int main(int argc, char ** argv) {
MPI_Init(&argc, &argv);
NcError error(NcError::silent_nonfatal);
try {
// Input filename
std::string strInputFile;
// Output filename
std::string strOutputFile;
// Separate topography file
std::string strTopographyFile;
// List of variables to extract
std::string strVariables;
// Extract geopotential height
bool fGeopotentialHeight;
// Pressure levels to extract
std::string strPressureLevels;
// Height levels to extract
std::string strHeightLevels;
// Extract variables at the surface
bool fExtractSurface;
// Extract total energy
bool fExtractTotalEnergy;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputFile, "in", "");
CommandLineString(strOutputFile, "out", "");
CommandLineString(strVariables, "var", "");
CommandLineBool(fGeopotentialHeight, "output_z");
CommandLineBool(fExtractTotalEnergy, "output_energy");
CommandLineString(strPressureLevels, "p", "");
CommandLineString(strHeightLevels, "z", "");
CommandLineBool(fExtractSurface, "surf");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check command line arguments
if (strInputFile == "") {
_EXCEPTIONT("No input file specified");
}
if (strOutputFile == "") {
_EXCEPTIONT("No output file specified");
}
if (strVariables == "") {
_EXCEPTIONT("No variables specified");
}
// Parse variable string
std::vector< std::string > vecVariableStrings;
ParseVariableList(strVariables, vecVariableStrings);
// Check variables
if (vecVariableStrings.size() == 0) {
_EXCEPTIONT("No variables specified");
}
// Parse pressure level string
std::vector<double> vecPressureLevels;
ParseLevelArray(strPressureLevels, vecPressureLevels);
int nPressureLevels = (int)(vecPressureLevels.size());
for (int k = 0; k < nPressureLevels; k++) {
if (vecPressureLevels[k] <= 0.0) {
_EXCEPTIONT("Non-positive pressure values not allowed");
}
}
// Parse height level string
std::vector<double> vecHeightLevels;
ParseLevelArray(strHeightLevels, vecHeightLevels);
int nHeightLevels = (int)(vecHeightLevels.size());
// Check pressure levels
if ((nPressureLevels == 0) &&
(nHeightLevels == 0) &&
(!fExtractSurface)
) {
_EXCEPTIONT("No pressure / height levels to process");
}
// Open input file
AnnounceStartBlock("Loading input file");
NcFile ncdf_in(strInputFile.c_str(), NcFile::ReadOnly);
if (!ncdf_in.is_valid()) {
_EXCEPTION1("Unable to open file \"%s\" for reading",
strInputFile.c_str());
}
// Load time array
Announce("Time");
NcVar * varTime = ncdf_in.get_var("time");
if (varTime == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"time\"",
strInputFile.c_str());
}
int nTime = varTime->get_dim(0)->size();
DataArray1D<double> dTime(nTime);
varTime->set_cur((long)0);
varTime->get(&(dTime[0]), nTime);
// Load latitude array
Announce("Latitude");
NcVar * varLat = ncdf_in.get_var("lat");
if (varLat == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"lat\"",
strInputFile.c_str());
}
int nLat = varLat->get_dim(0)->size();
DataArray1D<double> dLat(nLat);
varLat->set_cur((long)0);
varLat->get(&(dLat[0]), nLat);
// Load longitude array
Announce("Longitude");
NcVar * varLon = ncdf_in.get_var("lon");
if (varLon == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"lon\"",
strInputFile.c_str());
}
int nLon = varLon->get_dim(0)->size();
DataArray1D<double> dLon(nLon);
varLon->set_cur((long)0);
varLon->get(&(dLon[0]), nLon);
// Load level array
Announce("Level");
NcVar * varLev = ncdf_in.get_var("lev");
if (varLev == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"lev\"",
strInputFile.c_str());
}
int nLev = varLev->get_dim(0)->size();
DataArray1D<double> dLev(nLev);
varLev->set_cur((long)0);
varLev->get(&(dLev[0]), nLev);
// Load level interface array
Announce("Interface");
NcVar * varILev = ncdf_in.get_var("ilev");
int nILev = 0;
DataArray1D<double> dILev;
if (varILev == NULL) {
Announce("Warning: Variable \"ilev\" not found");
} else {
nILev = varILev->get_dim(0)->size();
if (nILev != nLev + 1) {
_EXCEPTIONT("Variable \"ilev\" must have size lev+1");
}
dILev.Allocate(nILev);
varILev->set_cur((long)0);
varILev->get(&(dILev[0]), nILev);
}
// Load topography
Announce("Topography");
NcVar * varZs = ncdf_in.get_var("Zs");
if (varZs == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"Zs\"",
strInputFile.c_str());
}
DataArray2D<double> dZs(nLat, nLon);
varZs->set_cur((long)0, (long)0);
varZs->get(&(dZs[0][0]), nLat, nLon);
AnnounceEndBlock("Done");
// Open output file
AnnounceStartBlock("Constructing output file");
NcFile ncdf_out(strOutputFile.c_str(), NcFile::Replace);
if (!ncdf_out.is_valid()) {
_EXCEPTION1("Unable to open file \"%s\" for writing",
strOutputFile.c_str());
}
