std::abs(ep->geo.Source));
if(!face_source){
Msg::Error("In IsValidQuadToTriTop(), unknown source face number %d.",
face->meshAttributes.extrude->geo.Source);
return 0;
}
if(numRegions > 2){
Msg::Error("In IsValidQuadToTriTop(), too many regions adjacent to surface %d.",
face->tag() );
return 0;
}
if( top_regions.size() ){
(*quadToTri) = top_regions[0]->meshAttributes.extrude->mesh.QuadToTri;
}
// Make sure that face is the top for only one region. if not, then there will likely
// be conflicts (two regions extruded into each other).
if( top_regions.size() > 1 ){
Msg::Error("In IsValidQuadToTriTop(), QuadToTri top surface %d identified as top "
"surface for more than one region. Likely conflict.", face->tag() );
return 0;
}
} // end of else that executes if NOT toroidal extrusion
// this is technically redundant...but if changes are made, it's good to keep this here at the end for safety
if( !(*detectQuadToTriTop) )
return 0;
if( !is_toroidal_quadtri )
return 1;
else if( is_toroidal_quadtri == 1 )
{ return 2;} // for toroidal extrusion
else
return 3;
}
MarkeredSurface MarkeredSurfaceGeoGenerator::generate(string fileName, real size)
{
Engine& engine = Engine::getInstance();
LOG_INFO("Generating markered surface from Geo file " << fileName);
GmshSetOption("General", "Terminal", 1.0);
GmshSetOption("General", "Verbosity", engine.getGmshVerbosity());
GmshSetOption("General", "ExpertMode", 1.0);
GModel gmshModel;
gmshModel.setFactory("Gmsh");
gmshModel.readGEO(fileName);
float clmin, clmax;
if (size > 0)
{
clmin = size*0.8;
clmax = size*1.2;
}
else
{
auto _min = gmshModel.bounds().min();
auto _max = gmshModel.bounds().max();
auto d1 = _max.x() - _min.x();
auto d2 = _max.y() - _min.y();
auto d3 = _max.z() - _min.z();
if ((d1/d2 >= 0.8) && (d1/d2 <= 1.2) && (d1/d3 >= 0.8) && (d1/d3 <= 1.2))
{
auto d = gmshModel.bounds().diag();
clmin = d/80;
clmax = d/60;
}
else
{
auto d = min({d1, d2, d3});
clmin = d/10;
clmax = d/5;
}
}
GmshSetOption("Mesh", "CharacteristicLengthMin", clmin);
GmshSetOption("Mesh", "CharacteristicLengthMax", clmax);
gmshModel.mesh(2);
vector<GEntity*> entities;
gmshModel.getEntities(entities);
auto nverts = gmshModel.getNumMeshVertices();
vector<CalcNode> markers;
vector<TriangleFirstOrder> faces;
vector<int> regions;
int *newVertNums = new int[nverts+1];
for (int i = 0; i <= nverts; i++)
newVertNums[i] = -1;
MVertex* verts[3];
int nf = 0;
int nv = 0;
for (auto e: entities)
{
if (e->geomType() == GEntity::RuledSurface || e->geomType() == GEntity::Plane)
{
regions.push_back(e->getNumMeshElements());
for (unsigned int i = 0; i < e->getNumMeshElements(); i++)
{
auto elem = e->getMeshElement(i);
assert_eq(elem->getNumFaces(), 1);
auto face = elem->getFace(0);
for (int j = 0; j < 3; j++)
verts[j] = face.getVertex(j);
int v[3];
for (int j = 0; j < 3; j++)
{
if (newVertNums[verts[j]->getNum()] == -1)
{
newVertNums[verts[j]->getNum()] = nv;
markers.push_back(CalcNode(nv, vector3r(verts[j]->x(), verts[j]->y(), verts[j]->z())));
nv++;
}
v[j] = newVertNums[verts[j]->getNum()];
}
faces.push_back(TriangleFirstOrder(nf++, v));
}
}
}
assert_gt(markers.size(), 0);
assert_gt(faces.size(), 0);
