void
EBMGAverage::averageFAB(EBCellFAB& a_coar,
const Box& a_boxCoar,
const EBCellFAB& a_refCoar,
const DataIndex& a_datInd,
const Interval& a_variables) const
{
CH_TIMERS("EBMGAverage::average");
CH_TIMER("regular_average", t1);
CH_TIMER("irregular_average", t2);
CH_assert(isDefined());
const Box& coarBox = a_boxCoar;
//do all cells as if they were regular
Box refBox(IntVect::Zero, IntVect::Zero);
refBox.refine(m_refRat);
int numFinePerCoar = refBox.numPts();
BaseFab<Real>& coarRegFAB = a_coar.getSingleValuedFAB();
const BaseFab<Real>& refCoarRegFAB = a_refCoar.getSingleValuedFAB();
//set to zero because the fortran is a bit simpleminded
//and does stuff additively
a_coar.setVal(0.);
CH_START(t1);
for (int comp = a_variables.begin(); comp <= a_variables.end(); comp++)
{
FORT_REGAVERAGE(CHF_FRA1(coarRegFAB,comp),
CHF_CONST_FRA1(refCoarRegFAB,comp),
CHF_BOX(coarBox),
CHF_BOX(refBox),
CHF_CONST_INT(numFinePerCoar),
CHF_CONST_INT(m_refRat));
}
CH_STOP(t1);
//this is really volume-weighted averaging even though it does
//not look that way.
//so (in the traditional sense) we want to preserve
//rhoc * volc = sum(rhof * volf)
//this translates to
//volfrac_C * rhoC = (1/numFinePerCoar)(sum(volFrac_F * rhoF))
//but the data input to this routine is all kappa weigthed so
//the volumefractions have already been multiplied
//which means
// rhoC = (1/numFinePerCoar)(sum(rhoF))
//which is what this does
CH_START(t2);
for (int comp = a_variables.begin(); comp <= a_variables.end(); comp++)
{
m_averageEBStencil[a_datInd]->apply(a_coar, a_refCoar, false, comp);
}
CH_STOP(t2);
}
void
EBMGInterp::pwcInterpFAB(EBCellFAB& a_refCoar,
const Box& a_coarBox,
const EBCellFAB& a_coar,
const DataIndex& a_datInd,
const Interval& a_variables) const
{
CH_TIMERS("EBMGInterp::interp");
CH_TIMER("regular_interp", t1);
CH_TIMER("irregular_interp", t2);
CH_assert(isDefined());
const Box& coarBox = a_coarBox;
for (int ivar = a_variables.begin(); ivar <= a_variables.end(); ivar++)
{
m_interpEBStencil[a_datInd]->cache(a_refCoar, ivar);
//do all cells as if they were regular
Box refBox(IntVect::Zero, IntVect::Zero);
refBox.refine(m_refRat);
const BaseFab<Real>& coarRegFAB = a_coar.getSingleValuedFAB();
BaseFab<Real>& refCoarRegFAB = a_refCoar.getSingleValuedFAB();
CH_START(t1);
FORT_REGPROLONG(CHF_FRA1(refCoarRegFAB,ivar),
CHF_CONST_FRA1(coarRegFAB,ivar),
CHF_BOX(coarBox),
CHF_BOX(refBox),
CHF_CONST_INT(m_refRat));
CH_STOP(t1);
m_interpEBStencil[a_datInd]->uncache(a_refCoar, ivar);
CH_START(t2);
m_interpEBStencil[a_datInd]->apply(a_refCoar, a_coar, true, ivar);
CH_STOP(t2);
}
}
void LargeMatrix::TxtMult(colVect& output, const colVect& arg) const
{
CH_TIMERS("Multiplication");
CH_TIMER("mult_file", t1);
std::ifstream mtx_file;
CH_START(t1);
mtx_file.open(m_filename.c_str());
//std::cout << "MATRIX LOADING: " << std::endl;
std::stringstream ss;
for (int i = 0 ; i < m_num_rows ; i++)
{
rowVect row(m_num_rows,0);
std::string line;
if (mtx_file.is_open())
{
getline(mtx_file,line);
}
ss.str(line);
std::string remain;
for (int j = 0 ; j < m_num_rows ; j++)
{
ss >> row[j];
//std::cout << row[j] << " \t";
ss.ignore(256,',');
}
//std::cout << std::endl;
output[i] = row*arg;
}
CH_STOP(t1);
mtx_file.close();
}
void ebamriTransport(const AMRParameters& a_params,
const ProblemDomain& a_coarsestDomain)
{
// begin define INS solver
CH_TIMERS("ebamriTransport_driver");
CH_TIMER("define_ebamrnosubcycle_solver", t3);
CH_TIMER("init_ebamrnosubcycle_solver", t4);
CH_TIMER("run ebamrnosubcycle_solver", t5);
// read inputs
ParmParse pp;
int flowDir;
pp.get("flow_dir", flowDir);
Vector<int> nCells;
pp.getarr("n_cell", nCells,0,SpaceDim);
Real jet1inflowVel;
pp.get("jet1_inflow_vel", jet1inflowVel);
int idoJet2;
pp.get("do_jet2", idoJet2);
bool doJet2 = idoJet2==1;
Real jet2inflowVel;
pp.get("jet2_inflow_vel", jet2inflowVel);
Real viscosity = 0.0;
pp.get("viscosity", viscosity);
int idoSlipWalls;
pp.get("do_slip_walls", idoSlipWalls);
bool doSlip = idoSlipWalls==1;
IntVect doSlipWallsLo = idoSlipWalls*IntVect::Unit;
IntVect doSlipWallsHi = idoSlipWalls*IntVect::Unit;
Vector<int> slipWallsLo,slipWallsHi;
if(doSlip)
{
pp.getarr("do_slip_walls_hi",slipWallsHi,0,SpaceDim);
pp.getarr("do_slip_walls_lo",slipWallsLo,0,SpaceDim);
for (int idir = 0; idir < SpaceDim; idir++)
{
doSlipWallsHi[idir] = slipWallsHi[idir];
doSlipWallsLo[idir] = slipWallsLo[idir];
}
}
int orderEBBC = 1;
pp.query("order_ebbc", orderEBBC);
bool doJet1PoiseInflow = false;
pp.query("jet1_poiseuille_inflow", doJet1PoiseInflow);
bool doJet2PoiseInflow = false;
pp.query("jet2_poiseuille_inflow", doJet2PoiseInflow);
bool initPoiseData = false;
pp.query("poiseuille_init", initPoiseData);
if(initPoiseData)
pout() << "Doing Poiseuille initialization" << endl;
RefCountedPtr<PoiseuilleInflowBCValue> jet1PoiseBCValue;//make this BaseBCValue if also doing constant values
RefCountedPtr<PoiseuilleInflowBCValue> jet2PoiseBCValue;
// if(doPoiseInflow)
// {
// pout() << "Doing Poiseuille inflow" << endl;
RealVect jet1centerPt, tubeAxis;
Real jet1tubeRadius;
Vector<Real> jet1centerPtVect, tubeAxisVect;
pp.get("jet1_poise_profile_radius", jet1tubeRadius);
pp.getarr("jet1_poise_profile_center_pt", jet1centerPtVect,0,SpaceDim);
