/**
* Create a netCdf-file
* Any existing file will be replaced.
*
* @param i_baseName base name of the netCDF-file to which the data will be written to.
* @param i_nX number of cells in the horizontal direction.
* @param i_nY number of cells in the vertical direction.
* @param i_dX cell size in x-direction.
* @param i_dY cell size in y-direction.
* @param i_originX
* @param i_originY
*/
io::NetCdfWriter::NetCdfWriter( const std::string &i_baseName,
const Float2D &i_b,
int i_nX, int i_nY,
float i_dX, float i_dY,
float i_originX, float i_originY) :
io::Writer(i_baseName + ".nc", i_b,{{1, 1, 1, 1}}, i_nX, i_nY),
flush(0) {
int status;
status = nc_create(fileName.c_str(), NC_NETCDF4, &dataFile);
//check if the netCDF-file open command succeeded.
if (status != NC_NOERR) {
assert(false);
return;
}
//dimensions
int l_timeDim, l_xDim, l_yDim;
nc_def_dim(dataFile, "time", NC_UNLIMITED, &l_timeDim);
nc_def_dim(dataFile, "x", nX, &l_xDim);
nc_def_dim(dataFile, "y", nY, &l_yDim);
//variables (TODO: add rest of CF-1.5)
int l_xVar, l_yVar;
nc_def_var(dataFile, "time", NC_FLOAT, 1, &l_timeDim, &timeVar);
ncPutAttText(timeVar, "long_name", "Time");
ncPutAttText(timeVar, "units", "seconds since simulation start"); // the word "since" is important for the paraview reader
nc_def_var(dataFile, "x", NC_FLOAT, 1, &l_xDim, &l_xVar);
nc_def_var(dataFile, "y", NC_FLOAT, 1, &l_yDim, &l_yVar);
//variables, fastest changing index is on the right (C syntax), will be mirrored by the library
int dims[] = {l_timeDim, l_yDim, l_xDim};
nc_def_var(dataFile, "b", NC_FLOAT, 3, dims, &bVar);
//set attributes to match CF-1.5 convention
ncPutAttText(NC_GLOBAL, "Conventions", "CF-1.5");
ncPutAttText(NC_GLOBAL, "title", "Computed tsunami solution");
ncPutAttText(NC_GLOBAL, "history", "SWE");
ncPutAttText(NC_GLOBAL, "institution", "Technische Universitaet Muenchen, Department of Informatics, Chair of Scientific Computing");
ncPutAttText(NC_GLOBAL, "source", "Bathymetry and displacement data.");
ncPutAttText(NC_GLOBAL, "references", "http://www5.in.tum.de/SWE");
ncPutAttText(NC_GLOBAL, "comment", "SWE is free software and licensed under the GNU General Public License. Remark: In general this does not hold for the used input data.");
//setup grid size
float gridPosition = i_originX + (float).5 * i_dX;
for(size_t i = 0; i < nX; i++) {
nc_put_var1_float(dataFile, l_xVar, &i, &gridPosition);
gridPosition += i_dX;
}
gridPosition = i_originY + (float).5 * i_dY;
for(size_t j = 0; j < nY; j++) {
nc_put_var1_float(dataFile, l_yVar, &j, &gridPosition);
gridPosition += i_dY;
}
nc_sync(dataFile);
}
/**
* Encodes a BoundaryType and writes it to an attribute in the NetCDF-File
*
* @param varid The NetCDF variable ID
* @param name The attribute name
* @param boundaryType The type of the boundary
*/
void io::NetCdfWriter::ncPutBoundaryTypeAtt(int varid, const char *name, BoundaryType boundaryType) {
std::string boundaryTypeName;
switch(boundaryType) {
case WALL:
boundaryTypeName = std::string("wall");
break;
case OUTFLOW:
boundaryTypeName = std::string("outflow");
break;
case INFLOW:
boundaryTypeName = std::string("inflow");
break;
case PASSIVE:
boundaryTypeName = std::string("passive");
break;
case CONNECT:
boundaryTypeName = std::string("connect");
break;
default:
std::cerr << "WARNING: Unsupported BoundaryType in Checkpointing!" << std::endl;
assert(false);
return;
break;
}
ncPutAttText(varid, name, boundaryTypeName.c_str());
}
/**
* Create a netCdf-file
* Any existing file will be replaced.
