MultiFab*
Nyx::build_fine_mask()
{
BL_ASSERT(level > 0); // because we are building a mask for the coarser level
if (fine_mask != 0) return fine_mask;
BoxArray baf = parent->boxArray(level);
baf.coarsen(crse_ratio);
const BoxArray& bac = parent->boxArray(level-1);
fine_mask = new MultiFab(bac,parent->DistributionMap(level-1), 1,0);
fine_mask->setVal(1.0);
#ifdef _OPENMP
#pragma omp parallel
#endif
for (MFIter mfi(*fine_mask); mfi.isValid(); ++mfi)
{
FArrayBox& fab = (*fine_mask)[mfi];
std::vector< std::pair<int,Box> > isects = baf.intersections(fab.box());
for (int ii = 0; ii < isects.size(); ii++)
{
fab.setVal(0.0,isects[ii].second,0);
}
}
return fine_mask;
}
//
// What's the slowest way I can think of to compute all the norms??
//
Real
MFNorm (const MultiFab& mfab,
const int exponent,
const int srcComp,
const int numComp,
const int numGrow)
{
BL_ASSERT (numGrow <= mfab.nGrow());
BoxArray boxes = mfab.boxArray();
boxes.grow(numGrow);
//
// Get a copy of the multifab
//
MultiFab mftmp(mfab.boxArray(), numComp, 0);
MultiFab::Copy(mftmp,mfab,srcComp,0,numComp,numGrow);
//
// Calculate the Norms
//
Real myNorm = 0;
if ( exponent == 0 )
{
for ( MFIter mftmpmfi(mftmp); mftmpmfi.isValid(); ++mftmpmfi)
{
mftmp[mftmpmfi].abs(boxes[mftmpmfi.index()], 0, numComp);
myNorm = std::max(myNorm, mftmp[mftmpmfi].norm(0, 0, numComp));
}
ParallelDescriptor::ReduceRealMax(myNorm);
} else if ( exponent == 1 )
{
for ( MFIter mftmpmfi(mftmp); mftmpmfi.isValid(); ++mftmpmfi)
{
mftmp[mftmpmfi].abs(boxes[mftmpmfi.index()], 0, numComp);
myNorm += mftmp[mftmpmfi].norm(1, 0, numComp);
}
ParallelDescriptor::ReduceRealSum(myNorm);
} else if ( exponent == 2 )
{
for ( MFIter mftmpmfi(mftmp); mftmpmfi.isValid(); ++mftmpmfi)
{
mftmp[mftmpmfi].abs(boxes[mftmpmfi.index()], 0, numComp);
myNorm += pow(mftmp[mftmpmfi].norm(2, 0, numComp), 2);
}
ParallelDescriptor::ReduceRealSum(myNorm);
myNorm = sqrt( myNorm );
} else {
BoxLib::Error("Invalid exponent to norm function");
}
return myNorm;
}
BoxList::BoxList (const BoxArray &ba)
:
lbox(),
btype()
{
if (ba.size() > 0)
btype = ba[0].ixType();
for (int i = 0, N = ba.size(); i < N; ++i)
push_back(ba[i]);
}
int
iMultiFab::norm0 (int comp, const BoxArray& ba, bool local) const
{
int nm0 = -std::numeric_limits<int>::max();
#ifdef _OPENMP
#pragma omp parallel
#endif
{
std::vector< std::pair<int,Box> > isects;
int priv_nm0 = -std::numeric_limits<int>::max();
for (MFIter mfi(*this); mfi.isValid(); ++mfi)
{
ba.intersections(mfi.validbox(),isects);
for (int i = 0, N = isects.size(); i < N; i++)
{
priv_nm0 = std::max(priv_nm0, get(mfi).norm(isects[i].second, 0, comp, 1));
}
}
#ifdef _OPENMP
#pragma omp critical (imultifab_norm0_ba)
#endif
{
nm0 = std::max(nm0, priv_nm0);
}
}
if (!local)
ParallelDescriptor::ReduceIntMax(nm0);
return nm0;
}
MultiFab_C_to_F::MultiFab_C_to_F (const Geometry& geom,
const DistributionMapping& dmap,
const BoxArray& ba)
{
BL_ASSERT(count == 0);
count++;
int nb = ba.size();
int dm = BL_SPACEDIM;
std::vector<int> lo(nb*dm);
std::vector<int> hi(nb*dm);
for ( int i = 0; i < nb; ++i ) {
const Box& bx = BoxLib::enclosedCells(ba[i]);
for ( int j = 0; j < dm; ++j ) {
lo[j + i*dm] = bx.smallEnd(j);
hi[j + i*dm] = bx.bigEnd(j);
}
}
