int main(int argc, char** argv) {
// Input mesh
std::string strMesh;
// Polynomial order
int nP;
// Use of bubble to adjust areas
bool fBubble;
// Output metadata file
std::string strOutput;
// Parse the command line
BeginCommandLine()
CommandLineString(strMesh, "mesh", "");
CommandLineInt(nP, "np", 4);
CommandLineString(strOutput, "out", "gllmeta.nc");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Calculate metadata
DataArray3D<int> dataGLLnodes;
DataArray3D<double> dataGLLJacobian;
Mesh mesh;
int err =
GenerateGLLMetaData(
strMesh,
mesh,
nP,
fBubble,
strOutput,
dataGLLnodes,
dataGLLJacobian);
if (err) exit(err);
// Done
AnnounceBanner();
return 0;
}
int main(int argc, char ** argv) {
// Initialize MPI
MPI_Init(&argc, &argv);
try {
// Input filename
std::string strInputFile;
// Output filename
std::string strOutputFile;
// 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();
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 {
// Resolution
int nResolution;
// Dual mesh
bool fDual;
// Output filename
std::string strOutputFile;
// Parse the command line
BeginCommandLine()
CommandLineInt(nResolution, "res", 10);
CommandLineBool(fDual, "dual");
CommandLineString(strOutputFile, "file", "outICOMesh.g");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
// Generate Mesh
AnnounceBanner();
AnnounceStartBlock("Generating Mesh");
Mesh mesh;
GenerateIcosahedralQuadGrid(nResolution, mesh.nodes, mesh.faces);
AnnounceEndBlock("Done");
// Generate the dual grid
if (fDual) {
Dual(mesh);
}
// Output the mesh
AnnounceStartBlock("Writing Mesh to file");
Announce("Mesh size: Nodes [%i] Elements [%i]",
mesh.nodes.size(), mesh.faces.size());
mesh.Write(strOutputFile);
AnnounceEndBlock("Done");
} catch(Exception & e) {
std::cout << e.ToString() << std::endl;
}
}
int main(int argc, char** argv) {
// Initialize Tempest
TempestInitialize(&argc, &argv);
try {
// Model height cap
double dZtop;
// Grid rotation angle
double dAlpha;
// Include tracer field
bool fTracersOn;
// Rayleigh layer
bool fRayleighFriction;
// Deep atmosphere flag
bool fDeepAtmosphere;
// Perturbation type
std::string strPerturbationType;
// Parse the command line
BeginTempestCommandLine("BaroclinicWaveUMJS");
SetDefaultResolution(20);
SetDefaultLevels(10);
SetDefaultOutputDeltaT("200s");
SetDefaultDeltaT("200s");
SetDefaultEndTime("200s");
SetDefaultHorizontalOrder(4);
SetDefaultVerticalOrder(1);
CommandLineDouble(dZtop, "ztop", 10000.0);
CommandLineDouble(dAlpha, "alpha", 0.0);
CommandLineBool(fDeepAtmosphere, "deep_atmosphere");
CommandLineBool(fRayleighFriction, "rayleigh");
CommandLineStringD(strPerturbationType, "pert",
"None", "(None | Exp | Sfn)");
ParseCommandLine(argc, argv);
EndTempestCommandLine(argv)
// Setup the Model
AnnounceBanner("MODEL SETUP");
Model model(EquationSet::PrimitiveNonhydrostaticEquations);
TempestSetupCubedSphereModel(model);
// Set the test case for the model
AnnounceStartBlock("Initializing test case");
BaroclinicWaveUMJSTest::PerturbationType ePerturbationType;
STLStringHelper::ToLower(strPerturbationType);
if (strPerturbationType == "none") {
ePerturbationType = BaroclinicWaveUMJSTest::PerturbationType_None;
} else if (strPerturbationType == "exp") {
ePerturbationType = BaroclinicWaveUMJSTest::PerturbationType_Exp;
} else if (strPerturbationType == "sfn") {
ePerturbationType = BaroclinicWaveUMJSTest::PerturbationType_StreamFn;
} else {
_EXCEPTIONT("Invalid perturbation type:"
" Expected \"None\", \"Exp\" or \"SFn\"");
}
model.SetTestCase(
new BaroclinicWaveUMJSTest(
dAlpha,
fDeepAtmosphere,
dZtop,
ePerturbationType,
fRayleighFriction));
AnnounceEndBlock("Done");
// Begin execution
AnnounceBanner("SIMULATION");
model.Go();
// Compute error norms
AnnounceBanner("RESULTS");
model.ComputeErrorNorms();
AnnounceBanner();
} catch(Exception & e) {
std::cout << e.ToString() << std::endl;
}
// Deinitialize
TempestDeinitialize();
}
int main(int argc, char** argv) {
NcError error(NcError::silent_nonfatal);
try {
// Input filename
std::string strInputFile;
// Output mesh filename
std::string strOutputMesh;
// Output connectivity filename
std::string strOutputConnectivity;
// Number of elements in mesh
int nP;
// Use uniformly spaced sub-volumes
bool fUniformSpacing = false;
// Do not merge faces
bool fNoMergeFaces = false;
// Nodes appear at GLL nodes
bool fCGLL = true;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputFile, "in", "");
CommandLineString(strOutputMesh, "out", "");
CommandLineString(strOutputConnectivity, "out_connect", "");
CommandLineInt(nP, "np", 2);
CommandLineBool(fUniformSpacing, "uniform");
//CommandLineBool(fNoMergeFaces, "no-merge-face");
//CommandLineBool(fCGLL, "cgll");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check file names
if (strInputFile == "") {
_EXCEPTIONT("No input file specified");
}
if (nP < 2) {
_EXCEPTIONT("--np must be >= 2");
}
if ((fNoMergeFaces) && (strOutputConnectivity != "")) {
_EXCEPTIONT("--out_connect and --no-merge-face not implemented");
}
// Load input mesh
std::cout << std::endl;
std::cout << "..Loading input mesh" << std::endl;
Mesh meshIn(strInputFile);
meshIn.RemoveZeroEdges();
// Number of elements
int nElements = meshIn.faces.size();
// Gauss-Lobatto quadrature nodes and weights
std::cout << "..Computing sub-volume boundaries" << std::endl;
DataArray1D<double> dG(nP);
DataArray1D<double> dW(nP);
// Uniformly spaced nodes
if (fUniformSpacing) {
for (int i = 0; i < nP; i++) {
dG[i] = (2.0 * static_cast<double>(i) + 1.0) / (2.0 * nP);
dW[i] = 1.0 / nP;
}
dG[0] = 0.0;
dG[1] = 1.0;
// Get Gauss-Lobatto Weights
} else {
GaussLobattoQuadrature::GetPoints(nP, 0.0, 1.0, dG, dW);
}
// Accumulated weight vector
DataArray1D<double> dAccumW(nP+1);
dAccumW[0] = 0.0;
for (int i = 1; i < nP+1; i++) {
dAccumW[i] = dAccumW[i-1] + dW[i-1];
}
if (fabs(dAccumW[dAccumW.GetRows()-1] - 1.0) > 1.0e-14) {
_EXCEPTIONT("Logic error in accumulated weight");
}
// Data structures used for generating connectivity
DataArray3D<int> dataGLLnodes(nP, nP, nElements);
std::vector<Node> vecNodes;
std::map<Node, int> mapFaces;
// Data structure for
// Data structure used for avoiding coincident nodes on the fly
std::map<Node, int> mapNewNodes;
// Generate new mesh
std::cout << "..Generating sub-volumes" << std::endl;
Mesh meshOut;
for (size_t f = 0; f < nElements; f++) {
const Face & face = meshIn.faces[f];
if (face.edges.size() != 4) {
_EXCEPTIONT("Input mesh must only contain quadrilaterals");
}
const Node & node0 = meshIn.nodes[face[0]];
