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Commit 7cac7d4c authored by Thomas Witkowski's avatar Thomas Witkowski
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Work on Rosenbrock methods.

parent 6fbfd7ec
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Showing with 276 additions and 161 deletions
AMDiS/src/ProblemStat.cc
View file @ 7cac7d4c
......@@ -515,17 +515,8 @@ namespace AMDiS {
solution->getDOFVector(i)));
}
// Check for serializer
int writeSerialization = 0;
Parameters::get(name + "->write serialization", writeSerialization);
if (writeSerialization) {
MSG("Use are using the obsolete parameter: %s->write serialization\n", name.c_str());
MSG("Please use instead the following parameter: %s->output->write serialization\n", name.c_str());
ERROR_EXIT("Usage of an obsolete parameter (see message above)!\n");
}
Parameters::get(name + "->output->write serialization", writeSerialization);
if (writeSerialization)
fileWriters.push_back(new Serializer<ProblemStatSeq>(this));
}
......
AMDiS/src/Serializer.h
View file @ 7cac7d4c
......@@ -45,7 +45,10 @@ namespace AMDiS {
: name(""),
problem(prob),
tsModulo(1),
timestepNumber(-1)
timestepNumber(-1),
appendIndex(0),
indexLength(5),
indexDecimals(3)
{
FUNCNAME("Serializer::Serializer()");
......@@ -55,9 +58,9 @@ namespace AMDiS {
tsModulo);
TEST_EXIT(name != "")("No filename!\n");
#if HAVE_PARALLEL_DOMAIN_AMDIS
name += ".p" + boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank());
#endif
Parameters::get(problem->getName() + "->output->append index", appendIndex);
Parameters::get(problem->getName() + "->output->index length", indexLength);
Parameters::get(problem->getName() + "->output->index decimals", indexDecimals);
}
......@@ -65,15 +68,18 @@ namespace AMDiS {
: name(filename),
problem(prob),
tsModulo(writeEveryIth),
timestepNumber(-1)
timestepNumber(-1),
appendIndex(0),
indexLength(5),
indexDecimals(3)
{
FUNCNAME("Serializer::Serializer()");
TEST_EXIT(name != "")("No filename!\n");
#if HAVE_PARALLEL_DOMAIN_AMDIS
name += ".p" + boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank());
#endif
Parameters::get(problem->getName() + "->output->append index", appendIndex);
Parameters::get(problem->getName() + "->output->index length", indexLength);
Parameters::get(problem->getName() + "->output->index decimals", indexDecimals);
}
......@@ -97,14 +103,35 @@ namespace AMDiS {
TEST_EXIT(adaptInfo)("No AdaptInfo\n");
std::ofstream out(name.c_str());
string filename = name;
if (appendIndex) {
TEST_EXIT(indexLength <= 99)("index lenght > 99\n");
TEST_EXIT(indexDecimals <= 97)("index decimals > 97\n");
TEST_EXIT(indexDecimals < indexLength)("index length <= index decimals\n");
char formatStr[9];
char timeStr[20];
sprintf(formatStr, "%%0%d.%df", indexLength, indexDecimals);
sprintf(timeStr, formatStr, adaptInfo ? adaptInfo->getTime() : 0.0);
filename += string(timeStr);
}
filename += ".ser";
#if HAVE_PARALLEL_DOMAIN_AMDIS
filename += ".p" + boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank());
#endif
std::ofstream out(filename.c_str());
TEST_EXIT(out.is_open())("Cannot open serialization file!\n");
out.write(reinterpret_cast<const char*>(&amdisRevisionNumber), sizeof(int));
problem->serialize(out);
adaptInfo->serialize(out);
out.close();
MSG("problem serialized to %s \n", name.c_str());
MSG("Problem serialized to %s \n", filename.c_str());
}
protected:
......@@ -117,6 +144,16 @@ namespace AMDiS {
/// The problem is serialized every tsModulo-th timestep.
int tsModulo;
/// 0: Don't append time index to filename prefix.
/// 1: Append time index to filename prefix.
int appendIndex;
/// Total length of appended time index.
int indexLength;
/// Number of decimals in time index.
int indexDecimals;
/// Current timestep number.
int timestepNumber;
};
......