const Box& domain = geom.Domain();
int pm[dm];
for ( int i = 0; i < dm; ++i ) {
pm[i] = geom.isPeriodic(i)? 1 : 0;
}
const Array<int>& pmap = dmap.ProcessorMap();
build_layout_from_c(nb, dm, &lo[0], &hi[0],
domain.loVect(), domain.hiVect(),
pm, pmap.dataPtr());
}
MCMultiGrid::MCMultiGrid (MCLinOp &_lp)
:
initialsolution(0),
Lp(_lp)
{
Initialize();
maxiter = def_maxiter;
numiter = def_numiter;
nu_0 = def_nu_0;
nu_1 = def_nu_1;
nu_2 = def_nu_2;
nu_f = def_nu_f;
usecg = def_usecg;
verbose = def_verbose;
rtol_b = def_rtol_b;
atol_b = def_atol_b;
nu_b = def_nu_b;
numLevelsMAX = def_numLevelsMAX;
numlevels = numLevels();
numcomps = _lp.numberComponents();
if ( ParallelDescriptor::IOProcessor() && (verbose > 2) )
{
BoxArray tmp = Lp.boxArray();
std::cout << "MCMultiGrid: numlevels = " << numlevels
<< ": ngrid = " << tmp.size() << ", npts = [";
for ( int i = 0; i < numlevels; ++i )
{
if ( i > 0 ) tmp.coarsen(2);
std::cout << tmp.d_numPts() << " ";
}
std::cout << "]" << '\n';
std::cout << "MCMultiGrid: " << numlevels
<< " multigrid levels created for this solve" << '\n';
}
if ( ParallelDescriptor::IOProcessor() && (verbose > 4) )
{
std::cout << "Grids: " << '\n';
BoxArray tmp = Lp.boxArray();
for (int i = 0; i < numlevels; ++i)
{
Orientation face(0, Orientation::low);
const DistributionMapping& map = Lp.bndryData().bndryValues(face).DistributionMap();
if (i > 0)
tmp.coarsen(2);
std::cout << " Level: " << i << '\n';
for (int k = 0; k < tmp.size(); k++)
{
const Box& b = tmp[k];
std::cout << " [" << k << "]: " << b << " ";
for (int j = 0; j < BL_SPACEDIM; j++)
std::cout << b.length(j) << ' ';
std::cout << ":: " << map[k] << '\n';
}
}
}
}
void
BndryRegister::setBoxes (const BoxArray& _grids)
{
BL_ASSERT(grids.size() == 0);
BL_ASSERT(_grids.size() > 0);
BL_ASSERT(_grids[0].cellCentered());
grids.define(_grids);
//
// Check that bndry regions are not allocated.
//
for (int k = 0; k < 2*BL_SPACEDIM; k++)
BL_ASSERT(bndry[k].size() == 0);
}
bool
ParticleBase::FineToCrse (const ParticleBase& p,
int flev,
const ParGDBBase* gdb,
const Array<IntVect>& fcells,
const BoxArray& fvalid,
const BoxArray& compfvalid_grown,
Array<IntVect>& ccells,
Array<Real>& cfracs,
Array<int>& which,
Array<int>& cgrid,
Array<IntVect>& pshifts,
std::vector< std::pair<int,Box> >& isects)
{
BL_ASSERT(gdb != 0);
BL_ASSERT(flev > 0);
//
// We're in AssignDensity(). We want to know whether or not updating
// with a particle we'll cross a fine->crse boundary. Note that crossing
// a periodic boundary, where the periodic shift lies in our valid region,
// is not considered a Fine->Crse crossing.
//
const int M = fcells.size();
which.resize(M);
cgrid.resize(M);
ccells.resize(M);
cfracs.resize(M);
for (int i = 0; i < M; i++)
{
cgrid[i] = -1;
which[i] = 0;
}
const Box& ibx = BoxLib::grow(gdb->ParticleBoxArray(flev)[p.m_grid],-1);
BL_ASSERT(ibx.ok());
if (ibx.contains(p.m_cell))
//
// We're strictly contained in our valid box.
// We can't cross a fine->crse boundary.
//
return false;
if (!compfvalid_grown.contains(p.m_cell))
//
// We're strictly contained in our "valid" region. Note that the valid
// region contains any periodically shifted ghost cells that intersect
// valid region.
//
return false;
//
// Otherwise ...