CopyNcFileAttributes(&ncdf_in, &ncdf_out);
// Output time array
Announce("Time");
NcDim * dimOutTime = ncdf_out.add_dim("time");
NcVar * varOutTime = ncdf_out.add_var("time", ncDouble, dimOutTime);
varOutTime->set_cur((long)0);
varOutTime->put(&(dTime[0]), nTime);
CopyNcVarAttributes(varTime, varOutTime);
// Output pressure array
NcDim * dimOutP = NULL;
NcVar * varOutP = NULL;
if (nPressureLevels > 0) {
Announce("Pressure");
dimOutP = ncdf_out.add_dim("p", nPressureLevels);
varOutP = ncdf_out.add_var("p", ncDouble, dimOutP);
varOutP->set_cur((long)0);
varOutP->put(&(vecPressureLevels[0]), nPressureLevels);
}
// Output height array
NcDim * dimOutZ = NULL;
NcVar * varOutZ = NULL;
if (nHeightLevels > 0) {
Announce("Height");
dimOutZ = ncdf_out.add_dim("z", nHeightLevels);
varOutZ = ncdf_out.add_var("z", ncDouble, dimOutZ);
varOutZ->set_cur((long)0);
varOutZ->put(&(vecHeightLevels[0]), nHeightLevels);
}
// Output latitude and longitude array
Announce("Latitude");
NcDim * dimOutLat = ncdf_out.add_dim("lat", nLat);
NcVar * varOutLat = ncdf_out.add_var("lat", ncDouble, dimOutLat);
varOutLat->set_cur((long)0);
varOutLat->put(&(dLat[0]), nLat);
CopyNcVarAttributes(varLat, varOutLat);
Announce("Longitude");
NcDim * dimOutLon = ncdf_out.add_dim("lon", nLon);
NcVar * varOutLon = ncdf_out.add_var("lon", ncDouble, dimOutLon);
varOutLon->set_cur((long)0);
varOutLon->put(&(dLon[0]), nLon);
CopyNcVarAttributes(varLon, varOutLon);
// Output topography
Announce("Topography");
NcVar * varOutZs = ncdf_out.add_var(
"Zs", ncDouble, dimOutLat, dimOutLon);
varOutZs->set_cur((long)0, (long)0);
varOutZs->put(&(dZs[0][0]), nLat, nLon);
AnnounceEndBlock("Done");
// Done
AnnounceEndBlock("Done");
// Load all variables
Announce("Loading variables");
std::vector<NcVar *> vecNcVar;
for (int v = 0; v < vecVariableStrings.size(); v++) {
vecNcVar.push_back(ncdf_in.get_var(vecVariableStrings[v].c_str()));
if (vecNcVar[v] == NULL) {
_EXCEPTION1("Unable to load variable \"%s\" from file",
vecVariableStrings[v].c_str());
}
}
// Physical constants
Announce("Initializing thermodynamic variables");
NcAtt * attEarthRadius = ncdf_in.get_att("earth_radius");
double dEarthRadius = attEarthRadius->as_double(0);
NcAtt * attRd = ncdf_in.get_att("Rd");
double dRd = attRd->as_double(0);
NcAtt * attCp = ncdf_in.get_att("Cp");
double dCp = attCp->as_double(0);
double dGamma = dCp / (dCp - dRd);
NcAtt * attP0 = ncdf_in.get_att("P0");
double dP0 = attP0->as_double(0);
double dPressureScaling = dP0 * std::pow(dRd / dP0, dGamma);
NcAtt * attZtop = ncdf_in.get_att("Ztop");
double dZtop = attZtop->as_double(0);
// Input data
DataArray3D<double> dataIn(nLev, nLat, nLon);
DataArray3D<double> dataInt(nILev, nLat, nLon);
// Output data
DataArray2D<double> dataOut(nLat, nLon);
// Pressure in column
DataArray1D<double> dataColumnP(nLev);
// Height in column
DataArray1D<double> dataColumnZ(nLev);
DataArray1D<double> dataColumnIZ(nILev);
// Column weights
DataArray1D<double> dW(nLev);
DataArray1D<double> dIW(nILev);
// Loop through all times, pressure levels and variables
AnnounceStartBlock("Interpolating");
// Add energy variable
NcVar * varEnergy;
if (fExtractTotalEnergy) {
varEnergy = ncdf_out.add_var("TE", ncDouble, dimOutTime);
}
// Create output pressure variables
std::vector<NcVar *> vecOutNcVarP;
if (nPressureLevels > 0) {
for (int v = 0; v < vecVariableStrings.size(); v++) {
vecOutNcVarP.push_back(
ncdf_out.add_var(
vecVariableStrings[v].c_str(), ncDouble,
dimOutTime, dimOutP, dimOutLat, dimOutLon));
// Copy attributes
CopyNcVarAttributes(vecNcVar[v], vecOutNcVarP[v]);
}
}
// Create output height variables
std::vector<NcVar *> vecOutNcVarZ;
if (nHeightLevels > 0) {
for (int v = 0; v < vecVariableStrings.size(); v++) {
std::string strVarName = vecVariableStrings[v];
if (nPressureLevels > 0) {
strVarName += "z";
}
vecOutNcVarZ.push_back(
ncdf_out.add_var(
strVarName.c_str(), ncDouble,
dimOutTime, dimOutZ, dimOutLat, dimOutLon));
// Copy attributes
CopyNcVarAttributes(vecNcVar[v], vecOutNcVarZ[v]);
}
}
// Create output surface variable
std::vector<NcVar *> vecOutNcVarS;
if (fExtractSurface) {
for (int v = 0; v < vecVariableStrings.size(); v++) {
std::string strVarName = vecVariableStrings[v];
strVarName += "S";
vecOutNcVarS.push_back(
ncdf_out.add_var(
strVarName.c_str(), ncDouble,
dimOutTime, dimOutLat, dimOutLon));
// Copy attributes
CopyNcVarAttributes(vecNcVar[v], vecOutNcVarS[v]);
}
}
// Loop over all times
for (int t = 0; t < nTime; t++) {
char szAnnounce[256];
sprintf(szAnnounce, "Time %i", t);
AnnounceStartBlock(szAnnounce);
// Rho
DataArray3D<double> dataRho(nLev, nLat, nLon);