AMDiS/src/ZeroOrderTerm.h
View file @ 7cac7d4c
......@@ -97,7 +97,7 @@ namespace AMDiS {
public:
/// Constructor.
VecAtQP_ZOT(DOFVectorBase<double> *dv,
AbstractFunction<double, double> *ab);
AbstractFunction<double, double> *ab = NULL);
/// Implementation of \ref OperatorTerm::initElement().
void initElement(const ElInfo* elInfo,
......
AMDiS/src/io/FileWriter.cc
View file @ 7cac7d4c
......@@ -261,14 +261,16 @@ namespace AMDiS {
#if HAVE_PARALLEL_DOMAIN_AMDIS
if (MPI::COMM_WORLD.Get_rank() == 0) {
VtkWriter vtkWriter(&dataCollectors);
vtkWriter.updateAnimationFile(paraFilename + paraviewParallelFileExt,
vtkWriter.updateAnimationFile(adaptInfo,
paraFilename + paraviewParallelFileExt,
&paraviewAnimationFrames,
filename + ".pvd");
}
#else
VtkWriter vtkWriter(&dataCollectors);
vtkWriter.updateAnimationFile(fn + paraviewFileExt,
vtkWriter.updateAnimationFile(adaptInfo,
fn + paraviewFileExt,
&paraviewAnimationFrames,
filename + ".pvd");
#endif
......
AMDiS/src/io/FileWriter.h
View file @ 7cac7d4c
......@@ -35,6 +35,8 @@
namespace AMDiS {
using namespace std;
typedef enum {
NONE = 0,
GZIP = 1,
......@@ -73,19 +75,19 @@ namespace AMDiS {
writeElement = writeElem;
}
std::string getFilename()
string getFilename()
{
return filename;
}
void setFilename(std::string n)
void setFilename(string n)
{
filename = n;
}
protected:
/// Used filename prefix.
std::string filename;
string filename;
int traverseLevel;
......@@ -105,18 +107,18 @@ namespace AMDiS {
{
public:
/// Constructor for a filewriter for one data component.
FileWriter(std::string name, Mesh *mesh, DOFVector<double> *vec);
FileWriter(string name, Mesh *mesh, DOFVector<double> *vec);
/// Constructor for a filewriter with more than one data component.
FileWriter(std::string name,
FileWriter(string name,
Mesh *mesh,
std::vector< DOFVector<double>* > vecs);
vector< DOFVector<double>* > vecs);
/** \brief
* Constructor for a filewriter, when the solution vector is a vector
* of WorldVectors.
*/
FileWriter(std::string name,
FileWriter(string name,
Mesh *mesh,
DOFVector< WorldVector<double> > *vec);
......@@ -137,22 +139,22 @@ namespace AMDiS {
void readParameters();
/// Name of the writer.
std::string name;
string name;
/// AMDiS mesh-file extension.
std::string amdisMeshExt;
string amdisMeshExt;
/// AMDiS solution-file extension.
std::string amdisDataExt;
string amdisDataExt;
/// VTK file extension.
std::string paraviewFileExt;
string paraviewFileExt;
/// Parallel VTK file extension.
std::string paraviewParallelFileExt;
string paraviewParallelFileExt;
/// Periodic file extension.
std::string periodicFileExt;
string periodicFileExt;
/// 0: Don't write AMDiS files; 1: Write AMDiS files.
int writeAMDiSFormat;
......@@ -182,18 +184,16 @@ namespace AMDiS {
int writeArhFormat;
/// camera position for povray script files
std::string povrayCameraLocation;
string povrayCameraLocation;
/// orientation for camera in povray script files
std::string povrayCameraLookAt;
string povrayCameraLookAt;
/// name of the template file that will be prepended to all created *.pov files
std::string povrayTemplate;
string povrayTemplate;
/** \brief
* 0: Don't append time index to filename prefix.
* 1: Append time index to filename prefix.
*/
/// 0: Don't append time index to filename prefix.
/// 1: Append time index to filename prefix.
int appendIndex;
/// Total length of appended time index.
