Files *File::match(FileName *n)
{
#if POSIX
return NULL;
#elif _WIN32
HANDLE h;
WIN32_FIND_DATAA fileinfo;
Files *a;
char *c;
char *name;
a = new Files();
c = n->toChars();
name = n->name();
h = FindFirstFileA(c,&fileinfo);
if (h != INVALID_HANDLE_VALUE)
{
do
{
// Glue path together with name
char *fn;
File *f;
fn = (char *)mem.malloc(name - c + strlen(fileinfo.cFileName) + 1);
memcpy(fn, c, name - c);
strcpy(fn + (name - c), fileinfo.cFileName);
f = new File(fn);
f->touchtime = mem.malloc(sizeof(WIN32_FIND_DATAA));
memcpy(f->touchtime, &fileinfo, sizeof(fileinfo));
a->push(f);
} while (FindNextFileA(h,&fileinfo) != FALSE);
FindClose(h);
}
return a;
#else
assert(0);
#endif
}
void DumpFiles( const Files& files, BOOL bOnlyFileName )
{
if(files.empty())
{
_tprintf(_T("Empty Files\r\n"));
}
else
{
int i=0;
for(Files::const_iterator it=files.begin(); it!=files.end(); ++it)
{
++i;
LPCTSTR szFile = *it;
if(bOnlyFileName)
{
LPCTSTR szName = _tcsrchr(szFile, _T('\\'));
if(szName)
szFile = ++szName;
}
_tprintf(_T("%d/%d %s\r\n"), i, files.size(), szFile);
}
}
}
// Get a list of files in the given directory
Files GetFilesInDirectory(const std::string &path, const std::vector<std::string> &extensions)
{
DIR *dir;
dirent *entry;
Files files;
std::string finalPath = path;
if (finalPath[path.size() - 1] != '/')
finalPath += '/';
if ((dir = opendir(path.c_str())))
{
while ((entry = readdir(dir)))
{
std::string filename = std::string(entry->d_name);
if (filename == "." || filename == "..")
continue;
std::string fullPath = finalPath + filename;
// Although the following function is for checking if a directory
// exists, it can also be used to check if a path is a directory,
// saving a little bit of extra code
if (DirExists(fullPath))
continue;
// We want to skip any files not matching the extensions we gave, if any
std::string thisExtension = GetExtension(filename);
auto extensionMatch = std::find_if(extensions.begin(), extensions.end(), [&](const std::string &extension)
{
return extension == thisExtension;
});
if (extensions.empty() || extensionMatch != extensions.end())
files.push_back(fullPath);
}
closedir(dir);
}
return files;
}
Files ParallelEnergyPlusSplitJob::outputFilesImpl() const
{
// Save off the set of requiredfiles, see below
std::vector<std::pair<QUrl, openstudio::path> > requiredFiles = inputFile().requiredFiles;
std::vector<openstudio::path> files = generateFileNames(outdir(), m_numSplits);
Files retval;
for (std::vector<openstudio::path>::const_iterator itr = files.begin();
itr != files.end();
++itr)
{
if (boost::filesystem::exists(*itr))
{
FileInfo fi = RunManager_Util::dirFile(*itr);
// we want to carry along the set of required files used in the original IDF to the children
// (ie, the epw file)
fi.requiredFiles = requiredFiles;
retval.append(fi);
}
}
return retval;
}
/**
* @brief Get the statistics and print them if necessary
*/
static Files &files() {
static std::ofstream log(logFileName);
static Files sinceLast;
static Files total;
// print the final statistics on exit
static DestructionExecutor finalExecutor([&]() {
log << "Statistics for thread " << getCurrentThreadId() << "\n";
printStatistics(log, sinceLast);
log << "Total statistics for thread " << getCurrentThreadId() << ":\n";
total += sinceLast;
printStatistics(log, total);
});
static DeltaTimeExecutor executor([&]() {
log << "Statistics for thread "
<< getCurrentThreadId() << "\n";
printStatistics(log, sinceLast);
total += sinceLast;
sinceLast.resetStatistics();
},
std::chrono::microseconds(1000 * 1000 *
10));
executor.callIfTimeOver();
return sinceLast;
}
EnergyPlusPreProcessJob::EnergyPlusPreProcessJob(const UUID &t_uuid,
const Tools &tools,
const JobParams ¶ms,
const Files &files,
const JobState &t_restoreData)
: Job_Impl(t_uuid, JobType::EnergyPlusPreProcess, tools, params, files, t_restoreData)
{
try {
m_idf = files.getLastByExtension("idf");
resetFiles(m_files, m_idf);
} catch (const std::runtime_error &) {
}
m_description = buildDescription("idf");
}
TEST_F(RunManagerTestFixture, Workflow_FromWorkItems)
{
ToolInfo ti("tool", openstudio::toPath("somepath"));
Tools tis;
tis.append(ti);
JobParam param("param1");
JobParams params;
params.append(param);
FileInfo fi(openstudio::toPath("somefile.txt"), "txt");
Files fis;
fis.append(fi);
std::vector<WorkItem> wi;
wi.push_back(WorkItem(JobType::Null, tis, params, fis));
wi.push_back(WorkItem(JobType::EnergyPlus));
Workflow wf(wi);
EXPECT_EQ(tis, wf.tools());
EXPECT_EQ(params, wf.params());
EXPECT_EQ(fis, wf.files());
}
ModelToRadPreProcessJob::ModelToRadPreProcessJob(const UUID &t_uuid,
const Tools &tools,
const JobParams ¶ms,
const Files &files,
const JobState &t_restoreData)
: Job_Impl(t_uuid, JobType::ModelToRadPreProcess, tools, params, files, t_restoreData)
{
try {
m_osm = files.getLastByExtension("osm");
resetFiles(m_files, m_osm);
} catch (const std::exception &) {
}
m_description = buildDescription("osm");
}
ModelToRadJob::ModelToRadJob(const UUID &t_uuid,
const Tools &tools,
const JobParams ¶ms,
const Files &files,
const JobState &t_restoreData)
: Job_Impl(t_uuid, JobType::ModelToRad, tools, params, files, t_restoreData)
{
try {
m_model = files.getLastByExtension("osm");
resetFiles(m_files, m_model);
} catch (const std::runtime_error &) {
}
m_description = buildDescription("osm");
}
void print(bool exportOnly=false) {
ofxSimplifyPath(path,simplifyIterations,simplifyMinNumPoints,simplifyMinDistance);
string hourMinutes = ofxFormatDateTime(ofxGetDateTime(),"%H.%M");
string outputFilename = gcodeFolder+files.getFilename()+"_"+hourMinutes+".gcode";
printer.print(outputFilename, resourceFolder+"gcode/start.gcode",resourceFolder+"gcode/end.gcode");
if (exportOnly) return;
// outputFilename = "/Users/rick/Documents/Doodle3D/gcode/hilde-mannetje.svg_19.47.gcode";
cout << "print from file: " << outputFilename << endl;
ultimaker.sendCommandsFromFile(outputFilename);
}
OpenStudioPostProcessJob::OpenStudioPostProcessJob(const UUID &t_uuid,
const Tools &tools,
const JobParams ¶ms,
const Files &files,
const JobState &t_restoreData)
: Job_Impl(t_uuid, JobType::OpenStudioPostProcess, tools, params, files, t_restoreData)
{
try {
m_sql = files.getLastByFilename("eplusout.sql");
resetFiles(m_files, m_sql);
} catch (const std::runtime_error &) {
}
// what should this be?
m_description = buildDescription("sql");
}
void keyPressed(int key) {
switch (key) {
case '/': case '\\': case '$': case '#': case '|': case '%': case '@': case '^': case '&': case '_': side.setShape(key); break;
case '3': side.is3D=!side.is3D; break;
case '<': twists-=.5; break;
case '>': twists+=.5; break;
case '\'': twists=0; break;
case '?': showHelp(); break;
case 'a': side.toggle(); break;
case 'b': useSubpathColors=!useSubpathColors; break;
case 'C': canvas.createCircle(); break;
case 'c': canvas.clear(); files.unloadFile(); break;
case 'd': debug=!debug; refreshDebugInfo(); break;
case 'e': print(true); break;
case 'f': ofToggleFullscreen(); break;
case 'k': path.setFilled(!path.isFilled()); path.flagShapeChanged(); break;
case 'h': objectHeight+=5; if (objectHeight>maxObjectHeight) objectHeight=maxObjectHeight; break;
case 'H': objectHeight-=5; if (objectHeight<3) objectHeight=3; break;
case 'G': ultimaker.sendCommand("G28 X0 Y0 Z0\nM84",2); break;
case 'A': ultimaker.sendCommand("M84"); break;
case 'T': ultimaker.sendCommand("M109 S230"); break;
case 'l': files.loadNext(); break;
case 'L': files.loadPrevious(); break;
case 'o': files.load(); break;
case 'p': case 'm': case OF_KEY_RETURN: print(); break;
case 'q': stop(); break;
// case 'r': ultimaker.setRelative(); break;
case 'S': files.save(); break;
case 's': files.saveAs(); break;
case '`': showSubPathLines=!showSubPathLines;
case 't': ultimaker.sendCommand("M105",1); break;
case 'u': case 'z': canvas.undo(); break;
case '~': files.deleteCurrentFile(); break;
case ' ': files.listDir(); break;
case 'x': files.saveSvg(resourceFolder+"template.svg",documentFolder+"output.svg"); break;
case 27: if (ultimaker.isThreadRunning()) ultimaker.stopThread(); break;
case 'n': cloneApp(); break; //run new instance of Doodle3D
case 'i': cout << getNumInstances() << endl; break;
}
}
ParallelEnergyPlusSplitJob::ParallelEnergyPlusSplitJob(const UUID &t_uuid,
const Tools &tools,
const JobParams ¶ms,
const Files &files,
const JobState &t_restoreData)
: Job_Impl(t_uuid, JobType::ParallelEnergyPlusSplit, tools, params, files, t_restoreData),
m_numSplits(boost::lexical_cast<int>(params.get("numsplits").children.at(0).value)),
m_offset(boost::lexical_cast<int>(params.get("offset").children.at(0).value))
{
try {
m_input = files.getLastByExtension("idf");
resetFiles(m_files, m_input);
} catch (const std::runtime_error &) {
}
m_description = buildDescription("idf");
}
TEST_F(FilesTest, AttachTest)
{
Files files;
ASSERT_SOME(os::write("file", "body"));
ASSERT_SOME(os::mkdir("dir"));
AWAIT_EXPECT_READY(files.attach("file", "myname")); // Valid file.
AWAIT_EXPECT_READY(files.attach("dir", "mydir")); // Valid dir.
AWAIT_EXPECT_READY(files.attach("file", "myname")); // Re-attach.
AWAIT_EXPECT_FAILED(files.attach("missing", "somename")); // Missing file.
ASSERT_SOME(os::write("file2", "body"));
AWAIT_EXPECT_READY(files.attach("file2", "myname")); // Overwrite.
AWAIT_EXPECT_FAILED(files.attach("$@", "foo")); // Bad path.