pp.getarr("poise_profile_axis", tubeAxisVect,0,SpaceDim);
for (int idir = 0; idir < SpaceDim; idir++)
{
jet1centerPt[idir] = jet1centerPtVect[idir];
tubeAxis[idir] = tubeAxisVect[idir];
}
Real maxVelFactor;//= 1.5 for planar geometry, = 2.0 for cylindrical
pp.get("poise_maxvel_factor", maxVelFactor);
Real jet1maxVel = maxVelFactor*jet1inflowVel;
jet1PoiseBCValue = RefCountedPtr<PoiseuilleInflowBCValue>(new PoiseuilleInflowBCValue(jet1centerPt,tubeAxis,jet1tubeRadius,jet1maxVel,flowDir));
// }
RealVect jet2centerPt;
Real jet2tubeRadius;
Vector<Real> jet2centerPtVect;
pp.get("jet2_poise_profile_radius", jet2tubeRadius);
pp.getarr("jet2_poise_profile_center_pt", jet2centerPtVect,0,SpaceDim);
for (int idir = 0; idir < SpaceDim; idir++)
{
jet2centerPt[idir] = jet2centerPtVect[idir];
}
Real jet2maxVel = maxVelFactor*jet2inflowVel;
jet2PoiseBCValue = RefCountedPtr<PoiseuilleInflowBCValue>(new PoiseuilleInflowBCValue(jet2centerPt,tubeAxis,jet2tubeRadius,jet2maxVel,flowDir));
InflowOutflowIBCFactory ibc(flowDir,
doJet2,
jet1inflowVel,
jet2inflowVel,
orderEBBC,
doSlipWallsHi,
doSlipWallsLo,
doJet1PoiseInflow,
doJet2PoiseInflow,
initPoiseData,
jet1PoiseBCValue,
jet2PoiseBCValue);
CH_START(t3);
EBAMRNoSubcycle kahuna(a_params, ibc, a_coarsestDomain, viscosity);
CH_STOP(t3);
// end define INS solver
// begin define transport solver
// 1. setup the ibc
Real scalarInflowValue = 0.0;
pp.get("scalar_inflow_value", scalarInflowValue);
RefCountedPtr<EBScalarAdvectBCFactory> advectBCFact =
RefCountedPtr<EBScalarAdvectBCFactory>
(new EBScalarAdvectBCFactory(flowDir, scalarInflowValue, jet2PoiseBCValue));
EBAMRTransportParams transParams;
// fillTransParams(transParams);
bool scalSlopeLimiting = true;
int ilimit;
pp.get("limit_scal_slope", ilimit);
scalSlopeLimiting = (ilimit==1);
Real maxScalVal = 1.0;
pp.get("max_scal_value", maxScalVal);
Real minScalVal = 0.0;
pp.get("min_scal_value", minScalVal);
bool setScalMaxMin = true;
int ilimit2;
pp.get("set_scal_maxmin", ilimit2);
setScalMaxMin = (ilimit2==1);
int ifourth, iflatten, iartvisc;
pp.get("scal_use_fourth_order_slopes", ifourth);
pp.get("scal_use_flatten", iflatten);
pp.get("scal_use_art_visc", iartvisc);
bool useFourthOrderSlopes = (ifourth == 1);
bool useFlattening = (iflatten == 1);
bool useArtificialVisc = (iartvisc == 1);
RefCountedPtr<EBPhysIBCFactory> ibcFact = static_cast<RefCountedPtr<EBPhysIBCFactory> >(advectBCFact);
RefCountedPtr<EBPatchTransportFactory> patchTransport =
RefCountedPtr<EBPatchTransportFactory>
(new EBPatchTransportFactory(ibcFact, scalSlopeLimiting, maxScalVal, minScalVal, setScalMaxMin, useFourthOrderSlopes, useFlattening, useArtificialVisc));
// 2. setup transport solver
EBAMRTransportFactory transSolverFact(transParams, patchTransport, true);
// end define transport solver
kahuna.defineExtraSolver(&transSolverFact);
CH_START(t4);
if (!pp.contains("restart_file"))
{
pout() << "starting fresh AMR run" << endl;
kahuna.setupForAMRRun();
}
else
{
std::string restart_file;
pp.get("restart_file",restart_file);
pout() << " restarting from file " << restart_file << endl;
kahuna.setupForRestart(restart_file);
}
CH_STOP(t4);
int maxStep;
pp.get("max_step", maxStep);
Real stopTime = 0.0;
pp.get("max_time",stopTime);
CH_START(t5);
Real fixedDt = 0.;
pp.query("fixed_dt", fixedDt);
if(fixedDt > 1.e-12)
{
kahuna.useFixedDt(fixedDt);
}
kahuna.run(stopTime, maxStep);
CH_STOP(t5);
}
int
main(int a_argc, char* a_argv[])
{
#ifdef CH_MPI
MPI_Init(&a_argc,&a_argv);
#endif
//Scoping trick
{
CH_TIMERS("uber_timers");
CH_TIMER("define_geometry", t1);
CH_TIMER("run", t2);
#ifdef CH_MPI
MPI_Barrier(Chombo_MPI::comm);
#endif
//Check for an input file
char* inFile = NULL;
if (a_argc > 1)
{
inFile = a_argv[1];
}
else
{
pout() << "Usage: <executable name> <inputfile>" << endl;
pout() << "No input file specified" << endl;
return -1;
}
//Parse the command line and the input file (if any)
ParmParse pp(a_argc-2,a_argv+2,NULL,inFile);
ProblemDomain coarsestDomain;
RealVect coarsestDx;
AMRParameters params;
getAMRINSParameters(params, coarsestDomain);
int numFilt;
pp.get("num_filter_iterations", numFilt);
params.m_numFilterIterations = numFilt;
int gphiIterations;
pp.get("num_gphi_iterations", gphiIterations);
params.m_gphiIterations = gphiIterations;
int initIterations;
pp.get("num_init_iterations", initIterations);
params.m_initIterations = initIterations;
bool doRegridSmoothing;
pp.get("do_regrid_smoothing", doRegridSmoothing);
params.m_doRegridSmoothing = doRegridSmoothing;
CH_START(t1);
//define geometry
AMRINSGeometry(params, coarsestDomain);
CH_STOP(t1);
CH_START(t2);
ebamriTransport(params, coarsestDomain);
CH_STOP(t2);
EBIndexSpace* ebisPtr = Chombo_EBIS::instance();
ebisPtr->clear();
}//end scoping trick
#ifdef CH_MPI
CH_TIMER_REPORT();
dumpmemoryatexit();
MPI_Finalize();
#endif
}
void
EBMGInterp::define(const DisjointBoxLayout& a_dblFine,
const DisjointBoxLayout& a_dblCoar,
const EBISLayout& a_ebislFine,
const EBISLayout& a_ebislCoar,
const ProblemDomain& a_domainCoar,
const int& a_nref,
const int& a_nvar,
const EBIndexSpace* ebisPtr,
const IntVect& a_ghostCellsPhi,
const bool& a_layoutChanged,
const bool& a_doLinear)
{
CH_TIMERS("EBMGInterp::define");
CH_TIMER("fillEBISLayout", t1);