NcVar * varRho = ncdf_in.get_var("Rho");
if (varRho == NULL) {
_EXCEPTIONT("Unable to load variable \"Rho\" from file");
}
varRho->set_cur(t, 0, 0, 0);
varRho->get(&(dataRho[0][0][0]), 1, nLev, nLat, nLon);
// Pressure
DataArray3D<double> dataP(nLev, nLat, nLon);
if (nPressureLevels != 0) {
NcVar * varP = ncdf_in.get_var("P");
if (varP == NULL) {
_EXCEPTIONT("Unable to load variable \"P\" from file");
}
varP->set_cur(t, 0, 0, 0);
varP->get(&(dataP[0][0][0]), 1, nLev, nLat, nLon);
}
/*
// Populate pressure array
if (nPressureLevels > 0) {
// Calculate pointwise pressure
for (int k = 0; k < nLev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataP[k][i][j] = dPressureScaling
* exp(log(dataRho[k][i][j] * dataP[k][i][j]) * dGamma);
}
}
}
}
*/
// Height everywhere
DataArray3D<double> dataZ(nLev, nLat, nLon);
DataArray3D<double> dataIZ;
if (nILev != 0) {
dataIZ.Allocate(nILev, nLat, nLon);
}
// Populate height array
if ((nHeightLevels > 0) || (fGeopotentialHeight)) {
for (int k = 0; k < nLev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataZ[k][i][j] = dZs[i][j] + dLev[k] * (dZtop - dZs[i][j]);
}
}
}
for (int k = 0; k < nILev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataIZ[k][i][j] = dZs[i][j] + dILev[k] * (dZtop - dZs[i][j]);
}
}
}
}
// Loop through all pressure levels and variables
for (int v = 0; v < vecNcVar.size(); v++) {
bool fOnInterfaces = false;
// Load in the data array
vecNcVar[v]->set_cur(t, 0, 0, 0);
if (vecNcVar[v]->get_dim(1)->size() == nLev) {
vecNcVar[v]->get(&(dataIn[0][0][0]), 1, nLev, nLat, nLon);
Announce("%s (n)", vecVariableStrings[v].c_str());
} else if (vecNcVar[v]->get_dim(1)->size() == nILev) {
vecNcVar[v]->get(&(dataInt[0][0][0]), 1, nILev, nLat, nLon);
fOnInterfaces = true;
Announce("%s (i)", vecVariableStrings[v].c_str());
} else {
_EXCEPTION1("Variable \"%s\" has invalid level dimension",
vecVariableStrings[v].c_str());
}
// At the physical surface
if (fExtractSurface) {
if (fOnInterfaces) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataOut[i][j] = dataInt[0][i][j];
}
}
} else {
int kBegin = 0;
int kEnd = 3;
PolynomialInterp::LagrangianPolynomialCoeffs(
3, dLev, dW, 0.0);
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataIn[k][i][j];
}
}
}
}
// Write variable
vecOutNcVarS[v]->set_cur(t, 0, 0);
vecOutNcVarS[v]->put(&(dataOut[0][0]), 1, nLat, nLon);
}
// Loop through all pressure levels
for (int p = 0; p < nPressureLevels; p++) {
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Store column pressure
for (int k = 0; k < nLev; k++) {
dataColumnP[k] = dataP[k][i][j];
}
// Find weights
int kBegin = 0;
int kEnd = 0;
// On a pressure surface
InterpolationWeightsLinear(
vecPressureLevels[p],
dataColumnP,
kBegin,
kEnd,
dW);
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataIn[k][i][j];
}
}
}
// Write variable
vecOutNcVarP[v]->set_cur(t, p, 0, 0);
vecOutNcVarP[v]->put(&(dataOut[0][0]), 1, 1, nLat, nLon);
}
// Loop through all height levels
for (int z = 0; z < nHeightLevels; z++) {
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Find weights
int kBegin = 0;
int kEnd = 0;
// Interpolate from levels to z surfaces
if (!fOnInterfaces) {
for (int k = 0; k < nLev; k++) {
dataColumnZ[k] = dataZ[k][i][j];
}
InterpolationWeightsLinear(
vecHeightLevels[z],
dataColumnZ,
kBegin,
kEnd,
dW);
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataIn[k][i][j];
}
// Interpolate from interfaces to z surfaces
} else {
for (int k = 0; k < nILev; k++) {
dataColumnIZ[k] = dataIZ[k][i][j];
}
InterpolationWeightsLinear(
vecHeightLevels[z],
dataColumnIZ,
kBegin,
kEnd,
dIW);
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dIW[k] * dataInt[k][i][j];
}
}
}
}
// Write variable
vecOutNcVarZ[v]->set_cur(t, z, 0, 0);
vecOutNcVarZ[v]->put(&(dataOut[0][0]), 1, 1, nLat, nLon);
}
}
// Output geopotential height
if (fGeopotentialHeight) {
Announce("Geopotential height");
// Output variables
NcVar * varOutZ;
NcVar * varOutZs;
if (nPressureLevels > 0) {
varOutZ = ncdf_out.add_var(
"PHIZ", ncDouble, dimOutTime, dimOutP, dimOutLat, dimOutLon);
}
if (fExtractSurface) {
varOutZs = ncdf_out.add_var(
"PHIZS", ncDouble, dimOutTime, dimOutLat, dimOutLon);
}
// Interpolate onto pressure levels
for (int p = 0; p < nPressureLevels; p++) {
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
int kBegin = 0;
int kEnd = 0;
for (int k = 0; k < nLev; k++) {
dataColumnP[k] = dataP[k][i][j];
}
InterpolationWeightsLinear(
vecPressureLevels[p],
dataColumnP,
kBegin,
kEnd,
dW);
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataZ[k][i][j];
}
}
}
// Write variable
varOutZ->set_cur(t, p, 0, 0);