//
const Geometry& cgm = gdb->Geom(flev-1);
const IntVect& rr = gdb->refRatio(flev-1);
const BoxArray& cba = gdb->ParticleBoxArray(flev-1);
ParticleBase::CIC_Cells_Fracs(p, cgm.ProbLo(), cgm.CellSize(), cfracs, ccells);
bool result = false;
for (int i = 0; i < M; i++)
{
IntVect ccell_refined = ccells[i]*rr;
//
// We've got to protect against the case when we're at the low
// end of the domain because coarsening & refining don't work right
// when indices go negative.
//
for (int dm = 0; dm < BL_SPACEDIM; dm++)
ccell_refined[dm] = std::max(ccell_refined[dm], -1);
if (!fvalid.contains(ccell_refined))
{
result = true;
which[i] = 1;
Box cbx(ccells[i],ccells[i]);
if (!cgm.Domain().contains(ccells[i]))
{
//
// We must be at a periodic boundary.
// Find valid box into which we can be periodically shifted.
//
BL_ASSERT(cgm.isAnyPeriodic());
cgm.periodicShift(cbx, cgm.Domain(), pshifts);
BL_ASSERT(pshifts.size() == 1);
cbx -= pshifts[0];
ccells[i] -= pshifts[0];
BL_ASSERT(cbx.ok());
BL_ASSERT(cgm.Domain().contains(cbx));
}
//
// Which grid at the crse level do we need to update?
//
cba.intersections(cbx,isects,true);
BL_ASSERT(!isects.empty());
cgrid[i] = isects[0].first; // The grid ID at crse level that we hit.
}
}
return result;
}
void
BndryRegister::defineDoit (Orientation _face,
IndexType _typ,
int _in_rad,
int _out_rad,
int _extent_rad,
BoxArray& fsBA)
{
BL_PROFILE("BndryRegister::defineDoit()");
BL_ASSERT(grids.size() > 0);
const int coord_dir = _face.coordDir();
const int lo_side = _face.isLow();
//
// Build the BoxArray on which to define the FabSet on this face.
//
const int N = grids.size();
fsBA.resize(N);
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (int idx = 0; idx < N; ++idx)
{
Box b;
//
// First construct proper box for direction normal to face.
//
if (_out_rad > 0)
{
if (_typ.ixType(coord_dir) == IndexType::CELL)
b = BoxLib::adjCell(grids[idx], _face, _out_rad);
else
b = BoxLib::bdryNode(grids[idx], _face, _out_rad);
if (_in_rad > 0)
b.grow(_face.flip(), _in_rad);
}
else
{
if (_in_rad > 0)
{
if (_typ.ixType(coord_dir) == IndexType::CELL)
b = BoxLib::adjCell(grids[idx], _face, _in_rad);
else
b = BoxLib::bdryNode(grids[idx], _face, _in_rad);
b.shift(coord_dir, lo_side ? _in_rad : -_in_rad);
}
else
BoxLib::Error("BndryRegister::define(): strange values for in_rad, out_rad");
}
//
// Now alter box in all other index directions.
//
for (int dir = 0; dir < BL_SPACEDIM; dir++)
{
if (dir == coord_dir)
continue;
if (_typ.ixType(dir) == IndexType::NODE)
b.surroundingNodes(dir);
if (_extent_rad > 0)
b.grow(dir,_extent_rad);
}
BL_ASSERT(b.ok());
fsBA.set(idx,b);
}
BL_ASSERT(fsBA.ok());
}
void
MCLinOp::applyBC (MultiFab& inout,
int level,
MCBC_Mode bc_mode)
{
//
// The inout MultiFab must have at least MCLinOp_grow ghost cells
// for applyBC()
//
BL_ASSERT(inout.nGrow() >= MCLinOp_grow);
//
// The inout MultiFab must have at least Periodic_BC_grow cells for the
// algorithms taking care of periodic boundary conditions.
//
BL_ASSERT(inout.nGrow() >= MCLinOp_grow);
//
// No coarsened boundary values, cannot apply inhomog at lev>0.
//
BL_ASSERT(!(level>0 && bc_mode == MCInhomogeneous_BC));
int flagden = 1; // fill in the bndry data and undrrelxr
int flagbc = 1; // with values
if (bc_mode == MCHomogeneous_BC)
flagbc = 0; // nodata if homog
int nc = inout.nComp();
BL_ASSERT(nc == numcomp );
inout.setBndry(-1.e30);
inout.FillBoundary();
prepareForLevel(level);
geomarray[level].FillPeriodicBoundary(inout,0,nc);
//
// Fill boundary cells.
