// -----------------------------------------------------------------------------
// Interpolate ghosts at CF interface using zeros on coarser grids.
// -----------------------------------------------------------------------------
void homogeneousCFInterp (LevelData<FArrayBox>& a_phif,
const RealVect& a_fineDx,
const RealVect& a_crseDx,
const CFRegion& a_cfRegion,
const IntVect& a_applyDirs)
{
CH_TIME("homogeneousCFInterp (full level)");
// Loop over grids, directions, and sides and call the worker function.
DataIterator dit = a_phif.dataIterator();
for (dit.begin(); dit.ok(); ++dit) {
if (a_phif[dit].box().isEmpty()) continue;
for (int dir = 0; dir < SpaceDim; ++dir) {
if (a_applyDirs[dir] == 0) continue;
SideIterator sit;
for (sit.begin(); sit.ok(); sit.next()) {
homogeneousCFInterp(a_phif,
dit(),
dir,
sit(),
a_fineDx[dir],
a_crseDx[dir],
a_cfRegion);
}
}
}
}
/// Set up initial conditions
void SWIBC::initializeBdry(LevelData<FArrayBox>& a_B)
{
const Real tmpVal = 0.0;
const Real tmpVal2 = 100;
for (DataIterator dit = a_B.dataIterator(); dit.ok(); ++dit)
{
// Storage for current grid
FArrayBox& B = a_B[dit()];
// Box of current grid
Box bBox = B.box();
bBox &= m_domain;
// Set up initial condition in this grid
FORT_LINELASTSETFAB(CHF_FRA1(B,4),
CHF_BOX(bBox),
CHF_CONST_REAL(tmpVal));
FORT_LINELASTSETFAB(CHF_FRA1(B,5),
CHF_BOX(bBox),
CHF_CONST_REAL(tmpVal));
FORT_LINELASTSETFAB(CHF_FRA1(B,6),
CHF_BOX(bBox),
CHF_CONST_REAL(tmpVal2));
}
}
// ---------------------------------------------------------
void
AMRNavierStokes::computeLapVel(LevelData<FArrayBox>& a_lapVel,
LevelData<FArrayBox>& a_vel,
const LevelData<FArrayBox>* a_crseVelPtr)
{
// set BC's
VelBCHolder velBC(m_physBCPtr->viscousVelFuncBC());
bool isHomogeneous = false;
m_velocityAMRPoissonOp.applyOp(a_lapVel, a_vel, a_crseVelPtr,
isHomogeneous, velBC);
// may need to extend lapVel to cover ghost cells as well
{
BCHolder viscBC = m_physBCPtr->viscousFuncBC();
const DisjointBoxLayout& grids = a_lapVel.getBoxes();
DataIterator dit = a_lapVel.dataIterator();
for (dit.reset(); dit.ok(); ++dit)
{
viscBC(a_lapVel[dit], grids[dit],
m_problem_domain, m_dx,
false); // not homogeneous
}
}
// finally, do exchange
a_lapVel.exchange(a_lapVel.interval());
}
void EBPoissonOp::
getJacobiRelaxCoeff(LevelData<EBCellFAB>& a_relaxCoeff)
{
// Diagonal weight for Jacobi on regular grid
Real weightBase = m_alpha;
for (int idir = 0; idir < SpaceDim; idir++)
{
weightBase += -2.0 * m_beta * m_invDx2[idir];
}
weightBase = 1.0 / weightBase; // Weight for plain (non-weighted) Jacobi
Real weightRegular = EBPOISSONOP_JACOBI_OMEGA * weightBase; // ... for weighted Jacobi
for (DataIterator dit = m_eblg.getDBL().dataIterator(); dit.ok(); ++dit)
{
// Most of the grid is regular, so set the regular weighting by default
a_relaxCoeff[dit()].setVal(weightRegular);
// Walk the EB cells, and correct their weighting
const BaseIVFAB<Real>& curAlphaWeight = m_alphaDiagWeight[dit()];
const BaseIVFAB<Real>& curBetaWeight = m_betaDiagWeight[dit()];
VoFIterator& ebvofit = m_vofItIrreg[dit()];
for (ebvofit.reset(); ebvofit.ok(); ++ebvofit)
{
const VolIndex& vof = ebvofit();
Real weightIrreg = EBPOISSONOP_JACOBI_OMEGA / (m_alpha*curAlphaWeight(vof, 0) + m_beta*curBetaWeight(vof, 0));
a_relaxCoeff[dit()](vof, 0) = weightIrreg;
}
}
}
// ---------------------------------------------------------
void
AMRNavierStokes::computeLapScal(LevelData<FArrayBox>& a_lapScal,
LevelData<FArrayBox>& a_scal,
const BCHolder& a_physBC,
const LevelData<FArrayBox>* a_crseScalPtr)
{
m_scalarsAMRPoissonOp.setBC(a_physBC);
bool isHomogeneous = false;
if (a_crseScalPtr != NULL)
{
m_scalarsAMRPoissonOp.AMROperatorNF(a_lapScal, a_scal, *a_crseScalPtr,
isHomogeneous);
}
else
{
m_scalarsAMRPoissonOp.applyOpI(a_lapScal, a_scal,
isHomogeneous);
}
BCHolder viscBC = m_physBCPtr->viscousFuncBC();
DataIterator dit = a_lapScal.dataIterator();
const DisjointBoxLayout& grids = a_lapScal.getBoxes();
for (dit.reset(); dit.ok(); ++dit)
{
viscBC(a_lapScal[dit],
grids[dit],
m_problem_domain, m_dx,
false); // not homogeneous
}
// finally, do exchange
a_lapScal.exchange(a_lapScal.interval());
}
int scopingTest()
{
Vector<Box> boxes;
int retflag = 0;
setGrids(boxes);
LevelData<FArrayBox> levelFab;
makeLevelData(boxes, levelFab);
const DisjointBoxLayout& dbl = levelFab.getBoxes();
DataIterator dit = dbl.dataIterator();
int ivec = 0;
for (dit.begin(); dit.ok(); ++dit)
{
if (!dbl.check(dit()))
{
if (verbose)
pout() << indent2 << pgmname
<< ": failed at box " << ivec << endl;
retflag = 1;
}
else
{
levelFab[dit].setVal(0.);
}
if (retflag > 0) break;
ivec++;
}
return retflag;
}
void
initData(LevelData<FArrayBox>& a_data, const Real a_dx)
{
DataIterator dit = a_data.dataIterator();
const DisjointBoxLayout& interiorBoxes = a_data.getBoxes();
for (dit.begin(); dit.ok(); ++dit)
{
// first set to a bogus value which will persist in ghost cells
// after initialization
a_data[dit()].setVal(1.0e9);
// this will be slow, but who cares?
