void OutputManager::PerformOutput(
const Time & time
) {
// Open the file
if (!m_fIsFileOpen) {
std::string strActiveFileName;
GetFileName(time, strActiveFileName);
m_fIsFileOpen = OpenFile(strActiveFileName);
if (!m_fIsFileOpen) {
_EXCEPTION1("Unable to open file \"%s\"",
strActiveFileName.c_str());
}
}
// Output
Output(time);
m_ixOutputTime ++;
// Check if time limit is reached
if (m_ixOutputTime == m_nOutputsPerFile) {
CloseFile();
m_fIsFileOpen = false;
m_ixOutputFile ++;
m_ixOutputTime = 0;
}
}
void ExchangeBuffer::Reset() {
if (m_dSendBuffer.GetByteSize() < sizeof(MessageHeader)) {
_EXCEPTION1("Invalid ExchangeBuffer send buffer (%i)",
m_dSendBuffer.GetByteSize());
}
if (sizeof(MessageHeader) % sizeof(double) != 0) {
_EXCEPTIONT("sizeof(MessageHeader) % sizeof(double) != 0");
}
// Store ExchangeBuffer::MessageHeader
GetSendMessageHeader((MessageHeader *)(&(m_dSendBuffer[0])));
// Set read and write indices to just beyond the MessageHeader
m_ixRecvBuffer = sizeof(MessageHeader) / sizeof(double);
m_ixSendBuffer = sizeof(MessageHeader) / sizeof(double);
}
GridSpacingGaussLobatto::GridSpacingGaussLobatto(
double dDeltaElement,
double dZeroCoord,
int nOrder
) :
GridSpacing(dDeltaElement, dZeroCoord),
m_nOrder(nOrder)
{
// Check order
if (m_nOrder < 2) {
_EXCEPTION1("Invalid order of accuracy %i (Order < 2)", m_nOrder);
}
// Obtain GLL nodes
GaussLobattoQuadrature::GetPoints(
nOrder, 0.0, dDeltaElement, m_dG, m_dW);
}
/// <summary>
/// Load in the contents of a text file containing one filename per
/// line and store in a vector of strings.
/// </summary>
void GetInputFileList(
const std::string & strInputFileList,
std::vector<std::string> & vecInputFiles
) {
FILE * fp = fopen(strInputFileList.c_str(), "r");
char szBuffer[1024];
for (;;) {
fgets(szBuffer, 1024, fp);
if (feof(fp)) {
break;
}
// Remove end-of-line characters
for (;;) {
int nLen = strlen(szBuffer);
if ((szBuffer[nLen-1] == '\n') ||
(szBuffer[nLen-1] == '\r') ||
(szBuffer[nLen-1] == ' ')
) {
szBuffer[nLen-1] = '\0';
continue;
}
break;
}
vecInputFiles.push_back(szBuffer);
}
if (vecInputFiles.size() == 0) {
_EXCEPTION1("No files found in file \"%s\"", strInputFileList.c_str());
}
fclose(fp);
}
bool OutputManagerComposite::OpenFile(
const std::string & strFileName
) {
#ifdef USE_MPI
// Determine processor rank
int nRank;
MPI_Comm_rank(MPI_COMM_WORLD, &nRank);
// Open file at root
if (nRank == 0) {
// Check for existing file
if (m_ofsActiveOutput.is_open()) {
_EXCEPTIONT("Restart file already open");
}
// Open new binary output stream
std::string strRestartFileName = strFileName + ".restart.dat";
m_ofsActiveOutput.open(
strRestartFileName.c_str(), std::ios::binary | std::ios::out);
if (!m_ofsActiveOutput) {
_EXCEPTION1("Error opening output file \"%s\"",
strRestartFileName.c_str());
}
}
// Wait for all processes to complete
MPI_Barrier(MPI_COMM_WORLD);
return true;
#else
_EXCEPTIONT("Not implemented without USE_MPI");
#endif
}
void CubedSphereTrans::CoVecTransRLLFromABP(
double dX,
double dY,
int nP,
double dUalpha,
double dUbeta,
double & dUlon,
double & dUlat
) {
double dDelta2 = 1.0 + dX * dX + dY * dY;
double dRadius;
double dRadius2;
double lat;
switch (nP) {
// Equatorial panels
case 0:
case 1:
case 2:
case 3:
// Calculate new vector components
dUlon =
dDelta2 / (1.0 + dX * dX) * dUalpha
+ dDelta2 * dX * dY / (1.0 + dX * dX) / (1.0 + dY * dY) * dUbeta;
dUlat =
dDelta2 / sqrt(1.0 + dX * dX) / (1.0 + dY * dY) * dUbeta;
// Convert spherical coords to geometric basis
lat = atan(dY / sqrt(1.0 + dX * dX));
dUlon *= cos(lat);
break;
// North polar panel
case 4:
// Calculate new vector components
dRadius2 = (dX * dX + dY * dY);
dRadius = sqrt(dRadius2);
dUlon =
- dDelta2 * dY / (1.0 + dX * dX) / dRadius2 * dUalpha
+ dDelta2 * dX / (1.0 + dY * dY) / dRadius2 * dUbeta;
dUlat =
- dDelta2 * dX / (1.0 + dX * dX) / dRadius * dUalpha
- dDelta2 * dY / (1.0 + dY * dY) / dRadius * dUbeta;
// Convert spherical coords to geometric basis
lat = 0.5 * M_PI - atan(sqrt(dX * dX + dY * dY));
dUlon *= cos(lat);
break;
// South polar panel
case 5:
// Calculate new vector components
dRadius2 = (dX * dX + dY * dY);
dRadius = sqrt(dRadius2);
dUlon =
+ dDelta2 * dY / (1.0 + dX * dX) / dRadius2 * dUalpha
- dDelta2 * dX / (1.0 + dY * dY) / dRadius2 * dUbeta;
dUlat =
+ dDelta2 * dX / (1.0 + dX * dX) / dRadius * dUalpha
+ dDelta2 * dY / (1.0 + dY * dY) / dRadius * dUbeta;
// Convert spherical coords to geometric basis
lat = 0.5 * M_PI - atan(sqrt(dX * dX + dY * dY));
dUlon *= cos(lat);
break;
// Invalid panel
default:
_EXCEPTION1(
"Invalid nP coordinate. Given: %d, Expected: [0-5].\n", nP);
}
}
void Connectivity::BuildFluxConnectivity() {
// PatchBox
const PatchBox & box = m_patch.GetPatchBox();
// Allocate space for edges
m_vecExteriorEdge[0].resize(box.GetBTotalWidth(), NULL);
m_vecExteriorEdge[1].resize(box.GetATotalWidth(), NULL);
m_vecExteriorEdge[2].resize(box.GetBTotalWidth(), NULL);
m_vecExteriorEdge[3].resize(box.GetATotalWidth(), NULL);
m_vecExteriorEdge[4].resize(1, NULL);
m_vecExteriorEdge[5].resize(1, NULL);
m_vecExteriorEdge[6].resize(1, NULL);
m_vecExteriorEdge[7].resize(1, NULL);
// Loop over all exterior edges, hook up pointers to ExteriorNeighbors
for (int n = 0; n < m_vecExteriorNeighbors.size(); n++) {
ExteriorNeighbor * pNeighbor = m_vecExteriorNeighbors[n];
int iDir = static_cast<int>(pNeighbor->m_dir);
// Right or Left side of this PatchBox
if ((pNeighbor->m_dir == Direction_Right) ||
(pNeighbor->m_dir == Direction_Left)
) {
int j = pNeighbor->m_ixFirst;
for (; j < pNeighbor->m_ixSecond; j++) {
if ((j < box.GetBInteriorBegin()) ||
(j >= box.GetBInteriorEnd())
) {
_EXCEPTIONT("Edge index out of range");
}
m_vecExteriorEdge[iDir][j] = pNeighbor;
}
// Top or Bottom side of this PatchBox
} else if (
(pNeighbor->m_dir == Direction_Top) ||
(pNeighbor->m_dir == Direction_Bottom)
) {
int i = pNeighbor->m_ixFirst;
for (; i < pNeighbor->m_ixSecond; i++) {
if ((i < box.GetAInteriorBegin()) ||
(i >= box.GetAInteriorEnd())
) {
_EXCEPTIONT("Edge index out of range");
}
m_vecExteriorEdge[iDir][i] = pNeighbor;
}
// Corners of this PatchBox
} else if (
(pNeighbor->m_dir == Direction_TopRight) ||
(pNeighbor->m_dir == Direction_TopLeft) ||
(pNeighbor->m_dir == Direction_BottomRight) ||
(pNeighbor->m_dir == Direction_BottomLeft)
) {
if (m_vecExteriorEdge[iDir][0] != NULL) {
_EXCEPTION1("Corner patch %i already set", iDir);
}
m_vecExteriorEdge[iDir][0] = pNeighbor;
} else {
_EXCEPTIONT("Invalid direction");
}
}
}
void CubedSphereTrans::RLLFromXYP(
double dX,
double dY,
int nP,
double &lon,
double &lat
) {
switch (nP) {
// Equatorial panel 1
case 0:
lon = atan(dX);
lat = atan(dY / sqrt(1.0 + dX * dX));
break;
// Equatorial panel 2
case 1:
lon = atan(dX) + 0.5 * M_PI;
lat = atan(dY / sqrt(1.0 + dX * dX));
break;
// Equatorial panel 3
case 2:
lon = atan(dX) + M_PI;
lat = atan(dY / sqrt(1.0 + dX * dX));
break;
// Equatorial panel 4
case 3:
lon = atan(dX) + 1.5 * M_PI;
lat = atan(dY / sqrt(1.0 + dX * dX));
break;
// North polar panel
case 4:
if (fabs(dX) > DBL_EPSILON) {
lon = atan2(dX, -dY);
} else if (dY <= 0.0) {
lon = 0.0;
} else {
lon = M_PI;
}
lat = 0.5 * M_PI - atan(sqrt(dX * dX + dY * dY));
break;
// South polar panel
case 5:
if (fabs(dX) > DBL_EPSILON) {
lon = atan2(dX, dY);
} else if (dY > 0.0) {
lon = 0.0;
} else {
lon = M_PI;
}
lat = -0.5 * M_PI + atan(sqrt(dX * dX + dY * dY));
break;
// Invalid panel
default:
_EXCEPTION1(
"Invalid nP coordinate. Given: %d, Expected: [0-5].\n", nP);
}
// Map to the interval [0, 2 pi]
if (lon < 0.0) {
lon += 2.0 * M_PI;
}
}
void CubedSphereTrans::CoVecTransABPFromRLL(
double dX,
double dY,
int nP,
double dUlon,
double dUlat,
double & dUalpha,
double & dUbeta
) {
double dDelta2 = 1.0 + dX * dX + dY * dY;
double dRadius;
double lat;
if ((nP > 3) && (fabs(dX) < 1.0e-13) && (fabs(dY) < 1.0e-13)) {
if (nP == 4) {
dUalpha = dUlon;
} else {
dUalpha = - dUlon;
}
dUbeta = dUlat;
return;
}
switch (nP) {
// Equatorial panels
case 0:
case 1:
case 2:
case 3:
// Convert Ulon from geometric basis
lat = atan(dY / sqrt(1.0 + dX * dX));
dUlon = dUlon / cos(lat);
// Calculate vector component
dUalpha =
(1.0 + dX * dX) / dDelta2 * dUlon
- dX * dY * sqrt(1.0 + dX * dX) / dDelta2 * dUlat;
dUbeta =
sqrt(1.0 + dX * dX) * (1.0 + dY * dY) / dDelta2 * dUlat;
break;
// North polar panel
case 4:
// Convert Ulon from geometric basis
lat = 0.5 * M_PI - atan(sqrt(dX * dX + dY * dY));
dUlon = dUlon / cos(lat);
// Calculate vector component
dRadius = sqrt(dX * dX + dY * dY);
dUalpha =
- dY * (1.0 + dX * dX) / dDelta2 * dUlon
- dX * (1.0 + dX * dX) / (dDelta2 * dRadius) * dUlat;
dUbeta =
+ dX * (1.0 + dY * dY) / dDelta2 * dUlon
- dY * (1.0 + dY * dY) / (dDelta2 * dRadius) * dUlat;
break;
// South polar panel
case 5:
// Convert Ulon from geometric basis
lat = -0.5 * M_PI + atan(sqrt(dX * dX + dY * dY));
dUlon = dUlon / cos(lat);
// Calculate vector component
dRadius = sqrt(dX * dX + dY * dY);
dUalpha =
+ dY * (1.0 + dX * dX) / dDelta2 * dUlon
+ dX * (1.0 + dX * dX) / (dDelta2 * dRadius) * dUlat;
dUbeta =
- dX * (1.0 + dY * dY) / dDelta2 * dUlon
+ dY * (1.0 + dY * dY) / (dDelta2 * dRadius) * dUlat;
break;
// Invalid panel
default:
_EXCEPTION1(
"Invalid nP coordinate. Given: %d, Expected: [0-5].\n", nP);
}
}
void ParseLevelArray(
const std::string & strLevels,
std::vector<double> & vecLevels
) {
int iLevelBegin = 0;
int iLevelCurrent = 0;
vecLevels.clear();
if (strLevels == "") {
return;
}
// Parse pressure levels
bool fRangeMode = false;
for (;;) {
if ((iLevelCurrent >= strLevels.length()) ||
(strLevels[iLevelCurrent] == ',') ||
(strLevels[iLevelCurrent] == ' ') ||
(strLevels[iLevelCurrent] == ':')
) {
// Range mode
if ((!fRangeMode) &&
(strLevels[iLevelCurrent] == ':')
) {
if (vecLevels.size() != 0) {
_EXCEPTIONT("Invalid set of pressure levels");
}
fRangeMode = true;
}
if (fRangeMode) {
if ((strLevels[iLevelCurrent] != ':') &&
(iLevelCurrent < strLevels.length())
) {
_EXCEPTION1("Invalid character in pressure range (%c)",
strLevels[iLevelCurrent]);
}
}
if (iLevelCurrent == iLevelBegin) {
if (iLevelCurrent >= strLevels.length()) {
break;
}
continue;
}
std::string strPressureLevelSubStr =
strLevels.substr(
iLevelBegin, iLevelCurrent - iLevelBegin);
vecLevels.push_back(atof(strPressureLevelSubStr.c_str()));
iLevelBegin = iLevelCurrent + 1;
}
iLevelCurrent++;
}
// Range mode -- repopulate array
if (fRangeMode) {
if (vecLevels.size() != 3) {
_EXCEPTIONT("Exactly three pressure level entries required "
"for range mode");
}
double dLevelBegin = vecLevels[0];
double dLevelStep = vecLevels[1];
double dLevelEnd = vecLevels[2];
if (dLevelStep == 0.0) {
_EXCEPTIONT("Level step size cannot be zero");
}
if ((dLevelEnd - dLevelBegin) / dLevelStep > 10000.0) {
_EXCEPTIONT("Too many levels in range (limit 10000)");
}
if ((dLevelEnd - dLevelBegin) / dLevelStep < 0.0) {
_EXCEPTIONT("Sign mismatch in level step");
}
vecLevels.clear();
for (int i = 0 ;; i++) {
double dLevel = dLevelBegin + static_cast<double>(i) * dLevelStep;
if ((dLevelStep > 0.0) && (dLevel > dLevelEnd)) {
break;
}
if ((dLevelStep < 0.0) && (dLevel < dLevelEnd)) {
break;
}
vecLevels.push_back(dLevel);
}
}
}
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 / 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);
}
}
int main(int argc, char** argv) {
NcError error(NcError::silent_nonfatal);
try {
// Input filename
std::string strInputFile;
// Output mesh filename
std::string strOutputFile;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputFile, "in", "");
CommandLineString(strOutputFile, "out", "");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
// Check file names
if (strInputFile == "") {
std::cout << "ERROR: No input file specified" << std::endl;
return (-1);
}
if (strOutputFile == "") {
std::cout << "ERROR: No output file specified" << std::endl;
return (-1);
}
AnnounceBanner();
// Load shapefile
AnnounceStartBlock("Loading shapefile");
std::ifstream shpfile(
strInputFile.c_str(), std::ios::in | std::ios::binary);
SHPHeader shphead;
shpfile.read((char*)(&shphead), sizeof(SHPHeader));
if (O32_HOST_ORDER == O32_LITTLE_ENDIAN) {
shphead.iFileCode = SwapEndianInt32(shphead.iFileCode);
shphead.iFileLength = SwapEndianInt32(shphead.iFileLength);
} else if (O32_HOST_ORDER == O32_BIG_ENDIAN) {
shphead.iVersion = SwapEndianInt32(shphead.iVersion);
shphead.iShapeType = SwapEndianInt32(shphead.iShapeType);
} else {
_EXCEPTIONT("Invalid system Endian");
}
if (shphead.iFileCode != SHPFileCodeRef) {
_EXCEPTIONT("Input file does not appear to be a ESRI Shapefile: "
"File code mismatch");
}
if (shphead.iVersion != SHPVersionRef) {
_EXCEPTIONT("Input file error: Version mismatch");
}
if (shphead.iShapeType != SHPPolygonType) {
_EXCEPTIONT("Input file error: Polygon type expected");
}
SHPBounds shpbounds;
shpfile.read((char*)(&shpbounds), sizeof(SHPBounds));
if (O32_HOST_ORDER == O32_BIG_ENDIAN) {
shpbounds.dXmin = SwapEndianDouble(shpbounds.dXmin);
shpbounds.dYmin = SwapEndianDouble(shpbounds.dYmin);
shpbounds.dXmax = SwapEndianDouble(shpbounds.dXmax);
shpbounds.dYmax = SwapEndianDouble(shpbounds.dXmax);
shpbounds.dZmin = SwapEndianDouble(shpbounds.dZmin);
shpbounds.dZmax = SwapEndianDouble(shpbounds.dZmax);
shpbounds.dMmin = SwapEndianDouble(shpbounds.dMmin);
shpbounds.dMmax = SwapEndianDouble(shpbounds.dMmax);
}
// Current position (in 16-bit words)
int32_t iCurrentPosition = 50;
int32_t iPolygonIx = 1;
// Exodus mesh
Mesh mesh;
// Load records
while (iCurrentPosition < shphead.iFileLength) {
// Read the record header
SHPRecordHeader shprechead;
shpfile.read((char*)(&shprechead), sizeof(SHPRecordHeader));
if (shpfile.eof()) {
break;
}
if (O32_HOST_ORDER == O32_LITTLE_ENDIAN) {
shprechead.iNumber = SwapEndianInt32(shprechead.iNumber);
shprechead.nLength = SwapEndianInt32(shprechead.nLength);
}
char szBuffer[128];
sprintf(szBuffer, "Polygon %i", shprechead.iNumber);
iPolygonIx++;
AnnounceStartBlock(szBuffer);
iCurrentPosition += shprechead.nLength;
// Read the shape type
int32_t iShapeType;
shpfile.read((char*)(&iShapeType), sizeof(int32_t));
if (shpfile.eof()) {
break;
}
if (O32_HOST_ORDER == O32_BIG_ENDIAN) {
iShapeType = SwapEndianInt32(iShapeType);
}
if (iShapeType != SHPPolygonType) {
_EXCEPTIONT("Input file error: Record Polygon type expected");
}
// Read the polygon header
SHPPolygonHeader shppolyhead;
shpfile.read((char*)(&shppolyhead), sizeof(SHPPolygonHeader));
if (shpfile.eof()) {
break;
}
if (O32_HOST_ORDER == O32_BIG_ENDIAN) {
shppolyhead.dXmin = SwapEndianDouble(shppolyhead.dXmin);
shppolyhead.dYmin = SwapEndianDouble(shppolyhead.dYmin);
shppolyhead.dXmax = SwapEndianDouble(shppolyhead.dXmax);
shppolyhead.dYmax = SwapEndianDouble(shppolyhead.dYmax);
shppolyhead.nNumParts = SwapEndianInt32(shppolyhead.nNumParts);
shppolyhead.nNumPoints = SwapEndianInt32(shppolyhead.nNumPoints);
}
// Sanity check
if (shppolyhead.nNumParts > 0x1000000) {
_EXCEPTION1("Polygon NumParts exceeds sanity bound (%i)",
shppolyhead.nNumParts);
}
if (shppolyhead.nNumPoints > 0x1000000) {
_EXCEPTION1("Polygon NumPoints exceeds sanity bound (%i)",
shppolyhead.nNumPoints);
}
Announce("containing %i part(s) with %i points",
shppolyhead.nNumParts,
shppolyhead.nNumPoints);
Announce("Xmin: %3.5f", shppolyhead.dXmin);
Announce("Ymin: %3.5f", shppolyhead.dYmin);
Announce("Xmax: %3.5f", shppolyhead.dXmax);
Announce("Ymax: %3.5f", shppolyhead.dYmax);
if (shppolyhead.nNumParts != 1) {
_EXCEPTIONT("Only polygons with 1 part currently supported"
" in Exodus format");
}
DataVector<int32_t> iParts(shppolyhead.nNumParts);
shpfile.read((char*)&(iParts[0]),
shppolyhead.nNumParts * sizeof(int32_t));
if (shpfile.eof()) {
break;
}
DataVector<double> dPoints(shppolyhead.nNumPoints * 2);
shpfile.read((char*)&(dPoints[0]),
shppolyhead.nNumPoints * 2 * sizeof(double));
if (shpfile.eof()) {
break;
}
if (O32_HOST_ORDER == O32_BIG_ENDIAN) {
for (int i = 0; i < shppolyhead.nNumParts; i++) {
iParts[i] = SwapEndianInt32(iParts[i]);
}
for (int i = 0; i < shppolyhead.nNumPoints * 2; i++) {
dPoints[i] = SwapEndianDouble(dPoints[i]);
}
}
// Convert to Exodus mesh
int nFaces = mesh.faces.size();
int nNodes = mesh.nodes.size();
mesh.faces.resize(nFaces+1);
mesh.nodes.resize(nNodes + shppolyhead.nNumPoints);
mesh.faces[nFaces] = Face(shppolyhead.nNumPoints);
for (int i = 0; i < shppolyhead.nNumPoints; i++) {
double dLonRad = dPoints[2*i] / 180.0 * M_PI;
double dLatRad = dPoints[2*i+1] / 180.0 * M_PI;
mesh.nodes[nNodes+i].x = cos(dLatRad) * cos(dLonRad);
mesh.nodes[nNodes+i].y = cos(dLatRad) * sin(dLonRad);
mesh.nodes[nNodes+i].z = sin(dLatRad);
mesh.faces[nFaces].SetNode(i, nNodes + i);
}
AnnounceEndBlock("Done");
}
AnnounceEndBlock("Done");
// Write to file
AnnounceStartBlock("Write Exodus mesh");
mesh.Write(strOutputFile);
AnnounceEndBlock("Done");
// Announce
AnnounceBanner();
return (0);
} catch(Exception & e) {
Announce(e.ToString().c_str());
return (-1);
} catch(...) {
return (-2);
}
}
void GridPatchCartesianGLL::EvaluateGeometricTerms() {
// Physical constants
const PhysicalConstants & phys = m_grid.GetModel().GetPhysicalConstants();
// Obtain Gauss Lobatto quadrature nodes and weights
DataVector<double> dGL;
DataVector<double> dWL;
GaussLobattoQuadrature::GetPoints(m_nHorizontalOrder, 0.0, 1.0, dGL, dWL);
// Obtain normalized areas in the vertical
const DataVector<double> & dWNode =
m_grid.GetREtaLevelsNormArea();
const DataVector<double> & dWREdge =
m_grid.GetREtaInterfacesNormArea();
// Verify that normalized areas are correct
double dWNodeSum = 0.0;
for (int k = 0; k < dWNode.GetRows(); k++) {