varOutZ->put(&(dataOut[0][0]), 1, 1, nLat, nLon);
}
// Interpolate onto the physical surface
if (fExtractSurface) {
int kBegin = 0;
int kEnd = 3;
PolynomialInterp::LagrangianPolynomialCoeffs(
3, dLev, dW, 0.0);
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataZ[k][i][j];
}
}
}
// Write variable
varOutZs->set_cur(t, 0, 0);
varOutZs->put(&(dataOut[0][0]), 1, nLat, nLon);
}
}
// Extract total energy
if (fExtractTotalEnergy) {
Announce("Total Energy");
// Zonal velocity
DataArray3D<double> dataU(nLev, nLat, nLon);
NcVar * varU = ncdf_in.get_var("U");
varU->set_cur(t, 0, 0, 0);
varU->get(&(dataU[0][0][0]), 1, nLev, nLat, nLon);
// Meridional velocity
DataArray3D<double> dataV(nLev, nLat, nLon);
NcVar * varV = ncdf_in.get_var("V");
varV->set_cur(t, 0, 0, 0);
varV->get(&(dataV[0][0][0]), 1, nLev, nLat, nLon);
// Vertical velocity
DataArray3D<double> dataW(nLev, nLat, nLon);
NcVar * varW = ncdf_in.get_var("W");
varW->set_cur(t, 0, 0, 0);
varW->get(&(dataW[0][0][0]), 1, nLev, nLat, nLon);
// Calculate total energy
double dTotalEnergy = 0.0;
double dElementRefArea =
dEarthRadius * dEarthRadius
* M_PI / static_cast<double>(nLat)
* 2.0 * M_PI / static_cast<double>(nLon);
for (int k = 0; k < nLev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
double dKineticEnergy =
0.5 * dataRho[k][i][j] *
( dataU[k][i][j] * dataU[k][i][j]
+ dataV[k][i][j] * dataV[k][i][j]
+ dataW[k][i][j] * dataW[k][i][j]);
double dInternalEnergy =
dataP[k][i][j] / (dGamma - 1.0);
dTotalEnergy +=
(dKineticEnergy + dInternalEnergy)
* std::cos(M_PI * dLat[i] / 180.0) * dElementRefArea
* (dZtop - dZs[i][j]) / static_cast<double>(nLev);
}
}
}
// Put total energy into file
varEnergy->set_cur(t);
varEnergy->put(&dTotalEnergy, 1);
}
AnnounceEndBlock("Done");
}
AnnounceEndBlock("Done");
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
// Finalize MPI
MPI_Finalize();
}
int main(int argc, char** argv) {
NcError error(NcError::silent_nonfatal);
try {
// Input data file
std::string strInputData;
// Input map file
std::string strInputMap;
// List of variables
std::string strVariables;
// Input data file (second instance)
std::string strInputData2;
// Input map file (second instance)
std::string strInputMap2;
// List of variables (second instance)
std::string strVariables2;
// Output data file
std::string strOutputData;
// Name of the ncol variable
std::string strNColName;
// Output as double
bool fOutputDouble;
// List of variables to preserve
std::string strPreserveVariables;
// Preserve all non-remapped variables
bool fPreserveAll;
// Fill value override
double dFillValueOverride;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputData, "in_data", "");
CommandLineString(strInputMap, "map", "");
CommandLineString(strVariables, "var", "");
CommandLineString(strInputData2, "in_data2", "");
CommandLineString(strInputMap2, "map2", "");
CommandLineString(strVariables2, "var2", "");
CommandLineString(strOutputData, "out_data", "");
CommandLineString(strNColName, "ncol_name", "ncol");
CommandLineBool(fOutputDouble, "out_double");
CommandLineString(strPreserveVariables, "preserve", "");
CommandLineBool(fPreserveAll, "preserveall");
CommandLineDouble(dFillValueOverride, "fillvalue", 0.0);
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check parameters
if (strInputMap == "") {
_EXCEPTIONT("No map specified");
}
if (strInputData == "") {
_EXCEPTIONT("No input data specified");
}
if (strOutputData == "") {
_EXCEPTIONT("No output data specified");
}
// Parse variable list
std::vector< std::string > vecVariableStrings;
ParseVariableList(strVariables, vecVariableStrings);
// Parse preserve variable list
std::vector< std::string > vecPreserveVariableStrings;
ParseVariableList(strPreserveVariables, vecPreserveVariableStrings);
if (fPreserveAll && (vecPreserveVariableStrings.size() != 0)) {
_EXCEPTIONT("--preserveall and --preserve cannot both be specified");
}
// Second input data file
std::vector< std::string > vecVariableStrings2;
if (strInputData2 != "") {
ParseVariableList(strVariables2, vecVariableStrings2);
if (vecVariableStrings2.size() == 0) {
_EXCEPTIONT("No variables specified for --in_data2");
}
if (strInputMap2 == "") {
_EXCEPTIONT("No map specified for --in_data2");
}
}
if ((strInputMap2 != "") && (strInputData2 == "")) {
_EXCEPTIONT("No input data specified for --map2");
}
// Apply OfflineMap to data
if (strInputMap2 == "") {
AnnounceStartBlock("Applying offline map to data");
} else {
AnnounceStartBlock("Applying first offline map to data");
}
// OfflineMap
OfflineMap mapRemap;
mapRemap.Read(strInputMap);
mapRemap.SetFillValueOverride(static_cast<float>(dFillValueOverride));