......@@ -205,8 +205,9 @@ namespace AMDiS {
/// Timestep modulo: write only every tsModulo-th timestep!
int tsModulo;
/// Stores all writen filename to a ParaView animation file.
std::vector< std::string > paraviewAnimationFrames;
/// Stores a set of pairs of timepoint and filename to write a ParaView
/// animation file.
vector<pair<double, string> > paraviewAnimationFrames;
///
int timestepNumber;
......@@ -218,7 +219,7 @@ namespace AMDiS {
const FiniteElemSpace *feSpace;
/// Pointers to the vectors which store the solution.
std::vector<DOFVector<double>*> solutionVecs;
vector<DOFVector<double>*> solutionVecs;
/** \brief
* Stores the number of temporal solutions vectors, which have been created
......
AMDiS/src/io/VtkWriter.cc
View file @ 7cac7d4c
......@@ -31,7 +31,9 @@
namespace AMDiS {
int VtkWriter::writeFile(std::string name)
using namespace std;
int VtkWriter::writeFile(string name)
{
FUNCNAME("VtkWriter::writeFile()");
......@@ -50,32 +52,32 @@ namespace AMDiS {
}
{
std::ofstream swapfile(name.c_str(), std::ios::out | std::ios::trunc);
ofstream swapfile(name.c_str(), ios::out | ios::trunc);
TEST_EXIT(swapfile.is_open())
("Cannot open file %s for writing!\n", name.c_str());
swapfile.close();
}
file.push(boost::iostreams::file_descriptor_sink(name, std::ios::trunc));
file.push(boost::iostreams::file_descriptor_sink(name, ios::trunc));
writeFileToStream(file);
return 0;
}
void VtkWriter::writeParallelFile(std::string name, int nRanks,
std::string fnPrefix, std::string fnPostfix)
void VtkWriter::writeParallelFile(string name, int nRanks,
string fnPrefix, string fnPostfix)
{
FUNCNAME("VtkWriter::writeParallelFile()");
boost::iostreams::filtering_ostream file;
{
std::ofstream swapfile(name.c_str(), std::ios::out | std::ios::trunc);
ofstream swapfile(name.c_str(), ios::out | ios::trunc);
TEST_EXIT(swapfile.is_open())
("Cannot open file %s for writing!\n", name.c_str());
swapfile.close();
}
file.push(boost::iostreams::file_descriptor_sink(name, std::ios::trunc));
file.push(boost::iostreams::file_descriptor_sink(name, ios::trunc));
file << "<?xml version=\"1.0\"?>\n";
file << "<VTKFile type=\"PUnstructuredGrid\">\n";
......@@ -97,7 +99,7 @@ namespace AMDiS {
file << " </PPointData>\n";
for (int i = 0; i < nRanks; i++) {
std::stringstream oss;
stringstream oss;
oss << fnPrefix << "-p" << i << "-" << fnPostfix;
boost::filesystem::path filepath(oss.str());
file << " <Piece Source=\""
......@@ -111,38 +113,36 @@ namespace AMDiS {
}
int VtkWriter::updateAnimationFile(std::string valueFilename,
std::vector< std::string > *paraViewAnimationFrames,
std::string animationFilename)
int VtkWriter::updateAnimationFile(AdaptInfo *adaptInfo,
string valueFilename,
vector<pair<double, string > > *paraViewAnimationFrames,
string animationFilename)
{
FUNCNAME("VtkWriter::updateAnimationFile()");
size_t found = valueFilename.find_last_of("/\\");
paraViewAnimationFrames->push_back(valueFilename.substr(found + 1));
paraViewAnimationFrames->push_back(make_pair(adaptInfo->getTime(),
valueFilename.substr(found + 1)));
boost::iostreams::filtering_ostream file;
{
std::ofstream swapfile(animationFilename.c_str(),
std::ios::out | std::ios::trunc);
ofstream swapfile(animationFilename.c_str(),
ios::out | ios::trunc);
TEST_EXIT(swapfile.is_open())
("Cannot open file %s for writing!\n", animationFilename.c_str());
swapfile.close();
}