dWNodeSum += dWNode[k];
}
if (fabs(dWNodeSum - 1.0) > 1.0e-13) {
_EXCEPTION1("Error in normalized areas (%1.15e)", dWNodeSum);
}
if (m_grid.GetVerticalStaggering() !=
Grid::VerticalStaggering_Interfaces
) {
double dWREdgeSum = 0.0;
for (int k = 0; k < dWREdge.GetRows(); k++) {
dWREdgeSum += dWREdge[k];
}
if (fabs(dWREdgeSum - 1.0) > 1.0e-13) {
_EXCEPTION1("Error in normalized areas (%1.15e)", dWREdgeSum);
}
}
// Derivatives of basis functions
GridCartesianGLL & gridCartesianGLL =
dynamic_cast<GridCartesianGLL &>(m_grid);
const DataMatrix<double> & dDxBasis1D = gridCartesianGLL.GetDxBasis1D();
double dy0 = 0.5 * fabs(m_dGDim[3] - m_dGDim[2]);
double dfp = 2.0 * phys.GetOmega() * sin(m_dRefLat);
double dbetap = 2.0 * phys.GetOmega() * cos(m_dRefLat) /
phys.GetEarthRadius();
// Initialize the Coriolis force at each node
for (int i = 0; i < m_box.GetATotalWidth(); i++) {
for (int j = 0; j < m_box.GetBTotalWidth(); j++) {
// Coriolis force by beta approximation
//m_dataCoriolisF[i][j] = dfp + dbetap * (m_dataLat[i][j] - dy0);
//m_dataCoriolisF[i][j] = dfp;
//m_dataCoriolisF[i][j] = 0.0;
}
}
// Initialize metric and Christoffel symbols in terrain-following coords
for (int a = 0; a < GetElementCountA(); a++) {
for (int b = 0; b < GetElementCountB(); b++) {
for (int i = 0; i < m_nHorizontalOrder; i++) {
for (int j = 0; j < m_nHorizontalOrder; j++) {
// Nodal points
int iElementA = m_box.GetAInteriorBegin() + a * m_nHorizontalOrder;
int iElementB = m_box.GetBInteriorBegin() + b * m_nHorizontalOrder;
int iA = iElementA + i;
int iB = iElementB + j;
// Topography height and its derivatives
double dZs = m_dataTopography[iA][iB];
double dDaZs = m_dataTopographyDeriv[0][iA][iB];
double dDbZs = m_dataTopographyDeriv[1][iA][iB];
// Initialize 2D Jacobian
m_dataJacobian2D[iA][iB] = 1.0;
// Initialize 2D contravariant metric
m_dataContraMetric2DA[iA][iB][0] = 1.0;
m_dataContraMetric2DA[iA][iB][1] = 0.0;
m_dataContraMetric2DB[iA][iB][0] = 0.0;
m_dataContraMetric2DB[iA][iB][1] = 1.0;
// Initialize 2D covariant metric
m_dataCovMetric2DA[iA][iB][0] = 1.0;
m_dataCovMetric2DA[iA][iB][1] = 0.0;
m_dataCovMetric2DB[iA][iB][0] = 0.0;
m_dataCovMetric2DB[iA][iB][1] = 1.0;
// Vertical coordinate transform and its derivatives
for (int k = 0; k < m_grid.GetRElements(); k++) {
// Gal-Chen and Somerville (1975) terrain following coord
// Schar Exponential Decay terrain following coord
double dREta = m_grid.GetREtaLevel(k);
double dREtaStretch;
double dDxREtaStretch;
m_grid.EvaluateVerticalStretchF(
dREta, dREtaStretch, dDxREtaStretch);
//double dZ = dZs + (m_grid.GetZtop() - dZs) * dREtaStretch;
//double dbZ = sinh(m_grid.GetZtop() * (1.0 - dREtaStretch) / m_dSL)
// / sinh(m_grid.GetZtop() / m_dSL);
//double dZ = m_grid.GetZtop() * dREtaStretch + dZs; // * dbZ;
double dZ = dZs + (m_grid.GetZtop() - dZs) * dREtaStretch;
double dDaZ = (1.0 - dREtaStretch) * dDaZs;
double dDbZ = (1.0 - dREtaStretch) * dDbZs;
double dDxZ = (m_grid.GetZtop() - dZs) * dDxREtaStretch;
/*
double dDaZ = dbZ * dDaZs;
double dDbZ = dbZ * dDbZs;
double dDxZ = m_grid.GetZtop() - dZs * m_grid.GetZtop() *
cosh(m_grid.GetZtop() * (1.0 - dREtaStretch) / m_dSL) /
(m_dSL * sinh(m_grid.GetZtop() / m_dSL));
dDxZ *= dDxREtaStretch;
*/
// Calculate pointwise Jacobian
m_dataJacobian[k][iA][iB] =
dDxZ * m_dataJacobian2D[iA][iB];
// Element area associated with each model level GLL node
m_dataElementArea[k][iA][iB] =
m_dataJacobian[k][iA][iB]
* dWL[i] * GetElementDeltaA()
* dWL[j] * GetElementDeltaB()
* dWNode[k];
// Contravariant metric components
m_dataContraMetricA[k][iA][iB][0] =
m_dataContraMetric2DA[iA][iB][0];
m_dataContraMetricA[k][iA][iB][1] =
m_dataContraMetric2DA[iA][iB][1];
m_dataContraMetricA[k][iA][iB][2] =
- dDaZ / dDxZ;
m_dataContraMetricB[k][iA][iB][0] =
m_dataContraMetric2DB[iA][iB][0];
m_dataContraMetricB[k][iA][iB][1] =
m_dataContraMetric2DB[iA][iB][1];
m_dataContraMetricB[k][iA][iB][2] =
- dDbZ / dDxZ;
m_dataContraMetricXi[k][iA][iB][0] =
m_dataContraMetricA[k][iA][iB][2];
m_dataContraMetricXi[k][iA][iB][1] =
m_dataContraMetricB[k][iA][iB][2];
m_dataContraMetricXi[k][iA][iB][2] =
(1.0 + dDaZ * dDaZ + dDbZ * dDbZ) / (dDxZ * dDxZ);
// Covariant metric components
m_dataCovMetricA[k][iA][iB][0] =
m_dataCovMetric2DA[iA][iB][0] + dDaZ * dDaZ;
m_dataCovMetricA[k][iA][iB][1] =
m_dataCovMetric2DA[iA][iB][1] + dDaZ * dDbZ;
m_dataCovMetricA[k][iA][iB][2] =
dDaZ * dDxZ;
m_dataCovMetricB[k][iA][iB][0] =
m_dataCovMetric2DB[iA][iB][0] + dDbZ * dDaZ;
m_dataCovMetricB[k][iA][iB][1] =
m_dataCovMetric2DB[iA][iB][1] + dDbZ * dDbZ;
m_dataCovMetricB[k][iA][iB][2] =
dDbZ * dDxZ;
m_dataCovMetricXi[k][iA][iB][0] =
dDaZ * dDxZ;
m_dataCovMetricXi[k][iA][iB][1] =
dDbZ * dDxZ;
m_dataCovMetricXi[k][iA][iB][2] =
dDxZ * dDxZ;
// Derivatives of the vertical coordinate transform
m_dataDerivRNode[k][iA][iB][0] = dDaZ;
m_dataDerivRNode[k][iA][iB][1] = dDbZ;
m_dataDerivRNode[k][iA][iB][2] = dDxZ;
}
// Metric terms at vertical interfaces
for (int k = 0; k <= m_grid.GetRElements(); k++) {
// Gal-Chen and Somerville (1975) terrain following coord
// Schar Exponential decay terrain following coord
double dREta = m_grid.GetREtaInterface(k);
/*
double dREtaStretch;
double dDxREtaStretch;
m_grid.EvaluateVerticalStretchF(
dREta, dREtaStretch, dDxREtaStretch);
double dZ = dZs + (m_grid.GetZtop() - dZs) * dREtaStretch;
double dDaZ = (1.0 - dREtaStretch) * dDaZs;
double dDbZ = (1.0 - dREtaStretch) * dDbZs;
double dDxZ = (m_grid.GetZtop() - dZs) * dDxREtaStretch;
*/
double dREtaStretch;
double dDxREtaStretch;
m_grid.EvaluateVerticalStretchF(
dREta, dREtaStretch, dDxREtaStretch);
/*
//double dZ = dZs + (m_grid.GetZtop() - dZs) * dREtaStretch;
double dbZ = sinh(m_grid.GetZtop() * (1.0 - dREtaStretch) / m_dSL) /
sinh(m_grid.GetZtop() / m_dSL);
double dZ = m_grid.GetZtop() * dREtaStretch + dZs * dbZ;
*/
double dDaZ = (1.0 - dREtaStretch) * dDaZs;
double dDbZ = (1.0 - dREtaStretch) * dDbZs;
double dDxZ = (m_grid.GetZtop() - dZs) * dDxREtaStretch;
/*
double dDaZ = dbZ * dDaZs;
double dDbZ = dbZ * dDbZs;
double dDxZ = m_grid.GetZtop() - dZs * m_grid.GetZtop() *
cosh(m_grid.GetZtop() * (1.0 - dREtaStretch) / m_dSL) /
(m_dSL * sinh(m_grid.GetZtop() / m_dSL));
dDxZ *= dDxREtaStretch;
*/
// Calculate pointwise Jacobian
m_dataJacobianREdge[k][iA][iB] =
dDxZ * m_dataJacobian2D[iA][iB];
// Element area associated with each model interface GLL node
m_dataElementAreaREdge[k][iA][iB] =
m_dataJacobianREdge[k][iA][iB]
* dWL[i] * GetElementDeltaA()
* dWL[j] * GetElementDeltaB()
* dWREdge[k];
// Components of the contravariant metric
m_dataContraMetricAREdge[k][iA][iB][0] =
m_dataContraMetric2DA[iA][iB][0];
m_dataContraMetricAREdge[k][iA][iB][1] =
m_dataContraMetric2DA[iA][iB][1];
m_dataContraMetricAREdge[k][iA][iB][2] =
- dDaZ / dDxZ;
m_dataContraMetricBREdge[k][iA][iB][0] =
m_dataContraMetric2DB[iA][iB][0];
m_dataContraMetricBREdge[k][iA][iB][1] =
m_dataContraMetric2DB[iA][iB][1];
m_dataContraMetricBREdge[k][iA][iB][2] =
- dDbZ / dDxZ;
m_dataContraMetricXiREdge[k][iA][iB][0] =
- dDaZ / dDxZ;
m_dataContraMetricXiREdge[k][iA][iB][1] =
- dDbZ / dDxZ;
m_dataContraMetricXiREdge[k][iA][iB][2] =
(1.0 + dDaZ * dDaZ + dDbZ * dDbZ) / (dDxZ * dDxZ);
// Derivatives of the vertical coordinate transform
m_dataDerivRREdge[k][iA][iB][0] = dDaZ;
m_dataDerivRREdge[k][iA][iB][1] = dDbZ;
m_dataDerivRREdge[k][iA][iB][2] = dDxZ;
}
}
}
}
}
}
void ReadCFTimeDataFromNcFile(
NcFile * ncfile,
const std::string & strFilename,
std::vector<Time> & vecTimes,
bool fWarnOnMissingCalendar
) {
// Empty existing Time vector
vecTimes.clear();
// Get time dimension
NcDim * dimTime = ncfile->get_dim("time");
if (dimTime == NULL) {
_EXCEPTION1("Dimension \"time\" not found in file \"%s\"",
strFilename.c_str());
}
// Get time variable
NcVar * varTime = ncfile->get_var("time");
if (varTime == NULL) {
_EXCEPTION1("Variable \"time\" not found in file \"%s\"",
strFilename.c_str());
}
if (varTime->num_dims() != 1) {
_EXCEPTION1("Variable \"time\" has more than one dimension in file \"%s\"",
strFilename.c_str());
}
if (strcmp(varTime->get_dim(0)->name(), "time") != 0) {
_EXCEPTION1("Variable \"time\" does not have dimension \"time\" in file \"%s\"",
strFilename.c_str());
}
// Calendar attribute
NcAtt * attTimeCal = varTime->get_att("calendar");
std::string strCalendar;
if (attTimeCal == NULL) {
if (fWarnOnMissingCalendar) {
Announce("WARNING: Variable \"time\" is missing \"calendar\" attribute; assuming \"standard\"");
}
strCalendar = "standard";
} else {
strCalendar = attTimeCal->as_string(0);
}
Time::CalendarType eCalendarType =
Time::CalendarTypeFromString(strCalendar);
// Units attribute
NcAtt * attTimeUnits = varTime->get_att("units");
if (attTimeUnits == NULL) {
_EXCEPTION1("Variable \"time\" is missing \"units\" attribute in file \"%s\"",