const Node & node1 = meshIn.nodes[face[1]];
const Node & node2 = meshIn.nodes[face[2]];
const Node & node3 = meshIn.nodes[face[3]];
for (int q = 0; q < nP; q++) {
for (int p = 0; p < nP; p++) {
bool fNewFace = true;
// Build unique node array if CGLL
if (fCGLL) {
// Get local nodal location
Node nodeGLL;
Node dDx1G;
Node dDx2G;
ApplyLocalMap(
face,
meshIn.nodes,
dG[p],
dG[q],
nodeGLL,
dDx1G,
dDx2G);
// Determine if this is a unique Node
std::map<Node, int>::const_iterator iter =
mapFaces.find(nodeGLL);
if (iter == mapFaces.end()) {
// Insert new unique node into map
int ixNode = static_cast<int>(mapFaces.size());
mapFaces.insert(std::pair<Node, int>(nodeGLL, ixNode));
dataGLLnodes[q][p][f] = ixNode + 1;
vecNodes.push_back(nodeGLL);
} else {
dataGLLnodes[q][p][f] = iter->second + 1;
fNewFace = false;
}
// Non-unique node array if DGLL
} else {
dataGLLnodes[q][p][f] = nP * nP * f + q * nP + p;
}
// Get volumetric region
Face faceNew(4);
for (int i = 0; i < 4; i++) {
int px = p+((i+1)/2)%2; // p,p+1,p+1,p
int qx = q+(i/2); // q,q,q+1,q+1
Node nodeOut =
InterpolateQuadrilateralNode(
node0, node1, node2, node3,
dAccumW[px], dAccumW[qx]);
std::map<Node, int>::const_iterator iterNode =
mapNewNodes.find(nodeOut);
if (iterNode == mapNewNodes.end()) {
mapNewNodes.insert(
std::pair<Node, int>(nodeOut, meshOut.nodes.size()));
faceNew.SetNode(i, meshOut.nodes.size());
meshOut.nodes.push_back(nodeOut);
} else {
faceNew.SetNode(i, iterNode->second);
}
}
// Insert new Face or merge with existing Face
meshOut.faces.push_back(faceNew);
/*
if ((fNoMergeFaces) || (fNewFace)) {
} else {
std::cout << dataGLLnodes[q][p][f]-1 << " " << mapFaces.size()-1 << std::endl;
meshOut.faces[dataGLLnodes[q][p][f]-1].Merge(faceNew);
}
*/
}
}
}
meshOut.RemoveCoincidentNodes();
// Build connectivity and write to file
if (strOutputConnectivity != "") {
std::cout << "..Constructing connectivity file" << std::endl;
std::vector< std::set<int> > vecConnectivity;
vecConnectivity.resize(mapFaces.size());
for (size_t f = 0; f < nElements; f++) {
for (int q = 0; q < nP; q++) {
for (int p = 0; p < nP; p++) {
std::set<int> & setLocalConnectivity =
vecConnectivity[dataGLLnodes[q][p][f]-1];
// Connect in all directions
if (p != 0) {
setLocalConnectivity.insert(
dataGLLnodes[q][p-1][f]);
}
if (p != (nP-1)) {
setLocalConnectivity.insert(
dataGLLnodes[q][p+1][f]);
}
if (q != 0) {
setLocalConnectivity.insert(
dataGLLnodes[q-1][p][f]);
}
if (q != (nP-1)) {
setLocalConnectivity.insert(
dataGLLnodes[q+1][p][f]);
}
}
}
}
// Open output file
FILE * fp = fopen(strOutputConnectivity.c_str(), "w");
fprintf(fp, "%lu\n", vecConnectivity.size());
for (size_t f = 0; f < vecConnectivity.size(); f++) {
const Node & node = vecNodes[f];
double dLon = atan2(node.y, node.x);
double dLat = asin(node.z);
if (dLon < 0.0) {
dLon += 2.0 * M_PI;
}
fprintf(fp, "%1.14f,", dLon / M_PI * 180.0);
fprintf(fp, "%1.14f,", dLat / M_PI * 180.0);
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);
}
// Remove coincident nodes
//std::cout << "..Removing coincident nodes" << std::endl;
//meshOut.RemoveCoincidentNodes();
// Write the mesh
if (strOutputMesh != "") {
std::cout << "..Writing mesh" << std::endl;
meshOut.Write(strOutputMesh);
}
// Announce
std::cout << "..Mesh generator exited successfully" << std::endl;
std::cout << "=========================================================";
std::cout << std::endl;
return (0);
} catch(Exception & e) {
Announce(e.ToString().c_str());
return (-1);
} catch(...) {
return (-2);
}
}
int main(int argc, char** argv) {
// Initialize Tempest
TempestInitialize(&argc, &argv);
try {
// Nondimensional vertical width parameter
double dbC;
// Uniform zonal velocity
double dU0;
// Magnitude of the zonal wind perturbation
double dUp;
// Lapse rate
double ddTdz;
// Reference absolute temperature
double dT0;
// Width parameter for the perturbation
double dLpC;
// Center position of the perturbation
double dXC;
// Center position of the perturbation
double dYC;
// No Rayleigh friction
bool fNoRayleighFriction;
// Parse the command line
BeginTempestCommandLine("Baroclinic3DCartesianTest");
SetDefaultResolutionX(288);
SetDefaultResolutionY(48);
SetDefaultLevels(32);
SetDefaultOutputDeltaT("3h");
SetDefaultDeltaT("300s");
SetDefaultEndTime("12d");
SetDefaultHorizontalOrder(4);
SetDefaultVerticalOrder(1);
CommandLineDouble(dbC, "b", 2.0);
CommandLineDouble(dU0, "u0", 35.0);
CommandLineDouble(dUp, "up", 1.0);
CommandLineDouble(ddTdz, "gamma", 0.005);
CommandLineDouble(dT0, "T0", 288.0);
CommandLineDouble(dLpC, "Lp", 600000.0);
CommandLineDouble(dXC, "Xc", 2000000.0);
CommandLineDouble(dYC, "Yc", 2500000.0);
CommandLineBool(fNoRayleighFriction, "norayleigh");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
// Create a new instance of the test
Baroclinic3DCartesianTest * test =
new Baroclinic3DCartesianTest(dbC,
dU0,
dUp,
ddTdz,
dT0,
dLpC,
dXC,
dYC,
fNoRayleighFriction);
// Setup the Model
AnnounceBanner("MODEL SETUP");
Model model(EquationSet::PrimitiveNonhydrostaticEquations);
// Setup the cartesian model with dimensions and reference latitude
TempestSetupCartesianModel(model, test->m_dGDim, test->m_dRefLat,
test->m_iLatBC);
// Set the reference length to reduce diffusion relative to global scale
const double XL = std::abs(test->m_dGDim[1] - test->m_dGDim[0]);
const double oneDegScale = 110000.0;
if (XL < oneDegScale) {
model.GetGrid()->SetReferenceLength(XL);
}
else {
model.GetGrid()->SetReferenceLength(oneDegScale);
}
// Set the test case for the model
AnnounceStartBlock("Initializing test case");
model.SetTestCase(test);
AnnounceEndBlock("Done");
// Begin execution
AnnounceBanner("SIMULATION");
model.Go();
// Compute error norms
AnnounceBanner("RESULTS");
model.ComputeErrorNorms();
AnnounceBanner();
} catch(Exception & e) {
std::cout << e.ToString() << std::endl;
std::cout << "Try/catch block in the main program!" << std::endl;
}
// Deinitialize Tempest
TempestDeinitialize();
}
int main(int argc, char ** argv) {
MPI_Init(&argc, &argv);
try {
// Number of latitudes
int nLat;
// Number of longitudes
int nLon;
// Zonal wavenumber
int nK;
// Meridional power
int nLpow;
// Output file
std::string strOutputFile;
// Parse the command line
BeginCommandLine()
CommandLineInt(nLat, "lat", 40);
CommandLineInt(nLon, "lon", 80);
CommandLineString(strOutputFile, "out", "topo.nc");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
// Generate longitude and latitude arrays
AnnounceBanner();
AnnounceStartBlock("Generating longitude and latitude arrays");
