void DataTest::
setInitialCondition(AdvectionManager &advectionManager) {
TimeLevelIndex<2> timeIdx;
io.open(dataIdx);
double *q = new double[numTracer*_mesh->totalNumGrid(CENTER)];
int j = 0;
for (arma::uword t = 0; t < numTracer; ++t) {
io.input<double>(dataIdx, timeIdx, {&advectionManager.density(t)});
for (arma::uword i = 0; i < _mesh->totalNumGrid(CENTER); ++i) {
q[j++] = advectionManager.density(t)(timeIdx, i);
}
}
io.close(dataIdx);
advectionManager.input(timeIdx, q);
setVelocityField(timeIdx);
} // setInitialCondition
void DataTest::
output(const TimeLevelIndex<2> &timeIdx,
const AdvectionManager &advectionManager) {
io.create(outputIdx);
for (arma::uword t = 0; t < numTracer; ++t) {
io.output<double>(outputIdx, timeIdx,
{&advectionManager.density(t)});
}
for (arma::uword m = 0; m < _domain->numDim(); ++m) {
io.output<double>(outputIdx, timeIdx, {&velocityField(m)});
}
io.output<double>(outputIdx, timeIdx, {&velocityField.divergence()});
if (io.isFileActive(outputIdx)) {
advectionManager.output(timeIdx, io.file(outputIdx).fileId);
}
io.close(outputIdx);
#ifdef LASM_USE_DIAG
Diagnostics::output();
#endif
} // output
void DataTest::
init(AdvectionManager &advectionManager) {
// Read in configuration.
auto caseName = ConfigManager::getValue<string>("common", "case_name");
auto dataRoot = ConfigManager::getValue<string>(caseName, "data_root");
auto dataPattern = ConfigManager::getValue<string>(caseName, "data_pattern");
auto outputPattern = ConfigManager::getValue<string>(caseName, "output_pattern");
auto freq = ConfigManager::getValue<string>(caseName, "output_frequency");
auto domainType = ConfigManager::getValue<string>(caseName, "domain_type");
// Create domain and mesh objects.
mark_tag tagDomainType(1), tagNumDomain(2);
sregex reDomainType = (tagDomainType= +_w) >> ' ' >> (tagNumDomain= +_d) >> "d";
smatch what;
if (!regex_match(domainType, what, reDomainType)) {
REPORT_ERROR("Invalid domain type attribute \"" << domainType << "\"!");
}
// Check if the domain type is matched.
if ((what[tagDomainType] == "Cartesian" && !is_same<Domain, geomtk::CartesianDomain>::value) ||
(what[tagDomainType] == "Sphere" && !is_same<Domain, geomtk::SphereDomain>::value)) {
REPORT_ERROR("Domain type is not matched!");
}
_domain = new Domain(atoi(what[tagNumDomain].str().c_str()));
_mesh = new Mesh(*_domain);
// Initialize IO manager.
IOManager::init(_timeManager);
// Initialize time manager.
vector<string> filePaths = geomtk::SystemTools::getFilePaths(dataRoot, geomtk::StampString::wildcard(dataPattern));
_startTime = io.getTime(filePaths.front());
_endTime = io.getTime(filePaths.back());
_stepSize = ConfigManager::getValue<double>(caseName, "time_step_size_in_seconds");
_timeManager.init(_startTime, _endTime, _stepSize);
// Add input and output files.
dataIdx = io.addInputFile(*_mesh, dataRoot+"/"+dataPattern);
outputIdx = io.addOutputFile(*_mesh, outputPattern, geomtk::durationFromString(freq));
// Read in domain from the first data.
_domain->init(io.file(dataIdx).currentFilePath());
// Read in mesh from the first data.
_mesh->init(io.file(dataIdx).currentFilePath());
// Initialize velocity field.
auto useStagger = ConfigManager::getValue<bool>(caseName, "velocity_stagger");
velocityField.create(*_mesh, useStagger, true);
for (int m = 0; m < _domain->numDim(); ++m) {
io.file(dataIdx).addField("double", FULL_DIMENSION, {&velocityField(m)});
io.file(outputIdx).addField("double", FULL_DIMENSION, {&velocityField(m)});
}
io.file(outputIdx).addField("double", FULL_DIMENSION, {&velocityField.divergence()});
#ifdef LASM_USE_DIAG
// Initialize diagnostics.
Diagnostics::init(*_mesh, io, caseName);
Diagnostics::addMetric<Field<int> >("nmp", "1", "mixed parcel number");
Diagnostics::addMetric<Field<int> >("ncp1", "1", "contained parcel number");
Diagnostics::addMetric<Field<int> >("ncp2", "1", "connected parcel number");
#endif
// Initialize advection manager.
advectionManager.init(*_mesh);
// Initialize density fields for input and output.
if (io.file(dataIdx).hasAttribute("num_tracer")) {
numTracer = io.file(dataIdx).getAttribute<int>("num_tracer");
for (int t = 0; t < numTracer; ++t) {
string name = "q"+to_string(t);
string longName = io.file(dataIdx).getAttribute<string>(name, "long_name");
string units = io.file(dataIdx).getAttribute<string>(name, "units");
advectionManager.addTracer(name, units, longName);
io.file(dataIdx).addField("double", FULL_DIMENSION,
{&advectionManager.density(t)});
io.file(outputIdx).addField("double", FULL_DIMENSION,
{&advectionManager.density(t)});
}
}
} // init