void Grid::Checksum( DataType eDataType, DataArray1D<double> & dChecksums, int iDataIndex, ChecksumType eChecksumType ) const { #ifdef USE_MPI // Identify root process int nRank; MPI_Comm_rank(MPI_COMM_WORLD, &nRank); // Initialize the local checksum array from DataType DataArray1D<double> dChecksumsLocal; if (eDataType == DataType_State) { dChecksumsLocal.Allocate(m_model.GetEquationSet().GetComponents()); } else if (eDataType == DataType_Tracers) { int nTracers = m_model.GetEquationSet().GetTracers(); if (nTracers == 0) { return; } dChecksumsLocal.Allocate(nTracers); } else { _EXCEPTIONT("Invalid DataType"); } // Loop over all patches and calculate local checksums for (int n = 0; n < m_vecActiveGridPatches.size(); n++) { m_vecActiveGridPatches[n]->Checksum( eDataType, dChecksumsLocal, iDataIndex, eChecksumType); } // Initialize global checksums array at root if (nRank == 0) { dChecksums.Allocate(dChecksumsLocal.GetRows()); } // Compute sum over all processors and send to root node MPI_Op nMPIOperator; if (eChecksumType == ChecksumType_Linf) { nMPIOperator = MPI_MAX; } else { nMPIOperator = MPI_SUM; } MPI_Reduce( &(dChecksumsLocal[0]), &(dChecksums[0]), dChecksumsLocal.GetRows(), MPI_DOUBLE, nMPIOperator, 0, MPI_COMM_WORLD); // Take the square root for the L2 norm sum if (nRank == 0) { if (eChecksumType == ChecksumType_L2) { for (int c = 0; c < dChecksums.GetRows(); c++) { dChecksums[c] = sqrt(dChecksums[c]); } } } #endif }
int main(int argc, char** argv) { NcError error(NcError::silent_nonfatal); try { // Input filename std::string strInputFile; // Output mesh filename std::string strOutputFile; // Polynomial degree per element int nP = 2; // Parse the command line BeginCommandLine() CommandLineString(strInputFile, "in", ""); CommandLineString(strOutputFile, "out", ""); //CommandLineInt(nP, "np", 2); //CommandLineBool(fCGLL, "cgll"); 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); } if (nP < 1) { std::cout << "ERROR: --np must be >= 2" << std::endl; return (-1); } AnnounceBanner(); // Load input mesh AnnounceStartBlock("Loading input mesh"); Mesh meshIn(strInputFile); meshIn.RemoveZeroEdges(); AnnounceEndBlock("Done"); // Construct edge map AnnounceStartBlock("Constructing edge map"); meshIn.ConstructEdgeMap(); AnnounceEndBlock("Done"); // Build connectivity vector using edge map AnnounceStartBlock("Constructing connectivity"); std::vector< std::set<int> > vecConnectivity; int err = GenerateConnectivityData(meshIn, vecConnectivity); if (err) return err; AnnounceEndBlock("Done"); // Open output file AnnounceStartBlock("Writing connectivity file"); NcFile ncmesh(strInputFile.c_str(), NcFile::ReadOnly); NcVar * varLat = ncmesh.get_var("grid_center_lat"); NcVar * varLon = ncmesh.get_var("grid_center_lon"); // Check if center latitudes and longitudes are already available DataArray1D<double> dAllLats; DataArray1D<double> dAllLons; bool fConvertLatToDegrees = true; bool fConvertLonToDegrees = true; if ((varLat == NULL) || (varLon == NULL)) { Announce("grid_center_lat not found, recalculating