*
* @param i_baseName base name of the netCDF-file to which the data will be written to.
* @param i_nX number of cells in the horizontal direction.
* @param i_nY number of cells in the vertical direction.
* @param i_dX cell size in x-direction.
* @param i_dY cell size in y-direction.
* @param i_originX
* @param i_originY
* @param i_flush If > 0, flush data to disk every i_flush write operation
* @param i_dynamicBathymetry
*/
io::NetCdfWriter::NetCdfWriter( const std::string &i_baseName,
const Float2D &i_b,
const BoundarySize &i_boundarySize,
int i_nX, int i_nY,
float i_dX, float i_dY,
float i_originX, float i_originY,
unsigned int i_flush,
size_t contTimestep,
unsigned int compression) :
//const bool &i_dynamicBathymetry) : //!TODO
io::Writer(i_baseName + ".nc", i_b, i_boundarySize, i_nX, i_nY, contTimestep),
flush(i_flush), compress(compression) {
int status;
if(contTimestep)
{
status = nc_open(fileName.c_str(), NC_WRITE, &dataFile);
//check if the netCDF-file open command succeeded.
if (status != NC_NOERR) {
assert(false);
return;
}
size_t l_length;
if(status = nc_inq_varid(dataFile, "time", &timeVar)) ERR(status);
if(status = nc_inq_varid(dataFile, "h", &hVar)) ERR(status);
if(status = nc_inq_varid(dataFile, "hu", &huVar)) ERR(status);
if(status = nc_inq_varid(dataFile, "hv", &hvVar)) ERR(status);
if(status = nc_inq_varid(dataFile, "b", &bVar)) ERR(status);
//if(status = nc_inq_dimlen(dataFile, timeVar, &timeStep)) ERR(status);
}
else {
//create a netCDF-file, an existing file will be replaced
status = nc_create(fileName.c_str(), NC_NETCDF4, &dataFile);
//check if the netCDF-file creation constructor succeeded.
if (status != NC_NOERR) {
assert(false);
return;
}
// std::cout << "i_nX, i_nY, i_dX, i_dY: " << nX << ", " << nY << ", " << i_dX << ", " << i_dY << std::endl;
adjust(nX, nY, i_dX, i_dY, compress);
// std::cout << "i_nX, i_nY, i_dX, i_dY: " << nX << ", " << nY << ", " << i_dX << ", " << i_dY << std::endl;
#ifdef PRINT_NETCDFWRITER_INFORMATION
std::cout << " *** io::NetCdfWriter::createNetCdfFile" << std::endl;
std::cout << " created/replaced: " << fileName << std::endl;
std::cout << " dimensions(nx, ny): " << nX << ", " << nY << std::endl;
std::cout << " cell width(dx,dy): " << i_dX << ", " << i_dY << std::endl;
std::cout << " origin(x,y): " << i_originX << ", " << i_originY << std::endl;
#endif
//dimensions
int l_timeDim, l_xDim, l_yDim;
nc_def_dim(dataFile, "time", NC_UNLIMITED, &l_timeDim);
nc_def_dim(dataFile, "x", nX, &l_xDim);
nc_def_dim(dataFile, "y", nY, &l_yDim);
//variables (TODO: add rest of CF-1.5)
int l_xVar, l_yVar;
nc_def_var(dataFile, "time", NC_FLOAT, 1, &l_timeDim, &timeVar);
ncPutAttText(timeVar, "long_name", "Time");
ncPutAttText(timeVar, "units", "seconds since simulation start"); // the word "since" is important for the paraview reader
nc_def_var(dataFile, "x", NC_FLOAT, 1, &l_xDim, &l_xVar);
nc_def_var(dataFile, "y", NC_FLOAT, 1, &l_yDim, &l_yVar);
//variables, fastest changing index is on the right (C syntax), will be mirrored by the library
int dims[] = {l_timeDim, l_yDim, l_xDim};
nc_def_var(dataFile, "h", NC_FLOAT, 3, dims, &hVar);
nc_def_var(dataFile, "hu", NC_FLOAT, 3, dims, &huVar);
nc_def_var(dataFile, "hv", NC_FLOAT, 3, dims, &hvVar);
nc_def_var(dataFile, "b", NC_FLOAT, 3, dims, &bVar);
//set attributes to match CF-1.5 convention
ncPutAttText(NC_GLOBAL, "Conventions", "CF-1.5");
ncPutAttText(NC_GLOBAL, "title", "Computed tsunami solution");