FArrayBox& localData = a_data[dit()];
BoxIterator boxIt(interiorBoxes[dit()]);
Real localVal;
for (boxIt.begin(); boxIt.ok(); ++boxIt)
{
const IntVect& loc = boxIt();
for (int comp=0; comp<localData.nComp(); comp++)
{
localVal = dataVal(loc, comp);
localData(loc, comp) = localVal;
}
}
}
}
void
NoFlowVortex::
initializeVelocity(LevelData<EBCellFAB>& a_velocity,
const DisjointBoxLayout& a_grids,
const EBISLayout& a_ebisl,
const ProblemDomain& a_domain,
const RealVect& a_origin,
const Real& a_time,
const RealVect& a_dx) const
{
Real pi = 4.0*atan(1.0);
for (DataIterator dit = a_grids.dataIterator(); dit.ok(); ++dit)
{
IntVectSet ivsBox(a_grids.get(dit()));
for (VoFIterator vofit(ivsBox, a_ebisl[dit()].getEBGraph()); vofit.ok(); ++vofit)
{
RealVect xval, velpt;
getXVal(xval, a_origin,vofit(), a_dx);
getVelPt(velpt, xval, pi);
for (int idir = 0; idir < SpaceDim; idir++)
{
a_velocity[dit()](vofit(), idir) = velpt[idir];
}
}
}
}
void LevelPluto::setGridLevel()
{
CH_TIME("LevelPluto::setGrid");
m_structs_grid.define(m_grids);
#if GEOMETRY != CARTESIAN
m_dV.define(m_grids,CHOMBO_NDV,m_numGhost*IntVect::Unit);
#endif
Real dlMinLoc = 1.e30;
for (DataIterator dit = m_grids.dataIterator(); dit.ok(); ++dit)
{
// The current box
Box curBox = m_grids.get(dit());
struct GRID* grid = m_structs_grid[dit].getGrid();
#if GEOMETRY != CARTESIAN
FArrayBox& curdV = m_dV[dit()];
#else
FArrayBox curdV;
#endif
m_patchPluto->setGrid(curBox, grid, curdV);
for (int idir = 0; idir < SpaceDim; idir++) dlMinLoc = Min(dlMinLoc,grid[idir].dl_min);
}
#if (GEOMETRY == CARTESIAN) || (GEOMETRY == CYLINDRICAL)
D_EXPAND(m_dl_min = m_dx; ,
// ---------------------------------------------------------
void levelDivergenceMAC(LevelData<FArrayBox>& a_div,
const LevelData<FluxBox>& a_uEdge,
const Real a_dx)
{
// silly way to do this until i figure out a better
// way to make this dimensionally-independent
CH_assert (a_uEdge.nComp() >= a_div.nComp());
DataIterator dit = a_div.dataIterator();
for (dit.reset(); dit.ok(); ++dit)
{
a_div[dit()].setVal(0.0);
const FluxBox& thisFluxBox = a_uEdge[dit()];
Box cellBox(thisFluxBox.box());
// just to be sure we don't accidentally trash memory...
cellBox &= a_div[dit()].box();
// now loop over coordinate directions and add to divergence
for (int dir=0; dir<SpaceDim; dir++)
{
const FArrayBox& uEdgeDir = thisFluxBox[dir];
FORT_DIVERGENCE(CHF_CONST_FRA(uEdgeDir),
CHF_FRA(a_div[dit()]),
CHF_BOX(cellBox),
CHF_CONST_REAL(a_dx),
CHF_INT(dir));
}
}
}
void
EBLevelAdvect::
computeNormalVel(LevelData<EBCellFAB>& a_normalVel,
const LevelData<EBFluxFAB>& a_advectionVel,
const LayoutData<Vector<BaseIVFAB<Real> * > >& a_coveredVeloLo,
const LayoutData<Vector<BaseIVFAB<Real> * > >& a_coveredVeloHi,
const LayoutData<Vector<Vector<VolIndex> > >& a_coveredFaceLo,
const LayoutData<Vector<Vector<VolIndex> > >& a_coveredFaceHi) const
{
CH_TIME("EBLevelAdvect::computeNormalVel");
for (DataIterator dit = m_thisGrids.dataIterator(); dit.ok(); ++dit)
{
const Box& cellBox = m_thisGrids.get(dit());
Box grownBox = grow(cellBox, 1);
grownBox &= m_domain;
m_ebPatchAdvect[dit]->averageVelToCC(a_normalVel[dit()],
a_advectionVel[dit()],
a_coveredVeloLo[dit()],
a_coveredVeloHi[dit()],
a_coveredFaceLo[dit()],
a_coveredFaceHi[dit()],
grownBox);
}
}
//-----------------------------------------------------------------------
// AMR Factory define function, with coefficient data allocated automagically
// for operators.