strFilename.c_str());
}
std::string strTimeUnits = attTimeUnits->as_string(0);
// Load in time data
DataVector<int> vecTimeInt;
DataVector<float> vecTimeFloat;
DataVector<double> vecTimeDouble;
DataVector<ncint64> vecTimeInt64;
if (varTime->type() == ncInt) {
vecTimeInt.Initialize(dimTime->size());
varTime->set_cur((long)0);
varTime->get(&(vecTimeInt[0]), dimTime->size());
} else if (varTime->type() == ncFloat) {
vecTimeFloat.Initialize(dimTime->size());
varTime->set_cur((long)0);
varTime->get(&(vecTimeFloat[0]), dimTime->size());
} else if (varTime->type() == ncDouble) {
vecTimeDouble.Initialize(dimTime->size());
varTime->set_cur((long)0);
varTime->get(&(vecTimeDouble[0]), dimTime->size());
} else if (varTime->type() == ncInt64) {
vecTimeInt64.Initialize(dimTime->size());
varTime->set_cur((long)0);
varTime->get(&(vecTimeInt64[0]), dimTime->size());
} else {
_EXCEPTION1("Variable \"time\" has invalid type "
"(expected \"int\", \"int64\", \"float\" or \"double\")"
" in file \"%s\"", strFilename.c_str());
}
for (int t = 0; t < dimTime->size(); t++) {
Time time(eCalendarType);
if (varTime->type() == ncInt) {
time.FromCFCompliantUnitsOffsetInt(
strTimeUnits,
vecTimeInt[t]);
} else if (varTime->type() == ncFloat) {
time.FromCFCompliantUnitsOffsetDouble(
strTimeUnits,
static_cast<double>(vecTimeFloat[t]));
} else if (varTime->type() == ncDouble) {
time.FromCFCompliantUnitsOffsetDouble(
strTimeUnits,
vecTimeDouble[t]);
} else if (varTime->type() == ncInt64) {
time.FromCFCompliantUnitsOffsetInt(
strTimeUnits,
(int)(vecTimeInt64[t]));
}
vecTimes.push_back(time);
}
}
Time OutputManagerComposite::Input(
const std::string & strFileName
) {
#ifdef USE_MPI
// Set the flag indicating that output came from a restart file
m_fFromRestartFile = true;
// Determine processor rank
int nRank;
MPI_Comm_rank(MPI_COMM_WORLD, &nRank);
// The active model
const Model & model = m_grid.GetModel();
// Open binary input stream
std::ifstream ifsActiveInput;
ifsActiveInput.open(
strFileName.c_str(), std::ios::binary | std::ios::in);
if (!ifsActiveInput) {
_EXCEPTION1("Unable to open input file \"%s\"",
strFileName.c_str());
}
// Read check bits
int iCheckInput;
ifsActiveInput.read((char *)(&iCheckInput), sizeof(int));
if (iCheckInput != m_iCheck) {
_EXCEPTION1("Invalid or incompatible input file \"%s\"",
strFileName.c_str());
}
// Read current time
Time timeCurrent;
ifsActiveInput.read((char *)(&(timeCurrent)), sizeof(Time));
// Read Grid parameters from file
DataContainer & dcGridParameters = m_grid.GetDataContainerParameters();
int nGridParametersByteSize =
dcGridParameters.GetTotalByteSize();
char * pGridParameters =
(char *)(dcGridParameters.GetPointer());
ifsActiveInput.read(pGridParameters, nGridParametersByteSize);
// Initialize the Grid from specified parameters
m_grid.InitializeDataLocal();
// Load Grid data from file
DataContainer & dcGridPatchData = m_grid.GetDataContainerPatchData();
int nGridPatchDataByteSize =
dcGridPatchData.GetTotalByteSize();
char * pGridPatchData =
(char *)(dcGridPatchData.GetPointer());
ifsActiveInput.read(pGridPatchData, nGridPatchDataByteSize);
// Distribute GridPatches to processors
m_grid.DistributePatches();
// Determine space allocation for each GridPatch
m_vecGridPatchByteSize.Allocate(m_grid.GetPatchCount(), 2);
for (int i = 0; i < m_grid.GetActivePatchCount(); i++) {
const GridPatch * pPatch = m_grid.GetActivePatch(i);
int iPatchIx = pPatch->GetPatchIndex();
if (iPatchIx > m_grid.GetPatchCount()) {
_EXCEPTION2("PatchIndex (%i) out of range [0,%i)",
iPatchIx, m_grid.GetPatchCount());
}
const DataContainer & dcGeometric =
pPatch->GetDataContainerGeometric();
m_vecGridPatchByteSize[iPatchIx][0] =
dcGeometric.GetTotalByteSize();
const DataContainer & dcActiveState =
pPatch->GetDataContainerActiveState();
m_vecGridPatchByteSize[iPatchIx][1] =
dcActiveState.GetTotalByteSize();
}
MPI_Allreduce(
MPI_IN_PLACE,
&(m_vecGridPatchByteSize[0][0]),
m_vecGridPatchByteSize.GetTotalSize(),
MPI_INT,
MPI_MAX,
MPI_COMM_WORLD);
// Initialize byte location for each GridPatch
m_vecGridPatchByteLoc.Allocate(m_grid.GetPatchCount(), 2);
m_vecGridPatchByteLoc[0][0] = 0;
m_vecGridPatchByteLoc[0][1] = m_vecGridPatchByteSize[0][0];
for (int i = 1; i < m_vecGridPatchByteSize.GetRows(); i++) {
m_vecGridPatchByteLoc[i][0] =
m_vecGridPatchByteLoc[i-1][1]
+ m_vecGridPatchByteSize[i-1][1];
m_vecGridPatchByteLoc[i][1] =
m_vecGridPatchByteLoc[i][0]
+ m_vecGridPatchByteSize[i][0];
}
// Reference position
std::streampos posRefFile = ifsActiveInput.tellg();
if (posRefFile == (-1)) {
_EXCEPTIONT("ActiveInput::tellg() fail");
}
// Load in GridPatch data from file
for (int i = 0; i < m_grid.GetActivePatchCount(); i++) {
GridPatch * pPatch = m_grid.GetActivePatch(i);
int iPatchIx = pPatch->GetPatchIndex();
if (iPatchIx > m_grid.GetPatchCount()) {
_EXCEPTION2("PatchIndex (%i) out of range [0,%i)",
iPatchIx, m_grid.GetPatchCount());
}
DataContainer & dcGeometric =
pPatch->GetDataContainerGeometric();
int nGeometricDataByteSize =
dcGeometric.GetTotalByteSize();
char * pGeometricData =
(char *)(dcGeometric.GetPointer());
ifsActiveInput.seekg(
posRefFile + m_vecGridPatchByteLoc[iPatchIx][0]);
ifsActiveInput.read(
pGeometricData, m_vecGridPatchByteSize[iPatchIx][0]);
DataContainer & dcActiveState =
pPatch->GetDataContainerActiveState();
int nActiveStateDataByteSize =
dcActiveState.GetTotalByteSize();
char * pActiveStateData =
(char *)(dcActiveState.GetPointer());
ifsActiveInput.seekg(
posRefFile + m_vecGridPatchByteLoc[iPatchIx][1]);
ifsActiveInput.read(
pActiveStateData, m_vecGridPatchByteSize[iPatchIx][1]);
}
// Close the file
ifsActiveInput.close();
// Barrier
MPI_Barrier(MPI_COMM_WORLD);
#else
_EXCEPTIONT("Not implemented without USE_MPI");
#endif
return timeCurrent;
}
void OutputManagerComposite::Output(
const Time & time
) {
#ifdef USE_MPI
// Check for open file
if (!IsFileOpen()) {
_EXCEPTIONT("No file available for output");
}
// Verify that only one output has been performed
if (m_ixOutputTime != 0) {
_EXCEPTIONT("Only one Composite output allowed per file");
}
// Determine processor rank
int nRank;
MPI_Comm_rank(MPI_COMM_WORLD, &nRank);
// Data types
const int ExchangeDataType_Geometric = 0;
const int ExchangeDataType_ActiveState = 1;
const int ExchangeDataType_Count = 2;
// Determine space allocation for each GridPatch
m_vecGridPatchByteSize.Allocate(m_grid.GetPatchCount(), 2);
for (int i = 0; i < m_grid.GetActivePatchCount(); i++) {
const GridPatch * pPatch = m_grid.GetActivePatch(i);
int iPatchIx = pPatch->GetPatchIndex();
if (iPatchIx > m_grid.GetPatchCount()) {
_EXCEPTION2("PatchIndex (%i) out of range [0,%i)",
iPatchIx, m_grid.GetPatchCount());
}
const DataContainer & dcGeometric =
pPatch->GetDataContainerGeometric();
m_vecGridPatchByteSize[iPatchIx][0] =
dcGeometric.GetTotalByteSize();
const DataContainer & dcActiveState =
pPatch->GetDataContainerActiveState();
m_vecGridPatchByteSize[iPatchIx][1] =
dcActiveState.GetTotalByteSize();
}
// Reduce GridPatch byte size
if (nRank != 0) {
MPI_Reduce(
&(m_vecGridPatchByteSize[0][0]),
&(m_vecGridPatchByteSize[0][0]),
m_vecGridPatchByteSize.GetTotalSize(),
MPI_INT,
MPI_MAX,
0,
MPI_COMM_WORLD);
// Reduce GridPatch byte size and write Grid information
} else if (nRank == 0) {
// Reduce
MPI_Reduce(
MPI_IN_PLACE,
&(m_vecGridPatchByteSize[0][0]),
m_vecGridPatchByteSize.GetTotalSize(),
MPI_INT,
MPI_MAX,
0,
MPI_COMM_WORLD);
// The active Model
const Model & model = m_grid.GetModel();
// Get maximum byte size for exchange
int sMaxRecvBufferByteSize = 0;
for (int i = 0; i < m_vecGridPatchByteSize.GetRows(); i++) {
if (m_vecGridPatchByteSize[i][0] > sMaxRecvBufferByteSize) {
sMaxRecvBufferByteSize = m_vecGridPatchByteSize[i][0];
}
if (m_vecGridPatchByteSize[i][1] > sMaxRecvBufferByteSize) {
sMaxRecvBufferByteSize = m_vecGridPatchByteSize[i][1];
}
}
// Allocate Recv buffer at root
if (m_vecRecvBuffer.GetRows() < sMaxRecvBufferByteSize) {
m_vecRecvBuffer.Allocate(sMaxRecvBufferByteSize);
}
// Initialize byte location for each GridPatch
m_vecGridPatchByteLoc.Allocate(m_grid.GetPatchCount(), 2);
m_vecGridPatchByteLoc[0][0] = 0;
m_vecGridPatchByteLoc[0][1] = m_vecGridPatchByteSize[0][0];
for (int i = 1; i < m_vecGridPatchByteSize.GetRows(); i++) {
m_vecGridPatchByteLoc[i][0] =
m_vecGridPatchByteLoc[i-1][1]
+ m_vecGridPatchByteSize[i-1][1];
m_vecGridPatchByteLoc[i][1] =
m_vecGridPatchByteLoc[i][0]
+ m_vecGridPatchByteSize[i][0];
}
// Write check bits
m_ofsActiveOutput.write((const char *)(&m_iCheck), sizeof(int));
// Write current time
const Time & timeCurrent = model.GetCurrentTime();
m_ofsActiveOutput.write((const char *)(&(timeCurrent)), sizeof(Time));
// Write Grid information to file
const DataContainer & dcGridParameters =