face centers"); } else { Announce("grid_center_lat found in file, loading values"); if (varLat->get_dim(0)->size() != vecConnectivity.size()) { _EXCEPTIONT("grid_center_lat dimension mismatch"); } if (varLon->get_dim(0)->size() != vecConnectivity.size()) { _EXCEPTIONT("grid_center_lon dimension mismatch"); } dAllLats.Allocate(vecConnectivity.size()); varLat->set_cur((long)0); varLat->get(dAllLats, vecConnectivity.size()); NcAtt * attLatUnits = varLat->get_att("units"); std::string strLatUnits = attLatUnits->as_string(0); if (strLatUnits == "degrees") { fConvertLatToDegrees = false; } dAllLons.Allocate(vecConnectivity.size()); varLon->set_cur((long)0); varLon->get(dAllLons, vecConnectivity.size()); NcAtt * attLonUnits = varLon->get_att("units"); std::string strLonUnits = attLonUnits->as_string(0); if (strLonUnits == "degrees") { fConvertLonToDegrees = false; } } // Write connectiivty file FILE * fp = fopen(strOutputFile.c_str(), "w"); fprintf(fp, "%lu\n", vecConnectivity.size()); for (size_t f = 0; f < vecConnectivity.size(); f++) { double dLon; double dLat; if ((varLat == NULL) || (varLon == NULL)) { Node nodeCentroid; for (int i = 0; i < meshIn.faces[f].edges.size(); i++) { nodeCentroid.x += meshIn.nodes[meshIn.faces[f][i]].x; nodeCentroid.y += meshIn.nodes[meshIn.faces[f][i]].y; nodeCentroid.z += meshIn.nodes[meshIn.faces[f][i]].z; } double dMagnitude = nodeCentroid.Magnitude(); nodeCentroid.x /= dMagnitude; nodeCentroid.y /= dMagnitude; nodeCentroid.z /= dMagnitude; dLon = atan2(nodeCentroid.y, nodeCentroid.x); dLat = asin(nodeCentroid.z); if (dLon < 0.0) { dLon += 2.0 * M_PI; } } else { dLon = dAllLons[f]; dLat = dAllLats[f]; } if (fConvertLonToDegrees) { dLon *= 180.0 / M_PI; } if (fConvertLatToDegrees) { dLat *= 180.0 / M_PI; } fprintf(fp, "%1.14f,", dLon); fprintf(fp, "%1.14f,", dLat); fprintf(fp, "%lu", vecConnectivity[f].size()); std::set<int>::const_iterator iter = vecConnectivity[f].begin(); for (; iter != vecConnectivity[f].end(); iter++) { fprintf(fp, ",%i", *iter); } if (f != vecConnectivity.size()-1) { fprintf(fp,"\n"); } } fclose(fp); AnnounceEndBlock("Done"); // Announce AnnounceBanner(); return (0); } catch(Exception & e) { Announce(e.ToString().c_str()); return (-1); } catch(...) { return (-2); } }
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(); }
void GridPatchCSGLL::EvaluateTestCase( const TestCase & test, const Time & time, int iDataIndex ) { // Initialize the data at each node if (m_datavecStateNode.size() == 0) { _EXCEPTIONT("InitializeData must be called before InitialConditions"); } if (iDataIndex >= m_datavecStateNode.size()) { _EXCEPTIONT("Invalid iDataIndex (out of range)"); } // 2D equation set bool fIs2DEquationSet = false; if (m_grid.GetModel().GetEquationSet().GetDimensionality() == 2) { fIs2DEquationSet = true; } // Check dimensionality if (fIs2DEquationSet && (m_nVerticalOrder != 1)) { _EXCEPTIONT("VerticalOrder / Dimensionality mismatch:\n" "For 2D problems vertical order must be 1."); } // Evaluate topography EvaluateTopography(test); // Physical