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first hdf5-file dump implementation

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This commit is contained in:
Thorsten Liebig 2010-04-05 20:22:03 +02:00
parent 6288ebca91
commit 924f0a6d40
7 changed files with 232 additions and 40 deletions
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116
FDTD/processfields.cpp
View File

@ -17,10 +17,14 @@
#include "processfields.h"
#include "H5Cpp.h"
ProcessFields::ProcessFields(Operator* op, Engine* eng) : Processing(op, eng)
{
DumpMode=0;
DumpType = 0;
m_DumpMode = NO_INTERPOLATION;
m_DumpType = E_FIELD_DUMP;
// vtk-file is default
m_fileType = VTK_FILETYPE;
// SetSubSampling(1);
for (int n=0;n<3;++n)
@ -42,9 +46,68 @@ ProcessFields::~ProcessFields()
}
}
void ProcessFields::InitProcess()
{
string names[] = {"x","y","z"};
if (m_fileType==HDF5_FILETYPE)
{
unsigned int* NrLines;
double** Lines;
if (m_DumpMode==CELL_INTERPOLATE)
{
NrLines = numDLines;
Lines = discDLines;
}
else if (m_DumpMode==NO_INTERPOLATION)
{
NrLines = numLines;
Lines = discLines;
}
else
return;
m_fileName+= ".h5";
H5::H5File* file = new H5::H5File( m_fileName , H5F_ACC_TRUNC );
H5::Group* group = new H5::Group( file->createGroup( "/Mesh" ));
for (int n=0;n<3;++n)
{
hsize_t dimsf[1]; // dataset dimensions
dimsf[0] = NrLines[n];
H5::DataSpace dataspace( 1, dimsf );
H5::FloatType datatype( H5::PredType::NATIVE_FLOAT );
H5::DataSet dataset = group->createDataSet( names[n].c_str(), datatype, dataspace );
//convert to float...
float* array = new float[NrLines[n]];
for (int i=0;i<NrLines[n];++i)
array[i] = Lines[n][i];
//write to dataset
dataset.write( array, H5::PredType::NATIVE_FLOAT );
}
delete group;
group = new H5::Group( file->createGroup( "/FieldData" ));
delete group;
delete file;
}
}
string ProcessFields::GetFieldNameByType(DumpType type)
{
switch (type)
{
case E_FIELD_DUMP:
return "E-Field";
case H_FIELD_DUMP:
return "H-Field";
}
return "unknown field";
}
void ProcessFields::DefineStartStopCoord(double* dstart, double* dstop)
{
if (DumpMode==0)
if (m_DumpMode==NO_INTERPOLATION)
{
if (Op->SnapToMesh(dstart,start)==false) cerr << "ProcessFields::DefineStartStopCoord: Warning: Snapping problem, check start value!!" << endl;
if (Op->SnapToMesh(dstop,stop)==false) cerr << "ProcessFields::DefineStartStopCoord: Warning: Snapping problem, check stop value!!" << endl;
@ -69,7 +132,7 @@ void ProcessFields::DefineStartStopCoord(double* dstart, double* dstop)
}
}
}
else if (DumpMode==2)
else if (m_DumpMode==CELL_INTERPOLATE)
{
if (Op->SnapToMesh(dstart,start,true)==false) cerr << "ProcessFields::DefineStartStopCoord: Warning: Snapping problem, check start value!!" << endl;
if (Op->SnapToMesh(dstop,stop,true)==false) cerr << "ProcessFields::DefineStartStopCoord: Warning: Snapping problem, check stop value!!" << endl;
@ -86,7 +149,7 @@ void ProcessFields::DefineStartStopCoord(double* dstart, double* dstop)
}
++stop[n];
numDLines[n]=stop[n]-start[n];
// cerr << " number of lines " << numDLines[n] << endl;
// cerr << " number of lines " << numDLines[n] << endl;
delete[] discDLines[n];
discDLines[n] = new double[numDLines[n]];
for (unsigned int i=0;i<numDLines[n];++i)
@ -238,4 +301,47 @@ bool ProcessFields::DumpMultiScalarArray2VTK(ofstream &file, string names[], FDT
return true;
}
bool ProcessFields::DumpVectorArray2HDF5(string filename, string name, FDTD_FLOAT**** array, unsigned int* numLines)
{
const H5std_string FILE_NAME(filename);
const H5std_string DATASET_NAME( name );
H5::H5File file( FILE_NAME, H5F_ACC_RDWR );
H5::Group group( file.openGroup( "/FieldData" ));
hsize_t dimsf[4]; // dataset dimensions
dimsf[0] = 3;
dimsf[1] = numLines[2];
dimsf[2] = numLines[1];
dimsf[3] = numLines[0];
H5::DataSpace dataspace( 4, dimsf );
H5::FloatType datatype( H5::PredType::NATIVE_FLOAT );
// datatype.setOrder( H5T_ORDER_LE );
H5::DataSet dataset = group.createDataSet( DATASET_NAME, datatype, dataspace );
// I have not the slightest idea why this array-copy action is necessary... but it's the only way hdf5 does what it is supposed to do anyway!!
// at least it is save in case FDTD_FLOAT was defined as double...
// why does hdf5 write the dimensions backwards??? or matlab???
float hdf5array[3][numLines[2]][numLines[1]][numLines[0]];
for (int n=0;n<3;++n)
{
for (unsigned int i=0;i<numLines[0];++i)
{
for (unsigned int j=0;j<numLines[1];++j)
{
for (unsigned int k=0;k<numLines[2];++k)
{
hdf5array[n][k][j][i] = array[n][i][j][k];
}
}
}
}
dataset.write( hdf5array, H5::PredType::NATIVE_FLOAT );
return true;
}