}
void ExpandObjectsJob::getFiles(const Files &t_files) const
{
if (!m_idf)
{
try {
m_idf = t_files.getLastByExtension("idf");
if (!m_idf->hasRequiredFile(toPath("Energy+.idd")))
{
m_idf->addRequiredFile( toPath("Energy+.idd"), toPath("Energy+.idd"));
}
} catch (const std::runtime_error &) {
// no idf set
}
}
}
void HiRes1Engine::initGameState() {
_state.vars.resize(IDI_HR1_NUM_VARS);
StreamPtr stream(_files->createReadStream(IDS_HR1_EXE_1));
// Load room data from executable
_roomDesc.clear();
stream->seek(IDI_HR1_OFS_ROOMS);
for (uint i = 0; i < IDI_HR1_NUM_ROOMS; ++i) {
Room room;
stream->readByte();
_roomDesc.push_back(stream->readByte());
for (uint j = 0; j < 6; ++j)
room.connections[j] = stream->readByte();
room.picture = stream->readByte();
room.curPicture = stream->readByte();
_state.rooms.push_back(room);
}
// Load item data from executable
stream->seek(IDI_HR1_OFS_ITEMS);
byte id;
while ((id = stream->readByte()) != 0xff) {
Item item = Item();
item.id = id;
item.noun = stream->readByte();
item.room = stream->readByte();
item.picture = stream->readByte();
item.isLineArt = stream->readByte();
item.position.x = stream->readByte();
item.position.y = stream->readByte();
item.state = stream->readByte();
item.description = stream->readByte();
stream->readByte();
byte size = stream->readByte();
for (uint i = 0; i < size; ++i)
item.roomPictures.push_back(stream->readByte());
_state.items.push_back(item);
}
}
int main(int argc,char **args) {
bool Vanka=0, Gmres=0, Asm=0;
if(argc >= 2) {
if( !strcmp("vanka",args[1])) Vanka=1;
else if( !strcmp("gmres",args[1])) Gmres=1;
else if( !strcmp("asm",args[1])) Asm=1;
if(Vanka+Gmres+Asm==0) {
cout << "wrong input arguments!" << endl;
exit(0);
}
}
else {
cout << "No input argument set default smoother = Gmres" << endl;
Gmres=1;
}
/// Init Petsc-MPI communicator
FemusInit mpinit(argc,args,MPI_COMM_WORLD);
Files files;
files.CheckIODirectories();
files.RedirectCout();
/// INIT MESH =================================
unsigned short nm,nr;
nm=2;
std::cout<<"MULTIGRID levels: "<< nm << endl;
nr=0;
std::cout<<"MAX_REFINEMENT levels: " << nr << endl<< endl;
int tmp=nm; nm+=nr; nr=tmp;
char *infile = new char [50];
sprintf(infile,"./input/nsbenc.neu");
//Adimensional quantity (Lref,Uref)
double Lref = 1.;
double Uref = 1.;
//Steadystate NonLinearMultiLevelProblem
//MultiLevelMesh ml_msh(nm,nr,infile,"seventh",Lref,SetRefinementFlag);
MultiLevelMesh ml_msh;
ml_msh.ReadCoarseMesh(infile,"seventh",Lref);
ml_msh.RefineMesh(nm,nr,NULL);
// ml_msh.EraseCoarseLevels(2);
MultiLevelSolution ml_sol(&ml_msh);
// generate solution vector
ml_sol.AddSolution("T",LAGRANGE,SECOND);
ml_sol.AddSolution("U",LAGRANGE,SECOND);
ml_sol.AddSolution("V",LAGRANGE,SECOND);
// the pressure variable should be the last for the Schur decomposition
ml_sol.AddSolution("P",DISCONTINOUS_POLYNOMIAL,FIRST);
ml_sol.AssociatePropertyToSolution("P","Pressure");
//Initialize (update Init(...) function)
ml_sol.Initialize("U",InitVariableU);
ml_sol.Initialize("V");
ml_sol.Initialize("P");
ml_sol.Initialize("T");
//Set Boundary (update Dirichlet(...) function)
ml_sol.AttachSetBoundaryConditionFunction(SetBoundaryCondition);
ml_sol.GenerateBdc("U");
ml_sol.GenerateBdc("V");
ml_sol.GenerateBdc("P");
ml_sol.GenerateBdc("T");
MultiLevelProblem ml_prob(&ml_sol);
// add fluid material
Parameter parameter(Lref,Uref);
// Generate fluid Object (Adimensional quantities,viscosity,density,fluid-model)
Fluid fluid(parameter,0.001,1,"Newtonian",0.001,1.);
cout << "Fluid properties: " << endl;
cout << fluid << endl;
ml_prob.parameters.set<Fluid>("Fluid") = fluid;
//BEGIN Navier-Stokes Multilevel Problem
std::cout << std::endl;
std::cout << " *********** Navier-Stokes ************ " << std::endl;
NonLinearImplicitSystem & system1 = ml_prob.add_system<NonLinearImplicitSystem> ("Navier-Stokes");
system1.AddSolutionToSystemPDE("U");
system1.AddSolutionToSystemPDE("V");
system1.AddSolutionToSystemPDE("P");
// Set MG Options
system1.SetAssembleFunction(AssembleMatrixResNS);
system1.SetMaxNumberOfNonLinearIterations(3);
system1.SetMaxNumberOfLinearIterations(2);
system1.SetLinearConvergenceTolerance(1.e-10);
system1.SetNonLinearConvergenceTolerance(1.e-04);
system1.SetMgType(F_CYCLE);
system1.SetNumberPreSmoothingStep(1);
system1.SetNumberPostSmoothingStep(1);
//Set Smoother Options
if(Gmres) system1.SetMgSmoother(GMRES_SMOOTHER);
else if(Asm) system1.SetMgSmoother(ASM_SMOOTHER);
else if(Vanka) system1.SetMgSmoother(VANKA_SMOOTHER);
system1.init();
std::string AMR = "yes";
unsigned int maxAMRlevels = 6;
std::string AMRnorm="l2";
double AMRthreshold =0.001;
system1.SetAMRSetOptions(AMR,maxAMRlevels,AMRnorm,AMRthreshold);
//common smoother options
system1.SetSolverFineGrids(GMRES);
system1.SetPreconditionerFineGrids(ILU_PRECOND);
system1.SetTolerances(1.e-12,1.e-20,1.e+50,4);
//for Vanka and ASM smoothers
system1.ClearVariablesToBeSolved();
system1.AddVariableToBeSolved("All");
//system1.AddVariableToBeSolved("U");
//system1.AddVariableToBeSolved("V");
//system1.AddVariableToBeSolved("P");
system1.SetNumberOfSchurVariables(1);
//system1.SetElementBlockNumber(4);
system1.SetElementBlockNumber("All",1);
//for Gmres smoother
system1.SetDirichletBCsHandling(PENALTY);
// Solve Navier-Stokes system
ml_prob.get_system("Navier-Stokes").solve();
//END Navier-Stokes Multilevel Problem
// //BEGIN Temperature MultiLevel Problem
// std::cout << std::endl;
// std::cout << " *********** Temperature ************* " << std::endl;
//
// LinearImplicitSystem & system2 = ml_prob.add_system<LinearImplicitSystem> ("Temperature");
// system2.AddSolutionToSystemPDE("T");
//
//
// // Set MG Options
// system2.SetAssembleFunction(AssembleMatrixResT);
// system2.SetMaxNumberOfLinearIterations(6);
// system2.SetLinearConvergenceTolerance(1.e-9);
// system2.SetMgType(V_CYCLE);
// system2.SetNumberPreSmoothingStep(1);
// system2.SetNumberPostSmoothingStep(1);
//
// //Set Smoother Options
// if(Gmres) system2.SetMgSmoother(GMRES_SMOOTHER);
// else if(Asm) system2.SetMgSmoother(ASM_SMOOTHER);
// else if(Vanka) system2.SetMgSmoother(VANKA_SMOOTHER);
//
// system2.init();
// //common smoother option
// system2.SetSolverFineGrids(GMRES);
// system2.SetTolerances(1.e-12,1.e-20,1.e+50,4);
// system2.SetPreconditionerFineGrids(ILU_PRECOND);
// //for Vanka and ASM smoothers
// system2.ClearVariablesToBeSolved();
// system2.AddVariableToBeSolved("All");
// system2.SetNumberOfSchurVariables(0);
// system2.SetElementBlockNumber(4);
// //for Gmres smoother
// system2.SetDirichletBCsHandling(PENALTY);
//
// // Solve Temperature system
// ml_prob.get_system("Temperature").solve();
// //END Temperature Multilevel Problem
//
// double l2normvarU = ml_sol.GetSolutionLevel(3)->GetSolutionName("U")->l2_norm();
//
// double l2normvarUStored = 16.313927822836003;
//
// std::cout << "Solution U l2norm: " << l2normvarU << std::endl;
//
// if( fabs((l2normvarU - l2normvarUStored )/l2normvarUStored) > 1.e-6)
// {
// exit(1);
// }
//
// double l2normvarV = ml_sol.GetSolutionLevel(3)->GetSolutionName("V")->l2_norm();
//
// double l2normvarVStored = 6.0644257018060355;
//
// std::cout << "Solution V l2norm: " << l2normvarV << std::endl;
//
// if( fabs((l2normvarV - l2normvarVStored )/l2normvarVStored )> 1.e-6)
// {
// exit(1);
// }
//
// double l2normvarP = ml_sol.GetSolutionLevel(3)->GetSolutionName("P")->l2_norm();
//
// double l2normvarPStored = 1.8202105018866834;
//
// std::cout << "Solution P l2norm: " << l2normvarP << std::endl;
//
// if( fabs((l2normvarP - l2normvarPStored )/l2normvarPStored) > 1.e-6)
// {
// exit(1);
// }
//
// double l2normvarT = ml_sol.GetSolutionLevel(3)->GetSolutionName("T")->l2_norm();
//
// double l2normvarTStored = 219.68194612060503;
//
// std::cout << "Solution T l2norm: " << l2normvarT <<std::endl;
//
// if( fabs((l2normvarT - l2normvarTStored )/l2normvarTStored) > 1.e-6)
// {
// exit(1);
// }
std::vector<std::string> print_vars;
print_vars.push_back("U");
print_vars.push_back("V");
print_vars.push_back("P");
print_vars.push_back("T");
GMVWriter gmvio(&ml_sol);
gmvio.write(files.GetOutputPath(),"biquadratic",print_vars);
//Destroy all the new systems
ml_prob.clear();
delete [] infile;
return 0;
}
int main(int argc,char **args) {
/// Init Petsc-MPI communicator
FemusInit mpinit(argc,args,MPI_COMM_WORLD);
Files files;
files.CheckIODirectories();
//files.RedirectCout();
bool Vanka=0, Gmres=0, Asm=0;
if(argc >= 2) {
if( !strcmp("vanka",args[1])) Vanka=1;
else if( !strcmp("gmres",args[1])) Gmres=1;
else if( !strcmp("asm",args[1])) Asm=1;
if(Vanka+Gmres+Asm==0) {