void
VCAMRPoissonOp2Factory::
define(const ProblemDomain& a_coarseDomain,
const Vector<DisjointBoxLayout>& a_grids,
const Vector<int>& a_refRatios,
const Real& a_coarsedx,
BCHolder a_bc,
const IntVect& a_ghostVect)
{
// This just allocates coefficient data, sets alpha = beta = 1, and calls
// the other define() method.
Vector<RefCountedPtr<LevelData<FArrayBox> > > aCoef(a_grids.size());
Vector<RefCountedPtr<LevelData<FluxBox> > > bCoef(a_grids.size());
for (int i = 0; i < a_grids.size(); ++i)
{
aCoef[i] = RefCountedPtr<LevelData<FArrayBox> >(
new LevelData<FArrayBox>(a_grids[i], 1, a_ghostVect));
bCoef[i] = RefCountedPtr<LevelData<FluxBox> >(
new LevelData<FluxBox>(a_grids[i], 1, a_ghostVect));
// Initialize the a and b coefficients to 1 for starters.
for (DataIterator dit = aCoef[i]->dataIterator(); dit.ok(); ++dit)
{
(*aCoef[i])[dit()].setVal(1.0);
for (int idir = 0; idir < SpaceDim; ++idir)
(*bCoef[i])[dit()][idir].setVal(1.0);
}
}
Real alpha = 1.0, beta = 1.0;
define(a_coarseDomain, a_grids, a_refRatios, a_coarsedx, a_bc,
alpha, aCoef, beta, bCoef);
}
// ---------------------------------------------------------
// 27 March 2003:
// This is called by other functions, and should not be called directly.
Real
maxnorm(const BoxLayoutData<NodeFArrayBox>& a_layout,
const Interval& a_interval,
bool a_verbose)
{
Real normTotal = 0.;
// a_p == 0: max norm
for (DataIterator it = a_layout.dataIterator(); it.ok(); ++it)
{
const Box& thisBox(a_layout.box(it())); // CELL-centered
const NodeFArrayBox& thisNfab = a_layout[it()];
Real thisNfabNorm =
maxnorm(thisNfab, thisBox, a_interval.begin(), a_interval.size());
if (a_verbose)
cout << "maxnorm(" << thisBox << ") = " << thisNfabNorm << endl;
normTotal = Max(normTotal, thisNfabNorm);
}
# ifdef CH_MPI
Real recv;
int result = MPI_Allreduce(&normTotal, &recv, 1, MPI_CH_REAL,
MPI_MAX, Chombo_MPI::comm);
if (result != MPI_SUCCESS)
{ //bark!!!
MayDay::Error("sorry, but I had a communication error on maxnorm");
}
normTotal = recv;
# endif
return normTotal;
}
// this preconditioner first initializes phihat to (IA)phihat = rhshat
// (diagonization of L -- A is the matrix version of L)
// then smooths with a couple of passes of levelGSRB
void VCAMRPoissonOp2::preCond(LevelData<FArrayBox>& a_phi,
const LevelData<FArrayBox>& a_rhs)
{
CH_TIME("VCAMRPoissonOp2::preCond");
// diagonal term of this operator in:
//
// alpha * a(i)
// + beta * sum_over_dir (b(i-1/2*e_dir) + b(i+1/2*e_dir)) / (dx*dx)
//
// The inverse of this is our initial multiplier.
int ncomp = a_phi.nComp();
CH_assert(m_lambda.isDefined());
CH_assert(a_rhs.nComp() == ncomp);
CH_assert(m_bCoef->nComp() == ncomp);
// Recompute the relaxation coefficient if needed.
resetLambda();
// don't need to use a Copier -- plain copy will do
DataIterator dit = a_phi.dataIterator();
for (dit.begin(); dit.ok(); ++dit)
{
// also need to average and sum face-centered bCoefs to cell-centers
Box gridBox = a_rhs[dit].box();
// approximate inverse
a_phi[dit].copy(a_rhs[dit]);
a_phi[dit].mult(m_lambda[dit], gridBox, 0, 0, ncomp);
}
relax(a_phi, a_rhs, 2);
}
// -----------------------------------------------------------------------------
// Semi-implicitly handles the gravity forcing and projection.
// The old* inputs should be the values at t^n.
// The new* inputs should be the updated values from the TGA solver.
// -----------------------------------------------------------------------------
void AMRNavierStokes::doCCIGProjection (LevelData<FArrayBox>& a_newVel,
LevelData<FArrayBox>& a_newB,
const LevelData<FArrayBox>& a_oldVel,
const LevelData<FArrayBox>& a_oldB,
const LevelData<FluxBox>& a_advVel,
const Real a_oldTime,
const Real a_dt,
const bool a_doProj)
{
CH_TIME("AMRNavierStokes::doCCIGProjection");
const Real halfTime = a_oldTime + 0.5 * a_dt;
const Real newTime = a_oldTime + 1.0 * a_dt;
const Real dummyTime = -1.0e300;
const GeoSourceInterface& geoSource = *(m_levGeoPtr->getGeoSourcePtr());
const RealVect& dx = m_levGeoPtr->getDx();
const DisjointBoxLayout& grids = a_newVel.getBoxes();
DataIterator dit = grids.dataIterator();
// 1. Compute the background buoyancy, N, Dinv, etc...