//
#ifdef _OPENMP
#pragma omp parallel
#endif
for (MFIter mfi(inout); mfi.isValid(); ++mfi)
{
const int gn = mfi.index();
BL_ASSERT(gbox[level][gn] == inout.box(gn));
const BndryData::RealTuple& bdl = bgb.bndryLocs(gn);
const Array< Array<BoundCond> >& bdc = bgb.bndryConds(gn);
const MaskTuple& msk = maskvals[level][gn];
for (OrientationIter oitr; oitr; ++oitr)
{
const Orientation face = oitr();
FabSet& f = (*undrrelxr[level])[face];
FabSet& td = (*tangderiv[level])[face];
int cdr(face);
const FabSet& fs = bgb.bndryValues(face);
Real bcl = bdl[face];
const Array<BoundCond>& bc = bdc[face];
const int *bct = (const int*) bc.dataPtr();
const FArrayBox& fsfab = fs[gn];
const Real* bcvalptr = fsfab.dataPtr();
//
// Way external derivs stored.
//
const Real* exttdptr = fsfab.dataPtr(numcomp);
const int* fslo = fsfab.loVect();
const int* fshi = fsfab.hiVect();
FArrayBox& inoutfab = inout[gn];
FArrayBox& denfab = f[gn];
FArrayBox& tdfab = td[gn];
#if BL_SPACEDIM==2
int cdir = face.coordDir(), perpdir = -1;
if (cdir == 0)
perpdir = 1;
else if (cdir == 1)
perpdir = 0;
else
BoxLib::Abort("MCLinOp::applyBC(): bad logic");
const Mask& m = *msk[face];
const Mask& mphi = *msk[Orientation(perpdir,Orientation::high)];
const Mask& mplo = *msk[Orientation(perpdir,Orientation::low)];
FORT_APPLYBC(
&flagden, &flagbc, &maxorder,
inoutfab.dataPtr(),
ARLIM(inoutfab.loVect()), ARLIM(inoutfab.hiVect()),
&cdr, bct, &bcl,
bcvalptr, ARLIM(fslo), ARLIM(fshi),
m.dataPtr(), ARLIM(m.loVect()), ARLIM(m.hiVect()),
mphi.dataPtr(), ARLIM(mphi.loVect()), ARLIM(mphi.hiVect()),
mplo.dataPtr(), ARLIM(mplo.loVect()), ARLIM(mplo.hiVect()),
denfab.dataPtr(),
ARLIM(denfab.loVect()), ARLIM(denfab.hiVect()),
exttdptr, ARLIM(fslo), ARLIM(fshi),
tdfab.dataPtr(),ARLIM(tdfab.loVect()),ARLIM(tdfab.hiVect()),
inout.box(gn).loVect(), inout.box(gn).hiVect(),
&nc, h[level]);
#elif BL_SPACEDIM==3
const Mask& mn = *msk[Orientation(1,Orientation::high)];
const Mask& me = *msk[Orientation(0,Orientation::high)];
const Mask& mw = *msk[Orientation(0,Orientation::low)];
const Mask& ms = *msk[Orientation(1,Orientation::low)];
const Mask& mt = *msk[Orientation(2,Orientation::high)];
const Mask& mb = *msk[Orientation(2,Orientation::low)];
FORT_APPLYBC(
&flagden, &flagbc, &maxorder,
inoutfab.dataPtr(),
ARLIM(inoutfab.loVect()), ARLIM(inoutfab.hiVect()),
&cdr, bct, &bcl,
bcvalptr, ARLIM(fslo), ARLIM(fshi),
mn.dataPtr(),ARLIM(mn.loVect()),ARLIM(mn.hiVect()),
me.dataPtr(),ARLIM(me.loVect()),ARLIM(me.hiVect()),
mw.dataPtr(),ARLIM(mw.loVect()),ARLIM(mw.hiVect()),
ms.dataPtr(),ARLIM(ms.loVect()),ARLIM(ms.hiVect()),
mt.dataPtr(),ARLIM(mt.loVect()),ARLIM(mt.hiVect()),
mb.dataPtr(),ARLIM(mb.loVect()),ARLIM(mb.hiVect()),
denfab.dataPtr(),
ARLIM(denfab.loVect()), ARLIM(denfab.hiVect()),
exttdptr, ARLIM(fslo), ARLIM(fshi),
tdfab.dataPtr(),ARLIM(tdfab.loVect()),ARLIM(tdfab.hiVect()),
inout.box(gn).loVect(), inout.box(gn).hiVect(),
&nc, h[level]);
#endif
}
}
#if 0
// This "probably" works, but is not strictly needed just because of the way Bill
// coded up the tangential derivative stuff. It's handy code though, so I want to
// keep it around/
// Clean up corners:
// The problem here is that APPLYBC fills only grow cells normal to the boundary.