cout << "wrong input arguments!" << endl;
exit(0);
}
}
else {
cout << "No input argument set default smoother = Gmres" << endl;
Gmres=1;
}
/// INIT MESH =================================
unsigned short nm,nr;
nm=4;
std::cout<<"MULTIGRID levels: "<< nm << endl;
nr=0;
std::cout<<"MAX_REFINEMENT levels: " << nr << endl<< endl;
int tmp=nm; nm+=nr; nr=tmp;
char *infile = new char [50];
sprintf(infile,"./input/box10x10.neu");
//Adimensional quantity (Lref,Uref)
double Lref = 1.;
double Uref = 1.;
//Steadystate NonLinearMultiLevelProblem
//MultiLevelMesh ml_msh(nm,nr,infile,"seventh",Lref,SetRefinementFlag);
MultiLevelMesh ml_msh;
ml_msh.ReadCoarseMesh(infile,"seventh",Lref);
ml_msh.RefineMesh(nm,nr,NULL);
ml_msh.EraseCoarseLevels(nm-1);
MultiLevelSolution ml_sol(&ml_msh);
// generate solution vector
FEOrder orderPre = FIRST;
FEOrder orderVel = FIRST;
FEOrder orderTemp = FIRST;
ml_sol.AddSolution("U", LAGRANGE, orderVel);
ml_sol.AddSolution("V", LAGRANGE, orderVel);
ml_sol.AddSolution("lmbd", DISCONTINOUS_POLYNOMIAL, ZERO, 0, false);
// the pressure variable should be the last for the Schur decomposition
// ml_sol.AddSolution("P",DISCONTINOUS_POLYNOMIAL,FIRST);
ml_sol.AddSolution("P",LAGRANGE, orderPre);
ml_sol.AssociatePropertyToSolution("P","Pressure");
ml_sol.AddSolution("T",LAGRANGE,orderTemp);
//Initialize (update Init(...) function)
ml_sol.Initialize("U");
ml_sol.Initialize("V");
ml_sol.Initialize("P");
ml_sol.Initialize("T");
ml_sol.Initialize("lmbd");
//Set Boundary (update Dirichlet(...) function)
ml_sol.AttachSetBoundaryConditionFunction(SetBoundaryConditionCavityFlow);
ml_sol.GenerateBdc("U");
ml_sol.GenerateBdc("V");
ml_sol.GenerateBdc("P");
ml_sol.GenerateBdc("T");
SetLambda(ml_sol, 0, orderVel, ELASTICITY);
//SetLambda(ml_sol, 0, 2,"diffusion");
MultiLevelProblem ml_prob(&ml_sol);
// add fluid material
Parameter parameter(Lref,Uref);
// Generate fluid Object (Adimensional quantities,viscosity,density,fluid-model)
Fluid fluid(parameter,0.001,1,"Newtonian",0.001,1.);
cout << "Fluid properties: " << endl;
cout << fluid << endl;
ml_prob.parameters.set<Fluid>("Fluid") = fluid;
//BEGIN Navier-Stokes Multilevel Problem
std::cout << std::endl;
std::cout << " *********** Navier-Stokes ************ " << std::endl;
NonLinearImplicitSystem & system1 = ml_prob.add_system<NonLinearImplicitSystem> ("Navier-Stokes");
system1.AddSolutionToSystemPDE("U");
system1.AddSolutionToSystemPDE("V");
system1.AddSolutionToSystemPDE("P");
// Set MG Options
system1.SetAssembleFunction(AssembleMatrixResNS);
system1.SetMaxNumberOfNonLinearIterations(90);
system1.SetMaxNumberOfLinearIterations(2);
system1.SetLinearConvergenceTolerance(1.e-10);
system1.SetNonLinearConvergenceTolerance(1.e-10);
system1.SetMgType(F_CYCLE);
system1.SetNumberPreSmoothingStep(1);
system1.SetNumberPostSmoothingStep(1);
//Set Smoother Options
if(Gmres) system1.SetMgSmoother(GMRES_SMOOTHER);
else if(Asm) system1.SetMgSmoother(ASM_SMOOTHER);
else if(Vanka) system1.SetMgSmoother(VANKA_SMOOTHER);
system1.init();
//common smoother options
// system1.AddStabilization(true);
system1.SetSolverFineGrids(GMRES);
system1.SetPreconditionerFineGrids(ILU_PRECOND);
system1.SetTolerances(1.e-12,1.e-20,1.e+50,4);
system1.ClearVariablesToBeSolved();
//system1.AddVariableToBeSolved("All");
system1.AddVariableToBeSolved("U");
system1.AddVariableToBeSolved("V");
system1.AddVariableToBeSolved("P");
//for Vanka and ASM smoothers
system1.SetNumberOfSchurVariables(0);
system1.SetElementBlockNumber(4);
//system1.SetElementBlockNumber("All",1);
//for Gmres smoother
system1.SetDirichletBCsHandling(PENALTY);
//system1.SetDirichletBCsHandling(ELIMINATION);
// Solve Navier-Stokes system
ml_prob.get_system("Navier-Stokes").solve();
//END Navier-Stokes Multilevel Problem
//BEGIN Temperature MultiLevel Problem
std::cout << std::endl;
std::cout << " *********** Temperature ************* " << std::endl;
LinearImplicitSystem & system2 = ml_prob.add_system<LinearImplicitSystem> ("Temperature");
system2.AddSolutionToSystemPDE("T");
// Set MG Options
system2.SetAssembleFunction(AssembleMatrixResT);
system2.SetMaxNumberOfLinearIterations(6);
system2.SetLinearConvergenceTolerance(1.e-9);
system2.SetMgType(V_CYCLE);
system2.SetNumberPreSmoothingStep(1);
system2.SetNumberPostSmoothingStep(1);
//Set Smoother Options
if(Gmres) system2.SetMgSmoother(GMRES_SMOOTHER);
else if(Asm) system2.SetMgSmoother(ASM_SMOOTHER);
else if(Vanka) system2.SetMgSmoother(VANKA_SMOOTHER);
system2.init();
//common smoother option
system2.SetSolverFineGrids(GMRES);
system2.SetTolerances(1.e-12,1.e-20,1.e+50,4);
system2.SetPreconditionerFineGrids(ILU_PRECOND);
//for Vanka and ASM smoothers
system2.ClearVariablesToBeSolved();
system2.AddVariableToBeSolved("All");
system2.SetNumberOfSchurVariables(0);
system2.SetElementBlockNumber(4);
//for Gmres smoother
system2.SetDirichletBCsHandling(PENALTY);
//system2.SetDirichletBCsHandling(ELIMINATION);
// Solve Temperature system
ml_prob.get_system("Temperature").solve();
//END Temperature Multilevel Problem
/// Print all solutions
std::vector<std::string> print_vars;
print_vars.push_back("U");
print_vars.push_back("V");
print_vars.push_back("P");
print_vars.push_back("T");
VTKWriter vtkio(&ml_sol);
vtkio.write(files.GetOutputPath(),"biquadratic",print_vars);
//vtkio.write(DEFAULT_OUTPUTDIR,"biquadratic",print_vars);
GMVWriter gmvio(&ml_sol);
gmvio.write(DEFAULT_OUTPUTDIR,"biquadratic",print_vars);
// gmvio.write(files.GetOutputPath(),"biquadratic",print_vars);
// XDMFWriter xdmfio(ml_sol);
// xdmfio.write(files.GetOutputPath(),"biquadratic",print_vars);
//Destroy all the new systems
ml_prob.clear();
delete [] infile;
return 0;
}
int main(int argc,char **args) {
/// Init Petsc-MPI communicator
FemusInit mpinit(argc,args,MPI_COMM_WORLD);
Files files;
files.CheckIODirectories();
files.RedirectCout();
/// INIT MESH =================================
unsigned short nm,nr;
nm=4;
std::cout<<"MULTIGRID levels: "<< nm << endl;
nr=0;
std::cout<<"MAX_REFINEMENT levels: " << nr << endl<< endl;
int tmp=nm; nm+=nr; nr=tmp;
char *infile = new char [50];
sprintf(infile,"./input/nsbenchreg.neu");
//Adimensional quantity (Lref,Uref)
double Lref = 1.;
double Uref = 1.;
MultiLevelMesh ml_msh(nm,nr,infile,"seventh",Lref,NULL);
MultiLevelSolution ml_sol(&ml_msh);
// generate solution vector
ml_sol.AddSolution("U",LAGRANGE,SECOND,2);
ml_sol.AddSolution("V",LAGRANGE,SECOND,2);
// the pressure variable should be the last for the Schur decomposition
ml_sol.AddSolution("P",DISCONTINOUS_POLYNOMIAL,FIRST,1);
ml_sol.AssociatePropertyToSolution("P","Pressure");
//Initialize (update Init(...) function)
ml_sol.Initialize("All");
//Set Boundary (update Dirichlet(...) function)
ml_sol.AttachSetBoundaryConditionFunction(SetBoundaryCondition);
ml_sol.GenerateBdc("U","Time_dependent");
ml_sol.GenerateBdc("V");
ml_sol.GenerateBdc("P");
MultiLevelProblem ml_prob(&ml_sol);
Parameter parameter(Lref,Uref);
// Generate fluid Object (Adimensional quantities,viscosity,density,fluid-model)
Fluid fluid(parameter,0.001,1.,"Newtonian");
cout << "Fluid properties: " << endl;
cout << fluid << endl;
// add fluid material
ml_prob.parameters.set<Fluid>("Fluid") = fluid;
//create systems
// add the system Navier-Stokes to the MultiLevel problem
TransientNonlinearImplicitSystem & system = ml_prob.add_system<TransientNonlinearImplicitSystem> ("Navier-Stokes");
system.AddSolutionToSystemPDE("U");
system.AddSolutionToSystemPDE("V");
system.AddSolutionToSystemPDE("P");
// init all the systems
system.init();
// System Navier-Stokes
system.SetAssembleFunction(AssembleMatrixResNS);
system.SetMaxNumberOfLinearIterations(1);
system.SetLinearConvergenceTolerance(1.e-8);
system.SetMgType(V_CYCLE);
system.SetMaxNumberOfNonLinearIterations(15);
// time loop parameter
system.SetIntervalTime(0.1);
const unsigned int n_timesteps = 20;
const unsigned int write_interval = 1;
for (unsigned time_step = 0; time_step < n_timesteps; time_step++) {
// Solving Navier-Stokes system
std::cout << std::endl;
std::cout << " *********** Navier-Stokes ************ " << std::endl;
ml_prob.get_system("Navier-Stokes").solve();
//update Solution
ml_prob.get_system<TransientNonlinearImplicitSystem>("Navier-Stokes").UpdateSolution();
// print solution
if ( !(time_step%write_interval) ) {
//print solution
std::vector<std::string> print_vars;
print_vars.push_back("U");
print_vars.push_back("V");
print_vars.push_back("P");
// ml_prob.printsol_vtu_inline("biquadratic",print_vars,time_step);
VTKWriter vtkio(&ml_sol);
vtkio.write(files.GetOutputPath(),"biquadratic",print_vars,time_step);
}