DataVector<double> dLon;
dLon.Initialize(nLon);
Parameters param;
param.GenerateLatituteArray(nLat);
std::vector<double> & dLat = param.vecNode;
double dDeltaLon = 2.0 * M_PI / static_cast<double>(nLon);
for (int i = 0; i < nLon; i++) {
dLon[i] = (static_cast<double>(i) + 0.5) * dDeltaLon;
}
AnnounceEndBlock("Done");
// Open NetCDF output file
AnnounceStartBlock("Writing to file");
NcFile ncdf_out(strOutputFile.c_str(), NcFile::Replace);
// Output coordinates
NcDim * dimLat = ncdf_out.add_dim("lat", nLat);
NcDim * dimLon = ncdf_out.add_dim("lon", nLon);
NcVar * varLat = ncdf_out.add_var("lat", ncDouble, dimLat);
varLat->set_cur((long)0);
varLat->put(&(param.vecNode[0]), nLat);
NcVar * varLon = ncdf_out.add_var("lon", ncDouble, dimLon);
varLon->set_cur((long)0);
varLon->put(&(dLon[0]), nLon);
// Generate topography
DataMatrix<double> dTopo;
dTopo.Initialize(nLat, nLon);
double dK = static_cast<double>(nK);
double dLpow = static_cast<double>(nLpow);
double dA = 6.37122e6;
double dX = 500.0;
double dLatM = 0.0;
double dLonM = M_PI / 4.0;
double dD = 5000.0;
double dH0 = 1.0;
double dXiM = 4000.0;
for (int j = 0; j < nLat; j++) {
for (int i = 0; i < nLon; i++) {
// Great circle distance
double dR = dA / dX * acos(sin(dLatM) * sin(dLat[j])
+ cos(dLatM) * cos(dLat[j]) * cos(dLon[i] - dLonM));
double dCosXi = 1.0; //cos(M_PI * dR / dXiM);
dTopo[j][i] = dH0 * exp(- dR * dR / (dD * dD))
* dCosXi * dCosXi;
}
}
// Write topography
NcVar * varZs = ncdf_out.add_var("Zs", ncDouble, dimLat, dimLon);
varZs->set_cur(0, 0);
varZs->put(&(dTopo[0][0]), nLat, nLon);
AnnounceEndBlock("Done");
Announce("Completed successfully!");
AnnounceBanner();
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
MPI_Finalize();
}
int main(int argc, char** argv) {
NcError error(NcError::silent_nonfatal);
try {
// Input data file
std::string strInputData;
// Input map file
std::string strInputMap;
// List of variables
std::string strVariables;
// Input data file (second instance)
std::string strInputData2;
// Input map file (second instance)
std::string strInputMap2;
// List of variables (second instance)
std::string strVariables2;
// Output data file
std::string strOutputData;
// Name of the ncol variable
std::string strNColName;
// Output as double
bool fOutputDouble;
// List of variables to preserve
std::string strPreserveVariables;
// Preserve all non-remapped variables
bool fPreserveAll;
// Fill value override
double dFillValueOverride;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputData, "in_data", "");
CommandLineString(strInputMap, "map", "");
CommandLineString(strVariables, "var", "");
CommandLineString(strInputData2, "in_data2", "");
CommandLineString(strInputMap2, "map2", "");
CommandLineString(strVariables2, "var2", "");
CommandLineString(strOutputData, "out_data", "");
CommandLineString(strNColName, "ncol_name", "ncol");
CommandLineBool(fOutputDouble, "out_double");
CommandLineString(strPreserveVariables, "preserve", "");
CommandLineBool(fPreserveAll, "preserveall");
CommandLineDouble(dFillValueOverride, "fillvalue", 0.0);
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check parameters
if (strInputMap == "") {
_EXCEPTIONT("No map specified");
}
if (strInputData == "") {
_EXCEPTIONT("No input data specified");
}
if (strOutputData == "") {
_EXCEPTIONT("No output data specified");
}
// Parse variable list
std::vector< std::string > vecVariableStrings;
ParseVariableList(strVariables, vecVariableStrings);
// Parse preserve variable list
std::vector< std::string > vecPreserveVariableStrings;
ParseVariableList(strPreserveVariables, vecPreserveVariableStrings);
if (fPreserveAll && (vecPreserveVariableStrings.size() != 0)) {
_EXCEPTIONT("--preserveall and --preserve cannot both be specified");
}
// Second input data file
std::vector< std::string > vecVariableStrings2;
if (strInputData2 != "") {
ParseVariableList(strVariables2, vecVariableStrings2);
if (vecVariableStrings2.size() == 0) {
_EXCEPTIONT("No variables specified for --in_data2");
}
if (strInputMap2 == "") {
_EXCEPTIONT("No map specified for --in_data2");
}
}
if ((strInputMap2 != "") && (strInputData2 == "")) {
_EXCEPTIONT("No input data specified for --map2");
}
// Apply OfflineMap to data
if (strInputMap2 == "") {
AnnounceStartBlock("Applying offline map to data");
} else {
AnnounceStartBlock("Applying first offline map to data");
}
// OfflineMap
OfflineMap mapRemap;
mapRemap.Read(strInputMap);
mapRemap.SetFillValueOverride(static_cast<float>(dFillValueOverride));
mapRemap.Apply(
strInputData,
strOutputData,
vecVariableStrings,
strNColName,
fOutputDouble,
false);
AnnounceEndBlock(NULL);
if (strInputMap2 != "") {
AnnounceStartBlock("Applying second offline map to data");
// OfflineMap
OfflineMap mapRemap2;
mapRemap2.Read(strInputMap2);
// Verify consistency of maps
SparseMatrix<double> & smatRemap = mapRemap .GetSparseMatrix();
SparseMatrix<double> & smatRemap2 = mapRemap2.GetSparseMatrix();
if ((smatRemap.GetRows() != smatRemap2.GetRows()) ||
(smatRemap.GetColumns() != smatRemap2.GetColumns())
) {
_EXCEPTIONT("Mismatch in dimensions of input maps "
"--map and --map2");
}
mapRemap2.Apply(
strInputData2,
strOutputData,
vecVariableStrings2,
strNColName,
false,
true);
AnnounceEndBlock(NULL);
}
// Copy variables from input file to output file
if (fPreserveAll) {
AnnounceStartBlock("Preserving variables");
mapRemap.PreserveAllVariables(strInputData, strOutputData);
AnnounceEndBlock(NULL);
} else if (vecPreserveVariableStrings.size() != 0) {
AnnounceStartBlock("Preserving variables");
mapRemap.PreserveVariables(
strInputData,
strOutputData,
vecPreserveVariableStrings);
AnnounceEndBlock(NULL);
}
AnnounceBanner();
return (0);
} catch(Exception & e) {
Announce(e.ToString().c_str());
return (-1);
} catch(...) {
return (-2);
}
}
int main(int argc, char** argv) {
NcError error(NcError::silent_nonfatal);
try {
// Input / Output types
enum DiscretizationType {
DiscretizationType_FV,
DiscretizationType_CGLL,
DiscretizationType_DGLL
};
// Input mesh file
std::string strInputMesh;
// Overlap mesh file
std::string strOverlapMesh;
// Input metadata file
std::string strInputMeta;
// Output metadata file
std::string strOutputMeta;
// Input data type
std::string strInputType;
// Output data type
std::string strOutputType;
// Order of polynomial in each element
int nPin;
// Order of polynomial in each output element
int nPout;
// Use bubble on interior of spectral element nodes
bool fBubble;
// Enforce monotonicity