m_isDefined = true;
m_doLinear = a_doLinear;
m_ghost = a_ghostCellsPhi;
m_nComp = a_nvar;
m_coarGrids = a_dblCoar;
m_fineGrids = a_dblFine;
m_coarEBISL = a_ebislCoar;
m_fineEBISL = a_ebislFine;
m_coarDomain = a_domainCoar;
m_refRat = a_nref;
m_fineDomain = refine(m_coarDomain, m_refRat);
m_layoutChanged = a_layoutChanged;
m_coarsenable = a_dblFine.coarsenable(m_refRat);
//only define ebislbuf and gridbuf if we are changing layouts
if (m_layoutChanged)
{
ProblemDomain domebisl;
if (m_coarsenable)
{
coarsen(m_buffGrids, m_fineGrids, m_refRat);
domebisl = m_coarDomain;
}
else
{
refine(m_buffGrids, m_coarGrids, m_refRat);
m_copierRCtoF.define(m_buffGrids, m_fineGrids, a_ghostCellsPhi);
m_copierFtoRC.define(m_fineGrids, m_buffGrids, a_ghostCellsPhi);
domebisl = m_fineDomain;
}
CH_START(t1);
int nghost = 4;
ebisPtr->fillEBISLayout(m_buffEBISL,
m_buffGrids,
domebisl, nghost);
if (m_refRat > 2)
{
if (m_coarsenable)
{
m_buffEBISL.setMaxRefinementRatio(m_refRat, ebisPtr);
}
else
{
m_buffEBISL.setMaxCoarseningRatio(m_refRat, ebisPtr);
}
}
CH_STOP(t1);
}
defineStencils();
}
void
EBMGInterp::pwlInterpFAB(EBCellFAB& a_refCoar,
const Box& a_coarBox,
const EBCellFAB& a_coar,
const DataIndex& a_datInd,
const Interval& a_variables) const
{
CH_TIMERS("EBMGInterp::pwlinterpfab");
CH_TIMER("regular_interp", t1);
CH_TIMER("irregular_interp", t2);
CH_assert(isDefined());
//first interpolate piecewise constant.
pwcInterpFAB(a_refCoar,
a_coarBox,
a_coar,
a_datInd,
a_variables);
//then add in slope*distance.
const Box& coarBox = a_coarBox;
for (int ivar = a_variables.begin(); ivar <= a_variables.end(); ivar++)
{
//save stuff at irreg cells because fortran result will be garbage
//and this is an incremental process
m_linearEBStencil[a_datInd]->cache(a_refCoar, ivar);
//do all cells as if they were regular
Box refBox(IntVect::Zero, IntVect::Zero);
refBox.refine(m_refRat);
const BaseFab<Real>& coarRegFAB = a_coar.getSingleValuedFAB();
BaseFab<Real>& refCoarRegFAB = a_refCoar.getSingleValuedFAB();
CH_START(t1);
Real dxf = 1.0/m_coarDomain.size(0);
Real dxc = 2.0*dxf;
//do every cell as regular
for (int idir = 0; idir < SpaceDim; idir++)
{
FORT_PROLONGADDSLOPE(CHF_FRA1(refCoarRegFAB,ivar),
CHF_CONST_FRA1(coarRegFAB,ivar),
CHF_BOX(coarBox),
CHF_BOX(refBox),
CHF_INT(idir),
CHF_REAL(dxf),
CHF_REAL(dxc),
CHF_CONST_INT(m_refRat));
}
CH_STOP(t1);
//replace garbage fortran put in with original values (at irregular cells)
m_linearEBStencil[a_datInd]->uncache(a_refCoar, ivar);
CH_START(t2);
//do what fortran should have done at irregular cells.
m_linearEBStencil[a_datInd]->apply(a_refCoar, a_coar, true, ivar);
CH_STOP(t2);
}
}
//
// VCAMRPoissonOp2::reflux()
// There are currently the new version (first) and the old version (second)
// in this file. Brian asked to preserve the old version in this way for
// now. - TJL (12/10/2007)
//
void VCAMRPoissonOp2::reflux(const LevelData<FArrayBox>& a_phiFine,
const LevelData<FArrayBox>& a_phi,
LevelData<FArrayBox>& a_residual,
AMRLevelOp<LevelData<FArrayBox> >* a_finerOp)
{
CH_TIMERS("VCAMRPoissonOp2::reflux");
m_levfluxreg.setToZero();
Interval interv(0,a_phi.nComp()-1);
CH_TIMER("VCAMRPoissonOp2::reflux::incrementCoarse", t2);
CH_START(t2);
DataIterator dit = a_phi.dataIterator();
for (dit.reset(); dit.ok(); ++dit)
{
const FArrayBox& coarfab = a_phi[dit];
const FluxBox& coarBCoef = (*m_bCoef)[dit];
const Box& gridBox = a_phi.getBoxes()[dit];
if (m_levfluxreg.hasCF(dit()))
{
for (int idir = 0; idir < SpaceDim; idir++)
{
FArrayBox coarflux;
Box faceBox = surroundingNodes(gridBox, idir);
getFlux(coarflux, coarfab, coarBCoef, faceBox, idir);
Real scale = 1.0;
m_levfluxreg.incrementCoarse(coarflux, scale,dit(),
interv, interv, idir);
}
}
}
CH_STOP(t2);
// const cast: OK because we're changing ghost cells only
LevelData<FArrayBox>& phiFineRef = ( LevelData<FArrayBox>&)a_phiFine;
VCAMRPoissonOp2* finerAMRPOp = (VCAMRPoissonOp2*) a_finerOp;
QuadCFInterp& quadCFI = finerAMRPOp->m_interpWithCoarser;
quadCFI.coarseFineInterp(phiFineRef, a_phi);
// I'm pretty sure this is not necessary. bvs -- flux calculations use
// outer ghost cells, but not inner ones
// phiFineRef.exchange(a_phiFine.interval());
IntVect phiGhost = phiFineRef.ghostVect();
int ncomps = a_phiFine.nComp();
CH_TIMER("VCAMRPoissonOp2::reflux::incrementFine", t3);
CH_START(t3);
DataIterator ditf = a_phiFine.dataIterator();
const DisjointBoxLayout& dblFine = a_phiFine.disjointBoxLayout();
for (ditf.reset(); ditf.ok(); ++ditf)
{
const FArrayBox& phifFab = a_phiFine[ditf];
const FluxBox& fineBCoef = (*(finerAMRPOp->m_bCoef))[ditf];
const Box& gridbox = dblFine.get(ditf());
for (int idir = 0; idir < SpaceDim; idir++)
{
//int normalGhost = phiGhost[idir];
SideIterator sit;
for (sit.begin(); sit.ok(); sit.next())
{
if (m_levfluxreg.hasCF(ditf(), sit()))
{
Side::LoHiSide hiorlo = sit();
Box fluxBox = bdryBox(gridbox,idir,hiorlo,1);
FArrayBox fineflux(fluxBox,ncomps);
getFlux(fineflux, phifFab, fineBCoef, fluxBox, idir,
m_refToFiner);
Real scale = 1.0;
m_levfluxreg.incrementFine(fineflux, scale, ditf(),
interv, interv, idir, hiorlo);
}
}
}
}
CH_STOP(t3);
Real scale = 1.0/m_dx;
m_levfluxreg.reflux(a_residual, scale);
}
// Advance the solution by "a_dt" by using an unsplit method.