// Fill the FC background buoyancy field.
LevelData<FluxBox> bbar(grids, 1, 2*IntVect::Unit);
for (dit.reset(); dit.ok(); ++dit) {
FluxBox& bbarFB = bbar[dit];
D_TERM(m_physBCPtr->setBackgroundScalar(bbarFB[0], 0, *m_levGeoPtr, dit(), dummyTime);,
m_physBCPtr->setBackgroundScalar(bbarFB[1], 0, *m_levGeoPtr, dit(), dummyTime);,
void
EBCoarToFineRedist::
defineDataHolders()
{
CH_TIME("EBCoarToFineRedist::defineDataHolders");
//make mass buffers
BaseIVFactory<Real> factCoar(m_ebislCoar, m_setsCoar);
IntVect noghost = IntVect::Zero;
m_regsCoar.define(m_gridsCoar, m_nComp, noghost, factCoar);
BaseIVFactory<Real> factCedFine(m_ebislCedFine, m_setsCedFine);
m_regsCedFine.define(m_gridsCedFine, m_nComp, m_redistRad*IntVect::Unit, factCedFine);
EBCellFactory ebcellfact(m_ebislCedFine);
m_densityCedFine.define(m_gridsCedFine, 1, 2*m_redistRad*IntVect::Unit, ebcellfact);
//define the stencils with volume weights.
//if you want mass weights or whatever, use reset weights
m_stenCedFine.define(m_gridsCedFine);
m_volumeStenc.define(m_gridsCedFine);
m_standardStenc.define(m_gridsCedFine);
RedistStencil stenCedFine(m_gridsCedFine, m_ebislCedFine,
m_domainCoar, m_redistRad);
for (DataIterator ditCedF = m_gridsCedFine.dataIterator();
ditCedF.ok(); ++ditCedF)
{
BaseIVFAB<VoFStencil>& stenFAB = m_stenCedFine[ditCedF()];
BaseIVFAB<VoFStencil>& volStenFAB = m_volumeStenc[ditCedF()];
BaseIVFAB<VoFStencil>& stanStenFAB = m_standardStenc[ditCedF()];
const EBISBox& ebisBox = m_ebislCedFine[ditCedF()];
const IntVectSet& ivs = m_setsCedFine[ditCedF()];
const BaseIVFAB<VoFStencil>& rdStenFAB = stenCedFine[ditCedF()];
const Box& gridCedFine = m_gridsCedFine.get(ditCedF());
stenFAB.define(ivs, ebisBox.getEBGraph(), 1);
volStenFAB.define(ivs, ebisBox.getEBGraph(), 1);
stanStenFAB.define(ivs, ebisBox.getEBGraph(), 1);
for (VoFIterator vofit(ivs, ebisBox.getEBGraph()); vofit.ok(); ++vofit)
{
const VolIndex& srcVoF = vofit();
VoFStencil newStencil;
const VoFStencil& stanSten = rdStenFAB(srcVoF, 0);
for (int istan = 0; istan < stanSten.size(); istan++)
{
const VolIndex& dstVoF = stanSten.vof(istan);
const Real& weight = stanSten.weight(istan);
if (gridCedFine.contains(dstVoF.gridIndex()))
{
newStencil.add(dstVoF, weight);
}
}
stenFAB(srcVoF, 0) = newStencil;
//need to keep these around to get mass redist right
volStenFAB(srcVoF, 0) = newStencil;
stanStenFAB(srcVoF,0) = stanSten;
}
}
}
// ---------------------------------------------------------
// 28 March 2003:
// This is called by other functions, and should not be called directly.
Real
integral(const BoxLayoutData<NodeFArrayBox>& a_layout,
const Real a_dx,
const Interval& a_interval,
bool a_verbose)
{
Real integralTotal = 0.;
for (DataIterator it = a_layout.dataIterator(); it.ok(); ++it)
{
const NodeFArrayBox& thisNfab = a_layout[it()];
const Box& thisBox(a_layout.box(it())); // CELL-centered
Real thisNfabIntegral =
integral(thisNfab, a_dx, thisBox,
a_interval.begin(), a_interval.size());
integralTotal += thisNfabIntegral;
}
# ifdef CH_MPI
Real recv;
// add up
int result = MPI_Allreduce(&integralTotal, &recv, 1, MPI_CH_REAL,
MPI_SUM, Chombo_MPI::comm);
if (result != MPI_SUCCESS)
{ //bark!!!