mapRemap.Apply(
strInputData,
strOutputData,
vecVariableStrings,
strNColName,
fOutputDouble,
false);
AnnounceEndBlock(NULL);
if (strInputMap2 != "") {
AnnounceStartBlock("Applying second offline map to data");
// OfflineMap
OfflineMap mapRemap2;
mapRemap2.Read(strInputMap2);
// Verify consistency of maps
SparseMatrix<double> & smatRemap = mapRemap .GetSparseMatrix();
SparseMatrix<double> & smatRemap2 = mapRemap2.GetSparseMatrix();
if ((smatRemap.GetRows() != smatRemap2.GetRows()) ||
(smatRemap.GetColumns() != smatRemap2.GetColumns())
) {
_EXCEPTIONT("Mismatch in dimensions of input maps "
"--map and --map2");
}
mapRemap2.Apply(
strInputData2,
strOutputData,
vecVariableStrings2,
strNColName,
false,
true);
AnnounceEndBlock(NULL);
}
// Copy variables from input file to output file
if (fPreserveAll) {
AnnounceStartBlock("Preserving variables");
mapRemap.PreserveAllVariables(strInputData, strOutputData);
AnnounceEndBlock(NULL);
} else if (vecPreserveVariableStrings.size() != 0) {
AnnounceStartBlock("Preserving variables");
mapRemap.PreserveVariables(
strInputData,
strOutputData,
vecPreserveVariableStrings);
AnnounceEndBlock(NULL);
}
AnnounceBanner();
return (0);
} catch(Exception & e) {
Announce(e.ToString().c_str());
return (-1);
} catch(...) {
return (-2);
}
}
int main(int argc, char** argv) {
NcError error(NcError::silent_nonfatal);
try {
// Input / Output types
enum DiscretizationType {
DiscretizationType_FV,
DiscretizationType_CGLL,
DiscretizationType_DGLL
};
// Input mesh file
std::string strInputMesh;
// Overlap mesh file
std::string strOverlapMesh;
// Input metadata file
std::string strInputMeta;
// Output metadata file
std::string strOutputMeta;
// Input data type
std::string strInputType;
// Output data type
std::string strOutputType;
// Order of polynomial in each element
int nPin;
// Order of polynomial in each output element
int nPout;
// Use bubble on interior of spectral element nodes
bool fBubble;
// Enforce monotonicity
bool fMonotoneType1;
// Enforce monotonicity
bool fMonotoneType2;
// Enforce monotonicity
bool fMonotoneType3;
// Volumetric remapping
bool fVolumetric;
// No conservation
bool fNoConservation;
// Turn off checking for conservation / consistency
bool fNoCheck;
// Output mesh file
std::string strOutputMesh;
// Variable list
std::string strVariables;
// Output map file
std::string strOutputMap;
// Input data file
std::string strInputData;
// Output data file
std::string strOutputData;
// Name of the ncol variable
std::string strNColName;
// Output as double
bool fOutputDouble;
// List of variables to preserve
std::string strPreserveVariables;
// Preserve all non-remapped variables
bool fPreserveAll;
// Fill value override
double dFillValueOverride;
// Parse the command line
BeginCommandLine()
//CommandLineStringD(strMethod, "method", "", "[se]");
CommandLineString(strInputMesh, "in_mesh", "");
CommandLineString(strOutputMesh, "out_mesh", "");
CommandLineString(strOverlapMesh, "ov_mesh", "");
CommandLineString(strInputMeta, "in_meta", "");
CommandLineString(strOutputMeta, "out_meta", "");
CommandLineStringD(strInputType, "in_type", "fv", "[fv|cgll|dgll]");
CommandLineStringD(strOutputType, "out_type", "fv", "[fv|cgll|dgll]");
CommandLineInt(nPin, "in_np", 4);
CommandLineInt(nPout, "out_np", 4);
CommandLineBool(fBubble, "bubble");
CommandLineBool(fMonotoneType1, "mono");
CommandLineBool(fMonotoneType2, "mono2");
CommandLineBool(fMonotoneType3, "mono3");
CommandLineBool(fVolumetric, "volumetric");
CommandLineBool(fNoConservation, "noconserve");
CommandLineBool(fNoCheck, "nocheck");
CommandLineString(strVariables, "var", "");
CommandLineString(strOutputMap, "out_map", "");
CommandLineString(strInputData, "in_data", "");
CommandLineString(strOutputData, "out_data", "");
CommandLineString(strNColName, "ncol_name", "ncol");
CommandLineBool(fOutputDouble, "out_double");
CommandLineString(strPreserveVariables, "preserve", "");
CommandLineBool(fPreserveAll, "preserveall");
CommandLineDouble(dFillValueOverride, "fillvalue", 0.0);
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check command line parameters (mesh arguments)
if (strInputMesh == "") {
_EXCEPTIONT("No input mesh (--in_mesh) specified");
}
if (strOutputMesh == "") {
_EXCEPTIONT("No output mesh (--out_mesh) specified");
}
// Overlap mesh
if (strOverlapMesh == "") {
_EXCEPTIONT("No overlap mesh specified");
}
// Check command line parameters (data arguments)
if ((strInputData != "") && (strOutputData == "")) {
_EXCEPTIONT("--in_data specified without --out_data");
}
if ((strInputData == "") && (strOutputData != "")) {