// As a result, any corner cell on the boundary (either coarse-fine or fine-fine)
// is not filled. For coarse-fine, the operator adjusts itself, sliding away from
// the box edge to avoid referencing that corner point. On the physical boundary
// though, the corner point is needed. Particularly if a fine-fine boundary intersects
// the physical boundary, since we want the stencil to be independent of the box
// blocking. FillBoundary operations wont fix the problem because the "good"
// data we need is living in the grow region of adjacent fabs. So, here we play
// the usual games to treat the newly filled grow cells as "valid" data.
// Note that we only need to do something where the grids touch the physical boundary.
const Geometry& geomlev = geomarray[level];
const BoxArray& grids = inout.boxArray();
const Box& domain = geomlev.Domain();
int nGrow = 1;
int src_comp = 0;
int num_comp = BL_SPACEDIM;
// Lets do a quick check to see if we need to do anything at all here
BoxArray BIGba = BoxArray(grids).grow(nGrow);
if (! (domain.contains(BIGba.minimalBox())) ) {
BoxArray boundary_pieces;
Array<int> proc_idxs;
Array<Array<int> > old_to_new(grids.size());
const DistributionMapping& dmap=inout.DistributionMap();
for (int d=0; d<BL_SPACEDIM; ++d) {
if (! (geomlev.isPeriodic(d)) ) {
BoxArray gba = BoxArray(grids).grow(d,nGrow);
for (int i=0; i<gba.size(); ++i) {
BoxArray new_pieces = BoxLib::boxComplement(gba[i],domain);
int size_new = new_pieces.size();
if (size_new>0) {
int size_old = boundary_pieces.size();
boundary_pieces.resize(size_old+size_new);
proc_idxs.resize(boundary_pieces.size());
for (int j=0; j<size_new; ++j) {
boundary_pieces.set(size_old+j,new_pieces[j]);
proc_idxs[size_old+j] = dmap[i];
old_to_new[i].push_back(size_old+j);
}
}
}
}
}
proc_idxs.push_back(ParallelDescriptor::MyProc());
MultiFab boundary_data(boundary_pieces,num_comp,nGrow,
DistributionMapping(proc_idxs));
for (MFIter mfi(inout); mfi.isValid(); ++mfi) {
const FArrayBox& src_fab = inout[mfi];
for (int j=0; j<old_to_new[mfi.index()].size(); ++j) {
int new_box_idx = old_to_new[mfi.index()][j];
boundary_data[new_box_idx].copy(src_fab,src_comp,0,num_comp);
}
}
boundary_data.FillBoundary();
// Use a hacked Geometry object to handle the periodic intersections for us.
// Here, the "domain" is the plane of cells on non-periodic boundary faces.
// and there may be cells over the periodic boundary in the remaining directions.
// We do a Geometry::PFB on each non-periodic face to sync these up.
if (geomlev.isAnyPeriodic()) {
Array<int> is_per(BL_SPACEDIM,0);
for (int d=0; d<BL_SPACEDIM; ++d) {
is_per[d] = geomlev.isPeriodic(d);
}
for (int d=0; d<BL_SPACEDIM; ++d) {
if (! is_per[d]) {
Box tmpLo = BoxLib::adjCellLo(geomlev.Domain(),d,1);
Geometry tmpGeomLo(tmpLo,&(geomlev.ProbDomain()),(int)geomlev.Coord(),is_per.dataPtr());
tmpGeomLo.FillPeriodicBoundary(boundary_data);
Box tmpHi = BoxLib::adjCellHi(geomlev.Domain(),d,1);
Geometry tmpGeomHi(tmpHi,&(geomlev.ProbDomain()),(int)geomlev.Coord(),is_per.dataPtr());
tmpGeomHi.FillPeriodicBoundary(boundary_data);
}
}
}
for (MFIter mfi(inout); mfi.isValid(); ++mfi) {
int idx = mfi.index();
FArrayBox& dst_fab = inout[mfi];
for (int j=0; j<old_to_new[idx].size(); ++j) {
int new_box_idx = old_to_new[mfi.index()][j];
const FArrayBox& src_fab = boundary_data[new_box_idx];
const Box& src_box = src_fab.box();
BoxArray pieces_outside_domain = BoxLib::boxComplement(src_box,domain);
for (int k=0; k<pieces_outside_domain.size(); ++k) {
const Box& outside = pieces_outside_domain[k] & dst_fab.box();
if (outside.ok()) {
dst_fab.copy(src_fab,outside,0,outside,src_comp,num_comp);
}
}
}
}
}
#endif
}
Real
Adv::advance (Real time,
Real dt,
int iteration,
int ncycle)
{
for (int k = 0; k < NUM_STATE_TYPE; k++) {
state[k].allocOldData();
state[k].swapTimeLevels(dt);
}
MultiFab& S_new = get_new_data(State_Type);
const Real prev_time = state[State_Type].prevTime();
const Real cur_time = state[State_Type].curTime();
const Real ctr_time = 0.5*(prev_time + cur_time);
const Real* dx = geom.CellSize();
const Real* prob_lo = geom.ProbLo();
//
// Get pointers to Flux registers, or set pointer to zero if not there.