m_grid.GetDataContainerParameters();
int nGridParametersByteSize =
dcGridParameters.GetTotalByteSize();
const char * pGridParameters =
(const char *)(dcGridParameters.GetPointer());
m_ofsActiveOutput.write(
pGridParameters, nGridParametersByteSize);
const DataContainer & dcGridPatchData =
m_grid.GetDataContainerPatchData();
int nGridPatchDataByteSize =
dcGridPatchData.GetTotalByteSize();
const char * pGridPatchData =
(const char *)(dcGridPatchData.GetPointer());
m_ofsActiveOutput.write(
pGridPatchData, nGridPatchDataByteSize);
}
// Send data from GridPatches to root
if (nRank != 0) {
int nActivePatches = m_grid.GetActivePatchCount();
if (nActivePatches == 0) {
_EXCEPTIONT("No GridPatches on processor");
}
DataArray1D<MPI_Request> vecSendReqGeo(nActivePatches);
DataArray1D<MPI_Request> vecSendReqAcS(nActivePatches);
for (int i = 0; i < nActivePatches; i++) {
const GridPatch * pPatch = m_grid.GetActivePatch(i);
const DataContainer & dcGeometric =
pPatch->GetDataContainerGeometric();
int nGeometricDataByteSize =
dcGeometric.GetTotalByteSize();
const unsigned char * pGeometricData =
dcGeometric.GetPointer();
MPI_Isend(
const_cast<unsigned char *>(pGeometricData),
nGeometricDataByteSize,
MPI_BYTE,
0,
ExchangeDataType_Geometric,
MPI_COMM_WORLD,
&(vecSendReqGeo[i]));
const DataContainer & dcActiveState =
pPatch->GetDataContainerActiveState();
int nActiveStateDataByteSize =
dcActiveState.GetTotalByteSize();
const unsigned char * pActiveStateData =
dcActiveState.GetPointer();
MPI_Isend(
const_cast<unsigned char *>(pActiveStateData),
nActiveStateDataByteSize,
MPI_BYTE,
0,
ExchangeDataType_ActiveState,
MPI_COMM_WORLD,
&(vecSendReqAcS[i]));
/*
printf("Send Geo %i %i\n", pPatch->GetPatchIndex(), nGeometricDataByteSize);
printf("Send AcS %i %i\n", pPatch->GetPatchIndex(), nActiveStateDataByteSize);
*/
}
int iWaitAllMsgGeo =
MPI_Waitall(
nActivePatches,
&(vecSendReqGeo[0]),
MPI_STATUSES_IGNORE);
if (iWaitAllMsgGeo == MPI_ERR_IN_STATUS) {
_EXCEPTIONT("MPI_Waitall returned MPI_ERR_IN_STATUS");
}
int iWaitAllMsgAcS =
MPI_Waitall(
nActivePatches,
&(vecSendReqAcS[0]),
MPI_STATUSES_IGNORE);
if (iWaitAllMsgAcS == MPI_ERR_IN_STATUS) {
_EXCEPTIONT("MPI_Waitall returned MPI_ERR_IN_STATUS");
}
//std::cout << "WAIT DONE" << std::endl;
// Receive data and output to file
} else {
// Reference position
std::streampos posRefFile = m_ofsActiveOutput.tellp();
if (posRefFile == (-1)) {
_EXCEPTIONT("ActiveOutput::tellp() fail");
}
// Write my GridPatch data to file
for (int i = 0; i < m_grid.GetActivePatchCount(); i++) {
const GridPatch * pPatch = m_grid.GetActivePatch(i);
int iPatchIx = pPatch->GetPatchIndex();
if (iPatchIx > m_grid.GetPatchCount()) {
_EXCEPTION2("PatchIndex (%i) out of range [0,%i)",
iPatchIx, m_grid.GetPatchCount());
}
/*
printf("Write %i %i %i %i %i\n",
iPatchIx,
m_vecGridPatchByteLoc[iPatchIx][0],
m_vecGridPatchByteSize[iPatchIx][0],
m_vecGridPatchByteLoc[iPatchIx][1],
m_vecGridPatchByteSize[iPatchIx][1]);
*/
const DataContainer & dcGeometric =
pPatch->GetDataContainerGeometric();
int nGeometricDataByteSize =
dcGeometric.GetTotalByteSize();
const char * pGeometricData =
(const char *)(dcGeometric.GetPointer());
m_ofsActiveOutput.seekp(
posRefFile + m_vecGridPatchByteLoc[iPatchIx][0]);
m_ofsActiveOutput.write(
pGeometricData, m_vecGridPatchByteSize[iPatchIx][0]);
const DataContainer & dcActiveState =
pPatch->GetDataContainerActiveState();
int nActiveStateDataByteSize =
dcActiveState.GetTotalByteSize();
const char * pActiveStateData =
(const char *)(dcActiveState.GetPointer());
m_ofsActiveOutput.seekp(
posRefFile + m_vecGridPatchByteLoc[iPatchIx][1]);
m_ofsActiveOutput.write(
pActiveStateData, m_vecGridPatchByteSize[iPatchIx][1]);
}
// Recieve all data objects from neighbors
int nRemainingMessages =
2 * (m_grid.GetPatchCount() - m_grid.GetActivePatchCount());
for (; nRemainingMessages > 0; nRemainingMessages--) {
// Receive a consolidation message
MPI_Status status;
MPI_Recv(
&(m_vecRecvBuffer[0]),
m_vecRecvBuffer.GetRows(),
MPI_CHAR,
MPI_ANY_SOURCE,
MPI_ANY_TAG,
MPI_COMM_WORLD,
&status);
// Data type from TAG
int iDataType = status.MPI_TAG;
if ((iDataType < 0) || (iDataType >= ExchangeDataType_Count)) {
_EXCEPTION1("MPI_TAG (%i) out of range", iDataType);
}
// Check patch index
int iPatchIx = *((int*)(&(m_vecRecvBuffer[0])));
if (iPatchIx > m_vecGridPatchByteLoc.GetRows()) {
_EXCEPTION2("PatchIndex (%i) out of range [0,%i)",
iPatchIx, m_vecGridPatchByteLoc.GetRows());
}
/*
if (iDataType == 0) {
printf("Recv Geo %i %i\n",
pPatchIx[0],
m_vecGridPatchByteSize[pPatchIx[0]][iDataType]);
} else {
printf("Recv AcS %i %i\n",
pPatchIx[0],
m_vecGridPatchByteSize[pPatchIx[0]][iDataType]);
}
*/
m_ofsActiveOutput.seekp(
posRefFile + m_vecGridPatchByteLoc[iPatchIx][iDataType]);
m_ofsActiveOutput.write(
(const char *)(&(m_vecRecvBuffer[0])),
m_vecGridPatchByteSize[iPatchIx][iDataType]);
}
}
// Barrier
MPI_Barrier(MPI_COMM_WORLD);
#else
_EXCEPTIONT("Not implemented without USE_MPI");
#endif
}
void MeshUtilities::FindFaceFromNode(
const Mesh & mesh,
const Node & node,
FindFaceStruct & aFindFaceStruct
) {
// Reset the FaceStruct
aFindFaceStruct.vecFaceIndices.clear();
aFindFaceStruct.vecFaceLocations.clear();
aFindFaceStruct.loc = Face::NodeLocation_Undefined;
// Loop through all faces to find overlaps
// Note: This algorithm can likely be dramatically improved
for (int l = 0; l < mesh.faces.size(); l++) {
Face::NodeLocation loc;
int ixLocation;
ContainsNode(
mesh.faces[l],
mesh.nodes,
node,
loc,
ixLocation);
if (loc == Face::NodeLocation_Exterior) {
continue;
}
#ifdef VERBOSE
printf("%i\n", l);
printf("n: %1.5e %1.5e %1.5e\n", node.x, node.y, node.z);
printf("n0: %1.5e %1.5e %1.5e\n",
mesh.nodes[mesh.faces[l][0]].x,
mesh.nodes[mesh.faces[l][0]].y,
mesh.nodes[mesh.faces[l][0]].z);
printf("n1: %1.5e %1.5e %1.5e\n",
mesh.nodes[mesh.faces[l][1]].x,
mesh.nodes[mesh.faces[l][1]].y,
mesh.nodes[mesh.faces[l][1]].z);
printf("n2: %1.5e %1.5e %1.5e\n",
mesh.nodes[mesh.faces[l][2]].x,
mesh.nodes[mesh.faces[l][2]].y,
mesh.nodes[mesh.faces[l][2]].z);
printf("n3: %1.5e %1.5e %1.5e\n",
mesh.nodes[mesh.faces[l][3]].x,
mesh.nodes[mesh.faces[l][3]].y,
mesh.nodes[mesh.faces[l][3]].z);
#endif
if (aFindFaceStruct.loc == Face::NodeLocation_Undefined) {
aFindFaceStruct.loc = loc;
}
// Node is in the interior of this face
if (loc == Face::NodeLocation_Interior) {
if (loc != aFindFaceStruct.loc) {
_EXCEPTIONT("No consensus on location of Node");
}
aFindFaceStruct.vecFaceIndices.push_back(l);
aFindFaceStruct.vecFaceLocations.push_back(ixLocation);
break;
}
// Node is on the edge of this face
if (loc == Face::NodeLocation_Edge) {
if (loc != aFindFaceStruct.loc) {
_EXCEPTIONT("No consensus on location of Node");
}
aFindFaceStruct.vecFaceIndices.push_back(l);
aFindFaceStruct.vecFaceLocations.push_back(ixLocation);
}
// Node is at the corner of this face
if (loc == Face::NodeLocation_Corner) {
if (loc != aFindFaceStruct.loc) {
_EXCEPTIONT("No consensus on location of Node");
}
aFindFaceStruct.vecFaceIndices.push_back(l);
aFindFaceStruct.vecFaceLocations.push_back(ixLocation);
}
}
// Edges can only have two adjacent Faces
if (aFindFaceStruct.loc == Face::NodeLocation_Edge) {
if (aFindFaceStruct.vecFaceIndices.size() != 2) {
printf("n: %1.5e %1.5e %1.5e\n", node.x, node.y, node.z);
_EXCEPTION2("Node found on edge with %i neighboring face(s) (%i)",
aFindFaceStruct.vecFaceIndices.size(),
(int)(aFindFaceStruct.vecFaceIndices.size()));
}
}
// Corners must have at least three adjacent Faces
if (aFindFaceStruct.loc == Face::NodeLocation_Corner) {
if (aFindFaceStruct.vecFaceIndices.size() < 3) {
printf("n: %1.5e %1.5e %1.5e\n", node.x, node.y, node.z);
_EXCEPTION1("Two Faced corner detected (%i)",
(int)(aFindFaceStruct.vecFaceIndices.size()));
}
}
}
bool OutputManagerReference::OpenFile(
const std::string & strFileName
) {
#ifdef TEMPEST_NETCDF
// Determine processor rank; only proceed if root node
int nRank = 0;
#ifdef TEMPEST_MPIOMP
MPI_Comm_rank(MPI_COMM_WORLD, &nRank);
#endif
// The active model
const Model & model = m_grid.GetModel();
// Open NetCDF file on root process
if (nRank == 0) {
// Check for existing NetCDF file
if (m_pActiveNcOutput != NULL) {
_EXCEPTIONT("NetCDF file already open");
}
// Append .nc extension to file
std::string strNcFileName = strFileName + ".nc";
// Open new NetCDF file
m_pActiveNcOutput = new NcFile(strNcFileName.c_str(), NcFile::Replace);
if (m_pActiveNcOutput == NULL) {
_EXCEPTION1("Error opening NetCDF file \"%s\"",
strNcFileName.c_str());
}
if (!m_pActiveNcOutput->is_valid()) {
_EXCEPTION1("Error opening NetCDF file \"%s\"",
strNcFileName.c_str());
}
// Create nodal time dimension
NcDim * dimTime = m_pActiveNcOutput->add_dim("time");
if (dimTime == NULL) {
_EXCEPTIONT("Error creating \"time\" dimension");