_EXCEPTIONT("--out_data specified without --in_data");
}
// Check metadata parameters
if ((strInputMeta != "") && (strInputType == "fv")) {
_EXCEPTIONT("--in_meta cannot be used with --in_type fv");
}
if ((strOutputMeta != "") && (strOutputType == "fv")) {
_EXCEPTIONT("--out_meta cannot be used with --out_type fv");
}
// Check command line parameters (data type arguments)
STLStringHelper::ToLower(strInputType);
STLStringHelper::ToLower(strOutputType);
DiscretizationType eInputType;
DiscretizationType eOutputType;
if (strInputType == "fv") {
eInputType = DiscretizationType_FV;
} else if (strInputType == "cgll") {
eInputType = DiscretizationType_CGLL;
} else if (strInputType == "dgll") {
eInputType = DiscretizationType_DGLL;
} else {
_EXCEPTION1("Invalid \"in_type\" value (%s), expected [fv|cgll|dgll]",
strInputType.c_str());
}
if (strOutputType == "fv") {
eOutputType = DiscretizationType_FV;
} else if (strOutputType == "cgll") {
eOutputType = DiscretizationType_CGLL;
} else if (strOutputType == "dgll") {
eOutputType = DiscretizationType_DGLL;
} else {
_EXCEPTION1("Invalid \"out_type\" value (%s), expected [fv|cgll|dgll]",
strOutputType.c_str());
}
// Monotonicity flags
int nMonotoneType = 0;
if (fMonotoneType1) {
nMonotoneType = 1;
}
if (fMonotoneType2) {
if (nMonotoneType != 0) {
_EXCEPTIONT("Only one of --mono, --mono2 and --mono3 may be set");
}
nMonotoneType = 2;
}
if (fMonotoneType3) {
if (nMonotoneType != 0) {
_EXCEPTIONT("Only one of --mono, --mono2 and --mono3 may be set");
}
nMonotoneType = 3;
}
/*
// Volumetric
if (fVolumetric && (nMonotoneType != 0)) {
_EXCEPTIONT("--volumetric cannot be used in conjunction with --mono#");
}
*/
// Create Offline Map
OfflineMap mapRemap;
// Initialize dimension information from file
AnnounceStartBlock("Initializing dimensions of map");
Announce("Input mesh");
mapRemap.InitializeSourceDimensionsFromFile(strInputMesh);
Announce("Output mesh");
mapRemap.InitializeTargetDimensionsFromFile(strOutputMesh);
AnnounceEndBlock(NULL);
// Parse variable list
std::vector< std::string > vecVariableStrings;
ParseVariableList(strVariables, vecVariableStrings);
// Parse preserve variable list
std::vector< std::string > vecPreserveVariableStrings;
ParseVariableList(strPreserveVariables, vecPreserveVariableStrings);
if (fPreserveAll && (vecPreserveVariableStrings.size() != 0)) {
_EXCEPTIONT("--preserveall and --preserve cannot both be specified");
}
// Load input mesh
AnnounceStartBlock("Loading input mesh");
Mesh meshInput(strInputMesh);
meshInput.RemoveZeroEdges();
AnnounceEndBlock(NULL);
// Calculate Face areas
AnnounceStartBlock("Calculating input mesh Face areas");
double dTotalAreaInput = meshInput.CalculateFaceAreas();
Announce("Input Mesh Geometric Area: %1.15e", dTotalAreaInput);
AnnounceEndBlock(NULL);
// Input mesh areas
if (eInputType == DiscretizationType_FV) {
mapRemap.SetSourceAreas(meshInput.vecFaceArea);
}
// Load output mesh
AnnounceStartBlock("Loading output mesh");
Mesh meshOutput(strOutputMesh);
meshOutput.RemoveZeroEdges();
AnnounceEndBlock(NULL);
// Calculate Face areas
AnnounceStartBlock("Calculating output mesh Face areas");
Real dTotalAreaOutput = meshOutput.CalculateFaceAreas();
Announce("Output Mesh Geometric Area: %1.15e", dTotalAreaOutput);
AnnounceEndBlock(NULL);
// Output mesh areas
if (eOutputType == DiscretizationType_FV) {
mapRemap.SetTargetAreas(meshOutput.vecFaceArea);
}
// Load overlap mesh
AnnounceStartBlock("Loading overlap mesh");
Mesh meshOverlap(strOverlapMesh);
meshOverlap.RemoveZeroEdges();
// Verify that overlap mesh is in the correct order
int ixSourceFaceMax = (-1);
int ixTargetFaceMax = (-1);
if (meshOverlap.vecSourceFaceIx.size() !=
meshOverlap.vecTargetFaceIx.size()
) {
_EXCEPTIONT("Invalid overlap mesh:\n"
" Possible mesh file corruption?");
}
for (int i = 0; i < meshOverlap.vecSourceFaceIx.size(); i++) {
if (meshOverlap.vecSourceFaceIx[i] + 1 > ixSourceFaceMax) {
ixSourceFaceMax = meshOverlap.vecSourceFaceIx[i] + 1;
}
if (meshOverlap.vecTargetFaceIx[i] + 1 > ixTargetFaceMax) {
ixTargetFaceMax = meshOverlap.vecTargetFaceIx[i] + 1;
}
}
// Check for forward correspondence in overlap mesh
if (ixSourceFaceMax == meshInput.faces.size() //&&
//(ixTargetFaceMax == meshOutput.faces.size())
) {
Announce("Overlap mesh forward correspondence found");
// Check for reverse correspondence in overlap mesh
} else if (
ixSourceFaceMax == meshOutput.faces.size() //&&
//(ixTargetFaceMax == meshInput.faces.size())
) {
Announce("Overlap mesh reverse correspondence found (reversing)");
// Reorder overlap mesh
meshOverlap.ExchangeFirstAndSecondMesh();
// No correspondence found
} else {