bool fMonotoneType1;
// Enforce monotonicity
bool fMonotoneType2;
// Enforce monotonicity
bool fMonotoneType3;
// Volumetric remapping
bool fVolumetric;
// No conservation
bool fNoConservation;
// Turn off checking for conservation / consistency
bool fNoCheck;
// Output mesh file
std::string strOutputMesh;
// Variable list
std::string strVariables;
// Output map file
std::string strOutputMap;
// Input data file
std::string strInputData;
// Output data file
std::string strOutputData;
// Name of the ncol variable
std::string strNColName;
// Output as double
bool fOutputDouble;
// List of variables to preserve
std::string strPreserveVariables;
// Preserve all non-remapped variables
bool fPreserveAll;
// Fill value override
double dFillValueOverride;
// Parse the command line
BeginCommandLine()
//CommandLineStringD(strMethod, "method", "", "[se]");
CommandLineString(strInputMesh, "in_mesh", "");
CommandLineString(strOutputMesh, "out_mesh", "");
CommandLineString(strOverlapMesh, "ov_mesh", "");
CommandLineString(strInputMeta, "in_meta", "");
CommandLineString(strOutputMeta, "out_meta", "");
CommandLineStringD(strInputType, "in_type", "fv", "[fv|cgll|dgll]");
CommandLineStringD(strOutputType, "out_type", "fv", "[fv|cgll|dgll]");
CommandLineInt(nPin, "in_np", 4);
CommandLineInt(nPout, "out_np", 4);
CommandLineBool(fBubble, "bubble");
CommandLineBool(fMonotoneType1, "mono");
CommandLineBool(fMonotoneType2, "mono2");
CommandLineBool(fMonotoneType3, "mono3");
CommandLineBool(fVolumetric, "volumetric");
CommandLineBool(fNoConservation, "noconserve");
CommandLineBool(fNoCheck, "nocheck");
CommandLineString(strVariables, "var", "");
CommandLineString(strOutputMap, "out_map", "");
CommandLineString(strInputData, "in_data", "");
CommandLineString(strOutputData, "out_data", "");
CommandLineString(strNColName, "ncol_name", "ncol");
CommandLineBool(fOutputDouble, "out_double");
CommandLineString(strPreserveVariables, "preserve", "");
CommandLineBool(fPreserveAll, "preserveall");
CommandLineDouble(dFillValueOverride, "fillvalue", 0.0);
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check command line parameters (mesh arguments)
if (strInputMesh == "") {
_EXCEPTIONT("No input mesh (--in_mesh) specified");
}
if (strOutputMesh == "") {
_EXCEPTIONT("No output mesh (--out_mesh) specified");
}
// Overlap mesh
if (strOverlapMesh == "") {
_EXCEPTIONT("No overlap mesh specified");
}
// Check command line parameters (data arguments)
if ((strInputData != "") && (strOutputData == "")) {
_EXCEPTIONT("--in_data specified without --out_data");
}
if ((strInputData == "") && (strOutputData != "")) {
_EXCEPTIONT("--out_data specified without --in_data");
}
// Check metadata parameters
if ((strInputMeta != "") && (strInputType == "fv")) {
_EXCEPTIONT("--in_meta cannot be used with --in_type fv");
}
if ((strOutputMeta != "") && (strOutputType == "fv")) {
_EXCEPTIONT("--out_meta cannot be used with --out_type fv");
}
// Check command line parameters (data type arguments)
STLStringHelper::ToLower(strInputType);
STLStringHelper::ToLower(strOutputType);
DiscretizationType eInputType;
DiscretizationType eOutputType;
if (strInputType == "fv") {
eInputType = DiscretizationType_FV;
} else if (strInputType == "cgll") {
eInputType = DiscretizationType_CGLL;
} else if (strInputType == "dgll") {
eInputType = DiscretizationType_DGLL;
} else {
_EXCEPTION1("Invalid \"in_type\" value (%s), expected [fv|cgll|dgll]",
strInputType.c_str());
}
if (strOutputType == "fv") {
eOutputType = DiscretizationType_FV;
} else if (strOutputType == "cgll") {
eOutputType = DiscretizationType_CGLL;
} else if (strOutputType == "dgll") {
eOutputType = DiscretizationType_DGLL;
} else {
_EXCEPTION1("Invalid \"out_type\" value (%s), expected [fv|cgll|dgll]",
strOutputType.c_str());
}
// Monotonicity flags
int nMonotoneType = 0;
if (fMonotoneType1) {
nMonotoneType = 1;
}
if (fMonotoneType2) {
if (nMonotoneType != 0) {
_EXCEPTIONT("Only one of --mono, --mono2 and --mono3 may be set");
}
nMonotoneType = 2;
}
if (fMonotoneType3) {
if (nMonotoneType != 0) {
_EXCEPTIONT("Only one of --mono, --mono2 and --mono3 may be set");
}
nMonotoneType = 3;
}
/*
// Volumetric
if (fVolumetric && (nMonotoneType != 0)) {
_EXCEPTIONT("--volumetric cannot be used in conjunction with --mono#");
}
*/
// Create Offline Map
OfflineMap mapRemap;
// Initialize dimension information from file
AnnounceStartBlock("Initializing dimensions of map");
Announce("Input mesh");
mapRemap.InitializeSourceDimensionsFromFile(strInputMesh);
Announce("Output mesh");
mapRemap.InitializeTargetDimensionsFromFile(strOutputMesh);
AnnounceEndBlock(NULL);
// Parse variable list
std::vector< std::string > vecVariableStrings;
ParseVariableList(strVariables, vecVariableStrings);
// Parse preserve variable list
std::vector< std::string > vecPreserveVariableStrings;
ParseVariableList(strPreserveVariables, vecPreserveVariableStrings);
if (fPreserveAll && (vecPreserveVariableStrings.size() != 0)) {
_EXCEPTIONT("--preserveall and --preserve cannot both be specified");
}
// Load input mesh
AnnounceStartBlock("Loading input mesh");
Mesh meshInput(strInputMesh);
meshInput.RemoveZeroEdges();
AnnounceEndBlock(NULL);
// Calculate Face areas
AnnounceStartBlock("Calculating input mesh Face areas");
double dTotalAreaInput = meshInput.CalculateFaceAreas();
Announce("Input Mesh Geometric Area: %1.15e", dTotalAreaInput);
AnnounceEndBlock(NULL);
// Input mesh areas
if (eInputType == DiscretizationType_FV) {
mapRemap.SetSourceAreas(meshInput.vecFaceArea);
}
// Load output mesh
AnnounceStartBlock("Loading output mesh");
Mesh meshOutput(strOutputMesh);
meshOutput.RemoveZeroEdges();
AnnounceEndBlock(NULL);
// Calculate Face areas
AnnounceStartBlock("Calculating output mesh Face areas");
Real dTotalAreaOutput = meshOutput.CalculateFaceAreas();
Announce("Output Mesh Geometric Area: %1.15e", dTotalAreaOutput);
AnnounceEndBlock(NULL);
// Output mesh areas
if (eOutputType == DiscretizationType_FV) {
mapRemap.SetTargetAreas(meshOutput.vecFaceArea);
}
// Load overlap mesh
AnnounceStartBlock("Loading overlap mesh");
Mesh meshOverlap(strOverlapMesh);
meshOverlap.RemoveZeroEdges();
// Verify that overlap mesh is in the correct order
int ixSourceFaceMax = (-1);
int ixTargetFaceMax = (-1);
if (meshOverlap.vecSourceFaceIx.size() !=
meshOverlap.vecTargetFaceIx.size()
) {
_EXCEPTIONT("Invalid overlap mesh:\n"
" Possible mesh file corruption?");
}
for (int i = 0; i < meshOverlap.vecSourceFaceIx.size(); i++) {