}
m_varTime = m_pActiveNcOutput->add_var("time", ncDouble, dimTime);
if (m_varTime == NULL) {
_EXCEPTIONT("Error creating \"time\" variable");
}
std::string strUnits =
"days since " + model.GetStartTime().ToDateString();
std::string strCalendarName = model.GetStartTime().GetCalendarName();
m_varTime->add_att("long_name", "time");
m_varTime->add_att("units", strUnits.c_str());
m_varTime->add_att("calendar", strCalendarName.c_str());
m_varTime->add_att("bounds", "time_bnds");
// Create levels dimension
NcDim * dimLev =
m_pActiveNcOutput->add_dim("lev", m_dREtaCoord.GetRows());
// Create interfaces dimension
NcDim * dimILev =
m_pActiveNcOutput->add_dim("ilev", m_grid.GetRElements()+1);
// Create latitude dimension
NcDim * dimLat =
m_pActiveNcOutput->add_dim("lat", m_nYReference);
// Create longitude dimension
NcDim * dimLon =
m_pActiveNcOutput->add_dim("lon", m_nXReference);
// Output physical constants
const PhysicalConstants & phys = model.GetPhysicalConstants();
m_pActiveNcOutput->add_att("earth_radius", phys.GetEarthRadius());
m_pActiveNcOutput->add_att("g", phys.GetG());
m_pActiveNcOutput->add_att("omega", phys.GetOmega());
m_pActiveNcOutput->add_att("alpha", phys.GetAlpha());
m_pActiveNcOutput->add_att("Rd", phys.GetR());
m_pActiveNcOutput->add_att("Cp", phys.GetCp());
m_pActiveNcOutput->add_att("T0", phys.GetT0());
m_pActiveNcOutput->add_att("P0", phys.GetP0());
m_pActiveNcOutput->add_att("rho_water", phys.GetRhoWater());
m_pActiveNcOutput->add_att("Rvap", phys.GetRvap());
m_pActiveNcOutput->add_att("Mvap", phys.GetMvap());
m_pActiveNcOutput->add_att("Lvap", phys.GetLvap());
// Output grid parameters
m_pActiveNcOutput->add_att("Ztop", m_grid.GetZtop());
// Output equation set
const EquationSet & eqn = model.GetEquationSet();
m_pActiveNcOutput->add_att("equation_set", eqn.GetName().c_str());
// Create variables
for (int c = 0; c < eqn.GetComponents(); c++) {
if ((m_fOutputAllVarsOnNodes) ||
(m_grid.GetVarLocation(c) == DataLocation_Node)
) {
m_vecComponentVar.push_back(
m_pActiveNcOutput->add_var(
eqn.GetComponentShortName(c).c_str(),
ncDouble, dimTime, dimLev, dimLat, dimLon));
} else {
m_vecComponentVar.push_back(
m_pActiveNcOutput->add_var(
eqn.GetComponentShortName(c).c_str(),
ncDouble, dimTime, dimILev, dimLat, dimLon));
}
}
for (int c = 0; c < eqn.GetTracers(); c++) {
m_vecTracersVar.push_back(
m_pActiveNcOutput->add_var(
eqn.GetTracerShortName(c).c_str(),
ncDouble, dimTime, dimLev, dimLat, dimLon));
}
// Vorticity variable
if (m_fOutputVorticity) {
m_varVorticity =
m_pActiveNcOutput->add_var(
"ZETA", ncDouble, dimTime, dimLev, dimLat, dimLon);
}
// Divergence variable
if (m_fOutputDivergence) {
m_varDivergence =
m_pActiveNcOutput->add_var(
"DELTA", ncDouble, dimTime, dimLev, dimLat, dimLon);
}
// Temperature variable
if (m_fOutputTemperature) {
m_varTemperature =
m_pActiveNcOutput->add_var(
"T", ncDouble, dimTime, dimLev, dimLat, dimLon);
}
// Surface pressure variable
if (m_fOutputSurfacePressure) {
m_varSurfacePressure =
m_pActiveNcOutput->add_var(
"PS", ncDouble, dimTime, dimLat, dimLon);
}
// Richardson number variable
if (m_fOutputRichardson) {
m_varRichardson =
m_pActiveNcOutput->add_var(
"Ri", ncDouble, dimTime, dimLev, dimLat, dimLon);
}
// User data variables
const UserDataMeta & metaUserData = model.GetUserDataMeta();
m_vecUserData2DVar.resize(metaUserData.GetUserData2DItemCount());
for (int i = 0; i < metaUserData.GetUserData2DItemCount(); i++) {
m_vecUserData2DVar[i] =
m_pActiveNcOutput->add_var(
metaUserData.GetUserData2DItemName(i).c_str(),
ncDouble, dimTime, dimLat, dimLon);
}
// Output longitudes and latitudes
NcVar * varLon = m_pActiveNcOutput->add_var("lon", ncDouble, dimLon);
NcVar * varLat = m_pActiveNcOutput->add_var("lat", ncDouble, dimLat);
varLon->put(m_dXCoord, m_dXCoord.GetRows());
varLat->put(m_dYCoord, m_dYCoord.GetRows());
varLon->add_att("long_name", "longitude");
varLon->add_att("units", "degrees_east");
varLat->add_att("long_name", "latitude");
varLat->add_att("units", "degrees_north");
// Output levels
NcVar * varLev =
m_pActiveNcOutput->add_var("lev", ncDouble, dimLev);
varLev->put(
m_dREtaCoord,
m_dREtaCoord.GetRows());
varLev->add_att("long_name", "level");
varLev->add_att("units", "level");
// Output interface levels
NcVar * varILev =
m_pActiveNcOutput->add_var("ilev", ncDouble, dimILev);
varILev->put(
m_grid.GetREtaStretchInterfaces(),
m_grid.GetREtaStretchInterfaces().GetRows());
varILev->add_att("long_name", "interface level");
varILev->add_att("units", "level");
// Topography variable
m_varTopography =
m_pActiveNcOutput->add_var("Zs", ncDouble, dimLat, dimLon);
// Fresh output file
m_fFreshOutputFile = true;
}
#ifdef TEMPEST_MPIOMP
// Wait for all processes to complete
MPI_Barrier(MPI_COMM_WORLD);
#endif
#endif
return true;
}
int main(int argc, char** argv) {
NcError error(NcError::verbose_nonfatal);
try {
// Input file
std::string strInputFile;
// Input file list
std::string strInputFileList;
// Input file format
std::string strInputFormat;
// NetCDF file containing latitude and longitude arrays
std::string strLatLonFile;
// Output file (NetCDF)
std::string strOutputFile;
// Output variable name
std::string strOutputVariable;
// Column in which the longitude index appears
int iLonIxCol;
// Column in which the latitude index appears
int iLatIxCol;
// Begin latitude
double dLatBegin;
// End latitude
double dLatEnd;
// Begin longitude
double dLonBegin;
// End longitude
double dLonEnd;
// Number of latitudes in output
int nLat;
// Number of longitudes in output
int nLon;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputFile, "in", "");
CommandLineString(strInputFileList, "inlist", "");
CommandLineStringD(strInputFormat, "in_format", "std", "(std|visit)");
CommandLineString(strOutputFile, "out", "");
CommandLineString(strOutputVariable, "outvar", "density");
CommandLineInt(iLonIxCol, "iloncol", 8);
CommandLineInt(iLatIxCol, "ilatcol", 9);
CommandLineDouble(dLatBegin, "lat_begin", -90.0);
CommandLineDouble(dLatEnd, "lat_end", 90.0);
CommandLineDouble(dLonBegin, "lon_begin", 0.0);
CommandLineDouble(dLonEnd, "lon_end", 360.0);
CommandLineInt(nLat, "nlat", 180);
CommandLineInt(nLon, "nlon", 360);
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check input
if ((strInputFile == "") && (strInputFileList == "")) {
_EXCEPTIONT("No input file (--in) or (--inlist) specified");
}
if ((strInputFile != "") && (strInputFileList != "")) {
_EXCEPTIONT("Only one input file (--in) or (--inlist) allowed");
}
if (strInputFormat != "std") {
_EXCEPTIONT("UNIMPLEMENTED: Only \"--in_format std\" supported");
}
// Check output
if (strOutputFile == "") {
_EXCEPTIONT("No output file (--out) specified");
}
// Check output variable
if (strOutputVariable == "") {
_EXCEPTIONT("No output variable name (--outvar) specified");
}
// Number of latitudes and longitudes
if (nLat == 0) {
_EXCEPTIONT("UNIMPLEMENTED: --nlat must be specified currently");
}
if (nLon == 0) {
_EXCEPTIONT("UNIMPLEMENTED: --nlon must be specified currently");
}
// Input file list
std::vector<std::string> vecInputFiles;
if (strInputFile != "") {
vecInputFiles.push_back(strInputFile);
}
if (strInputFileList != "") {
GetInputFileList(strInputFileList, vecInputFiles);
}
int nFiles = vecInputFiles.size();
// Density
DataMatrix<int> nCounts;
nCounts.Initialize(nLat, nLon);
// Loop through all files in list
AnnounceStartBlock("Processing files");
std::string strBuffer;
strBuffer.reserve(1024);
for (int f = 0; f < nFiles; f++) {
Announce("File \"%s\"", vecInputFiles[f].c_str());
FILE * fp = fopen(vecInputFiles[f].c_str(), "r");
if (fp == NULL) {
_EXCEPTION1("Unable to open input file \"%s\"",
vecInputFiles[f].c_str());
}
for (;;) {
// Read in the next line
fgets(&(strBuffer[0]), 1024, fp);
int nLength = strlen(&(strBuffer[0]));
// Check for end of file
if (feof(fp)) {
break;
}
// Check for comment line
if (strBuffer[0] == '#') {
continue;
}
// Check for new storm
if (strncmp(&(strBuffer[0]), "start", 5) == 0) {
continue;
}
// Parse line
double dLon;
double dLat;
int iCol = 0;
int iLast = 0;
bool fWhitespace = true;
for (int i = 0; i <= nLength; i++) {
if ((strBuffer[i] == ' ') ||
(strBuffer[i] == ',') ||
(strBuffer[i] == '\t') ||
(strBuffer[i] == '\0')
) {
if (!fWhitespace) {
if (iCol == iLonIxCol) {
strBuffer[i] = '\0';
dLon = atof(&(strBuffer[iLast]));
}
if (iCol == iLatIxCol) {
strBuffer[i] = '\0';
dLat = atof(&(strBuffer[iLast]));
}
}
fWhitespace = true;
} else {
if (fWhitespace) {
iLast = i;
iCol++;
}
fWhitespace = false;
}
}
// Latitude and longitude index
int iLon =
static_cast<int>(static_cast<double>(nLon)
* (dLon - dLonBegin) / (dLonEnd - dLonBegin));
int iLat =
static_cast<int>(static_cast<double>(nLat)
* (dLat - dLatBegin) / (dLatEnd - dLatBegin));