28
FDTD/processfields.h
View File

@ -27,37 +27,53 @@ public:
ProcessFields(Operator* op, Engine* eng);
virtual ~ProcessFields();
enum FileType { VTK_FILETYPE, HDF5_FILETYPE};
enum DumpType { E_FIELD_DUMP, H_FIELD_DUMP};
enum DumpMode { NO_INTERPOLATION, NODE_INTERPOLATE, CELL_INTERPOLATE};
virtual void InitProcess();
virtual void DefineStartStopCoord(double* dstart, double* dstop);
// virtual void SetSubSampling(unsigned int subSampleRate, int dir=-1);
//! Used file pattern e.g. pattern="tmp/efield_" --> "tmp/efield_000045.vtk" for timestep 45 or "tmp/efield_2.40000e9.vtk" for 2.4GHz E-field dump.
//! Used file pattern e.g. pattern="tmp/efield_" --> "tmp/efield_000045.vtk" for timestep 45 or "tmp/efield_2.40000e9.vtk" for 2.4GHz E-field dump. (VTK FileType only) \sa SetFileType
void SetFilePattern(string fp) {filePattern=fp;}
//! Set the filename for a hdf5 data group file (HDF5 FileType only) \sa SetFileType
void SetFileName(string fn) {m_fileName=fn;}
//! Define the Dump-Mode
void SetDumpMode(int mode) {DumpMode=mode;}
void SetDumpMode(DumpMode mode) {m_DumpMode=mode;}
//! This methode will dump all fields in the center of a main cell (dual-node) using 4 E-field and 2 H-fields per direction. (default)
void SetDumpMode2Cell() {DumpMode=2;}
void SetDumpMode2Cell() {m_DumpMode=CELL_INTERPOLATE;}
//! Set dump type: 0 for E-fields, 1 for H-fields, 2 for D-fields, 3 for B-fields, 4 for J-fields, etc...
void SetDumpType(int type) {DumpType=type;}
void SetDumpType(DumpType type) {m_DumpType=type;}
static bool DumpVectorArray2VTK(ofstream &file, string name, FDTD_FLOAT**** array, double** discLines, unsigned int* numLines);
static bool DumpMultiVectorArray2VTK(ofstream &file, string names[], FDTD_FLOAT**** array[], unsigned int numFields, double** discLines, unsigned int* numLines);
static bool DumpScalarArray2VTK(ofstream &file, string name, FDTD_FLOAT*** array, double** discLines, unsigned int* numLines);
static bool DumpMultiScalarArray2VTK(ofstream &file, string names[], FDTD_FLOAT*** array[], unsigned int numFields, double** discLines, unsigned int* numLines);
static bool DumpVectorArray2HDF5(string filename, string name, FDTD_FLOAT**** array, unsigned int* numLines);
double CalcTotalEnergy();
void SetFileType(FileType fileType) {m_fileType=fileType;}
// virtual void Process();
protected:
static void WriteVTKHeader(ofstream &file, double** discLines, unsigned int* numLines);
static void WriteVTKVectorArray(ofstream &file, string name, FDTD_FLOAT**** array, unsigned int* numLines);
static void WriteVTKScalarArray(ofstream &file, string name, FDTD_FLOAT*** array, unsigned int* numLines);
int DumpMode;
int DumpType;
static string GetFieldNameByType(DumpType type);
DumpMode m_DumpMode;
DumpType m_DumpType;
string filePattern;
string m_fileName;
FileType m_fileType;
// unsigned int subSample[3];