// "a_finerFluxRegister" is the flux register with the next finer level.
// "a_coarseFluxRegister" is flux register with the next coarser level.
// If source terms do not exist, "a_S" should be null constructed and not
// defined (i.e. its define() should not be called).
Real LevelPluto::step(LevelData<FArrayBox>& a_U,
LevelData<FArrayBox> a_flux[CH_SPACEDIM],
LevelFluxRegister& a_finerFluxRegister,
LevelFluxRegister& a_coarserFluxRegister,
LevelData<FArrayBox>& a_split_tags,
const LevelData<FArrayBox>& a_UCoarseOld,
const Real& a_TCoarseOld,
const LevelData<FArrayBox>& a_UCoarseNew,
const Real& a_TCoarseNew,
const Real& a_time,
const Real& a_dt,
const Real& a_cfl)
{
CH_TIMERS("LevelPluto::step");
CH_TIMER("LevelPluto::step::setup" ,timeSetup);
CH_TIMER("LevelPluto::step::update" ,timeUpdate);
CH_TIMER("LevelPluto::step::reflux" ,timeReflux);
CH_TIMER("LevelPluto::step::conclude",timeConclude);
// Make sure everything is defined
CH_assert(m_isDefined);
CH_START(timeSetup);
// Clear flux registers with next finer level
if (m_hasFiner && (g_intStage == 1))
{
a_finerFluxRegister.setToZero();
}
// Setup an interval corresponding to the conserved variables
Interval UInterval(0,m_numCons-1);
{
CH_TIME("setup::localU");
for (DataIterator dit = m_U.dataIterator(); dit.ok(); ++dit)
{
m_U[dit].setVal(0.0); // Gets rid of denormalized crap.
m_U[dit].copy(a_U[dit]);
}
m_U.exchange(m_exchangeCopier);
}
// Fill m_U's ghost cells using fillInterp
if (m_hasCoarser)
{
// Fraction "a_time" falls between the old and the new coarse times
Real alpha = (a_time - a_TCoarseOld) / (a_TCoarseNew - a_TCoarseOld);
// Truncate the fraction to the range [0,1] to remove floating-point
// subtraction roundoff effects
Real eps = 0.04 * a_dt / m_refineCoarse;
if (Abs(alpha) < eps) alpha = 0.0;
if (Abs(1.0-alpha) < eps) alpha = 1.0;
// Current time before old coarse time
if (alpha < 0.0)
{
MayDay::Error( "LevelPluto::step: alpha < 0.0");
}
// Current time after new coarse time
if (alpha > 1.0)
{
MayDay::Error( "LevelPluto::step: alpha > 1.0");
}
// Interpolate ghost cells from next coarser level using both space
// and time interpolation
m_patcher.fillInterp(m_U,
a_UCoarseOld,
a_UCoarseNew,
alpha,
0,0,m_numCons);
}
// Potentially used in boundary conditions
m_patchPluto->setCurrentTime(a_time);
// Use to restrict maximum wave speed away from zero
Real maxWaveSpeed = 1.e-12;
Real minDtCool = 1.e38;
// The grid structure
Grid *grid;
static Time_Step Dts;
Real inv_dt;
#ifdef GLM_MHD
glm_ch = g_coeff_dl_min*m_dx/(a_dt + 1.e-16)*a_cfl;
// glm_ch = g_coeff_dl_min/(a_dt + 1.e-16)*a_cfl; /* If subcycling is turned off */
glm_ch = MIN(glm_ch,glm_ch_max*g_coeff_dl_min);
#endif
CH_STOP(timeSetup);
g_level_dx = m_dx;
// Beginning of loop through patches/grids.
for (DataIterator dit = m_grids.dataIterator(); dit.ok(); ++dit){
CH_START(timeUpdate);
// The current box
Box curBox = m_grids.get(dit());
// The current grid of conserved variables
FArrayBox& curU = m_U[dit];
// The current grid of volumes
#if GEOMETRY != CARTESIAN
const FArrayBox& curdV = m_dV[dit()];
#else
const FArrayBox curdV;
#endif
#ifdef SKIP_SPLIT_CELLS
// The current grid of split/unsplit tags
FArrayBox& split_tags = a_split_tags[dit];
#else
FArrayBox split_tags;
#endif
#if (TIME_STEPPING == RK2)
// The current storage for flags (RK2 only)
BaseFab<unsigned char>& flags = m_Flags[dit];
// Local temporary storage for conserved variables
FArrayBox& curUtmp = m_Utmp[dit];
#else
BaseFab<unsigned char> flags;
FArrayBox curUtmp;
#endif
// The fluxes computed for this grid - used for refluxing and returning
// other face centered quantities
FluxBox flux;
// Set the current box for the patch integrator
m_patchPluto->setCurrentBox(curBox);
Real minDtCoolGrid;
grid = m_structs_grid[dit].getGrid();
IBEG = grid[IDIR].lbeg; IEND = grid[IDIR].lend;
JBEG = grid[JDIR].lbeg; JEND = grid[JDIR].lend;
KBEG = grid[KDIR].lbeg; KEND = grid[KDIR].lend;
NX1 = grid[IDIR].np_int;
NX2 = grid[JDIR].np_int;
NX3 = grid[KDIR].np_int;
NX1_TOT = grid[IDIR].np_tot;
NX2_TOT = grid[JDIR].np_tot;
NX3_TOT = grid[KDIR].np_tot;
SetRBox(); /* RBox structures must be redefined for each patch */
g_dt = a_dt;
g_time = a_time;
g_maxRiemannIter = 0;
PLM_CoefficientsSet (grid); /* -- these may be needed by
shock flattening algorithms */
#if RECONSTRUCTION == PARABOLIC
PPM_CoefficientsSet (grid);
#endif
// reset time step coefficients
if (Dts.cmax == NULL) Dts.cmax = ARRAY_1D(NMAX_POINT, double);
int id;
Dts.inv_dta = 1.e-18;
Dts.inv_dtp = 1.e-18;
Dts.dt_cool = 1.e18;
Dts.cfl = a_cfl;
Where(-1, grid); /* -- store grid for subsequent calls -- */
// Take one step
m_patchPluto->advanceStep (curU, curUtmp, curdV, split_tags, flags, flux,
&Dts, curBox, grid);
inv_dt = Dts.inv_dta + 2.0*Dts.inv_dtp;
maxWaveSpeed = Max(maxWaveSpeed, inv_dt); // Now the inverse of the timestep
minDtCool = Min(minDtCool, Dts.dt_cool/a_cfl);
CH_STOP(timeUpdate);
CH_START(timeReflux);
// Do flux register updates
for (int idir = 0; idir < SpaceDim; idir++) {
// Increment coarse flux register between this level and the next
// finer level - this level is the next coarser level with respect
// to the next finer level
if (m_hasFiner) {
a_finerFluxRegister.incrementCoarse(flux[idir],a_dt,dit(),
UInterval, UInterval,idir);
}
// Increment fine flux registers between this level and the next
// coarser level - this level is the next finer level with respect
// to the next coarser level
if (m_hasCoarser) {
a_coarserFluxRegister.incrementFine(flux[idir],a_dt,dit(),
UInterval, UInterval,idir);
}
}
CH_STOP(timeReflux);
}
CH_START(timeConclude);
{
CH_TIME("conclude::copyU");
// Now that we have completed the updates of all the patches, we copy the
// contents of temporary storage, U, into the permanent storage, a_U.