} //end loop timestep
// Destroy all the new systems
ml_prob.clear();
delete[] infile;
return 0;
}
void HiRes1Engine::init() {
if (Common::File::exists("MYSTHOUS.DSK")) {
_files = new Files_DOS33();
if (!static_cast<Files_DOS33 *>(_files)->open("MYSTHOUS.DSK"))
error("Failed to open MYSTHOUS.DSK");
} else
_files = new Files_Plain();
_graphics = new Graphics_v1(*_display);
StreamPtr stream(_files->createReadStream(IDS_HR1_EXE_1));
// Some messages have overrides inside the executable
_gameStrings.cantGoThere = readStringAt(*stream, IDI_HR1_OFS_STR_CANT_GO_THERE);
_gameStrings.dontHaveIt = readStringAt(*stream, IDI_HR1_OFS_STR_DONT_HAVE_IT);
_gameStrings.dontUnderstand = readStringAt(*stream, IDI_HR1_OFS_STR_DONT_UNDERSTAND);
_gameStrings.gettingDark = readStringAt(*stream, IDI_HR1_OFS_STR_GETTING_DARK);
// Load other strings from executable
_strings.enterCommand = readStringAt(*stream, IDI_HR1_OFS_STR_ENTER_COMMAND);
_strings.verbError = readStringAt(*stream, IDI_HR1_OFS_STR_VERB_ERROR);
_strings.nounError = readStringAt(*stream, IDI_HR1_OFS_STR_NOUN_ERROR);
_strings.playAgain = readStringAt(*stream, IDI_HR1_OFS_STR_PLAY_AGAIN);
_strings.pressReturn = readStringAt(*stream, IDI_HR1_OFS_STR_PRESS_RETURN);
_strings.lineFeeds = readStringAt(*stream, IDI_HR1_OFS_STR_LINE_FEEDS);
// Set message IDs
_messageIds.cantGoThere = IDI_HR1_MSG_CANT_GO_THERE;
_messageIds.dontUnderstand = IDI_HR1_MSG_DONT_UNDERSTAND;
_messageIds.itemDoesntMove = IDI_HR1_MSG_ITEM_DOESNT_MOVE;
_messageIds.itemNotHere = IDI_HR1_MSG_ITEM_NOT_HERE;
_messageIds.thanksForPlaying = IDI_HR1_MSG_THANKS_FOR_PLAYING;
// Load message offsets
stream->seek(IDI_HR1_OFS_MSGS);
for (uint i = 0; i < IDI_HR1_NUM_MESSAGES; ++i)
_messages.push_back(_files->getDataBlock(IDS_HR1_MESSAGES, stream->readUint16LE()));
// Load picture data from executable
stream->seek(IDI_HR1_OFS_PICS);
for (uint i = 1; i <= IDI_HR1_NUM_PICS; ++i) {
byte block = stream->readByte();
Common::String name = Common::String::format("BLOCK%i", block);
uint16 offset = stream->readUint16LE();
_pictures[i] = _files->getDataBlock(name, offset);
}
// Load commands from executable
stream->seek(IDI_HR1_OFS_CMDS_1);
readCommands(*stream, _roomCommands);
stream->seek(IDI_HR1_OFS_CMDS_0);
readCommands(*stream, _globalCommands);
// Load dropped item offsets
stream->seek(IDI_HR1_OFS_ITEM_OFFSETS);
loadDroppedItemOffsets(*stream, IDI_HR1_NUM_ITEM_OFFSETS);
// Load right-angle line art
stream->seek(IDI_HR1_OFS_CORNERS);
uint16 cornersCount = stream->readUint16LE();
for (uint i = 0; i < cornersCount; ++i)
_corners.push_back(_files->getDataBlock(IDS_HR1_EXE_1, IDI_HR1_OFS_CORNERS + stream->readUint16LE()));
if (stream->eos() || stream->err())
error("Failed to read game data from '" IDS_HR1_EXE_1 "'");
stream->seek(IDI_HR1_OFS_VERBS);
loadWords(*stream, _verbs, _priVerbs);
stream->seek(IDI_HR1_OFS_NOUNS);
loadWords(*stream, _nouns, _priNouns);
}
void dragEvent(ofDragInfo dragInfo) {
if (dragInfo.files.size()==1) {
files.loadFromImage(dragInfo.files[0]);
}
}
void ModelToRadJob::startImpl(const boost::shared_ptr<ProcessCreator> &)
{
openstudio::path outpath = outdir();
QWriteLocker l(&m_mutex);
JobErrors errors;
errors.result = ruleset::OSResultValue::Success;
try {
if (!m_model)
{
m_model = modelFile();
}
if (!m_sql)
{
m_sql = sqlFile();
}
resetFiles(m_files, m_model);
} catch (const std::runtime_error &e) {
errors.result = ruleset::OSResultValue::Fail;
errors.addError(ErrorType::Error, e.what());
}
if (!m_sql || !m_model)
{
errors.result = ruleset::OSResultValue::Fail;
errors.addError(ErrorType::Error, "Unable to find required model or sql file");
}
LOG(Info, "ModelToRad starting, filename: " << toString(m_model->fullPath));
LOG(Info, "ModelToRad starting, outdir: " << toString(outpath));
l.unlock();
emitStatusChanged(AdvancedStatus(AdvancedStatusEnum::Starting));
emitStarted();
emitStatusChanged(AdvancedStatus(AdvancedStatusEnum::Processing));
if (errors.result == ruleset::OSResultValue::Fail)
{
setErrors(errors);
return;
}
try {
boost::filesystem::create_directories(outpath);
//
// setup
//
LOG(Debug, "Working Directory: " + openstudio::toString(outpath));
// get model
boost::optional<openstudio::IdfFile> idf = openstudio::IdfFile::load(m_model->fullPath);
openstudio::model::Model model = openstudio::model::Model(idf.get());
// load the sql file
openstudio::SqlFile sqlFile(m_sql->fullPath);
if (!sqlFile.connectionOpen())
{
LOG(Error, "SqlFile connection is not open");
errors.result = ruleset::OSResultValue::Fail;
errors.addError(ErrorType::Error, "SqlFile collection is not open");
setErrors(errors);
return;
}
// set the sql file
model.setSqlFile(sqlFile);
if (!model.sqlFile())
{
LOG(Error, "SqlFile is not set on model");
errors.result = ruleset::OSResultValue::Fail;
errors.addError(ErrorType::Error, "SqlFile is not set on model");
setErrors(errors);
return;
}
openstudio::radiance::ForwardTranslator ft;
std::vector<openstudio::path> outfiles = ft.translateModel(outpath, model);
// capture translator errors and warnings?
//ft.errors();
//ft.warnings();
Files outfileinfos;
for (std::vector<openstudio::path>::const_iterator itr = outfiles.begin();
itr != outfiles.end();
++itr)
{
FileInfo fi = RunManager_Util::dirFile(*itr);
LOG(Info, "Output file generated: " << openstudio::toString(fi.fullPath));
emitOutputFileChanged(fi);
outfileinfos.append(fi);
}
l.relock();
m_outputfiles = outfileinfos;
/// Do work here - and be sure to set output files too
} catch (const std::runtime_error &e) {
errors.addError(ErrorType::Error, "Error with conversion (runtime_error): " + std::string(e.what()));
errors.result = ruleset::OSResultValue::Fail;
}
catch (const std::exception &e) {
errors.addError(ErrorType::Error, "Error with conversion: " + std::string(e.what()));
errors.result = ruleset::OSResultValue::Fail;
}
setErrors(errors);
}
//The Game
int main(int argc, char* args[]) {
Food Food;
GraphicFiles_Vars GF_Var;
InternalRandom IRand;
LoopControl Loop;
OptionsRandom ORand;
Map Map;
MidVars MidVar;
Snake Snake;
Timer Timer;
GMI_Vars GMI_Var;
Files File;
FoodSys FoodSys;
GameOver GameOver;
GraphicFiles_Main GF_Main;
Initializers Init;
Input Input;
Menu Menu;
NPC NPC;
Tail Tail;
//External variables initializers.
Init.ExternalVariableInitializers(Food, GMI_Var, IRand, Loop, Map, ORand, Snake);
//Gets saved options from a txt file.
File.ReadOptionsFile(IRand, Map, MidVar, ORand, Snake);
//Gets high scores from a txt file.
File.ReadHighScoresFile(IRand, MidVar);
//Initializes SDL
GF_Main.init_SDL(GMI_Var, GF_Var);
//Gets snake movement controls from a txt file.
File.ReadInputASCII(GF_Var, MidVar);
//The program (re)start point.
while (Loop.getGameReset()) {
//Menu, where the user can customize and start the game.
Menu.MainMenu(GMI_Var, GF_Var, IRand, Loop, Map, MidVar, ORand);
//Saves Options to a txt file.
File.WriteOptionsFile(Map, ORand, Snake);
//Saves snake movement controls to a txt file.
File.WriteInputASCII(GF_Var);
if (Loop.getGameReset()) {
//Initializes SDL components for the game loop.
GF_Main.init_SDL_GameLoop(GMI_Var, GF_Var, Map, ORand);
//Reads saved game txt file if game is loaded.
File.ReadSavedGame(Food, IRand, Map, MidVar, ORand, Snake);
//Defaults variables for the game loop.
Init.InternalVariableInitializers(Food, GMI_Var, GF_Var, IRand, Loop, Map, ORand, Snake);
//Constructes the borders of the map.
Init.MapBorderBuild(IRand, Map);
//Initializers for the game loop.
Init.FunctionInitializers(Food, IRand, Map, ORand, Snake, Timer);
//The game loop.
while (!Loop.getExitState()) {
//SDL based input system.
Input.GetInput(GMI_Var, GF_Var, IRand, Loop, Map, ORand, Snake, Timer);
//Saves game on exit if user chooses to.
File.WriteSavedGame(Food, IRand, Loop, Map, ORand, Snake);
//NPC AI
NPC.NPC_Move(Food, Map, ORand, Snake);
//Checks user input.
Tail.ProcessUserInput(IRand, Loop, Map, ORand, Snake);
//Deletes the snake right after death.
Tail.DeleteSnakeTail(IRand, Map, ORand, Snake);
//Places the food onto the map and processes it.
FoodSys.FoodProcess(Food, GF_Var, IRand, Loop, Map, ORand, Snake);
//Keeps the tail of the Snake the same size (becomes larger as you eat).
Tail.TailLengthMaintainer(IRand, Map, ORand, Snake);
//Draws the SDL game loop screen.
GF_Main.UpdateGameScreen(GMI_Var, GF_Var, Food, Loop, Map, ORand, Snake);
//Exits the game loop if a right condition is met.
GameOver.GameLoopExit(IRand, Loop, Map, ORand, Snake);
}
GF_Main.quit_SDL_GameLoop(GF_Var);
}
//Saves high scores to a txt file.
File.WriteHighScoresFile(IRand, Loop, MidVar, ORand);
//Tells you how you exited the game loop and shows final score(s).