if (iLon == (-1)) {
iLon = 0;
}
if (iLon == nLon) {
iLon = nLon - 1;
}
if (iLat == (-1)) {
iLat = 0;
}
if (iLat == nLat) {
iLat = nLat - 1;
}
if ((iLat < 0) || (iLat >= nLat)) {
_EXCEPTION1("Latitude index (%i) out of range", iLat);
}
if ((iLon < 0) || (iLon >= nLon)) {
_EXCEPTION1("Longitude index (%i) out of range", iLon);
}
nCounts[iLat][iLon]++;
}
fclose(fp);
}
AnnounceEndBlock("Done");
// Output results
AnnounceStartBlock("Output results");
// Load the netcdf output file
NcFile ncOutput(strOutputFile.c_str(), NcFile::Replace);
if (!ncOutput.is_valid()) {
_EXCEPTION1("Unable to open output file \"%s\"",
strOutputFile.c_str());
}
// Create output
NcDim * dimLat = ncOutput.add_dim("lat", nLat);
NcDim * dimLon = ncOutput.add_dim("lon", nLon);
NcVar * varLat = ncOutput.add_var("lat", ncDouble, dimLat);
NcVar * varLon = ncOutput.add_var("lon", ncDouble, dimLon);
varLat->add_att("units", "degrees_north");
varLon->add_att("units", "degrees_east");
DataVector<double> dLat(nLat);
DataVector<double> dLon(nLon);
for (int j = 0; j < nLat; j++) {
dLat[j] = dLatBegin
+ (dLatEnd - dLatBegin)
* (static_cast<double>(j) + 0.5)
/ static_cast<double>(nLat);
}
for (int i = 0; i < nLon; i++) {
dLon[i] = dLonBegin
+ (dLonEnd - dLonBegin)
* (static_cast<double>(i) + 0.5)
/ static_cast<double>(nLon);
}
varLat->put(&(dLat[0]), nLat);
varLon->put(&(dLon[0]), nLon);
// Output counts
NcVar * varCount =
ncOutput.add_var(
strOutputVariable.c_str(),
ncInt,
dimLat,
dimLon);
varCount->put(&(nCounts[0][0]), nLat, nLon);
ncOutput.close();
AnnounceEndBlock("Done");
AnnounceBanner();
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
}
void CopyNcVar(
NcFile & ncIn,
NcFile & ncOut,
const std::string & strVarName,
bool fCopyAttributes,
bool fCopyData
) {
if (!ncIn.is_valid()) {
_EXCEPTIONT("Invalid input file specified");
}
if (!ncOut.is_valid()) {
_EXCEPTIONT("Invalid output file specified");
}
NcVar * var = ncIn.get_var(strVarName.c_str());
if (var == NULL) {
_EXCEPTION1("NetCDF file does not contain variable \"%s\"",
strVarName.c_str());
}
NcVar * varOut;
std::vector<NcDim *> dimOut;
dimOut.resize(var->num_dims());
std::vector<long> counts;
counts.resize(var->num_dims());
long nDataSize = 1;
for (int d = 0; d < var->num_dims(); d++) {
NcDim * dimA = var->get_dim(d);
dimOut[d] = ncOut.get_dim(dimA->name());
if (dimOut[d] == NULL) {
if (dimA->is_unlimited()) {
dimOut[d] = ncOut.add_dim(dimA->name());
} else {
dimOut[d] = ncOut.add_dim(dimA->name(), dimA->size());
}
if (dimOut[d] == NULL) {
_EXCEPTION2("Failed to add dimension \"%s\" (%i) to file",
dimA->name(), dimA->size());
}
}
if (dimOut[d]->size() != dimA->size()) {
if (dimA->is_unlimited() && !dimOut[d]->is_unlimited()) {
_EXCEPTION2("Mismatch between input file dimension \"%s\" and "
"output file dimension (UNLIMITED / %i)",
dimA->name(), dimOut[d]->size());
} else if (!dimA->is_unlimited() && dimOut[d]->is_unlimited()) {
_EXCEPTION2("Mismatch between input file dimension \"%s\" and "
"output file dimension (%i / UNLIMITED)",
dimA->name(), dimA->size());
} else if (!dimA->is_unlimited() && !dimOut[d]->is_unlimited()) {
_EXCEPTION3("Mismatch between input file dimension \"%s\" and "
"output file dimension (%i / %i)",
dimA->name(), dimA->size(), dimOut[d]->size());
}
}
counts[d] = dimA->size();
nDataSize *= counts[d];
}
// ncByte / ncChar type
if ((var->type() == ncByte) || (var->type() == ncChar)) {
DataVector<char> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
// ncShort type
if (var->type() == ncShort) {
DataVector<short> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncInt type
if (var->type() == ncInt) {
DataVector<int> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncFloat type
if (var->type() == ncFloat) {
DataVector<float> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncDouble type
if (var->type() == ncDouble) {
DataVector<double> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// ncInt64 type
if (var->type() == ncInt64) {
DataVector<ncint64> data;
data.Initialize(nDataSize);
varOut =
ncOut.add_var(
var->name(), var->type(),
dimOut.size(), (const NcDim**)&(dimOut[0]));
if (varOut == NULL) {
_EXCEPTION1("Cannot create variable \"%s\"", var->name());
}
if (fCopyData) {
var->get(&(data[0]), &(counts[0]));
varOut->put(&(data[0]), &(counts[0]));
}
}
// Check output variable exists
if (varOut == NULL) {
_EXCEPTION1("Unable to create output variable \"%s\"",
var->name());
}
// Copy attributes
if (fCopyAttributes) {
CopyNcVarAttributes(var, varOut);
}
}
void LegendrePolynomial::AllDerivativeRoots(
int nDegree,
double * dRoots
) {
// Iteration tolerance
const double IterationTolerance = 1.0e-14;
// Check for degree 0 or 1
if ((nDegree == 0) || (nDegree == 1)) {
return;
}
// Check for negative degree
if (nDegree < 0) {
_EXCEPTION1("Invalid degree (%i)", nDegree);
}
// Check for NULL dRoots pointer
if (dRoots == NULL) {
_EXCEPTIONT("NULL pointer passed into AllRoots argument dRoots");
}
// Double degree
double dDegree = static_cast<double>(nDegree);
// Additional storage for roots
double * dBuffer = new double[nDegree-1];
// Set initial estimate
for (int k = 0; k < nDegree-1; k++) {
dRoots[k] = (static_cast<double>(k) + 0.5) * 2.0 / (dDegree - 1.0) - 1.0;
}
// Refine estimate using Aberth-Ehrlich method
for (int iter = 0; iter < nDegree + 10; iter++) {
/*
for (int k = 0; k < nDegree - 1; k++) {
printf("%i %i: %1.15e\n", iter, k, dRoots[k]);
}
*/
int nFoundRoots = 0;
for (int k = 0; k < nDegree - 1; k++) {
double dValue;
double dDerivative;
EvaluateValueAndDerivative(nDegree, dRoots[k], dValue, dDerivative);
if (fabs(dDerivative) < IterationTolerance) {
nFoundRoots++;
dBuffer[k] = dRoots[k];
continue;
}
double dMod = 0.0;
for (int l = 0; l < nDegree - 1; l++) {
if (l == k) {
continue;
}
dMod += 1.0 / (dRoots[k] - dRoots[l]);
}
// Second derivative obtained from
double dSecondDerivative =
1.0 / (1.0 - dRoots[k] * dRoots[k])
* (2.0 * dRoots[k] * dDerivative
- dDegree * (dDegree + 1.0) * dValue);
dBuffer[k] = dRoots[k]
- 1.0 / (dSecondDerivative / dDerivative - dMod);
}
// Copy buffer to roots
memcpy(dRoots, dBuffer, (nDegree - 1) * sizeof(double));
// Check if all roots have been found
if (nFoundRoots == nDegree - 1) {
break;
}
}
// Sort roots
std::sort(dRoots, dRoots + nDegree - 1);
// Delete buffer
delete[] dBuffer;
}
int main(int argc, char ** argv){
NcError error(NcError::verbose_nonfatal);
try{
std::string inFile;
std::string outFile;
std::string varName;
std::string inList;
// bool calcStdDev;
BeginCommandLine()
CommandLineString(inFile, "in", "");
CommandLineString(inList, "inlist","");
CommandLineString(varName, "var", "");
CommandLineString(outFile, "out", "");
// CommandLineBool(calcStdDev, "std");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
if ((inFile != "") && (inList != "")){
_EXCEPTIONT("Can only open one file (--in) or list (--inlist).");
}
//file list vector
std::vector<std::string> vecFiles;
if (inFile != ""){
vecFiles.push_back(inFile);
}
if (inList != ""){
GetInputFileList(inList,vecFiles);
}
//open up first file
NcFile readin(vecFiles[0].c_str());
if (!readin.is_valid()){
_EXCEPTION1("Unable to open file %s for reading",\
vecFiles[0].c_str());
}
int tLen,latLen,lonLen;
NcDim * time = readin.get_dim("time");
tLen = time->size();
NcVar * timeVar = readin.get_var("time");
NcDim * lat = readin.get_dim("lat");
latLen = lat->size();
NcVar * latVar = readin.get_var("lat");
NcDim * lon = readin.get_dim("lon");
lonLen = lon->size();
NcVar * lonVar = readin.get_var("lon");
//read input variable
NcVar * inVar = readin.get_var(varName.c_str());
//Create output matrix
DataMatrix<double> outMat(latLen,lonLen);
densCalc(inVar,outMat);
//Option for calculating the yearly standard deviation
/* if (calcStdDev){
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
storeMat[0][a][b] = outMat[a][b];
}
}
}
*/
//If multiple files, add these values to the output
if (vecFiles.size()>1){
DataMatrix<double> addMat(latLen,lonLen);
std::cout<<"There are "<<vecFiles.size()<<" files."<<std::endl;
for (int v=1; v<vecFiles.size(); v++){
NcFile addread(vecFiles[v].c_str());
NcVar * inVar = addread.get_var(varName.c_str());
densCalc(inVar,addMat);
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
outMat[a][b]+=addMat[a][b];
}
}
/* if (calcStdDev){
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
storeMat[v][a][b] = addMat[a][b];
}
}
}*/
addread.close();
}
//Divide output by number of files
double div = 1./((double) vecFiles.size());
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
outMat[a][b]*=div;
}
}
}
NcFile readout(outFile.c_str(),NcFile::Replace, NULL,0,NcFile::Offset64Bits);
NcDim * outLat = readout.add_dim("lat", latLen);
NcDim * outLon = readout.add_dim("lon", lonLen);