for(DataIterator dit = m_U.dataIterator(); dit.ok(); ++dit){
a_U[dit].copy(m_U[dit]);
}
}
// Find the minimum of dt's over this level
Real local_dtNew = 1. / maxWaveSpeed;
local_dtNew = Min(local_dtNew,minDtCool);
Real dtNew;
{
CH_TIME("conclude::getDt");
#ifdef CH_MPI
#if (TIME_STEPPING == RK2) && (COOLING == NO)
if (g_intStage == 1) {
#endif
int result = MPI_Allreduce(&local_dtNew, &dtNew, 1, MPI_CH_REAL,
MPI_MIN, Chombo_MPI::comm);
if(result != MPI_SUCCESS){ //bark!!!
MayDay::Error("sorry, but I had a communcation error on new dt");
}
#if (TIME_STEPPING == RK2) && (COOLING == NO)
} else {
dtNew = local_dtNew;
}
#endif
#else
dtNew = local_dtNew;
#endif
}
CH_STOP(timeConclude);
// Return the maximum stable time step
return dtNew;
}
void LargeMatrix::OptMult(colVect& output, const colVect& arg) const
{
CH_TIMERS("Multiplication");
CH_TIMER("trivial", t0);
CH_TIMER("file_read", t1);
CH_TIMER("line_splice", t2);
CH_TIMER("vec_multiply", t3);
//std::cout << "PERFORMING MULTIPLICATION!" << std::endl;
std::ifstream mtx_file;
mtx_file.open(m_filename.c_str(), std::ifstream::binary);
//std::cout << "MATRIX LOADING: " << std::endl;
char header_buffer[18];
mtx_file.read(header_buffer, 18);
if (!mtx_file)
{
mtx_file.close();
std::cout << "FATAL ERROR: could not read line from file" << std::endl;
abort();
}
//std::cout << "HEADER:: " << header_buffer << std::endl;
unsigned int dat_size = *(int*) (header_buffer + 9);
unsigned int num_row = *(int*) (header_buffer + 13);
//std::cout << "Dat Size:: " << dat_size << std::endl;
//std::cout << "Num rows:: " << num_row << std::endl;
assert(m_num_rows == num_row);
int Nchar_double = 8;
assert(Nchar_double == dat_size);
assert(sizeof(Real) == dat_size);
int max_lines_read = m_nums_in_memory / m_num_rows;
//std::cout << "Max nums in memory: " << m_nums_in_memory << std::endl;
//std::cout << "Max lines to read: " << max_lines_read << std::endl;
int line_size_char = m_num_rows * Nchar_double;
char buffer[ line_size_char * max_lines_read];
for (int i = 0 ; i < m_num_rows ; i+=max_lines_read)
{
CH_START(t0);
assert(mtx_file.is_open());
CH_STOP(t0);
CH_START(t1);
int num_lines_to_read = std::min(max_lines_read, m_num_rows - i);
int num_bytes_to_read = line_size_char * num_lines_to_read;
//std::cout << "Reading " << num_lines_to_read << " lines.\n Buffer call to read " << num_bytes_to_read << " Bytes." << std::endl;
rowVect row(m_num_rows,0);
mtx_file.read(buffer, num_bytes_to_read);
if (!mtx_file)
{
mtx_file.close();
std::cout << "FATAL ERROR: could not read line from file" << std::endl;
abort();
}
CH_STOP(t1);
for (int n_line = 0 ; n_line < num_lines_to_read ; n_line++)
{
CH_START(t2);
int line_displace = n_line * line_size_char;
Real* row_vect = (Real*) (buffer + line_displace);
//for (int j = 0 ; j < m_num_rows ; j++)
// {
// int float_displace = (j * Nchar_double) + line_displace;
// //assert(displace + Nchar_double < line_size_char);
// row[j] = *(Real*) (buffer + float_displace);
// if (n_line == num_lines_to_read-1 and j == m_num_rows-1)
// {
// std::cout << row[j] << std::endl;
// std::cout << float_displace << std::endl;
// }
// }
CH_STOP(t2);
CH_START(t3);
output[i+n_line] = cblas_ddot(m_num_rows, row_vect, 1, &*arg.begin(), 1);
CH_STOP(t3);
}
}
mtx_file.close();
}
void LargeMatrix::BinMult(colVect& output, const colVect& arg) const
{
CH_TIMERS("Multiplication");
CH_TIMER("file_read", t1);
CH_TIMER("line_splice", t2);
CH_TIMER("vec_multiply", t3);
//std::cout << "PERFORMING MULTIPLICATION!" << std::endl;
std::ifstream mtx_file;
mtx_file.open(m_filename.c_str(), std::ifstream::binary);
//std::cout << "MATRIX LOADING: " << std::endl;
int Nchar_double = 8;
assert(m_num_rows == 25*25);
int line_size = m_num_rows * Nchar_double;
char buffer[line_size + 1];
for (int i = 0 ; i < m_num_rows ; i++)
{
assert(mtx_file.is_open());
CH_START(t1);
rowVect row(m_num_rows,0);
mtx_file.read(buffer, line_size + 1);
if (!mtx_file)
{
mtx_file.close();
std::cout << "FATAL ERROR: could not read line from file" << std::endl;
abort();
}
assert(buffer[line_size] == '\n');
CH_STOP(t1);
CH_START(t2);
Real * row_vect = (Real*) buffer;
for (int j = 0 ; j < m_num_rows ; j++)
{
int displace = Nchar_double * j;
//assert(displace + Nchar_double < line_size);
row[j] = *(Real*) (buffer + Nchar_double * j);
//if (i == m_num_rows-1 and j == m_num_rows-1)
//{
// std::cout << row[j] << std::endl;
// std::cout << Nchar_double * j << std::endl;
//}
}
CH_STOP(t2);
CH_START(t3);
for (int q = 0 ; q < arg.size() ; q++)
{
//std::cout << "row["<<q<<"] vs row_vect["<<q<<"]:" <<row[q] << " VS "<<row_vect[q] << std::endl;
assert(row[q] == row_vect[q]);
}
output[i] = cblas_ddot(m_num_rows, row_vect, 1, &*arg.begin(), 1);
//output[i] = row*arg;
CH_STOP(t3);
}
mtx_file.close();
}