GameOver.GameOverMessage(GMI_Var, GF_Var, IRand, Loop, Map, ORand);
}
//Quits SDL
GF_Main.quit_SDL(GF_Var, ORand);
return 0;
}
virtual ReadResult readImage(const std::string& file, const osgDB::ReaderWriter::Options* options) const
{
notice()<<"Reading DICOM file "<<file<<" using DCMTK"<<std::endl;
std::string ext = osgDB::getLowerCaseFileExtension(file);
if (!acceptsExtension(ext)) return ReadResult::FILE_NOT_HANDLED;
std::string fileName = file;
if (ext=="dicom")
{
fileName = osgDB::getNameLessExtension(file);
}
fileName = osgDB::findDataFile( fileName, options );
if (fileName.empty()) return ReadResult::FILE_NOT_FOUND;
Files files;
osgDB::FileType fileType = osgDB::fileType(fileName);
if (fileType==osgDB::DIRECTORY)
{
getDicomFilesInDirectory(fileName, files);
}
else
{
#if 1
files.push_back(fileName);
#else
if (!getDicomFilesInDirectory(osgDB::getFilePath(fileName), files))
{
files.push_back(fileName);
}
#endif
}
if (files.empty())
{
return ReadResult::FILE_NOT_FOUND;
}
osg::ref_ptr<osg::RefMatrix> matrix = new osg::RefMatrix;
osg::ref_ptr<osg::Image> image;
unsigned int imageNum = 0;
EP_Representation pixelRep = EPR_Uint8;
int numPlanes = 0;
GLenum pixelFormat = 0;
GLenum dataType = 0;
unsigned int pixelSize = 0;
typedef std::list<FileInfo> FileInfoList;
FileInfoList fileInfoList;
typedef std::map<double, FileInfo> DistanceFileInfoMap;
typedef std::map<osg::Vec3d, DistanceFileInfoMap> OrientationFileInfoMap;
OrientationFileInfoMap orientationFileInfoMap;
unsigned int totalNumSlices = 0;
for(Files::iterator itr = files.begin();
itr != files.end();
++itr)
{
DcmFileFormat fileformat;
OFCondition status = fileformat.loadFile((*itr).c_str());
if(!status.good()) return ReadResult::ERROR_IN_READING_FILE;
FileInfo fileInfo;
fileInfo.filename = *itr;
double pixelSize_y = 1.0;
double pixelSize_x = 1.0;
double sliceThickness = 1.0;
double imagePositionPatient[3] = {0, 0, 0};
double imageOrientationPatient[6] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0 };
Uint16 numOfSlices = 1;
double value = 0.0;
if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, value,0).good())
{
pixelSize_y = value;
fileInfo.matrix(1,1) = pixelSize_y;
}
if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, value,1).good())
{
pixelSize_x = value;
fileInfo.matrix(0,0) = pixelSize_x;
}
// Get slice thickness
if (fileformat.getDataset()->findAndGetFloat64(DCM_SliceThickness, value).good())
{
sliceThickness = value;
notice()<<"sliceThickness = "<<sliceThickness<<std::endl;
fileInfo.sliceThickness = sliceThickness;
}
notice()<<"tagExistsWithValue(DCM_NumberOfFrames)="<<fileformat.getDataset()->tagExistsWithValue(DCM_NumberOfFrames)<<std::endl;
notice()<<"tagExistsWithValue(DCM_NumberOfSlices)="<<fileformat.getDataset()->tagExistsWithValue(DCM_NumberOfSlices)<<std::endl;
Uint32 numFrames;
if (fileformat.getDataset()->findAndGetUint32(DCM_NumberOfFrames, numFrames).good())
{
fileInfo.numSlices = numFrames;
notice()<<"Read number of frames = "<<numFrames<<std::endl;
}
OFString numFramesStr;
if (fileformat.getDataset()->findAndGetOFString(DCM_NumberOfFrames, numFramesStr).good())
{
fileInfo.numSlices = atoi(numFramesStr.c_str());
notice()<<"Read number of frames = "<<numFramesStr<<std::endl;
}
if (fileformat.getDataset()->findAndGetUint16(DCM_NumberOfFrames, numOfSlices).good())
{
fileInfo.numSlices = numOfSlices;
notice()<<"Read number of frames = "<<numOfSlices<<std::endl;
}
if (fileformat.getDataset()->findAndGetUint16(DCM_NumberOfSlices, numOfSlices).good())
{
fileInfo.numSlices = numOfSlices;
notice()<<"Read number of slices = "<<numOfSlices<<std::endl;
}
// patient position
for(int i=0; i<3; ++i)
{
if (fileformat.getDataset()->findAndGetFloat64(DCM_ImagePositionPatient, imagePositionPatient[i],i).good())
{
notice()<<"Read DCM_ImagePositionPatient["<<i<<"], "<<imagePositionPatient[i]<<std::endl;
}
else
{
notice()<<"Have not read DCM_ImagePositionPatient["<<i<<"]"<<std::endl;
}
}
//notice()<<"imagePositionPatient[2]="<<imagePositionPatient[2]<<std::endl;
fileInfo.matrix.setTrans(imagePositionPatient[0],imagePositionPatient[1],imagePositionPatient[2]);
for(int i=0; i<6; ++i)
{
double value = 0.0;
if (fileformat.getDataset()->findAndGetFloat64(DCM_ImageOrientationPatient, value,i).good())
{
imageOrientationPatient[i] = value;
notice()<<"Read imageOrientationPatient["<<i<<"], "<<imageOrientationPatient[i]<<std::endl;
}
else
{
notice()<<"Have not read imageOrientationPatient["<<i<<"]"<<std::endl;
}
}
osg::Vec3d dirX(imageOrientationPatient[0],imageOrientationPatient[1],imageOrientationPatient[2]);
osg::Vec3d dirY(imageOrientationPatient[3],imageOrientationPatient[4],imageOrientationPatient[5]);
osg::Vec3d dirZ = dirX ^ dirY;
dirZ.normalize();
dirX *= pixelSize_x;
dirY *= pixelSize_y;
fileInfo.matrix(0,0) = dirX[0];
fileInfo.matrix(1,0) = dirX[1];
fileInfo.matrix(2,0) = dirX[2];
fileInfo.matrix(0,1) = dirY[0];
fileInfo.matrix(1,1) = dirY[1];
fileInfo.matrix(2,1) = dirY[2];
fileInfo.matrix(0,2) = dirZ[0];
fileInfo.matrix(1,2) = dirZ[1];
fileInfo.matrix(2,2) = dirZ[2];
fileInfo.distance = dirZ * (osg::Vec3d(0.0,0.0,0.0)*fileInfo.matrix);
notice()<<"dirX = "<<dirX<<std::endl;
notice()<<"dirY = "<<dirY<<std::endl;
notice()<<"dirZ = "<<dirZ<<std::endl;
notice()<<"matrix = "<<fileInfo.matrix<<std::endl;
notice()<<"pos = "<<osg::Vec3d(0.0,0.0,0.0)*fileInfo.matrix<<std::endl;
notice()<<"dist = "<<fileInfo.distance<<std::endl;
notice()<<std::endl;
(orientationFileInfoMap[dirZ])[fileInfo.distance] = fileInfo;
totalNumSlices += fileInfo.numSlices;
}
if (orientationFileInfoMap.empty()) return 0;
typedef std::map<double, FileInfo> DistanceFileInfoMap;
typedef std::map<osg::Vec3d, DistanceFileInfoMap> OrientationFileInfoMap;
for(OrientationFileInfoMap::iterator itr = orientationFileInfoMap.begin();
itr != orientationFileInfoMap.end();
++itr)
{
notice()<<"Orientation = "<<itr->first<<std::endl;
DistanceFileInfoMap& dfim = itr->second;
for(DistanceFileInfoMap::iterator ditr = dfim.begin();
ditr != dfim.end();
++ditr)
{
FileInfo& fileInfo = ditr->second;
notice()<<" d = "<<fileInfo.distance<<" "<<fileInfo.filename<<std::endl;
}
}
DistanceFileInfoMap& dfim = orientationFileInfoMap.begin()->second;
if (dfim.empty()) return 0;
double totalDistance = 0.0;
if (dfim.size()>1)
{
totalDistance = fabs(dfim.rbegin()->first - dfim.begin()->first);
}
else
{
totalDistance = dfim.begin()->second.sliceThickness * double(dfim.begin()->second.numSlices);
}
notice()<<"Total Distance including ends "<<totalDistance<<std::endl;
double averageThickness = totalNumSlices<=1 ? 1.0 : totalDistance / double(totalNumSlices-1);
notice()<<"Average thickness "<<averageThickness<<std::endl;
for(DistanceFileInfoMap::iterator ditr = dfim.begin();
ditr != dfim.end();
++ditr)
{
FileInfo& fileInfo = ditr->second;
std::auto_ptr<DicomImage> dcmImage(new DicomImage(fileInfo.filename.c_str()));
if (dcmImage.get())
{
if (dcmImage->getStatus()==EIS_Normal)
{
// get the pixel data
const DiPixel* pixelData = dcmImage->getInterData();
if(!pixelData)
{
warning()<<"Error: no data in DicomImage object."<<std::endl;
return ReadResult::ERROR_IN_READING_FILE;
}
osg::ref_ptr<osg::Image> imageAdapter = new osg::Image;
EP_Representation curr_pixelRep;
int curr_numPlanes;
GLenum curr_pixelFormat;
GLenum curr_dataType;
unsigned int curr_pixelSize;
// create the new image
convertPixelTypes(pixelData,
curr_pixelRep, curr_numPlanes,
curr_dataType, curr_pixelFormat, curr_pixelSize);
imageAdapter->setImage(dcmImage->getWidth(), dcmImage->getHeight(), dcmImage->getFrameCount(),
curr_pixelFormat,
curr_pixelFormat,
curr_dataType,
(unsigned char*)(pixelData->getData()),
osg::Image::NO_DELETE);
if (!image)
{
pixelRep = curr_pixelRep;
numPlanes = curr_numPlanes;
dataType = curr_dataType;
pixelFormat = curr_pixelFormat;
pixelSize = curr_pixelSize;
(*matrix)(0,0) = fileInfo.matrix(0,0);
(*matrix)(1,0) = fileInfo.matrix(1,0);
(*matrix)(2,0) = fileInfo.matrix(2,0);
(*matrix)(0,1) = fileInfo.matrix(0,1);
(*matrix)(1,1) = fileInfo.matrix(1,1);
(*matrix)(2,1) = fileInfo.matrix(2,1);
(*matrix)(0,2) = fileInfo.matrix(0,2) * averageThickness;
(*matrix)(1,2) = fileInfo.matrix(1,2) * averageThickness;
(*matrix)(2,2) = fileInfo.matrix(2,2) * averageThickness;
image = new osg::Image;
image->setUserData(matrix.get());
image->setFileName(fileName.c_str());
image->allocateImage(dcmImage->getWidth(), dcmImage->getHeight(), totalNumSlices,
pixelFormat, dataType);
matrix->preMult(osg::Matrix::scale(double(image->s()), double(image->t()), double(image->r())));
notice()<<"Image dimensions = "<<image->s()<<", "<<image->t()<<", "<<image->r()<<" pixelFormat=0x"<<std::hex<<pixelFormat<<" dataType=0x"<<std::hex<<dataType<<std::dec<<std::endl;
}
else if (pixelData->getPlanes()>numPlanes ||
pixelData->getRepresentation()>pixelRep)
{
notice()<<"Need to reallocated "<<image->s()<<", "<<image->t()<<", "<<image->r()<<std::endl;
// record the previous image settings to use when we copy back the content.