if (meshOverlap.vecSourceFaceIx[i] + 1 > ixSourceFaceMax) {
ixSourceFaceMax = meshOverlap.vecSourceFaceIx[i] + 1;
}
if (meshOverlap.vecTargetFaceIx[i] + 1 > ixTargetFaceMax) {
ixTargetFaceMax = meshOverlap.vecTargetFaceIx[i] + 1;
}
}
// Check for forward correspondence in overlap mesh
if (ixSourceFaceMax == meshInput.faces.size() //&&
//(ixTargetFaceMax == meshOutput.faces.size())
) {
Announce("Overlap mesh forward correspondence found");
// Check for reverse correspondence in overlap mesh
} else if (
ixSourceFaceMax == meshOutput.faces.size() //&&
//(ixTargetFaceMax == meshInput.faces.size())
) {
Announce("Overlap mesh reverse correspondence found (reversing)");
// Reorder overlap mesh
meshOverlap.ExchangeFirstAndSecondMesh();
// No correspondence found
} else {
_EXCEPTION2("Invalid overlap mesh:\n"
" No correspondence found with input and output meshes (%i,%i)",
ixSourceFaceMax, ixTargetFaceMax);
}
AnnounceEndBlock(NULL);
// Calculate Face areas
AnnounceStartBlock("Calculating overlap mesh Face areas");
Real dTotalAreaOverlap = meshOverlap.CalculateFaceAreas();
Announce("Overlap Mesh Area: %1.15e", dTotalAreaOverlap);
AnnounceEndBlock(NULL);
// Partial cover
if (fabs(dTotalAreaOverlap - dTotalAreaInput) > 1.0e-10) {
if (!fNoCheck) {
Announce("WARNING: Significant mismatch between overlap mesh area "
"and input mesh area.\n Automatically enabling --nocheck");
fNoCheck = true;
}
}
/*
// Recalculate input mesh area from overlap mesh
if (fabs(dTotalAreaOverlap - dTotalAreaInput) > 1.0e-10) {
AnnounceStartBlock("Overlap mesh only covers a sub-area of the sphere");
Announce("Recalculating source mesh areas");
dTotalAreaInput = meshInput.CalculateFaceAreasFromOverlap(meshOverlap);
Announce("New Input Mesh Geometric Area: %1.15e", dTotalAreaInput);
AnnounceEndBlock(NULL);
}
*/
// Finite volume input / Finite volume output
if ((eInputType == DiscretizationType_FV) &&
(eOutputType == DiscretizationType_FV)
) {
// Generate reverse node array and edge map
meshInput.ConstructReverseNodeArray();
meshInput.ConstructEdgeMap();
// Initialize coordinates for map
mapRemap.InitializeSourceCoordinatesFromMeshFV(meshInput);
mapRemap.InitializeTargetCoordinatesFromMeshFV(meshOutput);
// Construct OfflineMap
AnnounceStartBlock("Calculating offline map");
LinearRemapFVtoFV(
meshInput, meshOutput, meshOverlap, nPin, mapRemap);
// Finite volume input / Finite element output
} else if (eInputType == DiscretizationType_FV) {
DataMatrix3D<int> dataGLLNodes;
DataMatrix3D<double> dataGLLJacobian;
if (strOutputMeta != "") {
AnnounceStartBlock("Loading meta data file");
LoadMetaDataFile(strOutputMeta, dataGLLNodes, dataGLLJacobian);
AnnounceEndBlock(NULL);
} else {
AnnounceStartBlock("Generating output mesh meta data");
double dNumericalArea =
GenerateMetaData(
meshOutput,
nPout,
fBubble,
dataGLLNodes,
dataGLLJacobian);
Announce("Output Mesh Numerical Area: %1.15e", dNumericalArea);
AnnounceEndBlock(NULL);
}
// Initialize coordinates for map
mapRemap.InitializeSourceCoordinatesFromMeshFV(meshInput);
mapRemap.InitializeTargetCoordinatesFromMeshFE(
meshOutput, nPout, dataGLLNodes);
// Generate the continuous Jacobian
bool fContinuous = (eOutputType == DiscretizationType_CGLL);
if (eOutputType == DiscretizationType_CGLL) {
GenerateUniqueJacobian(
dataGLLNodes,
dataGLLJacobian,
mapRemap.GetTargetAreas());
} else {
GenerateDiscontinuousJacobian(
dataGLLJacobian,
mapRemap.GetTargetAreas());
}
// Generate reverse node array and edge map
meshInput.ConstructReverseNodeArray();
meshInput.ConstructEdgeMap();
// Generate remap weights
AnnounceStartBlock("Calculating offline map");
if (fVolumetric) {
LinearRemapFVtoGLL_Volumetric(
meshInput,
meshOutput,
meshOverlap,
dataGLLNodes,
dataGLLJacobian,
mapRemap.GetTargetAreas(),
nPin,
mapRemap,
nMonotoneType,
fContinuous,
fNoConservation);
} else {
LinearRemapFVtoGLL(
meshInput,
meshOutput,
meshOverlap,
dataGLLNodes,
dataGLLJacobian,
mapRemap.GetTargetAreas(),
nPin,
mapRemap,
nMonotoneType,
fContinuous,
fNoConservation);
}
// Finite element input / Finite volume output
} else if (
(eInputType != DiscretizationType_FV) &&
(eOutputType == DiscretizationType_FV)
) {
DataMatrix3D<int> dataGLLNodes;
DataMatrix3D<double> dataGLLJacobian;
if (strInputMeta != "") {
AnnounceStartBlock("Loading meta data file");
LoadMetaDataFile(strInputMeta, dataGLLNodes, dataGLLJacobian);
AnnounceEndBlock(NULL);
} else {
AnnounceStartBlock("Generating input mesh meta data");
double dNumericalArea =
GenerateMetaData(
meshInput,
nPin,
fBubble,
dataGLLNodes,
dataGLLJacobian);
Announce("Input Mesh Numerical Area: %1.15e", dNumericalArea);
AnnounceEndBlock(NULL);
if (fabs(dNumericalArea - dTotalAreaInput) > 1.0e-12) {
Announce("WARNING: Significant mismatch between input mesh "
"numerical area and geometric area");
}
}
if (dataGLLNodes.GetSubColumns() != meshInput.faces.size()) {
_EXCEPTIONT("Number of element does not match between metadata and "
"input mesh");
}
// Initialize coordinates for map
mapRemap.InitializeSourceCoordinatesFromMeshFE(
meshInput, nPin, dataGLLNodes);
mapRemap.InitializeTargetCoordinatesFromMeshFV(meshOutput);
// Generate the continuous Jacobian for input mesh
bool fContinuousIn = (eInputType == DiscretizationType_CGLL);
if (eInputType == DiscretizationType_CGLL) {
GenerateUniqueJacobian(
dataGLLNodes,
dataGLLJacobian,
mapRemap.GetSourceAreas());
} else {
GenerateDiscontinuousJacobian(
dataGLLJacobian,
mapRemap.GetSourceAreas());
}
// Generate offline map
AnnounceStartBlock("Calculating offline map");
if (fVolumetric) {
_EXCEPTIONT("Unimplemented: Volumetric currently unavailable for"
"GLL input mesh");
}
LinearRemapSE4(
meshInput,
meshOutput,
meshOverlap,
dataGLLNodes,
dataGLLJacobian,
nMonotoneType,
fContinuousIn,
fNoConservation,
mapRemap
);
// Finite element input / Finite element output
} else if (
(eInputType != DiscretizationType_FV) &&
(eOutputType != DiscretizationType_FV)
) {
DataMatrix3D<int> dataGLLNodesIn;
DataMatrix3D<double> dataGLLJacobianIn;
DataMatrix3D<int> dataGLLNodesOut;
DataMatrix3D<double> dataGLLJacobianOut;
// Input metadata
if (strInputMeta != "") {
AnnounceStartBlock("Loading input meta data file");
LoadMetaDataFile(
strInputMeta, dataGLLNodesIn, dataGLLJacobianIn);
AnnounceEndBlock(NULL);
} else {
AnnounceStartBlock("Generating input mesh meta data");
double dNumericalAreaIn =
GenerateMetaData(
meshInput,
nPin,
fBubble,
dataGLLNodesIn,
dataGLLJacobianIn);
Announce("Input Mesh Numerical Area: %1.15e", dNumericalAreaIn);
AnnounceEndBlock(NULL);