constants const PhysicalConstants & phys = m_grid.GetModel().GetPhysicalConstants(); // Initialize the vertical height in each node if (fIs2DEquationSet) { for (int i = 0; i < m_box.GetATotalWidth(); i++) { for (int j = 0; j < m_box.GetBTotalWidth(); j++) { m_dataZLevels[0][i][j] = 0.0; m_dataZInterfaces[0][i][j] = 0.0; m_dataZInterfaces[1][i][j] = 1.0; } } } else { for (int i = 0; i < m_box.GetATotalWidth(); i++) { for (int j = 0; j < m_box.GetBTotalWidth(); j++) { // Gal-Chen and Sommerville (1975) vertical coordinate for (int k = 0; k < m_grid.GetRElements(); k++) { double dREta = m_grid.GetREtaLevel(k); /* double dREtaStretch; double dDxREtaStretch; m_grid.EvaluateVerticalStretchF( dREta, dREtaStretch, dDxREtaStretch); */ m_dataZLevels[k][i][j] = m_dataTopography[i][j] + dREta * (m_grid.GetZtop() - m_dataTopography[i][j]); } for (int k = 0; k <= m_grid.GetRElements(); k++) { double dREta = m_grid.GetREtaInterface(k); /* double dREtaStretch; double dDxREtaStretch; m_grid.EvaluateVerticalStretchF( dREta, dREtaStretch, dDxREtaStretch); */ m_dataZInterfaces[k][i][j] = m_dataTopography[i][j] + dREta * (m_grid.GetZtop() - m_dataTopography[i][j]); } } } } // Initialize the Rayleigh friction strength at each node if (test.HasRayleighFriction()) { for (int i = 0; i < m_box.GetATotalWidth(); i++) { for (int j = 0; j < m_box.GetBTotalWidth(); j++) { for (int k = 0; k < m_grid.GetRElements(); k++) { m_dataRayleighStrengthNode[k][i][j] = test.EvaluateRayleighStrength( m_dataZLevels[k][i][j], m_dataLon[i][j], m_dataLat[i][j]); } for (int k = 0; k < m_grid.GetRElements(); k++) { m_dataRayleighStrengthREdge[k][i][j] = test.EvaluateRayleighStrength( m_dataZInterfaces[k][i][j], m_dataLon[i][j], m_dataLat[i][j]); } } } } // Buffer vector for storing pointwise states const EquationSet & eqns = m_grid.GetModel().GetEquationSet(); int nComponents = m_grid.GetModel().GetEquationSet().GetComponents(); int nTracers = m_grid.GetModel().GetEquationSet().GetTracers(); DataArray1D<double> dPointwiseState(nComponents); DataArray1D<double> dPointwiseRefState(nComponents); DataArray1D<double> dPointwiseTracers; DataArray1D<double> dPointwiseRefTracers; if (m_datavecTracers.size() > 0) { if (nTracers > 0) { dPointwiseTracers.Allocate(nTracers); dPointwiseRefTracers.Allocate(nTracers); } } // Evaluate the state on model levels for (int k = 0; k < m_grid.GetRElements(); k++) { for (int i = 0; i < m_box.GetATotalWidth(); i++) { for (int j = 0; j < m_box.GetBTotalWidth(); j++) { // Evaluate pointwise state test.EvaluatePointwiseState( phys, time, m_dataZLevels[k][i][j], m_dataLon[i][j], m_dataLat[i][j], dPointwiseState, dPointwiseTracers); eqns.ConvertComponents( phys, dPointwiseState, dPointwiseTracers); for (int c = 0; c < dPointwiseState.GetRows(); c++) { m_datavecStateNode[iDataIndex][c][k][i][j] = dPointwiseState[c]; } // Transform state velocities double dUlon; double dUlat; dUlon = m_datavecStateNode[iDataIndex][0][k][i][j]; dUlat = m_datavecStateNode[iDataIndex][1][k][i][j]; dUlon *= phys.GetEarthRadius(); dUlat *= phys.GetEarthRadius(); CubedSphereTrans::CoVecTransABPFromRLL( tan(m_dANode[i]), tan(m_dBNode[j]), m_box.GetPanel(), dUlon, dUlat, m_datavecStateNode[iDataIndex][0][k][i][j], m_datavecStateNode[iDataIndex][1][k][i][j]); // Evaluate reference state if (m_grid.HasReferenceState()) { test.EvaluateReferenceState( m_grid.GetModel().GetPhysicalConstants(), m_dataZLevels[k][i][j], m_dataLon[i][j], m_dataLat[i][j], dPointwiseRefState, dPointwiseRefTracers); eqns.ConvertComponents( phys, dPointwiseRefState, dPointwiseRefTracers); for (int c = 0; c < dPointwiseRefState.GetRows(); c++) { m_dataRefStateNode[c][k][i][j] = dPointwiseRefState[c]; } for (int c = 0; c < dPointwiseRefTracers.GetRows(); c++) { m_dataRefTracers[c][k][i][j] = dPointwiseRefTracers[c]; } // Transform reference velocities dUlon = m_dataRefStateNode[0][k][i][j]; dUlat = m_dataRefStateNode[1][k][i][j]; dUlon *= phys.GetEarthRadius(); dUlat *= phys.GetEarthRadius(); CubedSphereTrans::CoVecTransABPFromRLL( tan(m_dANode[i]), tan(m_dBNode[j]), m_box.GetPanel(), dUlon, dUlat, m_dataRefStateNode[0][k][i][j], m_dataRefStateNode[1][k][i][j]); } // Evaluate tracers for (int c = 0; c < dPointwiseTracers.GetRows(); c++) { m_datavecTracers[iDataIndex][c][k][i][j] = dPointwiseTracers[c]; } } } } // Evaluate the state on model interfaces for (int k = 0; k <= m_grid.GetRElements(); k++) { for (int i = 0; i < m_box.GetATotalWidth(); i++) { for (int j = 0; j < m_box.GetBTotalWidth(); j++) { // Evaluate pointwise state test.EvaluatePointwiseState( m_grid.GetModel().GetPhysicalConstants(), time, m_dataZInterfaces[k][i][j], m_dataLon[i][j], m_dataLat[i][j], dPointwiseState, dPointwiseTracers); eqns.ConvertComponents( phys, dPointwiseState, dPointwiseTracers); for (int c = 0; c < dPointwiseState.GetRows(); c++) { m_datavecStateREdge[iDataIndex][c][k][i][j] = dPointwiseState[c]; } // Transform state velocities double dUlon; double dUlat; dUlon = m_datavecStateREdge[iDataIndex][0][k][i][j]; dUlat = m_datavecStateREdge[iDataIndex][1][k][i][j]; dUlon *= phys.GetEarthRadius(); dUlat *= phys.GetEarthRadius(); CubedSphereTrans::CoVecTransABPFromRLL( tan(m_dANode[i]), tan(m_dBNode[j]), m_box.GetPanel(), dUlon, dUlat, m_datavecStateREdge[iDataIndex][0][k][i][j], m_datavecStateREdge[iDataIndex][1][k][i][j]); if (m_grid.HasReferenceState()) { test.EvaluateReferenceState( m_grid.GetModel().GetPhysicalConstants(), m_dataZInterfaces[k][i][j], m_dataLon[i][j], m_dataLat[i][j], dPointwiseRefState, dPointwiseRefTracers); eqns.ConvertComponents( phys, dPointwiseRefState, dPointwiseRefTracers); for (int c = 0; c < dPointwiseState.GetRows(); c++) { m_dataRefStateREdge[c][k][i][j] = dPointwiseRefState[c]; } // Transform reference velocities dUlon = m_dataRefStateREdge[0][k][i][j]; dUlat = m_dataRefStateREdge[1][k][i][j]; dUlon *= phys.GetEarthRadius(); dUlat *= phys.GetEarthRadius(); CubedSphereTrans::CoVecTransABPFromRLL( tan(m_dANode[i]), tan(m_dBNode[j]), m_box.GetPanel(), dUlon, dUlat, m_dataRefStateREdge[0][k][i][j], m_dataRefStateREdge[1][k][i][j]); } } } } }