MayDay::Error("sorry, but I had a communication error on integral");
}
integralTotal = recv;
# endif
return integralTotal;
}
void
PoisselleTube::
initializeVelocity(LevelData<EBCellFAB>& a_velocity,
const DisjointBoxLayout& a_grids,
const EBISLayout& a_ebisl,
const ProblemDomain& a_domain,
const RealVect& a_origin,
const Real& a_time,
const RealVect& a_dx) const
{
for (DataIterator dit = a_grids.dataIterator(); dit.ok(); ++dit)
{
IntVectSet ivsBox(a_grids.get(dit()));
for (VoFIterator vofit(ivsBox, a_ebisl[dit()].getEBGraph()); vofit.ok(); ++vofit)
{
RealVect xval = EBArith::getVofLocation(vofit() , a_dx, RealVect::Zero);
for (int idir = 0; idir < SpaceDim; idir++)
{
//bogus values for normal and time because they do not matter
Real velComp = m_bcval[idir].value(xval, RealVect::Zero, a_time, idir);
a_velocity[dit()](vofit(), idir) = velComp;
}
}
}
}
// ---------------------------------------------------------
void
NodeQCFI::coarseFineInterp(LevelData<NodeFArrayBox>& a_phiFine,
const LevelData<NodeFArrayBox>& a_phiCoarse,
bool a_inhomogeneous)
{
CH_assert(isDefined());
CH_assert(a_phiFine.nComp() == m_ncomp);
CH_assert(a_phiCoarse.nComp() == m_ncomp);
if (m_coarsenings == 1)
{
m_qcfi2[0]->coarseFineInterp(a_phiFine, a_phiCoarse);
}
else // m_coarsenings >= 2
{
// if m_coarsenings == 2:
// m_qcfi2[1] = new NodeQuadCFInterp2(a_grids, true);
// m_qcfi2[0] = new NodeQuadCFInterp2(a_grids.coarsen(2), false);
// m_inter[0] = new LevelData(a_grids.coarsen(2));
// m_qcfi2[0] interpolates m_inter[0] from a_phiCoarse on all of it.
// m_qcfi2[1] interpolates a_phiFine from m_inter[0] on interface only.
m_qcfi2[0]->coarseFineInterp(*m_inter[0], a_phiCoarse);
m_inter[0]->exchange(m_inter[0]->interval());
// Set domain and dx for coarsest level refined by 2.
ProblemDomain domain(m_domainPenultimate);
Real dx = m_dxPenultimate;
bool homogeneous = !a_inhomogeneous;
const DisjointBoxLayout& dbl0 = m_inter[0]->disjointBoxLayout();
for (DataIterator dit = dbl0.dataIterator(); dit.ok(); ++dit)
{
m_bc((*m_inter[0])[dit()], dbl0.get(dit()), domain, dx, homogeneous);
}
for (int interlev = 1; interlev < m_coarsenings - 1; interlev++)
{
m_qcfi2[interlev]->coarseFineInterp(*m_inter[interlev],
*m_inter[interlev-1]);
m_inter[interlev]->exchange(m_inter[interlev]->interval());
domain.refine(2);
dx *= 0.5;
const DisjointBoxLayout& dbl = m_inter[interlev]->disjointBoxLayout();
for (DataIterator dit = dbl.dataIterator(); dit.ok(); ++dit)
{
m_bc((*m_inter[interlev])[dit()], dbl.get(dit()), domain, dx, homogeneous);
}
}
m_qcfi2[m_coarsenings-1]->coarseFineInterp(a_phiFine,
*m_inter[m_coarsenings-2]);
// Don't need to set boundary conditions for a_phiFine
// because the calling function will do that.
}
}
void
EBCompositeCCProjector::
averageVelocityToFaces(Vector<LevelData<EBFluxFAB>* >& a_macVeloc,
Vector<LevelData<EBCellFAB>* >& a_velocity)
{
CH_TIME("EBCompositeCCProjector::averageVelocityToFaces");
//interpolate and then send stuff on through to level function
// int ncomp = a_velocity[0]->nComp();
Interval interv(0, SpaceDim-1);
Vector<LevelData<EBCellFAB> *> amrPhi = m_macProjector->getPhi();
// Real time = 0.;
for (int ilev = 0; ilev < m_numLevels; ilev++)
{
if (ilev > 0)
{
//so it can be reused quadcfi is a one-variable animal
//when we have ebalias, we can accomplish this without copies.
//for now, tough luck
//use phi for scratch space
LevelData<EBCellFAB>& phiCoar = *amrPhi[ilev-1];
LevelData<EBCellFAB>& phiFine = *amrPhi[ilev ];
for (int idir = 0; idir < SpaceDim; idir++)
{
Interval phiInterv(0, 0);
Interval velInterv(idir, idir);
a_velocity[ilev-1]->copyTo(velInterv, phiCoar, phiInterv);
a_velocity[ilev ]->copyTo(velInterv, phiFine, phiInterv);
m_quadCFI[ilev]->interpolate(phiFine,
phiCoar,
phiInterv);
// m_pwlCFI[ilev]->interpolate(phiFine,
// phiCoar,
// phiCoar,
// time,
// time,
// time,
// phiInterv);
//on copy back, we need ghost cells, so do the data iterator loop
for (DataIterator dit = phiFine.dataIterator(); dit.ok(); ++dit)
{
Box region = phiFine[dit()].getRegion(); //includes ghost cells
(*a_velocity[ilev])[dit()].copy(region, velInterv, region, phiFine[dit()], phiInterv);
}
EBLevelDataOps::setVal(phiFine, 0.0);
EBLevelDataOps::setVal(phiCoar, 0.0);
}
}
a_velocity[ilev]->exchange(interv);
ccpAverageVelocityToFaces(*a_macVeloc[ilev],
*a_velocity[ilev],
m_eblg[ilev].getDBL(),
m_eblg[ilev].getEBISL(),
m_eblg[ilev].getDomain(),
m_dx[ilev],
*m_eblg[ilev].getCFIVS());
}
}
void VCAMRPoissonOp2::residualI(LevelData<FArrayBox>& a_lhs,
const LevelData<FArrayBox>& a_phi,
const LevelData<FArrayBox>& a_rhs,
bool a_homogeneous)
{
CH_TIME("VCAMRPoissonOp2::residualI");
LevelData<FArrayBox>& phi = (LevelData<FArrayBox>&)a_phi;
Real dx = m_dx;
const DisjointBoxLayout& dbl = a_lhs.disjointBoxLayout();
DataIterator dit = phi.dataIterator();
{
CH_TIME("VCAMRPoissonOp2::residualIBC");
for (dit.begin(); dit.ok(); ++dit)
{
m_bc(phi[dit], dbl[dit()],m_domain, dx, a_homogeneous);
}
}
phi.exchange(phi.interval(), m_exchangeCopier);
for (dit.begin(); dit.ok(); ++dit)
{
const Box& region = dbl[dit()];
const FluxBox& thisBCoef = (*m_bCoef)[dit];
#if CH_SPACEDIM == 1
FORT_VCCOMPUTERES1D
#elif CH_SPACEDIM == 2
FORT_VCCOMPUTERES2D
#elif CH_SPACEDIM == 3
FORT_VCCOMPUTERES3D
#else
This_will_not_compile!