//
FluxRegister *fine = 0;
FluxRegister *current = 0;
int finest_level = parent->finestLevel();
if (do_reflux && level < finest_level) {
fine = &getFluxReg(level+1);
fine->setVal(0.0);
}
if (do_reflux && level > 0) {
current = &getFluxReg(level);
}
MultiFab fluxes[BL_SPACEDIM];
if (do_reflux)
{
for (int j = 0; j < BL_SPACEDIM; j++)
{
BoxArray ba = S_new.boxArray();
ba.surroundingNodes(j);
fluxes[j].define(ba, NUM_STATE, 0, Fab_allocate);
}
}
// State with ghost cells
MultiFab Sborder(grids, NUM_STATE, NUM_GROW);
FillPatch(*this, Sborder, NUM_GROW, time, State_Type, 0, NUM_STATE);
#ifdef _OPENMP
#pragma omp parallel
#endif
{
FArrayBox flux[BL_SPACEDIM], uface[BL_SPACEDIM];
for (MFIter mfi(S_new, true); mfi.isValid(); ++mfi)
{
const Box& bx = mfi.tilebox();
const FArrayBox& statein = Sborder[mfi];
FArrayBox& stateout = S_new[mfi];
// Allocate fabs for fluxes and Godunov velocities.
for (int i = 0; i < BL_SPACEDIM ; i++) {
const Box& bxtmp = BoxLib::surroundingNodes(bx,i);
flux[i].resize(bxtmp,NUM_STATE);
uface[i].resize(BoxLib::grow(bxtmp,1),1);
}
get_face_velocity(level, ctr_time,
D_DECL(BL_TO_FORTRAN(uface[0]),
BL_TO_FORTRAN(uface[1]),
BL_TO_FORTRAN(uface[2])),
dx, prob_lo);
advect(time, bx.loVect(), bx.hiVect(),
BL_TO_FORTRAN_3D(statein),
BL_TO_FORTRAN_3D(stateout),
D_DECL(BL_TO_FORTRAN_3D(uface[0]),
BL_TO_FORTRAN_3D(uface[1]),
BL_TO_FORTRAN_3D(uface[2])),
D_DECL(BL_TO_FORTRAN_3D(flux[0]),
BL_TO_FORTRAN_3D(flux[1]),
BL_TO_FORTRAN_3D(flux[2])),
dx, dt);
if (do_reflux) {
for (int i = 0; i < BL_SPACEDIM ; i++)
fluxes[i][mfi].copy(flux[i],mfi.nodaltilebox(i));
}
}
}
if (do_reflux) {
if (current) {
for (int i = 0; i < BL_SPACEDIM ; i++)
current->FineAdd(fluxes[i],i,0,0,NUM_STATE,1.);
}
if (fine) {
for (int i = 0; i < BL_SPACEDIM ; i++)
fine->CrseInit(fluxes[i],i,0,0,NUM_STATE,-1.);
}
}
return dt;
}
bool
BoxList::contains (const BoxArray& ba) const
{
BoxArray tba(*this);
return ba.contains(tba);
}
static
BoxArray
GetBndryCells (const BoxArray& ba,
int ngrow,
const Geometry& geom)
{
//
// First get list of all ghost cells.
//
BoxList gcells, bcells;
for (int i = 0; i < ba.size(); ++i)
gcells.join(BoxLib::boxDiff(BoxLib::grow(ba[i],ngrow),ba[i]));
//
// Now strip out intersections with original BoxArray.
//
for (BoxList::const_iterator it = gcells.begin(); it != gcells.end(); ++it)
{
std::vector< std::pair<int,Box> > isects = ba.intersections(*it);
if (isects.empty())
bcells.push_back(*it);
else
{
//
// Collect all the intersection pieces.
//
BoxList pieces;
for (int i = 0; i < isects.size(); i++)
pieces.push_back(isects[i].second);
BoxList leftover = BoxLib::complementIn(*it,pieces);
bcells.catenate(leftover);
}
}
//
// Now strip out overlaps.
//
gcells.clear();
gcells = BoxLib::removeOverlap(bcells);
bcells.clear();
if (geom.isAnyPeriodic())
{
Array<IntVect> pshifts(27);
const Box& domain = geom.Domain();
for (BoxList::const_iterator it = gcells.begin(); it != gcells.end(); ++it)
{
if (!domain.contains(*it))
{
//
// Add in periodic ghost cells shifted to valid region.