ncPutAttText(NC_GLOBAL, "history", "SWE");
ncPutAttText(NC_GLOBAL, "institution", "Technische Universitaet Muenchen, Department of Informatics, Chair of Scientific Computing");
ncPutAttText(NC_GLOBAL, "source", "Bathymetry and displacement data.");
ncPutAttText(NC_GLOBAL, "references", "http://www5.in.tum.de/SWE");
ncPutAttText(NC_GLOBAL, "comment", "SWE is free software and licensed under the GNU General Public License. Remark: In general this does not hold for the used input data.");
//setup grid size
float gridPosition = i_originX + (float).5 * i_dX;
for(size_t i = 0; i < nX; i++) {
nc_put_var1_float(dataFile, l_xVar, &i, &gridPosition);
gridPosition += i_dX;
}
gridPosition = i_originY + (float).5 * i_dY;
for(size_t j = 0; j < nY; j++) {
nc_put_var1_float(dataFile, l_yVar, &j, &gridPosition);
gridPosition += i_dY;
}
nc_sync(dataFile);
}
}
/**
* Create or open an existing netCdf-file
*
* If i_baseName appended with the ".nc" extension represents an existing
* NetCDF file, the file is opened and it is tried to append to the
* file (e.g. open a checkpoint-file of a previously crashed run)
*
* @param i_baseName base name of the netCDF-file to which the data will be written to.
* @param i_nX number of cells in the horizontal direction.
* @param i_nY number of cells in the vertical direction.
* @param i_dX cell size in x-direction.
* @param i_dY cell size in y-direction.
* @param i_originX
* @param i_originY
* @param i_coarseness The coarseness factor
* @param i_flush If > 0, flush data to disk every i_flush write operation
* @param i_dynamicBathymetry
*/
io::NetCdfWriter::NetCdfWriter( const std::string &i_baseName,
const Float2D &i_b,
const BoundarySize &i_boundarySize,
int i_nX, int i_nY,
float i_dX, float i_dY,
float i_originX, float i_originY,
float i_coarseness,
unsigned int i_flush) :
//const bool &i_dynamicBathymetry) : //!TODO
io::Writer(i_baseName + ".nc", i_b, i_boundarySize, i_nX, i_nY, i_coarseness),
flush(i_flush)
{
int status;
// variables (TODO: add rest of CF-1.5)
int l_xVar, l_yVar;
// dimensions
int l_timeDim, l_xDim, l_yDim;
// Try to open the file (to see if it is an existing checkpoint file)
status = nc_open(fileName.c_str(), NC_WRITE, &dataFile);
if(status == NC_NOERR) {
// File exists and is a NetCDF file we can write to
// Read ID for time, x, y, h, hu, hv and b dimensions and variables
status = nc_inq_unlimdim(dataFile, &l_timeDim);
status = nc_inq_dimid(dataFile, "x", &l_xDim);
status = nc_inq_dimid(dataFile, "y", &l_yDim);
status = nc_inq_varid(dataFile, "time", &timeVar);
status = nc_inq_varid(dataFile, "x", &l_xVar);
status = nc_inq_varid(dataFile, "y", &l_yVar);
status = nc_inq_varid(dataFile, "h", &hVar);
status = nc_inq_varid(dataFile, "hu", &huVar);
status = nc_inq_varid(dataFile, "hv", &hvVar);
status = nc_inq_varid(dataFile, "b", &bVar);
// Read Dimensions for x and y variable
size_t l_xLen, l_yLen;
status = nc_inq_dimlen(dataFile, l_xDim, &l_xLen);
status = nc_inq_dimlen(dataFile, l_yDim, &l_yLen);
// Set next timeStep
status = nc_inq_dimlen(dataFile, l_timeDim, &timeStep);
// Check actual dimensions in file against supplied dimensions
assert(l_xLen == coarseX); assert(l_yLen == coarseY);
} else {
// File does not exist or is not a valid NetCDF file
//create a netCDF-file, an existing file will be replaced
status = nc_create(fileName.c_str(), NC_NETCDF4, &dataFile);
//check if the netCDF-file creation constructor succeeded.