#endif
(CHF_FRA(a_lhs[dit]),
CHF_CONST_FRA(phi[dit]),
CHF_CONST_FRA(a_rhs[dit]),
CHF_CONST_REAL(m_alpha),
CHF_CONST_FRA((*m_aCoef)[dit]),
CHF_CONST_REAL(m_beta),
#if CH_SPACEDIM >= 1
CHF_CONST_FRA(thisBCoef[0]),
#endif
#if CH_SPACEDIM >= 2
CHF_CONST_FRA(thisBCoef[1]),
#endif
#if CH_SPACEDIM >= 3
CHF_CONST_FRA(thisBCoef[2]),
#endif
#if CH_SPACEDIM >= 4
This_will_not_compile!
#endif
CHF_BOX(region),
CHF_CONST_REAL(m_dx));
} // end loop over boxes
}
void
EBCoarseAverage::average(LevelData<EBFluxFAB>& a_coarData,
const LevelData<EBFluxFAB>& a_fineData,
const Interval& a_variables)
{
CH_TIME("EBCoarseAverage::average(LD<EBFluxFAB>)");
LevelData<EBFluxFAB> coarFiData;
LevelData<EBFluxFAB> fineBuffer;
CH_assert(isDefined());
{
CH_TIME("buffer allocation");
EBFluxFactory factCoFi(m_eblgCoFi.getEBISL());
coarFiData.define( m_eblgCoFi.getDBL(), m_nComp, IntVect::Zero, factCoFi);
if (m_useFineBuffer)
{
EBFluxFactory factFine(m_eblgFine.getEBISL());
fineBuffer.define(m_eblgFine.getDBL(), m_nComp, IntVect::Zero, factFine);
}
}
if (m_useFineBuffer)
{
CH_TIME("fine_copy");
a_fineData.copyTo(a_variables, fineBuffer, a_variables);
}
{
CH_TIME("averaging");
for (DataIterator dit = m_eblgFine.getDBL().dataIterator(); dit.ok(); ++dit)
{
const EBFluxFAB* fineFABPtr = NULL;
if (m_useFineBuffer)
{
fineFABPtr = &fineBuffer[dit()];
}
else
{
fineFABPtr = &a_fineData[dit()];
}
EBFluxFAB& cofiFAB = coarFiData[dit()];
const EBFluxFAB& fineFAB = *fineFABPtr;
for (int idir = 0; idir < SpaceDim; idir++)
{
averageFAB(cofiFAB[idir],
fineFAB[idir],
dit(),
a_variables,
idir);
}
}
}
{
CH_TIME("copy_coar");
coarFiData.copyTo(a_variables, a_coarData, a_variables);
}
}
int
EBCompositeMACProjector::
project(Vector<LevelData<EBFluxFAB>* >& a_velocity,
Vector<LevelData<EBFluxFAB>* >& a_gradient,
const Real& a_gradCoef,
const Real& a_divuCoef,
const Vector<LevelData<BaseIVFAB<Real> >* >* a_boundaryVelo)
{
CH_TIME("EBCompositeMACProjector::project");
//compute divergence everywhere. This includes refluxing at coarse-fine boundaries
kappaDivergence(m_divu, a_velocity, a_boundaryVelo);
EBAMRDataOps::scale(m_divu,a_divuCoef);
//make an initial guess
initialize(m_phi);
//solve laplacian phi = div u
//zeroPhi=false is inconsequential in solveNoInit because of initialize above
bool zeroPhi = false;
m_solver.solveNoInit(m_phi, m_divu, m_numLevels-1, 0, zeroPhi);
//compute grad phi. This includes replacing coarse grad phi
//with average of fine at coarse-fine boundaries
gradient(a_gradient, m_phi);
enforceGradientBC(a_gradient,m_phi);
EBAMRDataOps::scale(a_gradient,a_gradCoef);
//average the gradient down to coarser levels
EBAMRDataOps::averageDown(a_gradient,m_eblg,m_refRat);
if (m_subtractOffMean)
{
//Subtract off mean of pressure so that convergence tests can make sense.