delete[] newVertNums;
return MarkeredSurface(markers, faces, regions);
}
void drawContext::drawMesh()
{
if(!CTX::instance()->mesh.draw) return;
// make sure to flag any model-dependent post-processing view as
// changed if the underlying mesh has, before resetting the changed
// flag
if(CTX::instance()->mesh.changed){
for(unsigned int i = 0; i < GModel::list.size(); i++)
for(unsigned int j = 0; j < PView::list.size(); j++)
if(PView::list[j]->getData()->hasModel(GModel::list[i]))
PView::list[j]->setChanged(true);
}
glPointSize((float)CTX::instance()->mesh.pointSize);
gl2psPointSize((float)(CTX::instance()->mesh.pointSize *
CTX::instance()->print.epsPointSizeFactor));
glLineWidth((float)CTX::instance()->mesh.lineWidth);
gl2psLineWidth((float)(CTX::instance()->mesh.lineWidth *
CTX::instance()->print.epsLineWidthFactor));
if(CTX::instance()->mesh.lightTwoSide)
glLightModelf(GL_LIGHT_MODEL_TWO_SIDE, GL_TRUE);
else
glLightModelf(GL_LIGHT_MODEL_TWO_SIDE, GL_FALSE);
if(!CTX::instance()->clipWholeElements){
for(int i = 0; i < 6; i++)
if(CTX::instance()->mesh.clip & (1 << i))
glEnable((GLenum)(GL_CLIP_PLANE0 + i));
else
glDisable((GLenum)(GL_CLIP_PLANE0 + i));
}
for(unsigned int i = 0; i < GModel::list.size(); i++){
GModel *m = GModel::list[i];
m->fillVertexArrays();
if(m->getVisibility() && isVisible(m)){
int status = m->getMeshStatus();
if(status >= 0)
std::for_each(m->firstVertex(), m->lastVertex(), drawMeshGVertex(this));
if(status >= 1)
std::for_each(m->firstEdge(), m->lastEdge(), drawMeshGEdge(this));
if(status >= 2){
beginFakeTransparency();
std::for_each(m->firstFace(), m->lastFace(), drawMeshGFace(this));
endFakeTransparency();
}
if(status >= 3)
std::for_each(m->firstRegion(), m->lastRegion(), drawMeshGRegion(this));
}
}
CTX::instance()->mesh.changed = 0;
for(int i = 0; i < 6; i++)
glDisable((GLenum)(GL_CLIP_PLANE0 + i));
}
bool OptHOM::addBndObjGrad(double factor, double &Obj, alglib::real_1d_array &gradObj)
{
// set the mesh to its present position
std::vector<SPoint3> xyz,uvw;
mesh.getGEntityPositions(xyz,uvw);
mesh.updateGEntityPositions();
//could be better (e.g. store the model in the Mesh:: datastrucure)
GModel *gm = GModel::current();
// for all model edges, compute the error between the geometry and the mesh
maxDistCAD = 0.0;
double distCAD = 0.0;
for (GModel::eiter it = gm->firstEdge(); it != gm->lastEdge(); ++it){
// do not do straight lines
if ((*it)->geomType() == GEntity::Line)continue;
// look at all mesh lines
std::vector<bool> doWeCompute((*it)->lines.size());
for (unsigned int i=0;i<(*it)->lines.size(); i++){
doWeCompute[i] = false;
for (unsigned int j=0;j<(*it)->lines[i]->getNumVertices(); j++){
int index = mesh.getFreeVertexStartIndex((*it)->lines[i]->getVertex(j));
if (index >=0){
doWeCompute[i] = true;
continue;
}
}
}
std::vector<double> dist((*it)->lines.size());
for (unsigned int i=0;i<(*it)->lines.size(); i++){
if (doWeCompute[i]){
// compute the distance from the geometry to the mesh
dist[i] = MLineGEdgeDistance ( (*it)->lines[i] , *it );
maxDistCAD = std::max(maxDistCAD,dist[i]);
distCAD += dist [i] * factor;
}
}
// be clever to compute the derivative : iterate on all