void EBPoissonOp::
applyOp(LevelData<EBCellFAB>& a_opPhi,
const LevelData<EBCellFAB>& a_phi,
bool a_homogeneousPhysBC,
DataIterator& dit,
bool a_do_exchange)
{
CH_TIMERS("EBPoissonOp::applyOp");
CH_TIMER("regular_apply", t1);
CH_TIMER("irregular_apply", t2);
CH_TIMER("eb_bcs_apply", t3);
CH_TIMER("dom_bcs_apply", t4);
CH_TIMER("alpha_apply", t5);
CH_assert(a_opPhi.ghostVect() == m_ghostCellsRHS);
CH_assert(a_phi.ghostVect() == m_ghostCellsPhi);
CH_assert(a_phi.nComp() == a_opPhi.nComp());
LevelData<EBCellFAB>& phi = const_cast<LevelData<EBCellFAB>&>(a_phi);
if (a_do_exchange)
{
phi.exchange(phi.interval());
}
int nComps = a_phi.nComp();
for (dit.reset(); dit.ok(); ++dit)
{
Box dblBox( m_eblg.getDBL().get(dit()) );
const EBCellFAB& phifab = phi[dit()];
Box curPhiBox = phifab.box();
const BaseFab<Real>& curPhiFAB = phifab.getSingleValuedFAB();
EBCellFAB& opphifab = a_opPhi[dit()];
BaseFab<Real>& curOpPhiFAB = opphifab.getSingleValuedFAB();
// Interval interv(0, nComps-1);
CH_START(t5);
if (m_alpha == 0)
{
opphifab.setVal(0.0);
}
else
{
opphifab.copy(phifab);
opphifab.mult(m_alpha);
}
CH_STOP(t5);
Box loBox[SpaceDim],hiBox[SpaceDim];
int hasLo[SpaceDim],hasHi[SpaceDim];
CH_START(t1);
applyOpRegularAllDirs( loBox, hiBox, hasLo, hasHi,
dblBox, curPhiBox, nComps,
curOpPhiFAB,
curPhiFAB,
a_homogeneousPhysBC,
dit(),
m_beta);
CH_STOP(t1);
CH_START(t2);
//apply stencil
m_opEBStencil[dit()]->apply(opphifab, phifab, false);
CH_STOP(t2);
//apply inhom boundary conditions
CH_START(t3);
if (!a_homogeneousPhysBC)
{
const Real factor = m_dxScale*m_beta;
m_ebBC->applyEBFlux(opphifab, phifab, m_vofItIrreg[dit()], (*m_eblg.getCFIVS()),
dit(), m_origin, m_dx, factor,
a_homogeneousPhysBC, m_time);
}
CH_STOP(t3);
CH_START(t4);
int comp = 0;
for (int idir = 0; idir < SpaceDim; idir++)
{
for (m_vofItIrregDomLo[idir][dit()].reset(); m_vofItIrregDomLo[idir][dit()].ok(); ++m_vofItIrregDomLo[idir][dit()])
{
Real flux;
const VolIndex& vof = m_vofItIrregDomLo[idir][dit()]();
m_domainBC->getFaceFlux(flux,vof,comp,a_phi[dit()],
m_origin,m_dx,idir,Side::Lo, dit(), m_time,
a_homogeneousPhysBC);
opphifab(vof,comp) -= flux * m_beta*m_invDx[idir];
}
for (m_vofItIrregDomHi[idir][dit()].reset(); m_vofItIrregDomHi[idir][dit()].ok(); ++m_vofItIrregDomHi[idir][dit()])
{
Real flux;
const VolIndex& vof = m_vofItIrregDomHi[idir][dit()]();
m_domainBC->getFaceFlux(flux,vof,comp,a_phi[dit()],
m_origin,m_dx,idir,Side::Hi,dit(), m_time,
a_homogeneousPhysBC);
opphifab(vof,comp) += flux * m_beta*m_invDx[idir];
}
}
CH_STOP(t4);
}
}
void
EBPoissonOp::
defineStencils()
{
CH_TIMERS("EBPoissonOp::defineStencils");
CH_TIMER("opStencil_define", t1);
CH_TIMER("colorStencil_define", t2);
// define ebstencil for irregular applyOp
m_opEBStencil.define(m_eblg.getDBL());
// create vofstencils for applyOp
LayoutData<BaseIVFAB<VoFStencil> > opStencil;
opStencil.define(m_eblg.getDBL());
//define bc stencils and create flux stencil
m_ebBC->define((*m_eblg.getCFIVS()), m_dxScale*m_beta);
LayoutData<BaseIVFAB<VoFStencil> >* fluxStencil = m_ebBC->getFluxStencil(0);
//create and define colored stencils (2 parts)
LayoutData<BaseIVFAB<VoFStencil> > colorStencil;
colorStencil.define(m_eblg.getDBL());
LayoutData<BaseIVFAB<VoFStencil> > rhsColorStencil;
rhsColorStencil.define(m_eblg.getDBL());
m_alphaDiagWeight.define( m_eblg.getDBL());
m_betaDiagWeight.define( m_eblg.getDBL());
m_vofItIrreg.define( m_eblg.getDBL()); // vofiterator cache
Box domainBox = m_eblg.getDomain().domainBox();
Box sideBoxLo[SpaceDim];
Box sideBoxHi[SpaceDim];
for (int idir = 0; idir < SpaceDim; idir++)
{
sideBoxLo[idir] = adjCellLo(domainBox, idir, 1);
sideBoxLo[idir].shift(idir, 1);
sideBoxHi[idir] = adjCellHi(domainBox, idir, 1);
sideBoxHi[idir].shift(idir, -1);
m_vofItIrregDomLo[idir].define( m_eblg.getDBL()); // vofiterator cache for domain lo
m_vofItIrregDomHi[idir].define( m_eblg.getDBL()); // vofiterator cache for domain hi
}
CH_START(t1);
for (DataIterator dit = m_eblg.getDBL().dataIterator(); dit.ok(); ++dit)
{
const Box& curBox = m_eblg.getDBL().get(dit());
const EBISBox& curEBISBox = m_eblg.getEBISL()[dit()];
const EBGraph& curEBGraph = curEBISBox.getEBGraph();
IntVectSet notRegular = curEBISBox.getIrregIVS (curBox);
BaseIVFAB<VoFStencil>& curStencilBaseIVFAB = opStencil[dit()];
BaseIVFAB<Real>& alphaWeight = m_alphaDiagWeight[dit()];
BaseIVFAB<Real>& betaWeight = m_betaDiagWeight[dit()];
curStencilBaseIVFAB.define(notRegular,curEBGraph, 1);
alphaWeight.define( notRegular,curEBGraph, 1);
betaWeight.define( notRegular,curEBGraph, 1);
//cache the vofIterators
m_vofItIrreg[dit()].define(notRegular,curEBISBox.getEBGraph());
for (int idir = 0; idir < SpaceDim; idir++)
{
IntVectSet loIrreg = notRegular;
IntVectSet hiIrreg = notRegular;
loIrreg &= sideBoxLo[idir];