//This is also useful if you are using initial guesses for m_phi with all Neumann bcs
EBAMRDataOps::subtractOffMean(m_phi, m_eblg, m_refRat);
}
//u := u - grad phi
for (int ilev = 0; ilev < m_numLevels; ilev++)
{
for (DataIterator dit = m_eblg[ilev].getDBL().dataIterator(); dit.ok(); ++dit)
{
for (int idir = 0; idir < SpaceDim; idir++)
{
EBFaceFAB& velFAB = (*a_velocity[ilev])[dit()][idir];
const EBFaceFAB& gradFAB = (*a_gradient[ilev])[dit()][idir];
velFAB -= gradFAB;
}
}
}
return m_solver.m_exitStatus;
}
// ----------------------------------------------------------------
void EdgeToCell(const LevelData<FluxBox>& a_edgeData,
LevelData<FArrayBox>& a_cellData)
{
// this is just a wrapper around the single-grid version
DataIterator dit = a_edgeData.dataIterator();
for (dit.reset(); dit.ok(); ++dit)
{
EdgeToCell(a_edgeData[dit()], a_cellData[dit()]);
}
}
void
EBCoarseAverage::average(LevelData<BaseIVFAB<Real> >& a_coarData,
const LevelData<BaseIVFAB<Real> >& a_fineData,
const Interval& a_variables)
{
CH_TIME("EBCoarseAverage::average(LD<BaseIVFAB>)");
LevelData<BaseIVFAB<Real> > coarFiData;
LevelData<BaseIVFAB<Real> > fineBuffer;
CH_assert(isDefined());
{
CH_TIME("buffer allocation");
BaseIVFactory<Real> factCoFi(m_eblgCoFi.getEBISL(), m_irregSetsCoFi);
coarFiData.define(m_eblgCoFi.getDBL(), m_nComp, IntVect::Zero, factCoFi);
if (m_useFineBuffer)
{
BaseIVFactory<Real> factFine(m_eblgFine.getEBISL(), m_irregSetsFine);
coarFiData.define(m_eblgFine.getDBL(), m_nComp, IntVect::Zero, factFine);
}
}
if (m_useFineBuffer)
{
CH_TIME("fine_copy");
a_fineData.copyTo(a_variables, fineBuffer, a_variables);
}
{
CH_TIME("averaging");
int ifnerg = 0;
for (DataIterator dit = m_eblgFine.getDBL().dataIterator(); dit.ok(); ++dit)
{
const BaseIVFAB<Real>* fineFABPtr = NULL;
if (m_useFineBuffer)
{
fineFABPtr = &fineBuffer[dit()];
}
else
{
fineFABPtr = &a_fineData[dit()];
}
BaseIVFAB<Real>& cofiFAB = coarFiData[dit()];
const BaseIVFAB<Real>& fineFAB = *fineFABPtr;
averageFAB(cofiFAB,
fineFAB,
dit(),
a_variables);
ifnerg++;
}
}
{
CH_TIME("copy_coar");
coarFiData.copyTo(a_variables, a_coarData, a_variables);
}
}
// Set up data on this level after regridding
void AMRLevelPluto::regrid(const Vector<Box>& a_newGrids)
{
CH_assert(allDefined());
if (s_verbosity >= 3)
{
pout() << "AMRLevelPluto::regrid " << m_level << endl;
}
// Save original grids and load balance
m_level_grids = a_newGrids;
m_grids = loadBalance(a_newGrids);
if (s_verbosity >= 4)
{
// Indicate/guarantee that the indexing below is only for reading
// otherwise an error/assertion failure occurs
const DisjointBoxLayout& constGrids = m_grids;
pout() << "new grids: " << endl;
for (LayoutIterator lit = constGrids.layoutIterator(); lit.ok(); ++lit)
{
pout() << constGrids[lit()] << endl;
}
}
// Save data for later
DataIterator dit = m_UNew.dataIterator();
for(;dit.ok(); ++dit){
m_UOld[dit()].copy(m_UNew[dit()]);
}
// Reshape state with new grids
IntVect ivGhost = m_numGhost*IntVect::Unit;
m_UNew.define(m_grids,m_numStates,ivGhost);
// Set up data structures
levelSetup();
// Interpolate from coarser level
if (m_hasCoarser)
{
AMRLevelPluto* amrGodCoarserPtr = getCoarserLevel();
m_fineInterp.interpToFine(m_UNew,amrGodCoarserPtr->m_UNew);
}
// Copy from old state
m_UOld.copyTo(m_UOld.interval(),
m_UNew,
m_UNew.interval());
m_UOld.define(m_grids,m_numStates,ivGhost);
}
void
EBCoarToFineRedist::
resetWeights(const LevelData<EBCellFAB>& a_modifierCoar,
const int& a_ivar)
{
CH_TIME("EBCoarToFineRedist::resetWeights");
Interval srcInterv(a_ivar, a_ivar);
Interval dstInterv(0,0);
a_modifierCoar.copyTo(srcInterv, m_densityCedFine, dstInterv);
//set the weights to mass weighting if the modifier
//is the fine density.