if (fabs(dNumericalAreaIn - dTotalAreaInput) > 1.0e-12) {
Announce("WARNING: Significant mismatch between input mesh "
"numerical area and geometric area");
}
}
// Output metadata
if (strOutputMeta != "") {
AnnounceStartBlock("Loading output meta data file");
LoadMetaDataFile(
strOutputMeta, dataGLLNodesOut, dataGLLJacobianOut);
AnnounceEndBlock(NULL);
} else {
AnnounceStartBlock("Generating output mesh meta data");
double dNumericalAreaOut =
GenerateMetaData(
meshOutput,
nPout,
fBubble,
dataGLLNodesOut,
dataGLLJacobianOut);
Announce("Output Mesh Numerical Area: %1.15e", dNumericalAreaOut);
AnnounceEndBlock(NULL);
if (fabs(dNumericalAreaOut - dTotalAreaOutput) > 1.0e-12) {
Announce("WARNING: Significant mismatch between output mesh "
"numerical area and geometric area");
}
}
// Initialize coordinates for map
mapRemap.InitializeSourceCoordinatesFromMeshFE(
meshInput, nPin, dataGLLNodesIn);
mapRemap.InitializeTargetCoordinatesFromMeshFE(
meshOutput, nPout, dataGLLNodesOut);
// Generate the continuous Jacobian for input mesh
bool fContinuousIn = (eInputType == DiscretizationType_CGLL);
if (eInputType == DiscretizationType_CGLL) {
GenerateUniqueJacobian(
dataGLLNodesIn,
dataGLLJacobianIn,
mapRemap.GetSourceAreas());
} else {
GenerateDiscontinuousJacobian(
dataGLLJacobianIn,
mapRemap.GetSourceAreas());
}
// Generate the continuous Jacobian for output mesh
bool fContinuousOut = (eOutputType == DiscretizationType_CGLL);
if (eOutputType == DiscretizationType_CGLL) {
GenerateUniqueJacobian(
dataGLLNodesOut,
dataGLLJacobianOut,
mapRemap.GetTargetAreas());
} else {
GenerateDiscontinuousJacobian(
dataGLLJacobianOut,
mapRemap.GetTargetAreas());
}
// Generate offline map
AnnounceStartBlock("Calculating offline map");
LinearRemapGLLtoGLL2(
meshInput,
meshOutput,
meshOverlap,
dataGLLNodesIn,
dataGLLJacobianIn,
dataGLLNodesOut,
dataGLLJacobianOut,
mapRemap.GetTargetAreas(),
nPin,
nPout,
nMonotoneType,
fContinuousIn,
fContinuousOut,
fNoConservation,
mapRemap
);
} else {
_EXCEPTIONT("Not implemented");
}
//#pragma warning "NOTE: VERIFICATION DISABLED"
// Verify consistency, conservation and monotonicity
if (!fNoCheck) {
AnnounceStartBlock("Verifying map");
mapRemap.IsConsistent(1.0e-8);
mapRemap.IsConservative(1.0e-8);
if (nMonotoneType != 0) {
mapRemap.IsMonotone(1.0e-12);
}
AnnounceEndBlock(NULL);
}
AnnounceEndBlock(NULL);
// Initialize element dimensions from input/output Mesh
AnnounceStartBlock("Writing output");
// Output the Offline Map
if (strOutputMap != "") {
AnnounceStartBlock("Writing offline map");
mapRemap.Write(strOutputMap);
AnnounceEndBlock(NULL);
}
// Apply Offline Map to data
if (strInputData != "") {
AnnounceStartBlock("Applying offline map to data");
mapRemap.SetFillValueOverride(static_cast<float>(dFillValueOverride));
mapRemap.Apply(
strInputData,
strOutputData,
vecVariableStrings,
strNColName,
fOutputDouble,
false);
AnnounceEndBlock(NULL);
}
AnnounceEndBlock(NULL);
// Copy variables from input file to output file
if ((strInputData != "") && (strOutputData != "")) {
if (fPreserveAll) {
AnnounceStartBlock("Preserving variables");
mapRemap.PreserveAllVariables(strInputData, strOutputData);
AnnounceEndBlock(NULL);
} else if (vecPreserveVariableStrings.size() != 0) {
AnnounceStartBlock("Preserving variables");
mapRemap.PreserveVariables(
strInputData,
strOutputData,
vecPreserveVariableStrings);
AnnounceEndBlock(NULL);
}
}
AnnounceBanner();
return (0);
} catch(Exception & e) {
Announce(e.ToString().c_str());
return (-1);
} catch(...) {
return (-2);
}
}
int main(int argc, char** argv) {
// Initialize Tempest
TempestInitialize(&argc, &argv);
try {
// Uniform +X flow field.
double dU0;
// Reference temperature
double dT0;
// Parameter reference height for temperature disturbance
double dhC;
// Parameter reference length a for temperature disturbance
double daC;
// Parameter reference length for mountain profile
double dxC;
// Parameter Archimede's Constant (essentially Pi but to some digits)
double dpiC;
// No Rayleigh friction
bool fNoRayleighFriction;
// Parse the command line
BeginTempestCommandLine("HydrostaticMountainCartesianTest");
SetDefaultResolutionX(40);
SetDefaultResolutionY(1);
SetDefaultLevels(48);
SetDefaultOutputDeltaT("1800s");
SetDefaultDeltaT("1s");
SetDefaultEndTime("36000s");
SetDefaultHorizontalOrder(4);
SetDefaultVerticalOrder(4);
CommandLineDouble(dU0, "u0", 20.0);
CommandLineDouble(dT0, "T0", 250.0);
CommandLineDouble(dhC, "hC", 1.0);
CommandLineDouble(daC, "aC", 10000.0);
CommandLineDouble(dxC, "xC", 1.2E+5);
CommandLineDouble(dpiC, "piC", 3.14159265);
CommandLineBool(fNoRayleighFriction, "norayleigh");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
// Create a new instance of the test
HydrostaticMountainCartesianTest * test =
new HydrostaticMountainCartesianTest(
dT0,
dU0,
dhC,
dxC,
daC,
dpiC,
fNoRayleighFriction);
// Setup the Model
AnnounceBanner("MODEL SETUP");
Model model(EquationSet::PrimitiveNonhydrostaticEquations);
// Setup the cartesian model with dimensions and reference latitude
TempestSetupCartesianModel(model, test->m_dGDim, 0.0,
test->m_iLatBC);
// Set the reference length to reduce diffusion relative to global scale
const double XL = std::abs(test->m_dGDim[1] - test->m_dGDim[0]);
const double oneDegScale = 110000.0;
if (XL < oneDegScale) {
model.GetGrid()->SetReferenceLength(XL);
}
else {
model.GetGrid()->SetReferenceLength(oneDegScale);
}
// Set the test case for the model
AnnounceStartBlock("Initializing test case");
model.SetTestCase(test);
AnnounceEndBlock("Done");
// Begin execution
AnnounceBanner("SIMULATION");
model.Go();
// Compute error norms
AnnounceBanner("RESULTS");
model.ComputeErrorNorms();
AnnounceBanner();
} catch(Exception & e) {
std::cout << e.ToString() << std::endl;
}
// Deinitialize Tempest
TempestDeinitialize();
}
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);
}
}
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) {
// Initialize MPI
TempestInitialize(&argc, &argv);
try {
// Model height cap.
double dZtop;
// Model scaling parameter
double dEarthScaling;
// Rotation rate of the Earth with X = 1.
double dOmega;
// Reference temperature.
double dT0;
// Temperature lapse rate.
double dGamma;
// Longitude of Schar-type mountain centerpoint.
double dLonM;
// Latitude of Schar-type mountain centerpoint.
double dLatM;
// Maximum Schar-type mountain height.
double dH0;
// Schar-type mountain radius (radians).
double dRM;
// Schar-type mountain oscillation half-width (radians).