NcVar * outLatVar = readout.add_var("lat",ncDouble,outLat);
NcVar * outLonVar = readout.add_var("lon",ncDouble,outLon);
std::cout<<"Copying dimension attributes."<<std::endl;
copy_dim_var(latVar,outLatVar);
copy_dim_var(lonVar,outLonVar);
std::cout<<"Creating density variable."<<std::endl;
NcVar * densVar = readout.add_var("dens",ncDouble,outLat,outLon);
densVar->set_cur(0,0);
densVar->put((&outMat[0][0]),latLen,lonLen);
/* if (calcStdDev){
NcVar * stdDevVar = readout.add_var("stddev", ncDouble,outLat,outLon);
DataMatrix<double> stdDevMat(latLen,lonLen);
yearlyStdDev(storeMat,vecFiles.size(),latLen,lonLen,stdDevMat);
stdDevVar->set_cur(0,0);
stdDevVar->put(&(stdDevMat[0][0]),latLen,lonLen);
std::cout<<" created sd variable"<<std::endl;
}
*/
readout.close();
readin.close();
}
catch (Exception &e){
std::cout<<e.ToString()<<std::endl;
}
}
void GridPatchCSGLL::EvaluateGeometricTerms() {
// Physical constants
const PhysicalConstants & phys = m_grid.GetModel().GetPhysicalConstants();
// 2D equation set
bool fIs2DEquationSet = false;
if (m_grid.GetModel().GetEquationSet().GetDimensionality() == 2) {
fIs2DEquationSet = true;
}
if ((fIs2DEquationSet) && (m_grid.GetZtop() != 1.0)) {
_EXCEPTIONT("Ztop must be 1.0 for 2D equation sets");
}
// Obtain Gauss Lobatto quadrature nodes and weights
DataArray1D<double> dGL;
DataArray1D<double> dWL;
GaussLobattoQuadrature::GetPoints(m_nHorizontalOrder, 0.0, 1.0, dGL, dWL);
// Obtain normalized areas in the vertical
const DataArray1D<double> & dWNode =
m_grid.GetREtaLevelsNormArea();
const DataArray1D<double> & dWREdge =
m_grid.GetREtaInterfacesNormArea();
// Verify that normalized areas are correct
double dWNodeSum = 0.0;
for (int k = 0; k < dWNode.GetRows(); k++) {
dWNodeSum += dWNode[k];
}
if (fabs(dWNodeSum - 1.0) > 1.0e-13) {
_EXCEPTION1("Error in normalized areas (%1.15e)", dWNodeSum);
}
if (m_grid.GetVerticalStaggering() !=
Grid::VerticalStaggering_Interfaces
) {
double dWREdgeSum = 0.0;
for (int k = 0; k < dWREdge.GetRows(); k++) {
dWREdgeSum += dWREdge[k];
}
if (fabs(dWREdgeSum - 1.0) > 1.0e-13) {
_EXCEPTION1("Error in normalized areas (%1.15e)", dWREdgeSum);
}
}
// Derivatives of basis functions
GridCSGLL & gridCSGLL = dynamic_cast<GridCSGLL &>(m_grid);
const DataArray2D<double> & dDxBasis1D = gridCSGLL.GetDxBasis1D();
// Initialize the Coriolis force at each node
for (int i = 0; i < m_box.GetATotalWidth(); i++) {
for (int j = 0; j < m_box.GetBTotalWidth(); j++) {
m_dataCoriolisF[i][j] = 2.0 * phys.GetOmega() * sin(m_dataLat[i][j]);
}
}
// Initialize metric in terrain-following coords
for (int a = 0; a < GetElementCountA(); a++) {
for (int b = 0; b < GetElementCountB(); b++) {
for (int i = 0; i < m_nHorizontalOrder; i++) {
for (int j = 0; j < m_nHorizontalOrder; j++) {
// Nodal points
int iElementA = m_box.GetAInteriorBegin() + a * m_nHorizontalOrder;
int iElementB = m_box.GetBInteriorBegin() + b * m_nHorizontalOrder;
int iA = iElementA + i;
int iB = iElementB + j;
// Gnomonic coordinates
double dX = tan(m_dANode[iA]);
double dY = tan(m_dBNode[iB]);
double dDelta2 = (1.0 + dX * dX + dY * dY);
double dDelta = sqrt(dDelta2);
// Topography height and its derivatives
double dZs = m_dataTopography[iA][iB];
double dDaZs = m_dataTopographyDeriv[0][iA][iB];
double dDbZs = m_dataTopographyDeriv[1][iA][iB];
// 2D equations
if (fIs2DEquationSet) {
dZs = 0.0;
dDaZs = 0.0;
dDbZs = 0.0;
}
// Initialize 2D Jacobian
m_dataJacobian2D[iA][iB] =
(1.0 + dX * dX) * (1.0 + dY * dY) / (dDelta * dDelta * dDelta);
m_dataJacobian2D[iA][iB] *=
phys.GetEarthRadius()
* phys.GetEarthRadius();
// Initialize 2D contravariant metric
double dContraMetricScale =
dDelta2 / (1.0 + dX * dX) / (1.0 + dY * dY)
/ (phys.GetEarthRadius() * phys.GetEarthRadius());
m_dataContraMetric2DA[iA][iB][0] =
dContraMetricScale * (1.0 + dY * dY);
m_dataContraMetric2DA[iA][iB][1] =
dContraMetricScale * dX * dY;
m_dataContraMetric2DB[iA][iB][0] =
dContraMetricScale * dX * dY;
m_dataContraMetric2DB[iA][iB][1] =
dContraMetricScale * (1.0 + dX * dX);
// Initialize 2D covariant metric
double dCovMetricScale =
phys.GetEarthRadius() * phys.GetEarthRadius()
* (1.0 + dX * dX) * (1.0 + dY * dY)
/ (dDelta2 * dDelta2);
m_dataCovMetric2DA[iA][iB][0] =
dCovMetricScale * (1.0 + dX * dX);
m_dataCovMetric2DA[iA][iB][1] =
dCovMetricScale * (- dX * dY);
m_dataCovMetric2DB[iA][iB][0] =
dCovMetricScale * (- dX * dY);
m_dataCovMetric2DB[iA][iB][1] =
dCovMetricScale * (1.0 + dY * dY);
// Vertical coordinate transform and its derivatives
for (int k = 0; k < m_grid.GetRElements(); k++) {
// Gal-Chen and Somerville (1975) linear terrain-following coord
double dREta = m_grid.GetREtaLevel(k);
/*
double dREtaStretch;
double dDxREtaStretch;
m_grid.EvaluateVerticalStretchF(
dREta, dREtaStretch, dDxREtaStretch);
double dZ = dZs + (m_grid.GetZtop() - dZs) * dREtaStretch;
double dDaR = (1.0 - dREtaStretch) * dDaZs;
double dDbR = (1.0 - dREtaStretch) * dDbZs;
double dDxR = (m_grid.GetZtop() - dZs) * dDxREtaStretch;
*/
double dZ = dZs + (m_grid.GetZtop() - dZs) * dREta;
double dDaR = (1.0 - dREta) * dDaZs;
double dDbR = (1.0 - dREta) * dDbZs;
double dDxR = (m_grid.GetZtop() - dZs);
// Calculate pointwise Jacobian
m_dataJacobian[k][iA][iB] = dDxR * m_dataJacobian2D[iA][iB];
// Element area associated with each model level GLL node
m_dataElementAreaNode[k][iA][iB] =
m_dataJacobian[k][iA][iB]
* dWL[i] * GetElementDeltaA()
* dWL[j] * GetElementDeltaB()
* dWNode[k];
// Contravariant metric components
m_dataContraMetricA[k][iA][iB][0] =
m_dataContraMetric2DA[iA][iB][0];
m_dataContraMetricA[k][iA][iB][1] =
m_dataContraMetric2DA[iA][iB][1];
m_dataContraMetricA[k][iA][iB][2] =
- dContraMetricScale / dDxR * (
(1.0 + dY * dY) * dDaR + dX * dY * dDbR);
m_dataContraMetricB[k][iA][iB][0] =
m_dataContraMetric2DB[iA][iB][0];
m_dataContraMetricB[k][iA][iB][1] =
m_dataContraMetric2DB[iA][iB][1];
m_dataContraMetricB[k][iA][iB][2] =
- dContraMetricScale / dDxR * (
dX * dY * dDaR + (1.0 + dX * dX) * dDbR);
m_dataContraMetricXi[k][iA][iB][0] =
m_dataContraMetricA[k][iA][iB][2];
m_dataContraMetricXi[k][iA][iB][1] =
m_dataContraMetricB[k][iA][iB][2];
m_dataContraMetricXi[k][iA][iB][2] =
1.0 / (dDxR * dDxR)
- 1.0 / dDxR * (
m_dataContraMetricXi[k][iA][iB][0] * dDaR
+ m_dataContraMetricXi[k][iA][iB][1] * dDbR);
// Derivatives of the vertical coordinate transform
m_dataDerivRNode[k][iA][iB][0] = dDaR;
m_dataDerivRNode[k][iA][iB][1] = dDbR;
m_dataDerivRNode[k][iA][iB][2] = dDxR;
}
// Metric terms at vertical interfaces
for (int k = 0; k <= m_grid.GetRElements(); k++) {
// Gal-Chen and Somerville (1975) linear terrain-following coord
double dREta = m_grid.GetREtaInterface(k);
/*
double dREtaStretch;
double dDxREtaStretch;
m_grid.EvaluateVerticalStretchF(
dREta, dREtaStretch, dDxREtaStretch);
double dZ = dZs + (m_grid.GetZtop() - dZs) * dREtaStretch;
double dDaR = (1.0 - dREtaStretch) * dDaZs;
double dDbR = (1.0 - dREtaStretch) * dDbZs;
double dDxR = (m_grid.GetZtop() - dZs) * dDxREtaStretch;
*/
double dZ = dZs + (m_grid.GetZtop() - dZs) * dREta;
double dDaR = (1.0 - dREta) * dDaZs;
double dDbR = (1.0 - dREta) * dDbZs;
double dDxR = (m_grid.GetZtop() - dZs);
// Calculate pointwise Jacobian
m_dataJacobianREdge[k][iA][iB] =
(1.0 + dX * dX) * (1.0 + dY * dY) / (dDelta * dDelta * dDelta);
m_dataJacobianREdge[k][iA][iB] *=
dDxR
* phys.GetEarthRadius()
* phys.GetEarthRadius();
// Element area associated with each model interface GLL node
m_dataElementAreaREdge[k][iA][iB] =
m_dataJacobianREdge[k][iA][iB]
* dWL[i] * GetElementDeltaA()
* dWL[j] * GetElementDeltaB()
* dWREdge[k];
// Contravariant metric (alpha)
m_dataContraMetricAREdge[k][iA][iB][0] =
m_dataContraMetric2DA[iA][iB][0];
m_dataContraMetricAREdge[k][iA][iB][1] =
m_dataContraMetric2DA[iA][iB][1];
m_dataContraMetricAREdge[k][iA][iB][2] =
- dContraMetricScale / dDxR * (
(1.0 + dY * dY) * dDaR + dX * dY * dDbR);
// Contravariant metric (beta)
m_dataContraMetricBREdge[k][iA][iB][0] =
m_dataContraMetric2DB[iA][iB][0];
m_dataContraMetricBREdge[k][iA][iB][1] =
m_dataContraMetric2DB[iA][iB][1];
m_dataContraMetricBREdge[k][iA][iB][2] =
- dContraMetricScale / dDxR * (
dX * dY * dDaR + (1.0 + dX * dX) * dDbR);
// Contravariant metric (xi)
m_dataContraMetricXiREdge[k][iA][iB][0] =
- dContraMetricScale / dDxR * (
(1.0 + dY * dY) * dDaR + dX * dY * dDbR);
m_dataContraMetricXiREdge[k][iA][iB][1] =
- dContraMetricScale / dDxR * (
dX * dY * dDaR + (1.0 + dX * dX) * dDbR);
m_dataContraMetricXiREdge[k][iA][iB][2] =
1.0 / (dDxR * dDxR)
- 1.0 / dDxR * (
m_dataContraMetricXiREdge[k][iA][iB][0] * dDaR
+ m_dataContraMetricXiREdge[k][iA][iB][1] * dDbR);
// Derivatives of the vertical coordinate transform
m_dataDerivRREdge[k][iA][iB][0] = dDaR;
m_dataDerivRREdge[k][iA][iB][1] = dDbR;
m_dataDerivRREdge[k][iA][iB][2] = dDxR;
}
}
}
}
}
}