// Distance = \sum_{lines} Distance (line, GEdge)
// For a high order vertex, we compute the derivative only by
// recomputing the distance to one only line
const double eps = 1.e-6;
for (unsigned int i=0;i<(*it)->lines.size(); i++){
if (doWeCompute[i]){
for (int j=2 ; j<(*it)->lines[i]->getNumVertices() ; j++){
MVertex *v = (*it)->lines[i]->getVertex(j);
int index = mesh.getFreeVertexStartIndex(v);
// printf("%d %d (%d %d)\n",v->getNum(),index,v->onWhat()->tag(),v->onWhat()->dim());
if (index >= 0){
double t;
v->getParameter(0,t);
SPoint3 pp (v->x(),v->y(),v->z());
GPoint gp = (*it)->point(t+eps);
v->setParameter(0,t+eps);
v->setXYZ(gp.x(),gp.y(),gp.z());
double dist2 = MLineGEdgeDistance ( (*it)->lines[i] , *it );
double deriv = (dist2 - dist[i])/eps;
v->setXYZ(pp.x(),pp.y(),pp.z());
v->setParameter(0,t);
// printf("%g %g %g\n",dist[i],dist2, MLineGEdgeDistance ( (*it)->lines[i] , *it ));
// get the index of the vertex
gradObj[index] += deriv * factor;
}
}
}
// printf("done\n");
// For a low order vertex classified on the GEdge, we recompute
// two distances for the two MLines connected to the vertex
for (unsigned int i=0;i<(*it)->lines.size()-1; i++){
MVertex *v = (*it)->lines[i]->getVertex(1);
int index = mesh.getFreeVertexStartIndex(v);
if (index >= 0){
double t;
v->getParameter(0,t);
SPoint3 pp (v->x(),v->y(),v->z());
GPoint gp = (*it)->point(t+eps);
v->setParameter(0,t+eps);
v->setXYZ(gp.x(),gp.y(),gp.z());
MLine *l1 = (*it)->lines[i];
MLine *l2 = (*it)->lines[i+1];
// printf("%d %d -- %d %d\n",l1->getVertex(0)->getNum(),l1->getVertex(1)->getNum(),l2->getVertex(0)->getNum(),l2->getVertex(1)->getNum());
double deriv =
(MLineGEdgeDistance ( l1 , *it ) - dist[i]) /eps +
(MLineGEdgeDistance ( l2 , *it ) - dist[i+1])/eps;
v->setXYZ(pp.x(),pp.y(),pp.z());
v->setParameter(0,t);
gradObj[index] += deriv * factor;
}
}
}
}
// printf("computing distance : 1D part %12.5E\n",distCAD);
// now the 3D part !
std::vector<std::vector<SVector3> > gsfT;
computeGradSFAtNodes ( (*gm->firstFace())->triangles[0],gsfT);
std::map<MVertex*,SVector3> normalsToCAD;
for(GModel::fiter it = gm->firstFace(); it != gm->lastFace(); ++it){
// do not do plane surfaces
if ((*it)->geomType() == GEntity::Plane)continue;
std::map<MTriangle*,double> dist;
std::vector<bool> doWeCompute((*it)->triangles.size());
for (unsigned int i=0;i<(*it)->triangles.size(); i++){
doWeCompute[i] = false;
for (unsigned int j=0;j<(*it)->triangles[i]->getNumVertices(); j++){
int index = mesh.getFreeVertexStartIndex((*it)->triangles[i]->getVertex(j));
if (index >=0){
doWeCompute[i] = true;
}
}
if (doWeCompute[i]){
for (unsigned int j=0;j<(*it)->triangles[i]->getNumVertices(); j++){
MVertex *v = (*it)->triangles[i]->getVertex(j);
if (normalsToCAD.find(v) == normalsToCAD.end()){
SPoint2 p_cad;
reparamMeshVertexOnFace(v, *it, p_cad);
SVector3 tg_cad = (*it)->normal(p_cad);
tg_cad.normalize();
normalsToCAD[v] = tg_cad;
}
}
}
}
for (unsigned int i=0;i<(*it)->triangles.size(); i++){
// compute the distance from the geometry to the mesh
if(doWeCompute[i]){
const double d = MFaceGFaceDistanceOld((*it)->triangles[i], *it, &gsfT, &normalsToCAD);