double dZetaM;
// Parse the command line
BeginTempestCommandLine("StationaryMountainFlowTest");
SetDefaultResolution(30);
SetDefaultLevels(30);
SetDefaultOutputDeltaT("1d");
SetDefaultDeltaT("300s");
SetDefaultEndTime("6d");
SetDefaultHorizontalOrder(4);
SetDefaultVerticalOrder(1);
CommandLineDouble(dZtop, "ztop", 30000.0);
CommandLineDouble(dEarthScaling, "X", 1.0);
CommandLineDouble(dOmega, "omega", 0.0);
CommandLineDouble(dT0, "T0", 300.0);
CommandLineDouble(dGamma, "Gamma", 0.0065);
CommandLineDouble(dLonM, "lonm", 270.0);
CommandLineDouble(dLatM, "latm", 0.0);
CommandLineDouble(dH0, "h0", 2000.0);
CommandLineDouble(dRM, "rm", 135.0);
CommandLineDouble(dZetaM, "zetam", 11.25);
ParseCommandLine(argc, argv);
EndTempestCommandLine(argv)
// Setup the Model
AnnounceBanner("MODEL SETUP");
Model model(EquationSet::PrimitiveNonhydrostaticEquations);
TempestSetupCubedSphereModel(model);
// Set the test case for the model
AnnounceStartBlock("Initializing test case");
model.SetTestCase(
new StationaryMountainFlowTest(
dZtop,
dEarthScaling,
dOmega,
dT0,
dGamma,
dLonM,
dLatM,
dH0,
dRM,
dZetaM));
AnnounceEndBlock("Done");
// Set the reference length
model.GetGrid()->SetReferenceLength(0.5 * M_PI / 30.0 * dEarthScaling);
// Begin execution
AnnounceBanner("SIMULATION");
model.Go();
// Compute error norms
AnnounceBanner("RESULTS");
model.ComputeErrorNorms();
AnnounceBanner();
} catch(Exception & e) {
std::cout << e.ToString() << std::endl;
}
// Deinitialize Tempest
TempestDeinitialize();
}
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());
}
}
int main(int argc, char ** argv) {
try {
// Parameters
Parameters param;
// Output filename
std::string strOutputFile;
// Horizontal minimum wave number
int nKmin;
// Horizontal maximum wave number
int nKmax;
// Parse the command line
BeginCommandLine()
CommandLineInt(param.nPhiElements, "n", 40);
CommandLineInt(nKmin, "kmin", 1);
CommandLineInt(nKmax, "kmax", 20);
CommandLineDouble(param.dXscale, "X", 1.0);
CommandLineDouble(param.dT0, "T0", 300.0);
CommandLineDouble(param.dU0, "U0", 20.0);
CommandLineDouble(param.dG, "G", 9.80616);
CommandLineDouble(param.dOmega, "omega", 7.29212e-5);
CommandLineDouble(param.dGamma, "gamma", 1.4);
CommandLineString(strOutputFile, "out", "wave.nc");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Generate latitude values
param.GenerateLatituteArray(param.nPhiElements);
// Open NetCDF file
NcFile ncdf_out(strOutputFile.c_str(), NcFile::Replace);
NcDim *dimK = ncdf_out.add_dim("k", nKmax - nKmin + 1);
NcDim *dimLat = ncdf_out.add_dim("lat", param.nPhiElements);
NcDim *dimEig = ncdf_out.add_dim("eig", param.nPhiElements);
// Write parameters and latitudes to file
param.WriteToNcFile(ncdf_out, dimLat, dimLatS);
// Wave numbers
NcVar *varK = ncdf_out.add_var("k", ncInt, dimK);
DataVector<int> vecK;
vecK.Initialize(nKmax - nKmin + 1);
for (int nK = nKmin; nK <= nKmax; nK++) {
vecK[nK - nKmin] = nK;
}
varK->set_cur((long)0);
varK->put(vecK, nKmax - nKmin + 1);
// Eigenvalues
NcVar *varMR = ncdf_out.add_var("mR", ncDouble, dimK, dimEig);
NcVar *varMI = ncdf_out.add_var("mI", ncDouble, dimK, dimEig);
NcVar *varUR = ncdf_out.add_var("uR", ncDouble, dimK, dimEig, dimLat);
NcVar *varUI = ncdf_out.add_var("uI", ncDouble, dimK, dimEig, dimLat);
NcVar *varVR = ncdf_out.add_var("vR", ncDouble, dimK, dimEig, dimLatS);
NcVar *varVI = ncdf_out.add_var("vI", ncDouble, dimK, dimEig, dimLatS);
NcVar *varPR = ncdf_out.add_var("pR", ncDouble, dimK, dimEig, dimLat);
NcVar *varPI = ncdf_out.add_var("pI", ncDouble, dimK, dimEig, dimLat);
NcVar *varWR = ncdf_out.add_var("wR", ncDouble, dimK, dimEig, dimLat);
NcVar *varWI = ncdf_out.add_var("wI", ncDouble, dimK, dimEig, dimLat);
NcVar *varRhoR = ncdf_out.add_var("rhoR", ncDouble, dimK, dimEig, dimLat);
NcVar *varRhoI = ncdf_out.add_var("rhoI", ncDouble, dimK, dimEig, dimLat);
// Allocate temporary arrays
DataVector<double> dUR;
dUR.Initialize(param.nPhiElements);
DataVector<double> dUI;
dUI.Initialize(param.nPhiElements);
DataVector<double> dVR;
dVR.Initialize(param.nPhiElements-1);
DataVector<double> dVI;
dVI.Initialize(param.nPhiElements-1);
DataVector<double> dPR;
dPR.Initialize(param.nPhiElements);
DataVector<double> dPI;
dPI.Initialize(param.nPhiElements);
DataVector<double> dWR;
dWR.Initialize(param.nPhiElements);
DataVector<double> dWI;
dWI.Initialize(param.nPhiElements);
DataVector<double> dRhoR;
dRhoR.Initialize(param.nPhiElements);
DataVector<double> dRhoI;
dRhoI.Initialize(param.nPhiElements);
// Loop over all horizontal wave numbers
for (int nK = nKmin; nK <= nKmax; nK++) {
// Build matrices
char szMessage[100];
sprintf(szMessage, "Building evolution matrices (k = %i)", nK);
AnnounceStartBlock(szMessage);
DataMatrix<double> matM;
DataMatrix<double> matB;
GenerateEvolutionMatrix(nK, param, matM, matB);
AnnounceEndBlock("Done");
// Solve the matrices
AnnounceStartBlock("Solving evolution matrices");
DataVector<double> vecAlphaR;
DataVector<double> vecAlphaI;
DataVector<double> vecBeta;
DataMatrix<double> matVR;
vecAlphaR.Initialize(matM.GetRows());
vecAlphaI.Initialize(matM.GetRows());
vecBeta .Initialize(matM.GetRows());
matVR .Initialize(matM.GetRows(), matM.GetColumns());
SolveEvolutionMatrix(
matM,
matB,
vecAlphaR,
vecAlphaI,
vecBeta,
matVR);
// Sort eigenvalues
std::multimap<double, int> mapSortedRows;
for (int i = 0; i < vecBeta.GetRows(); i++) {
if (vecBeta[i] != 0.0) {
double dLambdaR = vecAlphaR[i] / vecBeta[i];
double dLambdaI = vecAlphaI[i] / vecBeta[i];
double dMR = dLambdaI;
double dMI = - dLambdaR - 1.0;
double dEvalMagnitude = fabs(dMR);
//printf("\n%1.5e %1.5e ", dMR, dMI);
// Purely imaginary eigenvalue
if (dMR == 0.0) {
// Wave must decay with height
if (dMI < 0.0) {
continue;
}
// Complex-conjugate pair of eigenvalues
} else {
// Phase propagation must be downward, and energy
// propagation upwards
if (dMR < 0.0) {
continue;
}
}
//printf("(OK)");
mapSortedRows.insert(
std::pair<double, int>(dEvalMagnitude, i));
// Only store one entry for complex-conjugate pairs
if (vecAlphaI[i] != 0.0) {
i++;
}
}
}
Announce("%i eigenmodes found to satisfy entropy condition",
mapSortedRows.size());
/*
if (mapSortedRows.size() != param.nPhiElements) {
_EXCEPTIONT("Mismatch between eigenmode count and latitude count");
}
*/
AnnounceEndBlock("Done");
// Write the matrices to a file
AnnounceStartBlock("Writing results");
int iKix = nK - nKmin;
int iWave = 0;
std::map<double, int>::const_iterator it;
for (it = mapSortedRows.begin(); it != mapSortedRows.end(); it++) {
int i = it->second;
double dLambdaR = vecAlphaR[i] / vecBeta[i];
double dLambdaI = vecAlphaI[i] / vecBeta[i];