file.push(boost::iostreams::file_descriptor_sink(animationFilename,
std::ios::trunc));
ios::trunc));
file << "<?xml version=\"1.0\"?>\n";
file << "<VTKFile type=\"Collection\" version=\"0.1\" >" << "\n";
file << "<Collection>\n";
int counter = 0;
std::vector< std::string >::iterator it;
for (it = paraViewAnimationFrames->begin();
it < paraViewAnimationFrames->end();
++it, counter++) {
file << "<DataSet timestep=\"" << counter
<< "\" part=\"0\" file=\"" << (*it) << "\"/>\n";
}
for (vector<pair<double, string> >::iterator it = paraViewAnimationFrames->begin();
it < paraViewAnimationFrames->end(); ++it)
file << "<DataSet timestep=\"" << it->first
<< "\" part=\"0\" file=\"" << it->second << "\"/>\n";
file << "</Collection>\n";
file << "</VTKFile>\n";
......@@ -152,23 +152,23 @@ namespace AMDiS {
void VtkWriter::writeFile(DOFVector<double> *values,
std::string filename,
string filename,
bool writeParallel)
{
FUNCNAME("VtkWriter::writeFile()");
DataCollector dc(values->getFeSpace(), values);
std::vector<DataCollector*> dcList(0);
vector<DataCollector*> dcList(0);
dcList.push_back(&dc);
writeFile(dcList, filename, writeParallel);
}
void VtkWriter::writeFile(std::vector<DOFVector<double>* > &values,
std::string filename,
void VtkWriter::writeFile(vector<DOFVector<double>* > &values,
string filename,
bool writeParallel)
{
std::vector<DataCollector*> dcList(0);
vector<DataCollector*> dcList(0);
for (unsigned int i = 0; i < values.size(); i++)
dcList.push_back(new DataCollector(values[i]->getFeSpace(), values[i]));
writeFile(dcList, filename, writeParallel);
......@@ -178,10 +178,10 @@ namespace AMDiS {
void VtkWriter::writeFile(WorldVector<DOFVector<double>* > &values,
std::string filename,
string filename,
bool writeParallel)
{
std::vector<DataCollector*> dcList(0);
vector<DataCollector*> dcList(0);
for (int i = 0; i < values.getSize(); i++)
dcList.push_back(new DataCollector(values[i]->getFeSpace(), values[i]));
writeFile(dcList, filename, writeParallel);
......@@ -191,7 +191,7 @@ namespace AMDiS {
void VtkWriter::writeFile(DOFVector<WorldVector<double> > *values,
std::string filename,
string filename,
bool writeParallel)
{
WorldVector<DOFVector<double>*> valuesWV;
......@@ -205,10 +205,10 @@ namespace AMDiS {
void VtkWriter::writeFile(SystemVector *values,
std::string filename,
string filename,
bool writeParallel)
{
std::vector<DataCollector*> dcList(0);
vector<DataCollector*> dcList(0);
for (int i = 0; i < values->getSize(); i++)
dcList.push_back(new DataCollector(values->getDOFVector(i)->getFeSpace(),
values->getDOFVector(i)));
......@@ -218,8 +218,8 @@ namespace AMDiS {
}
void VtkWriter::writeFile(std::vector<DataCollector*> &dcList,
std::string filename,
void VtkWriter::writeFile(vector<DataCollector*> &dcList,
string filename,
bool writeParallel)
{
VtkWriter writer(&dcList);
......@@ -230,12 +230,12 @@ namespace AMDiS {
int sPos = filename.find(".vtu");
TEST_EXIT(sPos >= 0)("Failed to find file postfix!\n");
std::string name = filename.substr(0, sPos);
string name = filename.substr(0, sPos);
if (MPI::COMM_WORLD.Get_rank() == 0)
writer.writeParallelFile(name + ".pvtu", MPI::COMM_WORLD.Get_size(), name, ".vtu");
filename = name + "-p" + lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank()) + "-.vtu";
filename = name + "-p" + lexical_cast<string>(MPI::COMM_WORLD.Get_rank()) + "-.vtu";
}
#endif
writer.writeFile(filename);
......