//
geom.periodicShift(domain, *it, pshifts);
for (int i = 0; i < pshifts.size(); i++)
{
const Box& shftbox = *it + pshifts[i];
const Box& ovlp = domain & shftbox;
BoxList bl = BoxLib::complementIn(ovlp,BoxList(ba));
bcells.catenate(bl);
}
}
}
gcells.catenate(bcells);
}
return BoxArray(gcells);
}
int
main (int argc,
char* argv[])
{
BoxLib::Initialize(argc,argv);
if (argc < 2)
print_usage(argc,argv);
ParmParse pp;
if (pp.contains("help"))
print_usage(argc,argv);
bool verbose = false;
pp.query("verbose",verbose);
if (verbose>1)
AmrData::SetVerbose(true);
std::string infile; pp.get("infile",infile);
std::string outfile_DEF;
std::string outType = "tec";
#ifdef USE_TEC_BIN_IO
bool doBin = true;
pp.query("doBin",doBin);
outfile_DEF = infile+(doBin ? ".plt" : ".dat" );
#else
bool doBin=false;
outfile_DEF = infile+".dat";
#endif
//
bool connect_cc = true; pp.query("connect_cc",connect_cc);
std::string outfile(outfile_DEF); pp.query("outfile",outfile);
DataServices::SetBatchMode();
Amrvis::FileType fileType(Amrvis::NEWPLT);
DataServices dataServices(infile, fileType);
if (!dataServices.AmrDataOk())
DataServices::Dispatch(DataServices::ExitRequest, NULL);
AmrData& amrData = dataServices.AmrDataRef();
const Array<std::string>& names = amrData.PlotVarNames();
Array<int> comps;
if (int nc = pp.countval("comps"))
{
comps.resize(nc);
pp.getarr("comps",comps,0,nc);
}
else
{
int sComp = 0;
pp.query("sComp",sComp);
int nComp = amrData.NComp();
pp.query("nComp",nComp);
BL_ASSERT(sComp+nComp <= amrData.NComp());
comps.resize(nComp);
for (int i=0; i<nComp; ++i)
comps[i] = sComp + i;
}
Box subbox;
if (int nx=pp.countval("box"))
{
Array<int> barr;
pp.getarr("box",barr,0,nx);
int d=BL_SPACEDIM;
BL_ASSERT(barr.size()==2*d);
subbox=Box(IntVect(D_DECL(barr[0],barr[1],barr[2])),
IntVect(D_DECL(barr[d],barr[d+1],barr[d+2]))) & amrData.ProbDomain()[0];
} else {
subbox = amrData.ProbDomain()[0];
}
int finestLevel = amrData.FinestLevel(); pp.query("finestLevel",finestLevel);
int Nlev = finestLevel + 1;
Array<BoxArray> gridArray(Nlev);
Array<Box> subboxArray(Nlev);
int nGrowPer = 0; pp.query("nGrowPer",nGrowPer);
PArray<Geometry> geom(Nlev);
Array<Real> LO(BL_SPACEDIM,0);
Array<Real> HI(BL_SPACEDIM,1);
RealBox rb(LO.dataPtr(),HI.dataPtr());
int coordSys = 0;
Array<int> isPer(BL_SPACEDIM,0);
for (int lev=0; lev<Nlev; ++lev)
{
subboxArray[lev]
= (lev==0 ? subbox
: Box(subboxArray[lev-1]).refine(amrData.RefRatio()[lev-1]));
geom.set(lev,new Geometry(amrData.ProbDomain()[lev],&rb,coordSys,const_cast<int*>(isPer.dataPtr())));
if (nGrowPer>0 && lev==0)
{
for (int i=0; i<BL_SPACEDIM; ++i)
{
if (geom[lev].isPeriodic(i))
{
if (subboxArray[lev].smallEnd()[i] == amrData.ProbDomain()[lev].smallEnd()[i])
subboxArray[lev].growLo(i,nGrowPer);
if (subboxArray[lev].bigEnd()[i] == amrData.ProbDomain()[lev].bigEnd()[i])
subboxArray[lev].growHi(i,nGrowPer);
}
}
}
gridArray[lev] = BoxLib::intersect(amrData.boxArray(lev), subboxArray[lev]);
if (nGrowPer>0 && geom[lev].isAnyPeriodic() && gridArray[lev].size()>0)
{
//const Box& probDomain = amrData.ProbDomain()[lev];
const BoxArray& ba = amrData.boxArray(lev);
BoxList bladd;
Array<IntVect> shifts;