hiIrreg &= sideBoxHi[idir];
m_vofItIrregDomLo[idir][dit()].define(loIrreg,curEBISBox.getEBGraph());
m_vofItIrregDomHi[idir][dit()].define(hiIrreg,curEBISBox.getEBGraph());
}
//Operator vofstencil
VoFIterator& vofit = m_vofItIrreg[dit()];
for (vofit.reset(); vofit.ok(); ++vofit)
{
const VolIndex& VoF = vofit();
VoFStencil& curStencil = curStencilBaseIVFAB(VoF,0);
getOpVoFStencil(curStencil,curEBISBox,VoF);
Real& curAlphaWeight = alphaWeight(VoF,0);
Real& curBetaWeight = betaWeight(VoF,0);
const Real kappa = curEBISBox.volFrac(VoF);
curAlphaWeight = kappa;
curBetaWeight = 0.0;
for (int i = 0; i < curStencil.size(); i++)
{
if (curStencil.vof(i) == VoF)
{
curBetaWeight += curStencil.weight(i);
break;
}
}
curStencil *= m_beta;
if (m_alpha != 0)
{
curStencil.add(VoF, kappa*m_alpha);
}
const IntVect& iv = VoF.gridIndex();
for (int idir = 0; idir < SpaceDim; idir++)
{
Box loSide = bdryLo(m_eblg.getDomain(),idir);
loSide.shiftHalf(idir,1);
if (loSide.contains(iv))
{
Real faceAreaFrac = 0.0;
Vector<FaceIndex> faces = curEBISBox.getFaces(VoF,idir,Side::Lo);
for (int i = 0; i < faces.size(); i++)
{
faceAreaFrac += curEBISBox.areaFrac(faces[i]);
}
curBetaWeight += -faceAreaFrac * m_invDx2[idir];
}
Box hiSide = bdryHi(m_eblg.getDomain(),idir);
hiSide.shiftHalf(idir,-1);
if (hiSide.contains(iv))
{
Real faceAreaFrac = 0.0;
Vector<FaceIndex> faces = curEBISBox.getFaces(VoF,idir,Side::Hi);
for (int i = 0; i < faces.size(); i++)
{
faceAreaFrac += curEBISBox.areaFrac(faces[i]);
}
curBetaWeight += -faceAreaFrac * m_invDx2[idir];
}
}
if (curBetaWeight == 0.0)
{
curBetaWeight = -1.0;
}
if (fluxStencil != NULL)
{
BaseIVFAB<VoFStencil>& fluxStencilBaseIVFAB = (*fluxStencil)[dit()];
VoFStencil& fluxStencilPt = fluxStencilBaseIVFAB(VoF,0);
curStencil += fluxStencilPt;
}
}//vofit
//Operator ebstencil
m_opEBStencil[dit()] = RefCountedPtr<EBStencil>(new EBStencil(m_vofItIrreg[dit()].getVector(), opStencil[dit()], m_eblg.getDBL().get(dit()), m_eblg.getEBISL()[dit()], m_ghostCellsPhi, m_ghostCellsRHS));
}//dit
CH_STOP(t1);
//color vofstencils and ebstencils
IntVect color = IntVect::Zero;
IntVect limit = IntVect::Unit;
color[0]=-1;
// Loop over all possibilities (in all dimensions)
CH_START(t2);
for (int icolor = 0; icolor < m_colors.size(); icolor++)
{
m_colorEBStencil[icolor].define(m_eblg.getDBL());
m_rhsColorEBStencil[icolor].define(m_eblg.getDBL());
m_vofItIrregColor[icolor].define( m_eblg.getDBL());
for (int idir = 0; idir < SpaceDim; idir++)
{
m_vofItIrregColorDomLo[icolor][idir].define( m_eblg.getDBL());
m_vofItIrregColorDomHi[icolor][idir].define( m_eblg.getDBL());
}
for (DataIterator dit = m_eblg.getDBL().dataIterator(); dit.ok(); ++dit)
{
IntVectSet ivsColor;
const EBISBox& curEBISBox = m_eblg.getEBISL()[dit()];
const EBGraph& curEBGraph = curEBISBox.getEBGraph();
Box dblBox( m_eblg.getDBL().get(dit()) );
BaseIVFAB<VoFStencil>& curStencilBaseIVFAB = opStencil[dit()];
BaseIVFAB<VoFStencil>& colorStencilBaseIVFAB = colorStencil[dit()];
BaseIVFAB<VoFStencil>& rhsColorStencilBaseIVFAB = rhsColorStencil[dit()];
const BaseIVFAB<Real>& curAlphaWeight = m_alphaDiagWeight[dit()];
const BaseIVFAB<Real>& curBetaWeight = m_betaDiagWeight[dit()];
VoFIterator& vofit = m_vofItIrreg[dit()];
int vofOrdinal = 0;
for (vofit.reset(); vofit.ok(); ++vofit, ++vofOrdinal)
{
const VolIndex& vof = vofit();
const IntVect& iv = vof.gridIndex();
bool doThisVoF = true;
for (int idir = 0; idir < SpaceDim; idir++)
{
if (iv[idir] % 2 != color[idir])
{
doThisVoF = false;
break;
}
}
if (doThisVoF)
{
ivsColor |= iv;
}
}
m_vofItIrregColor[icolor][dit()].define(ivsColor, curEBGraph);
colorStencilBaseIVFAB.define(ivsColor, curEBGraph, 1);
rhsColorStencilBaseIVFAB.define(ivsColor, curEBGraph, 1);
for (int idir = 0; idir < SpaceDim; idir++)
{
IntVectSet loIrregColor = ivsColor;
IntVectSet hiIrregColor = ivsColor;
loIrregColor &= sideBoxLo[idir];
hiIrregColor &= sideBoxHi[idir];
m_vofItIrregColorDomLo[icolor][idir][dit()].define(loIrregColor,curEBISBox.getEBGraph());
m_vofItIrregColorDomHi[icolor][idir][dit()].define(hiIrregColor,curEBISBox.getEBGraph());
}
VoFIterator& vofitcolor = m_vofItIrregColor[icolor][dit()];
for (vofitcolor.reset(); vofitcolor.ok(); ++vofitcolor)
{
const VolIndex& vof = vofitcolor();
VoFStencil& curStencil = curStencilBaseIVFAB(vof,0);
VoFStencil& colorStencil = colorStencilBaseIVFAB(vof,0);
VoFStencil& rhsColorStencil = rhsColorStencilBaseIVFAB(vof,0);
Real weightIrreg = m_alpha*curAlphaWeight(vof,0) + m_beta*curBetaWeight(vof,0);
colorStencil = curStencil;
colorStencil *= (-1.0/weightIrreg);
colorStencil.add(vof, 1.0);
rhsColorStencil.add(vof, 1.0/weightIrreg);
}
Vector<VolIndex> srcVofs = m_vofItIrregColor[icolor][dit()].getVector();
//color ebstencils