AMDiS/src/io/VtkWriter.h
View file @ 7cac7d4c
......@@ -36,10 +36,12 @@
namespace AMDiS {
using namespace std;
class VtkWriter
{
public:
VtkWriter(std::vector<DataCollector*> *dc)
VtkWriter(vector<DataCollector*> *dc)
: dataCollector(dc),
compress(NONE)
{
......@@ -48,51 +50,51 @@ namespace AMDiS {
}
/// Writes a ParaView-VTK file.
int writeFile(std::string name);
int writeFile(string name);
/// Writes a pvtu file, which contains the links to all the rank files.
void writeParallelFile(std::string name, int nRanks,
std::string fnPrefix, std::string fnPostfix);
void writeParallelFile(string name, int nRanks,
string fnPrefix, string fnPostfix);
/// May be used to simply write ParaView files.
static void writeFile(DOFVector<double> *values,
std::string filename,
string filename,
bool writeParallel = true);
/// May be used to simply write ParaView files.
static void writeFile(DOFVector<double> &values,
std::string filename,
string filename,
bool writeParallel = true)
{
writeFile(&values, filename, writeParallel);
}
/// May be used to simply write ParaView files with a list of values.
static void writeFile(std::vector<DOFVector<double>*> &values,
std::string filename,
static void writeFile(vector<DOFVector<double>*> &values,
string filename,
bool writeParallel = true);
static void writeFile(WorldVector<DOFVector<double>*> &values,
std::string filename,
string filename,
bool writeParallel = true);
static void writeFile(DOFVector<WorldVector<double> > *values,
std::string filename,
string filename,
bool writeParallel = true);
static void writeFile(DOFVector<WorldVector<double> > &values,
std::string filename,
string filename,
bool writeParallel = true)
{
writeFile(&values, filename, writeParallel);
}
static void writeFile(SystemVector *values,
std::string filename,
string filename,
bool writeParallel = true);
static void writeFile(std::vector<DataCollector*> &dcList,
std::string filename,
static void writeFile(vector<DataCollector*> &dcList,
string filename,
bool writeParallel = true);
/// Set a compressing method for file output.
......@@ -102,9 +104,10 @@ namespace AMDiS {
}
/// Adds a new entry to a ParaView animation file.
static int updateAnimationFile(std::string valueFilename,
std::vector< std::string > *paraViewAnimationFrames,
std::string animationFilename);
static int updateAnimationFile(AdaptInfo *adaptInfo,
string valueFilename,
vector<pair<double, string> > *paraViewAnimationFrames,
string animationFilename);
protected:
/// Writes the VTK file to an arbitrary stream.
template<typename T>
......@@ -139,7 +142,7 @@ namespace AMDiS {
WorldVector<double> coord)
{
for (int i = 0; i < Global::getGeo(WORLD); i++)
file << " " << std::scientific << coord[i];
file << " " << scientific << coord[i];
for (int i = Global::getGeo(WORLD); i < 3; i++)
file << " "<<0.0;
......@@ -147,10 +150,10 @@ namespace AMDiS {
}
/// Writes a world coordinate to a given file.
inline void writeCoord(std::ofstream &file, WorldVector<double> coord)
inline void writeCoord(ofstream &file, WorldVector<double> coord)
{
for (int i = 0; i < Global::getGeo(WORLD); i++)
file << " " << std::scientific << coord[i];
file << " " << scientific << coord[i];
for (int i = Global::getGeo(WORLD); i < 3; i++)
file << " "<<0.0;
......@@ -159,7 +162,7 @@ namespace AMDiS {
private:
/// List of DataCollectors, for each component of the problem one.
std::vector<DataCollector*> *dataCollector;
vector<DataCollector*> *dataCollector;
/** \brief
* Defines if the file has to be compressed for ouput, and with which
......
AMDiS/src/io/VtkWriter.hh
View file @ 7cac7d4c
......@@ -16,6 +16,8 @@
namespace AMDiS {
using namespace std;
template<typename T>
void VtkWriter::writeFileToStream(T &file)
{
......@@ -98,15 +100,15 @@ namespace AMDiS {
template<typename T>
void VtkWriter::writeVertexCoords(T &file)
{
DOFVector< std::list<VertexInfo> > *vertexInfos =
DOFVector<list<VertexInfo> > *vertexInfos =