105
FDTD/processfields_td.cpp
View File

@ -29,12 +29,12 @@ ProcessFieldsTD::~ProcessFieldsTD()
{
}
void ProcessFieldsTD::DumpCellInterpol(ofstream &file)
void ProcessFieldsTD::DumpCellInterpol(string filename)
{
FDTD_FLOAT**** volt = Eng->GetVoltages();
FDTD_FLOAT**** curr = Eng->GetCurrents();
if (DumpType==0)
if (m_DumpType==E_FIELD_DUMP)
{
//create array
FDTD_FLOAT**** E_T = Create_N_3DArray(numDLines);
@ -66,12 +66,27 @@ void ProcessFieldsTD::DumpCellInterpol(ofstream &file)
}
}
}
DumpVectorArray2VTK(file,string("E-Field"),E_T,discDLines,numDLines);
if (m_fileType==VTK_FILETYPE)
{
ofstream file(filename.c_str());
if (file.is_open()==false) { cerr << "ProcessFieldsTD::Process: can't open file '" << filename << "' for writing... abort! " << endl;};
DumpVectorArray2VTK(file,string("E-Field"),E_T,discDLines,numDLines);
file.close();
}
else if (m_fileType==HDF5_FILETYPE)
{
stringstream ss;
ss << std::setw( pad_length ) << std::setfill( '0' ) << Eng->GetNumberOfTimesteps();
DumpVectorArray2HDF5(filename.c_str(),string( ss.str() ),E_T,numDLines);
}
else
cerr << "ProcessFieldsTD::DumpCellInterpol: unknown File-Type" << endl;
Delete_N_3DArray(E_T,numDLines);
E_T = NULL;
}
if (DumpType==1)
if (m_DumpType==1)
{
//create array
FDTD_FLOAT**** H_T = Create_N_3DArray(numDLines);
@ -104,20 +119,34 @@ void ProcessFieldsTD::DumpCellInterpol(ofstream &file)
}
}
}
DumpVectorArray2VTK(file,string("H-Field"),H_T,discDLines,numDLines);
if (m_fileType==VTK_FILETYPE)
{
ofstream file(filename.c_str());
if (file.is_open()==false) { cerr << "ProcessFieldsTD::Process: can't open file '" << filename << "' for writing... abort! " << endl;};
DumpVectorArray2VTK(file,string("H-Field"),H_T,discDLines,numDLines);
file.close();
}
else if (m_fileType==HDF5_FILETYPE)
{
stringstream ss;
ss << std::setw( pad_length ) << std::setfill( '0' ) << Eng->GetNumberOfTimesteps();
DumpVectorArray2HDF5(filename.c_str(),string( ss.str() ),H_T,numDLines);
}
else
cerr << "ProcessFieldsTD::DumpCellInterpol: unknown File-Type" << endl;
Delete_N_3DArray(H_T,numDLines);
H_T = NULL;
}
}
void ProcessFieldsTD::DumpNoInterpol(ofstream &file)
void ProcessFieldsTD::DumpNoInterpol(string filename)
{
FDTD_FLOAT**** volt = Eng->GetVoltages();
FDTD_FLOAT**** curr = Eng->GetCurrents();
unsigned int pos[3];
double delta[3];
if (DumpType==0)
if (m_DumpType==E_FIELD_DUMP)
{
//create array
FDTD_FLOAT**** E_T = Create_N_3DArray(numLines);
@ -136,12 +165,27 @@ void ProcessFieldsTD::DumpNoInterpol(ofstream &file)
}
}
}
DumpVectorArray2VTK(file,string("E-Field"),E_T,discLines,numLines);
if (m_fileType==VTK_FILETYPE)
{
ofstream file(filename.c_str());
if (file.is_open()==false) { cerr << "ProcessFieldsTD::Process: can't open file '" << filename << "' for writing... abort! " << endl;};
DumpVectorArray2VTK(file,string("E-Field"),E_T,discLines,numLines);
file.close();
}
else if (m_fileType==HDF5_FILETYPE)
{
stringstream ss;
ss << std::setw( pad_length ) << std::setfill( '0' ) << Eng->GetNumberOfTimesteps();
DumpVectorArray2HDF5(filename.c_str(),string( ss.str() ),E_T,numLines);
}
else
cerr << "ProcessFieldsTD::DumpCellInterpol: unknown File-Type" << endl;
Delete_N_3DArray(E_T,numLines);
E_T = NULL;
}
if (DumpType==1)
if (m_DumpType==H_FIELD_DUMP)
{
//create array
FDTD_FLOAT**** H_T = Create_N_3DArray(numLines);
@ -161,7 +205,22 @@ void ProcessFieldsTD::DumpNoInterpol(ofstream &file)
}
}
}
DumpVectorArray2VTK(file,string("H-Field"),H_T,discLines,numLines);
if (m_fileType==VTK_FILETYPE)
{
ofstream file(filename.c_str());
if (file.is_open()==false) { cerr << "ProcessFieldsTD::Process: can't open file '" << filename << "' for writing... abort! " << endl;};
DumpVectorArray2VTK(file,string("H-Field"),H_T,discLines,numLines);
file.close();
}
else if (m_fileType==HDF5_FILETYPE)
{
stringstream ss;
ss << std::setw( pad_length ) << std::setfill( '0' ) << Eng->GetNumberOfTimesteps();
DumpVectorArray2HDF5(filename.c_str(),string( ss.str() ),H_T,numLines);
}
else
cerr << "ProcessFieldsTD::DumpCellInterpol: unknown File-Type" << endl;
Delete_N_3DArray(H_T,numLines);
H_T = NULL;
}
@ -173,16 +232,22 @@ int ProcessFieldsTD::Process()
if (filePattern.empty()) return -1;
if (CheckTimestep()==false) return GetNextInterval();
stringstream ss;
ss << std::setw( pad_length ) << std::setfill( '0' ) << Eng->GetNumberOfTimesteps();
ss << filePattern << std::setw( pad_length ) << std::setfill( '0' ) << Eng->GetNumberOfTimesteps();
string filename = filePattern + ss.str() + ".vtk";
ofstream file(filename.c_str());
if (file.is_open()==false) { cerr << "ProcessFieldsTD::Process: can't open file '" << filename << "' for writing... abort! " << endl; return GetNextInterval();};
if (DumpMode==0)
DumpNoInterpol(file);
if (DumpMode==2)
DumpCellInterpol(file);
file.close();
if (m_fileType==VTK_FILETYPE)
{
ss << ".vtk";
if (m_DumpMode==NO_INTERPOLATION)
DumpNoInterpol(ss.str());
if (m_DumpMode==CELL_INTERPOLATE)
DumpCellInterpol(ss.str());
}
else if (m_fileType==HDF5_FILETYPE)
{
if (m_DumpMode==NO_INTERPOLATION)
DumpNoInterpol(m_fileName);
if (m_DumpMode==CELL_INTERPOLATE)
DumpCellInterpol(m_fileName);
}
return GetNextInterval();
}