m_colorEBStencil[icolor][dit()] = RefCountedPtr<EBStencil>(new EBStencil(srcVofs, colorStencil[dit()] , m_eblg.getDBL().get(dit()), m_eblg.getEBISL()[dit()], m_ghostCellsPhi, m_ghostCellsPhi));
m_rhsColorEBStencil[icolor][dit()] = RefCountedPtr<EBStencil>(new EBStencil(srcVofs, rhsColorStencil[dit()] , m_eblg.getDBL().get(dit()) , m_eblg.getEBISL()[dit()], m_ghostCellsRHS, m_ghostCellsPhi));
}//dit
}//color
CH_STOP(t2);
}
void ebamrieuler(const AMRParameters& a_params,
const ProblemDomain& a_coarsestDomain)
{
CH_TIMERS("ebamrins_driver");
CH_TIMER("define_ebamrnosubcycle_solver", t3);
CH_TIMER("init_ebamrnosubcycle_solver", t4);
CH_TIMER("run ebamrnosubcycle_solver", t5);
// read inputs
ParmParse pp;
int flowDir;
pp.get("flow_dir", flowDir);
Vector<int> nCells;
pp.getarr("n_cell", nCells,0,SpaceDim);
Real inflowVel;
pp.get("inflow_vel", inflowVel);
Real viscosity = 0.0;
pp.get("viscosity", viscosity);
int idoSlipWalls;
pp.get("do_slip_walls", idoSlipWalls);
bool doSlip = idoSlipWalls==1;
IntVect doSlipWallsLo = idoSlipWalls*IntVect::Unit;
IntVect doSlipWallsHi = idoSlipWalls*IntVect::Unit;
Vector<int> slipWallsLo,slipWallsHi;
if (doSlip)
{
pp.getarr("do_slip_walls_hi",slipWallsHi,0,SpaceDim);
pp.getarr("do_slip_walls_lo",slipWallsLo,0,SpaceDim);
for (int idir = 0; idir < SpaceDim; idir++)
{
doSlipWallsHi[idir] = slipWallsHi[idir];
doSlipWallsLo[idir] = slipWallsLo[idir];
}
}
int orderEBBC = 1;
pp.query("order_ebbc", orderEBBC);
bool doPoiseInflow = false;
pp.query("poiseuille_inflow", doPoiseInflow);
bool initPoiseData = false;
pp.query("poiseuille_init", initPoiseData);
if (initPoiseData)
pout() << "Doing Poiseuille initialization" << endl;
RefCountedPtr<PoiseuilleInflowBCValue> poiseBCValue;//make this BaseBCValue if also doing constant values
if (doPoiseInflow)
{
pout() << "Doing Poiseuille inflow" << endl;
RealVect centerPt, tubeAxis;
Real tubeRadius;
Vector<Real> centerPtVect, tubeAxisVect;
pp.get("poise_profile_radius", tubeRadius);
pp.getarr("poise_profile_center_pt", centerPtVect,0,SpaceDim);
pp.getarr("poise_profile_axis", tubeAxisVect,0,SpaceDim);
for (int idir = 0; idir < SpaceDim; idir++)
{
centerPt[idir] = centerPtVect[idir];
tubeAxis[idir] = tubeAxisVect[idir];
}
Real maxVelFactor;//= 1.5 for planar geometry, = 2.0 for cylindrical
pp.get("poise_maxvel_factor", maxVelFactor);
Real maxVel = maxVelFactor*inflowVel;
poiseBCValue = RefCountedPtr<PoiseuilleInflowBCValue>(new PoiseuilleInflowBCValue(centerPt,tubeAxis,tubeRadius,maxVel,flowDir));
}
bool doWomersleyInflow = false;
pp.query("womersley_inflow", doWomersleyInflow);
InflowOutflowIBCFactory ibc(flowDir,
inflowVel,
orderEBBC,
doSlipWallsHi,
doSlipWallsLo,
doPoiseInflow,
initPoiseData,
poiseBCValue,
doWomersleyInflow);
CH_START(t3);
EBAMRNoSubcycle kahuna(a_params, ibc, a_coarsestDomain, viscosity);
CH_STOP(t3);
CH_START(t4);
if (!pp.contains("restart_file"))
{
pout() << "starting fresh AMR run" << endl;
kahuna.setupForAMRRun();
}
else
{
std::string restart_file;
pp.get("restart_file",restart_file);
pout() << " restarting from file " << restart_file << endl;
kahuna.setupForRestart(restart_file);
}
CH_STOP(t4);
int maxStep;
pp.get("max_step", maxStep);
Real stopTime = 0.0;
pp.get("max_time",stopTime);
CH_START(t5);
Real fixedDt = 0.;
pp.query("fixed_dt", fixedDt);
if (fixedDt > 1.e-12)
{
kahuna.useFixedDt(fixedDt);
}
kahuna.run(stopTime, maxStep);
CH_STOP(t5);
}
void
EBMGAverage::average(LevelData<EBCellFAB>& a_coarData,
const LevelData<EBCellFAB>& a_fineData,
const Interval& a_variables)
{
CH_TIMERS("EBMGAverage::average");
CH_TIMER("layout_changed_coarsenable", t1);
CH_TIMER("layout_changed_not_coarsenable", t2);
CH_TIMER("not_layout_changed", t3);
CH_assert(a_fineData.ghostVect() == m_ghost);
//CH_assert(a_coarData.ghostVect() == m_ghost);
CH_assert(isDefined());
if (m_layoutChanged)
{
if (m_coarsenable)
{
CH_START(t1);
EBCellFactory ebcellfact(m_buffEBISL);
LevelData<EBCellFAB> coarsenedFineData(m_buffGrids, m_nComp, m_ghost, ebcellfact);
EBLevelDataOps::setVal(coarsenedFineData, 0.0);
for (DataIterator dit = m_fineGrids.dataIterator(); dit.ok(); ++dit)
{
averageFAB(coarsenedFineData[dit()],
m_buffGrids[dit()],
a_fineData[dit()],
dit(),
a_variables);
}
coarsenedFineData.copyTo(a_variables, a_coarData, a_variables, m_copier);
CH_STOP(t1);
}
else
{
CH_START(t2);
EBCellFactory ebcellfact(m_buffEBISL);
LevelData<EBCellFAB> refinedCoarseData(m_buffGrids, m_nComp, m_ghost, ebcellfact);
EBLevelDataOps::setVal(refinedCoarseData, 0.0);
a_fineData.copyTo(a_variables, refinedCoarseData, a_variables, m_copier);
for (DataIterator dit = m_coarGrids.dataIterator(); dit.ok(); ++dit)
{
averageFAB(a_coarData[dit()],
m_coarGrids[dit()],
refinedCoarseData[dit()],
dit(),
a_variables);
}
CH_STOP(t2);
}
}
else
{
CH_START(t3);
averageMG(a_coarData, a_fineData, a_variables);
CH_STOP(t3);
}
}