double dMR = dLambdaI;
double dMI = - dLambdaR - 1.0;
// Dump eigenvalue to NetCDF file
varMR->set_cur(iKix, iWave);
varMR->put(&dMR, 1, 1);
varMI->set_cur(iKix, iWave);
varMI->put(&dMI, 1, 1);
// Store real part of eigenfunction
for (int j = 0; j < param.nPhiElements; j++) {
dUR [j] = matVR[i][4*j ];
dPR [j] = matVR[i][4*j+1];
dWR [j] = matVR[i][4*j+2];
dRhoR[j] = matVR[i][4*j+3];
}
for (int j = 0; j < param.nPhiElements-1; j++) {
dVR[j] = matVR[i][4 * param.nPhiElements + j];
}
// Complex eigenvalue / eigenfunction pair
if (dLambdaI != 0.0) {
// Eigenvalue Lambda is complex conjugate
dMR = -dMR;
// Dump eigenvalue to NetCDF file
varMR->set_cur(iKix, iWave+1);
varMR->put(&dMR, 1, 1);
varMI->set_cur(iKix, iWave+1);
varMI->put(&dMI, 1, 1);
// Store imaginary component of vector
for (int j = 0; j < param.nPhiElements; j++) {
dUI [j] = matVR[i+1][4*j ];
dPI [j] = matVR[i+1][4*j+1];
dWI [j] = matVR[i+1][4*j+2];
dRhoI[j] = matVR[i+1][4*j+3];
}
for (int j = 0; j < param.nPhiElements-1; j++) {
dVI[j] = matVR[i+1][4 * param.nPhiElements + j];
}
// Real eigenvalue / eigenvector pair
} else {
dUI.Zero();
dPI.Zero();
dWI.Zero();
dRhoI.Zero();
dVI.Zero();
}
// Dump the first eigenfunction to the file
varUR->set_cur(iKix, iWave, 0);
varUR->put(dUR, 1, 1, param.nPhiElements);
varVR->set_cur(iKix, iWave, 0);
varVR->put(dVR, 1, 1, param.nPhiElements-1);
varPR->set_cur(iKix, iWave, 0);
varPR->put(dPR, 1, 1, param.nPhiElements);
varWR->set_cur(iKix, iWave, 0);
varWR->put(dWR, 1, 1, param.nPhiElements);
varRhoR->set_cur(iKix, iWave, 0);
varRhoR->put(dRhoR, 1, 1, param.nPhiElements);
varUI->set_cur(iKix, iWave, 0);
varUI->put(dUI, 1, 1, param.nPhiElements);
varVI->set_cur(iKix, iWave, 0);
varVI->put(dVI, 1, 1, param.nPhiElements-1);
varPI->set_cur(iKix, iWave, 0);
varPI->put(dPI, 1, 1, param.nPhiElements);
varWI->set_cur(iKix, iWave, 0);
varWI->put(dWI, 1, 1, param.nPhiElements);
varRhoI->set_cur(iKix, iWave, 0);
varRhoI->put(dRhoI, 1, 1, param.nPhiElements);
// Complex eigenvalue / eigenvector pair
if (dLambdaI != 0.0) {
for (int j = 0; j < param.nPhiElements; j++) {
dUI [j] = - dUI [j];
dPI [j] = - dPI [j];
dWI [j] = - dWI [j];
dRhoI[j] = - dRhoI[j];
}
for (int j = 0; j < param.nPhiElements-1; j++) {
dVI[j] = - dVI[j];
}
varUR->set_cur(iKix, iWave+1, 0);
varUR->put(dUR, 1, 1, param.nPhiElements);
varVR->set_cur(iKix, iWave+1, 0);
varVR->put(dVR, 1, 1, param.nPhiElements-1);
varPR->set_cur(iKix, iWave+1, 0);
varPR->put(dPR, 1, 1, param.nPhiElements);
varWR->set_cur(iKix, iWave+1, 0);
varWR->put(dWR, 1, 1, param.nPhiElements);
varRhoR->set_cur(iKix, iWave+1, 0);
varRhoR->put(dRhoR, 1, 1, param.nPhiElements);
varUI->set_cur(iKix, iWave+1, 0);
varUI->put(dUI, 1, 1, param.nPhiElements);
varVI->set_cur(iKix, iWave+1, 0);
varVI->put(dVI, 1, 1, param.nPhiElements-1);
varPI->set_cur(iKix, iWave+1, 0);
varPI->put(dPI, 1, 1, param.nPhiElements);
varWI->set_cur(iKix, iWave+1, 0);
varWI->put(dWI, 1, 1, param.nPhiElements);
varRhoI->set_cur(iKix, iWave+1, 0);
varRhoI->put(dRhoI, 1, 1, param.nPhiElements);
}
// Increment wave index
iWave++;
if (dLambdaI != 0.0) {
iWave++;
}
}
AnnounceEndBlock("Done");
AnnounceBanner();
}
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
}
int main(int argc, char** argv) {
// Initialize Tempest
TempestInitialize(&argc, &argv);
try {
// Model cap.
double dZtop;
// Earth radius scaling parameter.
double dEarthScaling;
// Deactivate physics
bool fNoPhysics;
// Bryan Boundary Layer
bool fBryanPBL;
// Reed-Jablonowksi precipitation
bool fReedJablonowskiPrecip;
// Parse the command line
BeginTempestCommandLine("TropicalCycloneTest");
SetDefaultResolution(20);
SetDefaultLevels(30);
SetDefaultOutputDeltaT("1h");
SetDefaultDeltaT("200s");
SetDefaultEndTime("10d");
SetDefaultHorizontalOrder(4);
SetDefaultVerticalOrder(1);
CommandLineDouble(dZtop, "ztop", 30000.0);
CommandLineDouble(dEarthScaling, "X", 1.0);
CommandLineBool(fNoPhysics, "nophys");
CommandLineBool(fBryanPBL, "bryanpbl");
CommandLineBool(fReedJablonowskiPrecip, "rjprecip");
ParseCommandLine(argc, argv);
EndTempestCommandLine(argv)
// Setup the Model
AnnounceBanner("MODEL SETUP");
EquationSet eqn(EquationSet::PrimitiveNonhydrostaticEquations);
eqn.InsertTracer("RhoQv", "RhoQv");
eqn.InsertTracer("RhoQc", "RhoQc");
eqn.InsertTracer("RhoQr", "RhoQr");
UserDataMeta metaUserData;
metaUserData.InsertDataItem2D("PRECT");
Model model(eqn, metaUserData);
TempestSetupCubedSphereModel(model);
// Set the test case for the model
AnnounceStartBlock("Initializing test case");
model.SetTestCase(
new TropicalCycloneTest(
dZtop,
dEarthScaling));
AnnounceEndBlock("Done");
// Add DCMIP physics
if (!fNoPhysics) {
model.AttachWorkflowProcess(
new DCMIPPhysics(
model,
model.GetDeltaT(),
2,
(fBryanPBL)?(1):(0),
(fReedJablonowskiPrecip)?(1):(0)));
}
// Begin execution
AnnounceBanner("SIMULATION");
model.Go();
// Compute error norms
AnnounceBanner("RESULTS");
model.ComputeErrorNorms();
AnnounceBanner();
} catch(Exception & e) {
std::cout << e.ToString() << std::endl;
}
// Deinitialize Tempest
TempestDeinitialize();
}
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::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;
}
}
int main(int argc, char** argv) {
try {
// Input mesh file
std::string strInputMesh;
// Output node file
std::string strOutputNodes;
// Output face file
std::string strOutputFaces;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputMesh, "in", "");
CommandLineString(strOutputNodes, "out_nodes", "nodes.dat");
CommandLineString(strOutputFaces, "out_faces", "faces.dat");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
if (strInputMesh == "") {
return (-1);
}
AnnounceBanner();
// Load input mesh
AnnounceStartBlock("Loading input mesh");
Mesh meshInput(strInputMesh);
AnnounceEndBlock(NULL);
// Output nodes
AnnounceStartBlock("Writing nodes");
FILE * fpNodes = fopen(strOutputNodes.c_str(), "w");
for (int i = 0; i < meshInput.nodes.size(); i++) {
fprintf(fpNodes, "%1.10e %1.10e %1.10e\n",
static_cast<double>(meshInput.nodes[i].x),
static_cast<double>(meshInput.nodes[i].y),
static_cast<double>(meshInput.nodes[i].z));
}
fclose(fpNodes);
AnnounceEndBlock("Done!");
// Output faces
AnnounceStartBlock("Writing faces");
FILE * fpFaces = fopen(strOutputFaces.c_str(), "w");
for (int i = 0; i < meshInput.faces.size(); i++) {
for (int j = 0; j < meshInput.faces[i].edges.size(); j++) {
fprintf(fpFaces, "%i", meshInput.faces[i][j] + 1);
if (j != meshInput.faces[i].edges.size()-1) {
fprintf(fpFaces, " ");
}
}
fprintf(fpFaces, "\n");
}
fclose(fpFaces);
AnnounceEndBlock("Done!");
AnnounceBanner();
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
}