dist[(*it)->triangles[i]] = d;
maxDistCAD = std::max(maxDistCAD,d);
distCAD += d * factor;
}
}
// be clever again to compute the derivatives
const double eps = 1.e-6;
for (unsigned int i=0;i<(*it)->triangles.size(); i++){
if(doWeCompute[i]){
for (unsigned int j=0;j<(*it)->triangles[i]->getNumVertices(); j++){
// for (; itm !=v2t.end(); ++itm){
MVertex *v = (*it)->triangles[i]->getVertex(j);
if(v->onWhat()->dim() == 1){
int index = mesh.getFreeVertexStartIndex(v);
if (index >= 0){
MTriangle *t = (*it)->triangles[i];
GEdge *ge = v->onWhat()->cast2Edge();
double t_;
v->getParameter(0,t_);
SPoint3 pp (v->x(),v->y(),v->z());
GPoint gp = ge->point(t_+eps);
v->setParameter(0,t_+eps);
v->setXYZ(gp.x(),gp.y(),gp.z());
const double distT = dist[t];
double deriv = (MFaceGFaceDistanceOld(t, *it, &gsfT, &normalsToCAD) - distT) /eps;
v->setXYZ(pp.x(),pp.y(),pp.z());
v->setParameter(0,t_);
gradObj[index] += deriv * factor;
}
}
if(v->onWhat() == *it){
int index = mesh.getFreeVertexStartIndex(v);
if (index >= 0){
MTriangle *t = (*it)->triangles[i];
double uu,vv;
v->getParameter(0,uu);
v->getParameter(1,vv);
SPoint3 pp (v->x(),v->y(),v->z());
const double distT = dist[t];
GPoint gp = (*it)->point(uu+eps,vv);
v->setParameter(0,uu+eps);
v->setXYZ(gp.x(),gp.y(),gp.z());
double deriv = (MFaceGFaceDistanceOld(t, *it, &gsfT, &normalsToCAD) - distT) /eps;
v->setXYZ(pp.x(),pp.y(),pp.z());
v->setParameter(0,uu);
gradObj[index] += deriv * factor;
gp = (*it)->point(uu,vv+eps);
v->setParameter(1,vv+eps);
v->setXYZ(gp.x(),gp.y(),gp.z());
deriv = (MFaceGFaceDistanceOld(t, *it, &gsfT, &normalsToCAD) - distT) /eps;
v->setXYZ(pp.x(),pp.y(),pp.z());
v->setParameter(1,vv);
gradObj[index+1] += deriv * factor;
}
}
}
}
}
}
mesh.updateGEntityPositions(xyz,uvw);
Obj +=distCAD;
// printf("computing distance : 2D part %12.5E\n",distCAD);
// printf("%22.15E\n",distCAD);
return true;
}
bool PView::readMSH(const std::string &fileName, int fileIndex)
{
FILE *fp = Fopen(fileName.c_str(), "rb");
if(!fp){
Msg::Error("Unable to open file '%s'", fileName.c_str());
return false;
}
GModel *model = GModel::current();
if(model->empty()){
Msg::Error("Model is empty: please load a mesh before loading the dataset");
fclose(fp);
return false;
}
char str[256] = "XXX";
int index = -1;
bool binary = false, swap = false;
while(1) {
while(str[0] != '$'){
if(!fgets(str, sizeof(str), fp) || feof(fp))
break;
}
if(feof(fp))
break;
if(!strncmp(&str[1], "MeshFormat", 10)) {
double version;
if(!fgets(str, sizeof(str), fp)){ fclose(fp); return false; }
int format, size;
if(sscanf(str, "%lf %d %d", &version, &format, &size) != 3){
fclose(fp);
return false;
}
if(format){
binary = true;
Msg::Info("View data is in binary format");
int one;
if(fread(&one, sizeof(int), 1, fp) != 1){ fclose(fp); return 0; }
if(one != 1){
swap = true;
Msg::Info("Swapping bytes from binary file");
}
}
}
else if(!strncmp(&str[1], "InterpolationScheme", 19)){
std::string name;
if(!fgets(str, sizeof(str), fp)){ fclose(fp); return false; }
name = ExtractDoubleQuotedString(str, sizeof(str));
Msg::Info("Reading interpolation scheme '%s'", name.c_str());