_EXCEPTION2("Invalid overlap mesh:\n"
" No correspondence found with input and output meshes (%i,%i)",
ixSourceFaceMax, ixTargetFaceMax);
}
AnnounceEndBlock(NULL);
// Calculate Face areas
AnnounceStartBlock("Calculating overlap mesh Face areas");
Real dTotalAreaOverlap = meshOverlap.CalculateFaceAreas();
Announce("Overlap Mesh Area: %1.15e", dTotalAreaOverlap);
AnnounceEndBlock(NULL);
// Partial cover
if (fabs(dTotalAreaOverlap - dTotalAreaInput) > 1.0e-10) {
if (!fNoCheck) {
Announce("WARNING: Significant mismatch between overlap mesh area "
"and input mesh area.\n Automatically enabling --nocheck");
fNoCheck = true;
}
}
/*
// Recalculate input mesh area from overlap mesh
if (fabs(dTotalAreaOverlap - dTotalAreaInput) > 1.0e-10) {
AnnounceStartBlock("Overlap mesh only covers a sub-area of the sphere");
Announce("Recalculating source mesh areas");
dTotalAreaInput = meshInput.CalculateFaceAreasFromOverlap(meshOverlap);
Announce("New Input Mesh Geometric Area: %1.15e", dTotalAreaInput);
AnnounceEndBlock(NULL);
}
*/
// Finite volume input / Finite volume output
if ((eInputType == DiscretizationType_FV) &&
(eOutputType == DiscretizationType_FV)
) {
// Generate reverse node array and edge map
meshInput.ConstructReverseNodeArray();
meshInput.ConstructEdgeMap();
// Initialize coordinates for map
mapRemap.InitializeSourceCoordinatesFromMeshFV(meshInput);
mapRemap.InitializeTargetCoordinatesFromMeshFV(meshOutput);
// Construct OfflineMap
AnnounceStartBlock("Calculating offline map");
LinearRemapFVtoFV(
meshInput, meshOutput, meshOverlap, nPin, mapRemap);
// Finite volume input / Finite element output
} else if (eInputType == DiscretizationType_FV) {
DataMatrix3D<int> dataGLLNodes;
DataMatrix3D<double> dataGLLJacobian;
if (strOutputMeta != "") {
AnnounceStartBlock("Loading meta data file");
LoadMetaDataFile(strOutputMeta, dataGLLNodes, dataGLLJacobian);
AnnounceEndBlock(NULL);
} else {
AnnounceStartBlock("Generating output mesh meta data");
double dNumericalArea =
GenerateMetaData(
meshOutput,
nPout,
fBubble,
dataGLLNodes,
dataGLLJacobian);
Announce("Output Mesh Numerical Area: %1.15e", dNumericalArea);
AnnounceEndBlock(NULL);
}
// Initialize coordinates for map
mapRemap.InitializeSourceCoordinatesFromMeshFV(meshInput);
mapRemap.InitializeTargetCoordinatesFromMeshFE(
meshOutput, nPout, dataGLLNodes);
// Generate the continuous Jacobian
bool fContinuous = (eOutputType == DiscretizationType_CGLL);
if (eOutputType == DiscretizationType_CGLL) {
GenerateUniqueJacobian(
dataGLLNodes,
dataGLLJacobian,
mapRemap.GetTargetAreas());
} else {
GenerateDiscontinuousJacobian(
dataGLLJacobian,
mapRemap.GetTargetAreas());
}
// Generate reverse node array and edge map
meshInput.ConstructReverseNodeArray();
meshInput.ConstructEdgeMap();
// Generate remap weights
AnnounceStartBlock("Calculating offline map");
if (fVolumetric) {
LinearRemapFVtoGLL_Volumetric(
meshInput,
meshOutput,
meshOverlap,
dataGLLNodes,
dataGLLJacobian,
mapRemap.GetTargetAreas(),
nPin,
mapRemap,
nMonotoneType,
fContinuous,
fNoConservation);
} else {
LinearRemapFVtoGLL(
meshInput,
meshOutput,
meshOverlap,
dataGLLNodes,
dataGLLJacobian,
mapRemap.GetTargetAreas(),
nPin,
mapRemap,
nMonotoneType,
fContinuous,
fNoConservation);
}
// Finite element input / Finite volume output
} else if (
(eInputType != DiscretizationType_FV) &&
(eOutputType == DiscretizationType_FV)
) {
DataMatrix3D<int> dataGLLNodes;
DataMatrix3D<double> dataGLLJacobian;
if (strInputMeta != "") {
AnnounceStartBlock("Loading meta data file");
LoadMetaDataFile(strInputMeta, dataGLLNodes, dataGLLJacobian);
AnnounceEndBlock(NULL);
} else {
AnnounceStartBlock("Generating input mesh meta data");
double dNumericalArea =
GenerateMetaData(
meshInput,
nPin,
fBubble,
dataGLLNodes,
dataGLLJacobian);
Announce("Input Mesh Numerical Area: %1.15e", dNumericalArea);
AnnounceEndBlock(NULL);
if (fabs(dNumericalArea - dTotalAreaInput) > 1.0e-12) {
Announce("WARNING: Significant mismatch between input mesh "
"numerical area and geometric area");
}
}
if (dataGLLNodes.GetSubColumns() != meshInput.faces.size()) {
_EXCEPTIONT("Number of element does not match between metadata and "
"input mesh");
}
// Initialize coordinates for map
mapRemap.InitializeSourceCoordinatesFromMeshFE(
meshInput, nPin, dataGLLNodes);
mapRemap.InitializeTargetCoordinatesFromMeshFV(meshOutput);
// Generate the continuous Jacobian for input mesh
bool fContinuousIn = (eInputType == DiscretizationType_CGLL);
if (eInputType == DiscretizationType_CGLL) {
GenerateUniqueJacobian(
dataGLLNodes,
dataGLLJacobian,
mapRemap.GetSourceAreas());
} else {
GenerateDiscontinuousJacobian(
dataGLLJacobian,