osg::ref_ptr<osg::Image> previous_image = image;
// create the new image
convertPixelTypes(pixelData,
pixelRep, numPlanes,
dataType, pixelFormat, pixelSize);
image = new osg::Image;
image->setUserData(previous_image->getUserData());
image->setFileName(fileName.c_str());
image->allocateImage(dcmImage->getWidth(), dcmImage->getHeight(), totalNumSlices,
pixelFormat, dataType);
osg::copyImage(previous_image.get(), 0,0,0, previous_image->s(), previous_image->t(), imageNum,
image.get(), 0, 0, 0,
false);
}
osg::copyImage(imageAdapter.get(), 0,0,0, imageAdapter->s(), imageAdapter->t(), imageAdapter->r(),
image.get(), 0, 0, imageNum,
false);
imageNum += dcmImage->getFrameCount();
}
else
{
warning()<<"Error in reading dicom file "<<fileName.c_str()<<", error = "<<DicomImage::getString(dcmImage->getStatus())<<std::endl;
}
}
}
if (!image)
{
return ReadResult::ERROR_IN_READING_FILE;
}
notice()<<"Spacing = "<<*matrix<<std::endl;
return image.get();
}
int main(int argc, char** argv) {
#ifdef HAVE_LIBMESH
libMesh::LibMeshInit init(argc,argv);
#else
FemusInit init(argc,argv);
#endif
// ======= Files ========================
Files files;
files.ConfigureRestart();
files.CheckIODirectories();
files.CopyInputFiles();
files.RedirectCout();
// ======= Physics Input Parser ========================
FemusInputParser<double> physics_map("Physics",files.GetOutputPath());
const double rhof = physics_map.get("rho0");
const double Uref = physics_map.get("Uref");
const double Lref = physics_map.get("Lref");
const double muf = physics_map.get("mu0");
const double _pref = rhof*Uref*Uref; physics_map.set("pref",_pref);
const double _Re = (rhof*Uref*Lref)/muf; physics_map.set("Re",_Re);
const double _Fr = (Uref*Uref)/(9.81*Lref); physics_map.set("Fr",_Fr);
const double _Pr = muf/rhof; physics_map.set("Pr",_Pr);
// ======= Mesh =====
const unsigned NoLevels = 3;
const unsigned dim = 2;
const GeomElType geomel_type = QUAD;
GenCase mesh(NoLevels,dim,geomel_type,"inclQ2D2x2.gam");
mesh.SetLref(1.);
// ======= MyDomainShape (optional, implemented as child of Domain) ====================
FemusInputParser<double> box_map("Box",files.GetOutputPath());
Box mybox(mesh.get_dim(),box_map);
mybox.InitAndNondimensionalize(mesh.get_Lref());
mesh.SetDomain(&mybox);
mesh.GenerateCase(files.GetOutputPath());
mesh.SetLref(Lref);
mybox.InitAndNondimensionalize(mesh.get_Lref());
XDMFWriter::ReadMeshAndNondimensionalizeBiquadraticHDF5(files.GetOutputPath(),mesh);
XDMFWriter::PrintMeshXDMF(files.GetOutputPath(),mesh,BIQUADR_FE);
XDMFWriter::PrintMeshLinear(files.GetOutputPath(),mesh);
//gencase is dimensionalized, meshtwo is nondimensionalized
//since the meshtwo is nondimensionalized, all the BC and IC are gonna be implemented on a nondimensionalized mesh
//now, a mesh may or may not have an associated domain
//moreover, a mesh may or may not be read from file
//the generation is dimensional, the nondimensionalization occurs later
//Both the Mesh and the optional domain must be nondimensionalized
//first, we have to say if the mesh has a shape or not
//that depends on the application, it must be put at the main level
//then, after you know the shape, you may or may not generate the mesh with that shape
//the two things are totally independent, and related to the application, not to the library
// ===== QuantityMap : this is like the MultilevelSolution =========================================
QuantityMap qty_map;
qty_map.SetMeshTwo(&mesh);
qty_map.SetInputParser(&physics_map);
Pressure pressure("Qty_Pressure",qty_map,1,LL); qty_map.AddQuantity(&pressure);
VelocityX velocityX("Qty_Velocity0",qty_map,1,QQ); qty_map.AddQuantity(&velocityX);
VelocityY velocityY("Qty_Velocity1",qty_map,1,QQ); qty_map.AddQuantity(&velocityY);
Temperature temperature("Qty_Temperature",qty_map,1,QQ); qty_map.AddQuantity(&temperature);
TempLift templift("Qty_TempLift",qty_map,1,QQ); qty_map.AddQuantity(&templift);
TempAdj tempadj("Qty_TempAdj",qty_map,1,QQ); qty_map.AddQuantity(&tempadj);
// ===== end QuantityMap =========================================
// ====== Start new main =================================
MultiLevelMesh ml_msh;
ml_msh.GenerateCoarseBoxMesh(8,8,0,0,1,0,2,0,0,QUAD9,"fifth"); // ml_msh.GenerateCoarseBoxMesh(numelemx,numelemy,numelemz,xa,xb,ya,yb,za,zb,elemtype,"fifth");
ml_msh.RefineMesh(NoLevels,NoLevels,NULL);
ml_msh.PrintInfo();
ml_msh.SetWriter(XDMF);
//ml_msh.GetWriter()->write(files.GetOutputPath(),"biquadratic");
ml_msh.SetDomain(&mybox);
MultiLevelSolution ml_sol(&ml_msh);
ml_sol.AddSolution("Qty_Temperature",LAGRANGE,SECOND,0);
ml_sol.AddSolution("Qty_TempLift",LAGRANGE,SECOND,0);
ml_sol.AddSolution("Qty_TempAdj",LAGRANGE,SECOND,0);
ml_sol.AddSolutionVector(ml_msh.GetDimension(),"Qty_Velocity",LAGRANGE,SECOND,0);
ml_sol.AddSolution("Qty_Pressure",LAGRANGE,FIRST,0);
ml_sol.AddSolution("Qty_TempDes",LAGRANGE,SECOND,0,false); //this is not going to be an Unknown! //moreover, this is not going to need any BC (i think they are excluded with "false") // I would like to have a Solution that is NOT EVEN related to the mesh at all... just like a function "on-the-fly"
// ******* Set problem *******
MultiLevelProblem ml_prob(&ml_sol);
ml_prob.SetMeshTwo(&mesh);
ml_prob.SetQruleAndElemType("fifth");
ml_prob.SetInputParser(&physics_map);
ml_prob.SetQtyMap(&qty_map);
// ******* Initial condition *******
ml_sol.InitializeMLProb(&ml_prob,"Qty_Temperature",SetInitialCondition);
ml_sol.InitializeMLProb(&ml_prob,"Qty_TempLift",SetInitialCondition);
ml_sol.InitializeMLProb(&ml_prob,"Qty_TempAdj",SetInitialCondition);
ml_sol.InitializeMLProb(&ml_prob,"Qty_Velocity0",SetInitialCondition);
ml_sol.InitializeMLProb(&ml_prob,"Qty_Velocity1",SetInitialCondition);
ml_sol.InitializeMLProb(&ml_prob,"Qty_Pressure",SetInitialCondition);
ml_sol.InitializeMLProb(&ml_prob,"Qty_TempDes",SetInitialCondition);
/// @todo you have to call this before you can print
/// @todo I can also call it after instantiation MLProblem
/// @todo I cannot call it with "All" and with a FUNCTION, because I need the string for "All" as a variable
/// @todo Have to say that you have to call this initialize BEFORE the generation of the boundary conditions;
/// if you called this after, it would superimpose the BOUNDARY VALUES
/// @todo you have to initialize also those variables which are NOT unknowns!
// ******* Set boundary function function *******
ml_sol.AttachSetBoundaryConditionFunctionMLProb(SetBoundaryCondition);
// ******* Generate boundary conditions *******
ml_sol.GenerateBdc("Qty_Temperature","Steady",&ml_prob);
ml_sol.GenerateBdc("Qty_TempLift","Steady",&ml_prob);
ml_sol.GenerateBdc("Qty_TempAdj","Steady",&ml_prob);
ml_sol.GenerateBdc("Qty_Velocity0","Steady",&ml_prob);
ml_sol.GenerateBdc("Qty_Velocity1","Steady",&ml_prob);
ml_sol.GenerateBdc("Qty_Pressure","Steady",&ml_prob);
// ******* Debug *******
ml_sol.SetWriter(VTK);
std::vector<std::string> print_vars(1); print_vars[0] = "All"; // we should find a way to make this easier
ml_sol.GetWriter()->write(files.GetOutputPath(),"biquadratic",print_vars);
//===============================================
//================== Add EQUATIONS AND ======================
//========= associate an EQUATION to QUANTITIES ========
//========================================================
// not all the Quantities need to be unknowns of an equation
SystemTwo & eqnNS = ml_prob.add_system<SystemTwo>("Eqn_NS");
eqnNS.AddSolutionToSystemPDEVector(ml_msh.GetDimension(),"Qty_Velocity");
eqnNS.AddSolutionToSystemPDE("Qty_Pressure");
eqnNS.AddUnknownToSystemPDE(&velocityX);
eqnNS.AddUnknownToSystemPDE(&velocityY);
eqnNS.AddUnknownToSystemPDE(&pressure);
eqnNS.SetAssembleFunction(GenMatRhsNS);
SystemTwo & eqnT = ml_prob.add_system<SystemTwo>("Eqn_T");
eqnT.AddSolutionToSystemPDE("Qty_Temperature");
eqnT.AddSolutionToSystemPDE("Qty_TempLift");
eqnT.AddSolutionToSystemPDE("Qty_TempAdj");
eqnT.AddUnknownToSystemPDE(&temperature);
eqnT.AddUnknownToSystemPDE(&templift);
eqnT.AddUnknownToSystemPDE(&tempadj); //the order in which you add defines the order in the matrix as well, so it is in tune with the assemble function
eqnT.SetAssembleFunction(GenMatRhsT);
//================================
//========= End add EQUATIONS and ========
//========= associate an EQUATION to QUANTITIES ========
//================================
//Ok now that the mesh file is there i want to COMPUTE the MG OPERATORS... but I want to compute them ONCE and FOR ALL,
//not for every equation... but the functions belong to the single equation... I need to make them EXTERNAL
// then I'll have A from the equation, PRL and REST from a MG object.