4
FDTD/processfields_td.h
View File

@ -34,8 +34,8 @@ public:
protected:
int pad_length;
void DumpNoInterpol(ofstream &file);
void DumpCellInterpol(ofstream &file);
void DumpNoInterpol(string filename);
void DumpCellInterpol(string filename);
};
#endif // PROCESSFIELDS_TD_H

8
matlab/examples/PlaneWave.m
View File

@ -53,13 +53,13 @@ CSX = AddExcitation(CSX,'excite',0,[0 1 0]);
CSX = AddBox(CSX,'excite',0 ,start,stop);
%dump
CSX = AddDump(CSX,'Et_',0,0);
CSX = AddDump(CSX,'Et',0,0,1);
start = [mesh.x(1) , 0 , mesh.z(1)];
stop = [mesh.x(end) , 0 , mesh.z(end)];
CSX = AddBox(CSX,'Et_',0 , start,stop);
CSX = AddBox(CSX,'Et',0 , start,stop);
CSX = AddDump(CSX,'Ht_',1,0);
CSX = AddBox(CSX,'Ht_',0,start,stop);
CSX = AddDump(CSX,'Ht',1,0,1);
CSX = AddBox(CSX,'Ht',0,start,stop);
%Write openEMS compatoble xml-file
WriteOpenEMS([Sim_Path '/' Sim_CSX],FDTD,CSX);

4
openEMS.pro
View File

@ -15,10 +15,12 @@ LIBS += -L../CSXCAD \
-lfparser \
-L../tinyxml \
-ltinyxml \
-lboost_thread
-lboost_thread \
-lhdf5_cpp
QMAKE_LFLAGS += \'-Wl,-rpath,\$$ORIGIN/../CSXCAD\'
QMAKE_LFLAGS += \'-Wl,-rpath,\$$ORIGIN/../fparser\'
QMAKE_LFLAGS += \'-Wl,-rpath,\$$ORIGIN/../tinyxml\'
SOURCES += main.cpp \
tools/ErrorMsg.cpp \
tools/AdrOp.cpp \

7
openems.cpp
View File

@ -346,10 +346,13 @@ int openEMS::SetupFDTD(const char* file)
CSPropDumpBox* db = DumpProps.at(i)->ToDumpBox();
if (db)
{
ProcTD->SetDumpType(db->GetDumpType());
ProcTD->SetDumpMode(db->GetDumpMode());
ProcTD->SetDumpType((ProcessFields::DumpType)db->GetDumpType());
ProcTD->SetDumpMode((ProcessFields::DumpMode)db->GetDumpMode());
ProcTD->SetFileType((ProcessFields::FileType)db->GetFileType());
ProcTD->SetFilePattern(db->GetName());
ProcTD->SetFileName(db->GetName());
ProcTD->DefineStartStopCoord(start,stop);
ProcTD->InitProcess();
PA->AddProcessing(ProcTD);
}
else