mapRemap.GetSourceAreas());
}
// Generate offline map
AnnounceStartBlock("Calculating offline map");
if (fVolumetric) {
_EXCEPTIONT("Unimplemented: Volumetric currently unavailable for"
"GLL input mesh");
}
LinearRemapSE4(
meshInput,
meshOutput,
meshOverlap,
dataGLLNodes,
dataGLLJacobian,
nMonotoneType,
fContinuousIn,
fNoConservation,
mapRemap
);
// Finite element input / Finite element output
} else if (
(eInputType != DiscretizationType_FV) &&
(eOutputType != DiscretizationType_FV)
) {
DataMatrix3D<int> dataGLLNodesIn;
DataMatrix3D<double> dataGLLJacobianIn;
DataMatrix3D<int> dataGLLNodesOut;
DataMatrix3D<double> dataGLLJacobianOut;
// Input metadata
if (strInputMeta != "") {
AnnounceStartBlock("Loading input meta data file");
LoadMetaDataFile(
strInputMeta, dataGLLNodesIn, dataGLLJacobianIn);
AnnounceEndBlock(NULL);
} else {
AnnounceStartBlock("Generating input mesh meta data");
double dNumericalAreaIn =
GenerateMetaData(
meshInput,
nPin,
fBubble,
dataGLLNodesIn,
dataGLLJacobianIn);
Announce("Input Mesh Numerical Area: %1.15e", dNumericalAreaIn);
AnnounceEndBlock(NULL);
if (fabs(dNumericalAreaIn - dTotalAreaInput) > 1.0e-12) {
Announce("WARNING: Significant mismatch between input mesh "
"numerical area and geometric area");
}
}
// Output metadata
if (strOutputMeta != "") {
AnnounceStartBlock("Loading output meta data file");
LoadMetaDataFile(
strOutputMeta, dataGLLNodesOut, dataGLLJacobianOut);
AnnounceEndBlock(NULL);
} else {
AnnounceStartBlock("Generating output mesh meta data");
double dNumericalAreaOut =
GenerateMetaData(
meshOutput,
nPout,
fBubble,
dataGLLNodesOut,
dataGLLJacobianOut);
Announce("Output Mesh Numerical Area: %1.15e", dNumericalAreaOut);
AnnounceEndBlock(NULL);
if (fabs(dNumericalAreaOut - dTotalAreaOutput) > 1.0e-12) {
Announce("WARNING: Significant mismatch between output mesh "
"numerical area and geometric area");
}
}
// Initialize coordinates for map
mapRemap.InitializeSourceCoordinatesFromMeshFE(
meshInput, nPin, dataGLLNodesIn);
mapRemap.InitializeTargetCoordinatesFromMeshFE(
meshOutput, nPout, dataGLLNodesOut);
// Generate the continuous Jacobian for input mesh
bool fContinuousIn = (eInputType == DiscretizationType_CGLL);
if (eInputType == DiscretizationType_CGLL) {
GenerateUniqueJacobian(
dataGLLNodesIn,
dataGLLJacobianIn,
mapRemap.GetSourceAreas());
} else {
GenerateDiscontinuousJacobian(
dataGLLJacobianIn,
mapRemap.GetSourceAreas());
}
// Generate the continuous Jacobian for output mesh
bool fContinuousOut = (eOutputType == DiscretizationType_CGLL);
if (eOutputType == DiscretizationType_CGLL) {
GenerateUniqueJacobian(
dataGLLNodesOut,
dataGLLJacobianOut,
mapRemap.GetTargetAreas());
} else {
GenerateDiscontinuousJacobian(
dataGLLJacobianOut,
mapRemap.GetTargetAreas());
}
// Generate offline map
AnnounceStartBlock("Calculating offline map");
LinearRemapGLLtoGLL2(
meshInput,
meshOutput,
meshOverlap,
dataGLLNodesIn,
dataGLLJacobianIn,
dataGLLNodesOut,
dataGLLJacobianOut,
mapRemap.GetTargetAreas(),
nPin,
nPout,
nMonotoneType,
fContinuousIn,
fContinuousOut,
fNoConservation,
mapRemap
);
} else {
_EXCEPTIONT("Not implemented");
}
//#pragma warning "NOTE: VERIFICATION DISABLED"
// Verify consistency, conservation and monotonicity
if (!fNoCheck) {
AnnounceStartBlock("Verifying map");
mapRemap.IsConsistent(1.0e-8);
mapRemap.IsConservative(1.0e-8);
if (nMonotoneType != 0) {
mapRemap.IsMonotone(1.0e-12);
}
AnnounceEndBlock(NULL);
}
AnnounceEndBlock(NULL);
// Initialize element dimensions from input/output Mesh
AnnounceStartBlock("Writing output");
// Output the Offline Map
if (strOutputMap != "") {
AnnounceStartBlock("Writing offline map");
mapRemap.Write(strOutputMap);
AnnounceEndBlock(NULL);
}
// Apply Offline Map to data
if (strInputData != "") {
AnnounceStartBlock("Applying offline map to data");
mapRemap.SetFillValueOverride(static_cast<float>(dFillValueOverride));
mapRemap.Apply(
strInputData,
strOutputData,
vecVariableStrings,
strNColName,
fOutputDouble,
false);
AnnounceEndBlock(NULL);
}
AnnounceEndBlock(NULL);
// Copy variables from input file to output file
if ((strInputData != "") && (strOutputData != "")) {
if (fPreserveAll) {
AnnounceStartBlock("Preserving variables");
mapRemap.PreserveAllVariables(strInputData, strOutputData);
AnnounceEndBlock(NULL);
} else if (vecPreserveVariableStrings.size() != 0) {
AnnounceStartBlock("Preserving variables");
mapRemap.PreserveVariables(
strInputData,
strOutputData,
vecPreserveVariableStrings);
AnnounceEndBlock(NULL);
}
}
AnnounceBanner();
return (0);
} catch(Exception & e) {
Announce(e.ToString().c_str());
return (-1);
} catch(...) {
return (-2);
}
}