for (DataIterator dit = m_gridsFine.dataIterator(); dit.ok(); ++dit)
{
const IntVectSet& coarSet = m_setsCedFine[dit()];
BaseIVFAB<VoFStencil>& massStenFAB = m_stenCedFine[dit()];
const BaseIVFAB<VoFStencil>& volStenFAB = m_volumeStenc[dit()];
const BaseIVFAB<VoFStencil>& stanStenFAB = m_standardStenc[dit()];
const EBISBox& ebisBoxCoar = m_ebislCedFine[dit()];
const EBCellFAB& modFAB = m_densityCedFine[dit()];
for (VoFIterator vofit(coarSet, ebisBoxCoar.getEBGraph()); vofit.ok(); ++vofit)
{
const VolIndex& vofCoar = vofit();
const VoFStencil& stanSten = stanStenFAB(vofCoar, 0);
const VoFStencil& volSten = volStenFAB(vofCoar, 0);
VoFStencil newSten;
for (int isten = 0; isten < volSten.size(); isten++)
{
const VolIndex& thatVoFCoar = volSten.vof(isten);
Real weight = modFAB(thatVoFCoar, 0);
//average fine weights onto coarse weight
newSten.add(thatVoFCoar, weight);
}
//need normalize by the whole standard stencil
Real sum = 0.0;
for (int isten = 0; isten < stanSten.size(); isten++)
{
const VolIndex& thatVoFCoar = stanSten.vof(isten);
Real weight = modFAB(thatVoFCoar, 0);
Real volfrac = ebisBoxCoar.volFrac(thatVoFCoar);
//it is weight*volfrac that is normalized
sum += weight*volfrac;
}
if (Abs(sum) > 0.0)
{
Real scaling = 1.0/sum;
newSten *= scaling;
}
massStenFAB(vofCoar, 0) = newSten;
}
}
}
// ---------------------------------------------------------
// 27 March 2003:
// This is called by other functions, and should not be called directly.
Real
norm(const BoxLayoutData<NodeFArrayBox>& a_layout,
const Real a_dx,
const int a_p,
const Interval& a_interval,
bool a_verbose)
{
if (a_p == 0)
return maxnorm(a_layout, a_interval, a_verbose);
Real normTotal = 0.;
for (DataIterator it = a_layout.dataIterator(); it.ok(); ++it)
{
const NodeFArrayBox& thisNfab = a_layout[it()];
const Box& thisBox(a_layout.box(it())); // CELL-centered
Real thisNfabNorm = norm(thisNfab, a_dx, thisBox, a_p,
a_interval.begin(), a_interval.size());
if (a_verbose)
cout << a_p << "norm(" << thisBox << ") = " << thisNfabNorm << endl;
if (a_p == 1)
{
normTotal += thisNfabNorm;
}
else if (a_p == 2)
{
normTotal += thisNfabNorm * thisNfabNorm;
}
else
{
normTotal += pow(thisNfabNorm, Real(a_p));
}
}
# ifdef CH_MPI
Real recv;
// add up (a_p is not 0)
int result = MPI_Allreduce(&normTotal, &recv, 1, MPI_CH_REAL,
MPI_SUM, Chombo_MPI::comm);
if (result != MPI_SUCCESS)
{ //bark!!!
MayDay::Error("sorry, but I had a communication error on norm");
}
normTotal = recv;
# endif
// now do sqrt, etc
if (a_p == 2)
normTotal = sqrt(normTotal);
else
if ((a_p != 0) && (a_p != 1))
normTotal = pow(normTotal, (Real)1.0/Real(a_p));
return normTotal;
}
void
EBMGInterp::pwlInterp(LevelData<EBCellFAB>& a_fineData,
const LevelData<EBCellFAB>& a_coarData,
const Interval& a_variables)
{
CH_TIME("EBMGInterp::pwlInterp");
CH_assert(a_fineData.ghostVect() == m_ghost);
CH_assert(a_coarData.ghostVect() == m_ghost);
CH_assert(m_doLinear); //otherwise stencils have not been defined
if (m_layoutChanged)
{
if (m_coarsenable)
{
CH_TIME("EBMGInterp::pwlInterp::coarsenable");
EBCellFactory ebcellfact(m_buffEBISL);
LevelData<EBCellFAB> coarsenedFineData(m_buffGrids, m_nComp, m_ghost, ebcellfact);
a_coarData.copyTo(a_variables, coarsenedFineData, a_variables);
fillGhostCellsPWC(coarsenedFineData, m_buffEBISL, m_coarDomain);
for (DataIterator dit = m_fineGrids.dataIterator(); dit.ok(); ++dit)
{
//does incrementonly = true
pwlInterpFAB(a_fineData[dit()],
m_buffGrids[dit()],
coarsenedFineData[dit()],
dit(),
a_variables);
}
}
else
{
CH_TIME("EBMGInterp::pwlInterp::uncoarsenable");
EBCellFactory ebcellfact(m_buffEBISL);
fillGhostCellsPWC((LevelData<EBCellFAB>&)a_coarData, m_coarEBISL, m_coarDomain);
LevelData<EBCellFAB> refinedCoarseData(m_buffGrids, m_nComp, m_ghost, ebcellfact);
for (DataIterator dit = m_coarGrids.dataIterator(); dit.ok(); ++dit)
{
refinedCoarseData[dit()].setVal(0.);
pwlInterpFAB(refinedCoarseData[dit()],
m_coarGrids[dit()],
a_coarData[dit()],
dit(),
a_variables);
}
EBAddOp op;
refinedCoarseData.copyTo(a_variables, a_fineData, a_variables, m_copierRCtoF, op);
}
}
else
{
pwcInterpMG(a_fineData, a_coarData, a_variables);
}
}
void
EBLevelAdvect::
resetBCs(const RefCountedPtr<EBPhysIBCFactory>& a_advectBC)
{
if (m_isDefined)
{
for (DataIterator dit = m_ebPatchAdvect.dataIterator(); dit.ok(); ++dit)
{
m_ebPatchAdvect[dit()]->setEBPhysIBC(*a_advectBC);
}
}
}