//So somehow i'll have to put these objects at a higher level... but so far let us see if we can COMPUTE and PRINT from HERE and not from the gencase
//once you have the list of the equations, you loop over them to initialize everything
for (MultiLevelProblem::const_system_iterator eqn = ml_prob.begin(); eqn != ml_prob.end(); eqn++) {
SystemTwo* sys = static_cast<SystemTwo*>(eqn->second);
// ******* set MG-Solver *******
sys->SetMgType(F_CYCLE);
sys->SetLinearConvergenceTolerance(1.e-10);
sys->SetNonLinearConvergenceTolerance(1.e-10);//1.e-5
sys->SetNumberPreSmoothingStep(1);
sys->SetNumberPostSmoothingStep(1);
sys->SetMaxNumberOfLinearIterations(8); //2
sys->SetMaxNumberOfNonLinearIterations(15); //10
// ******* Set Preconditioner *******
sys->SetMgSmoother(GMRES_SMOOTHER);//ASM_SMOOTHER,VANKA_SMOOTHER
// ******* init *******
sys->init();
// ******* Set Smoother *******
sys->SetSolverFineGrids(GMRES);
sys->SetPreconditionerFineGrids(ILU_PRECOND);
sys->SetTolerances(1.e-12,1.e-20,1.e+50,20); /// what the heck do these parameters mean?
// ******* Add variables to be solved ******* /// do we always need this?
sys->ClearVariablesToBeSolved();
sys->AddVariableToBeSolved("All");
// ******* For Gmres Preconditioner only *******
sys->SetDirichletBCsHandling(ELIMINATION);
// ******* For Gmres Preconditioner only *******
// sys->solve();
//=====================
sys -> init_two(); //the dof map is built here based on all the solutions associated with that system
sys -> _LinSolver[0]->set_solver_type(GMRES); //if I keep PREONLY it doesn't run
//=====================
sys -> init_unknown_vars();
//=====================
sys -> _dofmap.ComputeMeshToDof();
//=====================
sys -> initVectors();
//=====================
sys -> Initialize();
///=====================
sys -> _bcond.GenerateBdc();
//=====================
GenCase::ReadMGOps(files.GetOutputPath(),sys);
}
// ======== Loop ===================================
FemusInputParser<double> loop_map("TimeLoop",files.GetOutputPath());
OptLoop opt_loop(files, loop_map);
opt_loop.TransientSetup(ml_prob); // reset the initial state (if restart) and print the Case
opt_loop.optimization_loop(ml_prob);
// at this point, the run has been completed
files.PrintRunForRestart(DEFAULT_LAST_RUN);
files.log_petsc();
// ============ clean ================================
ml_prob.clear();
mesh.clear();
return 0;
}
int main(int argc, char** args) {
// ======= Init ========================
// init Petsc-MPI communicator
FemusInit mpinit(argc, args, MPI_COMM_WORLD);
// ======= Files ========================
Files files;
files.CheckIODirectories();
files.RedirectCout();
// ======= Quad Rule ========================
std::string fe_quad_rule("seventh");
/* "seventh" is the order of accuracy that is used in the gauss integration scheme
In the future it is not going to be an argument of the mesh function */
// ======= Mesh ========================
MultiLevelMesh ml_mesh;
ml_mesh.GenerateCoarseBoxMesh(NSUB_X,NSUB_Y,0,0.,1.,0.,1.,0.,0.,QUAD9,fe_quad_rule.c_str());
unsigned numberOfUniformLevels = 1;
unsigned numberOfSelectiveLevels = 0;
ml_mesh.RefineMesh(numberOfUniformLevels , numberOfUniformLevels + numberOfSelectiveLevels, NULL);
ml_mesh.PrintInfo();
// ======= Solution ========================
MultiLevelSolution ml_sol(&ml_mesh); // define the multilevel solution and attach the ml_mesh object to it
// add variables to ml_sol
ml_sol.AddSolution("state", LAGRANGE, FIRST);
ml_sol.AddSolution("control", LAGRANGE, FIRST);
ml_sol.AddSolution("adjoint", LAGRANGE, FIRST);
ml_sol.AddSolution("mu", LAGRANGE, FIRST);
ml_sol.AddSolution("TargReg", DISCONTINUOUS_POLYNOMIAL, ZERO); //this variable is not solution of any eqn, it's just a given field
ml_sol.AddSolution("ContReg", DISCONTINUOUS_POLYNOMIAL, ZERO); //this variable is not solution of any eqn, it's just a given field
const unsigned int fake_time_dep_flag = 2; //this is needed to be able to use _SolOld
const std::string act_set_flag_name = "act_flag";
ml_sol.AddSolution(act_set_flag_name.c_str(), LAGRANGE, FIRST,fake_time_dep_flag);
// ======= Problem ========================
MultiLevelProblem ml_prob(&ml_sol); // define the multilevel problem attach the ml_sol object to it
ml_prob.SetQuadratureRuleAllGeomElems(fe_quad_rule);
ml_prob.SetFilesHandler(&files);
// ======= Initial values ========================
ml_sol.Initialize("All"); // initialize all variables to zero
// ml_sol.Initialize("All", SetInitialCondition, &ml_prob); //unfortunately if I do this it sets all to zero //I would like to do an attach function similar to the BC
ml_sol.Initialize("state", SetInitialCondition, &ml_prob);
ml_sol.Initialize("control", SetInitialCondition, &ml_prob);
ml_sol.Initialize("adjoint", SetInitialCondition, &ml_prob);
ml_sol.Initialize("mu", SetInitialCondition, &ml_prob);
ml_sol.Initialize("TargReg", SetInitialCondition, &ml_prob);
ml_sol.Initialize("ContReg", SetInitialCondition, &ml_prob);
ml_sol.Initialize(act_set_flag_name.c_str(), SetInitialCondition, &ml_prob);
// ======= Boundary Conditions ========================
ml_sol.AttachSetBoundaryConditionFunction(SetBoundaryCondition); // attach the boundary condition function and generate boundary data
// ml_sol.GenerateBdc("All"); //this would do it also for the non-equation-related variables
ml_sol.GenerateBdc("state");
ml_sol.GenerateBdc("control");
ml_sol.GenerateBdc("adjoint");
ml_sol.GenerateBdc("mu"); //we need this for all Pde variables to make the matrix iterations work... but this should be related to the matrix and not to the sol... The same for the initial condition
// ======= System ========================
NonLinearImplicitSystemWithPrimalDualActiveSetMethod& system = ml_prob.add_system < NonLinearImplicitSystemWithPrimalDualActiveSetMethod > ("OptSys");
system.SetActiveSetFlagName(act_set_flag_name);
//here we decide the order in the matrix!
const std::vector < std::string > sol_matrix_pos = {"state","control","adjoint","mu"};
for (unsigned k = 0; k < sol_matrix_pos.size(); k++) system.AddSolutionToSystemPDE(sol_matrix_pos[k].c_str());
// attach the assembling function to system
system.SetAssembleFunction(AssembleProblem);
ml_sol.SetWriter(VTK); //need to move this here for the DebugNonlinear function
ml_sol.GetWriter()->SetDebugOutput(true);
system.SetDebugNonlinear(true);
system.SetDebugFunction(ComputeIntegral);
// system.SetMaxNumberOfNonLinearIterations(2);
// ======= Solve ========================
system.init(); // initialize and solve the system
system.MGsolve();
// ComputeIntegral(ml_prob);
// ======= Final Print ========================
std::vector < std::string > variablesToBePrinted;
variablesToBePrinted.push_back("all");
ml_sol.GetWriter()->Write(files.GetOutputPath()/*DEFAULT_OUTPUTDIR*/, "biquadratic", variablesToBePrinted); // print solutions
return 0;
}
void HiRes1Engine::runIntro() const {
StreamPtr stream(_files->createReadStream(IDS_HR1_EXE_0));
stream->seek(IDI_HR1_OFS_LOGO_0);
_display->setMode(DISPLAY_MODE_HIRES);
_display->loadFrameBuffer(*stream);
_display->updateHiResScreen();
delay(4000);
if (shouldQuit())
return;
_display->setMode(DISPLAY_MODE_TEXT);
StreamPtr basic(_files->createReadStream(IDS_HR1_LOADER));
Common::String str;
str = readStringAt(*basic, IDI_HR1_OFS_PD_TEXT_0, '"');
_display->printAsciiString(str + '\r');
str = readStringAt(*basic, IDI_HR1_OFS_PD_TEXT_1, '"');
_display->printAsciiString(str + "\r\r");
str = readStringAt(*basic, IDI_HR1_OFS_PD_TEXT_2, '"');
_display->printAsciiString(str + "\r\r");
str = readStringAt(*basic, IDI_HR1_OFS_PD_TEXT_3, '"');
_display->printAsciiString(str + '\r');
inputKey();
if (g_engine->shouldQuit())
return;
_display->setMode(DISPLAY_MODE_MIXED);
str = readStringAt(*stream, IDI_HR1_OFS_GAME_OR_HELP);
bool instructions = false;
while (1) {
_display->printString(str);
Common::String s = inputString();
if (g_engine->shouldQuit())
break;
if (s.empty())
continue;
if (s[0] == APPLECHAR('I')) {
instructions = true;
break;
} else if (s[0] == APPLECHAR('G')) {
break;
}
};
if (instructions) {
_display->setMode(DISPLAY_MODE_TEXT);
stream->seek(IDI_HR1_OFS_INTRO_TEXT);
const uint pages[] = { 6, 6, 4, 5, 8, 7, 0 };
uint page = 0;
while (pages[page] != 0) {
_display->home();
uint count = pages[page++];
for (uint i = 0; i < count; ++i) {
str = readString(*stream);
_display->printString(str);
stream->seek(3, SEEK_CUR);
}
inputString();
if (g_engine->shouldQuit())
return;
stream->seek(6, SEEK_CUR);
}
}
_display->printAsciiString("\r");
_display->setMode(DISPLAY_MODE_MIXED);
// Title screen shown during loading
stream.reset(_files->createReadStream(IDS_HR1_EXE_1));
stream->seek(IDI_HR1_OFS_LOGO_1);
_display->loadFrameBuffer(*stream);
_display->updateHiResScreen();
delay(2000);
}
TEST_F(FilesTest, ResolveTest)
{
Files files;
process::UPID upid("files", process::node());
// Test the directory / file resolution.
ASSERT_SOME(os::mkdir("1/2"));
ASSERT_SOME(os::write("1/two", "two"));
ASSERT_SOME(os::write("1/2/three", "three"));
// Attach some paths.
AWAIT_EXPECT_READY(files.attach("1", "one"));
AWAIT_EXPECT_READY(files.attach("1", "/one/"));
AWAIT_EXPECT_READY(files.attach("1/2", "two"));
AWAIT_EXPECT_READY(files.attach("1/2", "one/two"));
// Resolve 1/2/3 via each attached path.