PViewData::removeInterpolationScheme(name);
int numTypes;
if(fscanf(fp, "%d", &numTypes) != 1){ fclose(fp); return false; }
for(int i = 0; i < numTypes; i++){
int type, numMatrices;
if(fscanf(fp, "%d %d", &type, &numMatrices) != 2){ fclose(fp); return false; }
for(int j = 0; j < numMatrices; j++){
int m, n;
if(fscanf(fp, "%d %d", &m, &n) != 2){ fclose(fp); return false; }
fullMatrix<double> mat(m, n);
for(int k = 0; k < m; k++){
for(int l = 0; l < n; l++){
double d;
if(fscanf(fp, "%lf", &d) != 1){ fclose(fp); return false; }
mat.set(k, l, d);
}
}
PViewData::addMatrixToInterpolationScheme(name, type, mat);
}
}
}
else if(!strncmp(&str[1], "NodeData", 8) ||
!strncmp(&str[1], "ElementData", 11) ||
!strncmp(&str[1], "ElementNodeData", 15)) {
index++;
if(fileIndex < 0 || fileIndex == index){
PViewDataGModel::DataType type;
if(!strncmp(&str[1], "NodeData", 8))
type = PViewDataGModel::NodeData;
else if(!strncmp(&str[1], "ElementData", 11))
type = PViewDataGModel::ElementData;
else
type = PViewDataGModel::ElementNodeData;
int numTags;
// string tags
std::string viewName, interpolationScheme;
if(!fgets(str, sizeof(str), fp)){ fclose(fp); return false; }
if(sscanf(str, "%d", &numTags) != 1){ fclose(fp); return false; }
for(int i = 0; i < numTags; i++){
if(!fgets(str, sizeof(str), fp)){ fclose(fp); return false; }
if(i == 0)
viewName = ExtractDoubleQuotedString(str, sizeof(str));
else if(i == 1)
interpolationScheme = ExtractDoubleQuotedString(str, sizeof(str));
}
// double tags
double time = 0.;
if(!fgets(str, sizeof(str), fp)){ fclose(fp); return false; }
if(sscanf(str, "%d", &numTags) != 1){ fclose(fp); return false; }
for(int i = 0; i < numTags; i++){
if(!fgets(str, sizeof(str), fp)){ fclose(fp); return false; }
if(i == 0){
if(sscanf(str, "%lf", &time) != 1){ fclose(fp); return false; }
}
}
// integer tags
int timeStep = 0, numComp = 0, numEnt = 0, partition = 0;
if(!fgets(str, sizeof(str), fp)){ fclose(fp); return false; }
if(sscanf(str, "%d", &numTags) != 1){ fclose(fp); return false; }
for(int i = 0; i < numTags; i++){
if(!fgets(str, sizeof(str), fp)){ fclose(fp); return false; }
if(i == 0){
if(sscanf(str, "%d", &timeStep) != 1){ fclose(fp); return false; }
}
else if(i == 1){
if(sscanf(str, "%d", &numComp) != 1){ fclose(fp); return false; }
}
else if(i == 2){
if(sscanf(str, "%d", &numEnt) != 1){ fclose(fp); return false; }
}
else if(i == 3){
if(sscanf(str, "%d", &partition) != 1){ fclose(fp); return false; }
}
}
// either get existing viewData, or create new one
PView *p = getViewByName(viewName, timeStep, partition);
PViewDataGModel *d = 0;
if(p) d = dynamic_cast<PViewDataGModel*>(p->getData());
bool create = d ? false : true;
if(create) d = new PViewDataGModel(type);
if(!d->readMSH(viewName, fileName, fileIndex, fp, binary, swap, timeStep,
time, partition, numComp, numEnt, interpolationScheme)){
Msg::Error("Could not read data in msh file");
if(create) delete d;
fclose(fp);
return false;
}
else{
d->setName(viewName);
d->setFileName(fileName);
d->setFileIndex(index);
if(create) new PView(d);
}
}
}
do {
if(!fgets(str, sizeof(str), fp) || feof(fp))
break;
} while(str[0] != '$');
}
fclose(fp);
return true;
}