if (status != NC_NOERR) {
assert(false);
return;
}
#ifdef PRINT_NETCDFWRITER_INFORMATION
std::cout << " *** io::NetCdfWriter::createNetCdfFile" << std::endl;
std::cout << " created/replaced: " << fileName << std::endl;
std::cout << " internal dimensions(nx, ny): " << nX << ", " << nY << std::endl;
std::cout << " dimensions(nx, ny): " << coarseX << ", " << coarseY << std::endl;
std::cout << " coarseness: " << coarseness << std::endl;
std::cout << " cell width(dx,dy): " << i_dX << ", " << i_dY << std::endl;
std::cout << " origin(x,y): " << i_originX << ", " << i_originY << std::endl;
#endif
nc_def_dim(dataFile, "time", NC_UNLIMITED, &l_timeDim);
nc_def_dim(dataFile, "x", coarseX, &l_xDim);
nc_def_dim(dataFile, "y", coarseY, &l_yDim);
nc_def_var(dataFile, "time", NC_FLOAT, 1, &l_timeDim, &timeVar);
ncPutAttText(timeVar, "long_name", "Time");
ncPutAttText(timeVar, "units", "seconds since simulation start"); // the word "since" is important for the paraview reader
nc_def_var(dataFile, "x", NC_FLOAT, 1, &l_xDim, &l_xVar);
nc_def_var(dataFile, "y", NC_FLOAT, 1, &l_yDim, &l_yVar);
//variables, fastest changing index is on the right (C syntax), will be mirrored by the library
int dims[] = {l_timeDim, l_yDim, l_xDim};
nc_def_var(dataFile, "h", NC_FLOAT, 3, dims, &hVar);
nc_def_var(dataFile, "hu", NC_FLOAT, 3, dims, &huVar);
nc_def_var(dataFile, "hv", NC_FLOAT, 3, dims, &hvVar);
nc_def_var(dataFile, "b", NC_FLOAT, 2, &dims[1], &bVar);
//set attributes to match CF-1.5 convention
ncPutAttText(NC_GLOBAL, "Conventions", "CF-1.5");
ncPutAttText(NC_GLOBAL, "title", "Computed tsunami solution");
ncPutAttText(NC_GLOBAL, "history", "SWE");
ncPutAttText(NC_GLOBAL, "institution", "Technische Universitaet Muenchen, Department of Informatics, Chair of Scientific Computing");
ncPutAttText(NC_GLOBAL, "source", "Bathymetry and displacement data.");
ncPutAttText(NC_GLOBAL, "references", "http://www5.in.tum.de/SWE");
ncPutAttText(NC_GLOBAL, "comment", "SWE is free software and licensed under the GNU General Public License. Remark: In general this does not hold for the used input data.");
//setup grid size
float gridPosition = i_originX + (float).5 * i_dX;
for(size_t i = 0; i < coarseX; i++) {
nc_put_var1_float(dataFile, l_xVar, &i, &gridPosition);
gridPosition += i_dX;
}
gridPosition = i_originY + (float).5 * i_dY;
for(size_t j = 0; j < coarseY; j++) {
nc_put_var1_float(dataFile, l_yVar, &j, &gridPosition);
gridPosition += i_dY;
}
}
}