JSON::Object expected;
expected.values["offset"] = 0;
expected.values["data"] = "three";
Future<Response> response =
process::http::get(upid, "read.json", "path=one/2/three&offset=0");
AWAIT_EXPECT_RESPONSE_STATUS_EQ(OK().status, response);
AWAIT_EXPECT_RESPONSE_BODY_EQ(stringify(expected), response);
response =
process::http::get(upid, "read.json", "path=/one/2/three&offset=0");
AWAIT_EXPECT_RESPONSE_STATUS_EQ(OK().status, response);
AWAIT_EXPECT_RESPONSE_BODY_EQ(stringify(expected), response);
response =
process::http::get(upid, "read.json", "path=two/three&offset=0");
AWAIT_EXPECT_RESPONSE_STATUS_EQ(OK().status, response);
AWAIT_EXPECT_RESPONSE_BODY_EQ(stringify(expected), response);
response =
process::http::get(upid, "read.json", "path=one/two/three&offset=0");
AWAIT_EXPECT_RESPONSE_STATUS_EQ(OK().status, response);
AWAIT_EXPECT_RESPONSE_BODY_EQ(stringify(expected), response);
// Percent encoded '/' urls.
response =
process::http::get(upid, "read.json", "path=%2Fone%2F2%2Fthree&offset=0");
AWAIT_EXPECT_RESPONSE_STATUS_EQ(OK().status, response);
AWAIT_EXPECT_RESPONSE_BODY_EQ(stringify(expected), response);
response =
process::http::get(upid, "read.json", "path=one%2Ftwo%2Fthree&offset=0");
AWAIT_EXPECT_RESPONSE_STATUS_EQ(OK().status, response);
AWAIT_EXPECT_RESPONSE_BODY_EQ(stringify(expected), response);
// Reading dirs not allowed.
AWAIT_EXPECT_RESPONSE_STATUS_EQ(
BadRequest().status,
process::http::get(upid, "read.json", "path=one/2"));
AWAIT_EXPECT_RESPONSE_STATUS_EQ(
BadRequest().status,
process::http::get(upid, "read.json", "path=one"));
AWAIT_EXPECT_RESPONSE_STATUS_EQ(
BadRequest().status,
process::http::get(upid, "read.json", "path=one/"));
// Breaking out of sandbox.
AWAIT_EXPECT_RESPONSE_STATUS_EQ(
BadRequest().status,
process::http::get(upid, "read.json", "path=two/../two"));
}
ribi::foam::Mesh::Mesh(
const Files& files,
const std::vector<boost::shared_ptr<ribi::Coordinat3D>>& points
)
: m_boundaries{},
m_cells{CreateEmptyCells(files)},
m_faces{CreateFacesWithPoints(files,points)},
m_points(points)
{
#ifndef NDEBUG
Test();
#endif
//Add Cell owner to Faces
{
assert(!m_cells.empty());
const FaceIndex n_faces = files.GetFaces()->GetMaxFaceIndex();
for (FaceIndex i = FaceIndex(0); i!=n_faces; ++i)
{
const CellIndex owner_cell_index { files.GetOwner()->GetItem(i).GetCellIndex() };
#ifndef NDEBUG
if (owner_cell_index.Get() >= static_cast<int>(m_cells.size()))
{
TRACE("ERROR");
TRACE(owner_cell_index);
TRACE(m_cells.size());
}
#endif
assert(owner_cell_index.Get() >= 0);
assert(owner_cell_index.Get() < static_cast<int>(m_cells.size()));
assert(m_cells[ owner_cell_index.Get() ]);
const boost::shared_ptr<Cell> owner { m_cells[ owner_cell_index.Get() ] };
assert(owner);
assert(!m_faces[i.Get()]->GetOwner() );
m_faces[i.Get()]->AssignOwner(owner);
assert( m_faces[i.Get()]->GetOwner() );
}
}
#ifndef NDEBUG
for (const boost::shared_ptr<Face> face: m_faces) { assert(face); assert(face->GetOwner()); }
#endif
//Add owned Faces to Cells
{
std::map<boost::shared_ptr<Cell>,std::vector<boost::shared_ptr<Face>>> m;
for (const boost::shared_ptr<Face> face: m_faces)
{
assert(face);
const boost::shared_ptr<Cell> owner { face->GetOwner() };
assert(owner);
//if (!owner) continue;
if (m.find(owner) == m.end()) { m.insert(std::make_pair(owner, std::vector<boost::shared_ptr<Face>>() ) ); }
assert(m.find(owner) != m.end());
(*m.find(owner)).second.push_back(face);
}
for (auto p: m)
{
p.first->AssignOwnedFaces(p.second);
}
}
//Add neighbours to Faces
{
const int n_faces = static_cast<int>(m_faces.size());
for (int i=0; i!=n_faces; ++i)
{
const FaceIndex index(i);
assert(files.GetNeighbour());
//Not all Faces have a neighbour
if (!files.GetNeighbour()->CanGetItem(index)) continue;
assert(files.GetNeighbour()->CanGetItem(index));
const CellIndex neighbour_index {
files.GetNeighbour()->GetItem(index).GetCellIndex()
};
assert(i >= 0);
assert(i < static_cast<int>(m_faces.size()));
assert(neighbour_index.Get() < static_cast<int>(m_cells.size()));
assert(!m_faces[i]->GetNeighbour());
m_faces[i]->AssignNeighbour( m_cells[ neighbour_index.Get() ] );
assert(m_faces[i]->GetNeighbour());
}
}
//Assign boundaries
m_boundaries = CreateBoundaries(files,m_faces);
//Check
#ifndef NDEBUG
for (boost::shared_ptr<Cell> cell: m_cells)
{
assert(cell);
//assert( (cell->GetNeighbour() || !cell->GetNeighbour())
// && "Not all cells have a neighbour, for example in a 1x1x1 mesh");
}
if (GetNumberOfBoundaries() != files.GetBoundary()->GetMaxBoundaryIndex().Get())
{
TRACE("ERROR");
TRACE(GetNumberOfBoundaries());
TRACE(files.GetBoundary()->GetMaxBoundaryIndex());
}
#endif
assert(GetNumberOfBoundaries() == files.GetBoundary()->GetMaxBoundaryIndex().Get());
assert(GetNumberOfFaces() == files.GetFaces()->GetMaxFaceIndex().Get());
}
int main(int argc,char **args) {
/// Init Petsc-MPI communicator
FemusInit mpinit(argc,args,MPI_COMM_WORLD);
Files files;
files.CheckIODirectories();
files.RedirectCout();
unsigned short nm,nr;
std::cout<<"#MULTIGRID levels? (>=1) \n";
//std::cin>>nm;
nm=4;
std::cout<<"#MAX_REFINEMENT levels? (>=0) \n";
//std::cin>>nr;
nr=0;
int tmp=nm;
nm+=nr;
nr=tmp;
const std::string infile = "./input/fsifirst.neu";
double Lref = 1.;
double Uref = 1.;
double rhof = 1000.;
double muf = 1.;
double rhos = 1000;
double ni = 0.4;
double E = 5600000;
MultiLevelMesh ml_msh(nm,nr,infile.c_str(),"fifth",Lref,SetRefinementFlag);
MultiLevelSolution ml_sol(&ml_msh);
//Start System Variables
ml_sol.AddSolution("DX",LAGRANGE,SECOND,2);
ml_sol.AddSolution("DY",LAGRANGE,SECOND,2);
// ml_sol.AssociatePropertyToSolution("DX","Displacement"); // Add this line
// ml_sol.AssociatePropertyToSolution("DY","Displacement"); // Add this line
ml_sol.AddSolution("U",LAGRANGE,SECOND,2);
ml_sol.AddSolution("V",LAGRANGE,SECOND,2);
// ml_sol.PairSolution("U","DX"); // Add this line
// ml_sol.PairSolution("V","DY"); // Add this line
ml_sol.AddSolution("AX",LAGRANGE,SECOND,1,0);
ml_sol.AddSolution("AY",LAGRANGE,SECOND,1,0);
// Since the Pressure is a Lagrange multiplier it is used as an implicit variable
ml_sol.AddSolution("P",DISCONTINOUS_POLYNOMIAL,FIRST,1);
ml_sol.AssociatePropertyToSolution("P","Pressure"); // Add this line
//Initialize (update Init(...) function)
ml_sol.Initialize("All");
//Set Boundary (update Dirichlet(...) function)
ml_sol.AttachSetBoundaryConditionFunction(SetBoundaryCondition);
ml_sol.GenerateBdc("DX","Steady");
ml_sol.GenerateBdc("DY","Steady");
ml_sol.GenerateBdc("U","Time_dependent");
ml_sol.GenerateBdc("V","Steady");
ml_sol.GenerateBdc("AX","Steady");
ml_sol.GenerateBdc("AY","Steady");
ml_sol.GenerateBdc("P","Steady");
MultiLevelProblem ml_prob(&ml_sol);
Parameter par(Lref,Uref);
// Generate Solid Object
Solid solid(par,E,ni,rhos,"Neo-Hookean");
cout << "Solid properties: " << endl;
cout << solid << endl;
// Generate Fluid Object
Fluid fluid(par,muf,rhof,"Newtonian");
cout << "Fluid properties: " << endl;
cout << fluid << endl;
// Add fluid object
ml_prob.parameters.set<Fluid>("Fluid") = fluid;
// Add Solid Object
ml_prob.parameters.set<Solid>("Solid") = solid;
ml_msh.MarkStructureNode();
//create systems
// add the system FSI to the MultiLevel problem
TransientMonolithicFSINonlinearImplicitSystem & system = ml_prob.add_system<TransientMonolithicFSINonlinearImplicitSystem> ("Fluid-Structure-Interaction");
system.AddSolutionToSystemPDE("DX");
system.AddSolutionToSystemPDE("DY");
system.AddSolutionToSystemPDE("U");
system.AddSolutionToSystemPDE("V");
system.AddSolutionToSystemPDE("P");
// init all the systems
system.init();
// System Fluid-Structure-Interaction
system.SetAssembleFunction(AssembleMatrixResFSI);
system.SetMaxNumberOfLinearIterations(1);
system.SetLinearConvergenceTolerance(1.e-8);
system.SetMgType(V_CYCLE);
system.SetMaxNumberOfNonLinearIterations(4);
system.SetNonLinearConvergenceTolerance(1.e-5);
system.SetDirichletBCsHandling(PENALTY);
//system.SetDirichletBCsHandling(ELIMINATION);
// time loop parameter
system.AttachGetTimeIntervalFunction(SetVariableTimeStep);
const unsigned int n_timesteps = 5;
const unsigned int write_interval = 1;
std::vector<std::string> mov_vars;
mov_vars.push_back("DX");
mov_vars.push_back("DY");
VTKWriter vtkio(&ml_sol);
vtkio.SetMovingMesh(mov_vars);
for (unsigned time_step = 0; time_step < n_timesteps; time_step++) {
// Solving Fluid-Structure-Interaction system
std::cout << std::endl;
std::cout << " *********** Fluid-Structure-Interaction ************ " << std::endl;
system.solve();
//The update of the acceleration must be done before the update of the other variables
system.NewmarkAccUpdate();
//update Solution
system.UpdateSolution();
// print solution
if ( !(time_step%write_interval) ) {
//print solution
std::vector<std::string> print_vars;
print_vars.push_back("DX");
print_vars.push_back("DY");
print_vars.push_back("U");
print_vars.push_back("V");
print_vars.push_back("P");
// ml_prob.printsol_vtu_inline("biquadratic",print_vars,time_step);
vtkio.write(files.GetOutputPath(),"biquadratic",print_vars,time_step);
}
} //end loop timestep
// Destroy all the new systems
ml_prob.clear();
return 0;
}