for (int i=0; i<ba.size(); ++i)
{
geom[lev].periodicShift(subboxArray[lev],ba[i],shifts);
for (int j=0; j<shifts.size(); ++j)
{
Box ovlp = Box(ba[i]).shift(shifts[j]) & subboxArray[lev];
if (ovlp.ok())
bladd.push_back(ovlp);
}
}
bladd.simplify();
BoxList blnew(gridArray[lev]);
blnew.join(bladd);
gridArray[lev] = BoxArray(blnew);
}
if (!gridArray[lev].size())
{
Nlev = lev;
finestLevel = Nlev-1;
gridArray.resize(Nlev);
subboxArray.resize(Nlev);
}
}
const int nGrow = 1;
typedef BaseFab<Node> NodeFab;
typedef FabArray<NodeFab> MultiNodeFab;
PArray<MultiNodeFab> nodes(Nlev,PArrayManage);
std::cerr << "Before nodes allocated" << endl;
for (int lev=0; lev<Nlev; ++lev)
nodes.set(lev,new MultiNodeFab(gridArray[lev],1,nGrow));
std::cerr << "After nodes allocated" << endl;
int cnt = 0;
typedef std::map<Node,int> NodeMap;
NodeMap nodeMap;
for (int lev=0; lev<Nlev; ++lev)
{
for (MFIter fai(nodes[lev]); fai.isValid(); ++fai)
{
NodeFab& ifab = nodes[lev][fai];
const Box& box = ifab.box() & subboxArray[lev];
for (IntVect iv=box.smallEnd(); iv<=box.bigEnd(); box.next(iv))
ifab(iv,0) = Node(iv,lev,fai.index(),Node::VALID);
}
if (lev != 0)
{
const int ref = amrData.RefRatio()[lev-1];
const Box& rangeBox = Box(IntVect::TheZeroVector(),
(ref-1)*IntVect::TheUnitVector());
BoxArray bndryCells = GetBndryCells(nodes[lev].boxArray(),ref,geom[lev]);
for (MFIter fai(nodes[lev]); fai.isValid(); ++fai)
{
const Box& box = BoxLib::grow(fai.validbox(),ref) & subboxArray[lev];
NodeFab& ifab = nodes[lev][fai];
std::vector< std::pair<int,Box> > isects = bndryCells.intersections(box);
for (int i = 0; i < isects.size(); i++)
{
Box co = isects[i].second & fai.validbox();
if (co.ok())
std::cout << "BAD ISECTS: " << co << std::endl;
const Box& dstBox = isects[i].second;
const Box& srcBox = BoxLib::coarsen(dstBox,ref);
NodeFab dst(dstBox,1);
for (IntVect iv(srcBox.smallEnd());
iv<=srcBox.bigEnd();
srcBox.next(iv))
{
const IntVect& baseIV = ref*iv;
for (IntVect ivt(rangeBox.smallEnd());ivt<=rangeBox.bigEnd();rangeBox.next(ivt))
dst(baseIV + ivt,0) = Node(iv,lev-1,-1,Node::VALID);
}
const Box& ovlp = dstBox & ifab.box();
Box mo = ovlp & fai.validbox();
if (mo.ok())
{
std::cout << "BAD OVERLAP: " << mo << std::endl;
std::cout << " vb: " << fai.validbox() << std::endl;
}
if (ovlp.ok())
ifab.copy(dst,ovlp,0,ovlp,0,1);
}
}
}
// Block out cells covered by finer grid
if (lev < finestLevel)
{
const BoxArray coarsenedFineBoxes =
BoxArray(gridArray[lev+1]).coarsen(amrData.RefRatio()[lev]);
for (MFIter fai(nodes[lev]); fai.isValid(); ++fai)
{
NodeFab& ifab = nodes[lev][fai];
const Box& box = ifab.box();
std::vector< std::pair<int,Box> > isects = coarsenedFineBoxes.intersections(box);
for (int i = 0; i < isects.size(); i++)
{
const Box& ovlp = isects[i].second;
for (IntVect iv=ovlp.smallEnd(); iv<=ovlp.bigEnd(); ovlp.next(iv))
ifab(iv,0) = Node(iv,lev,fai.index(),Node::COVERED);
}
}
}
// Add the unique nodes from this level to the list
for (MFIter fai(nodes[lev]); fai.isValid(); ++fai)
{
NodeFab& ifab = nodes[lev][fai];
const Box& box = fai.validbox() & subboxArray[lev];
for (IntVect iv(box.smallEnd()); iv<=box.bigEnd(); box.next(iv))
{
if (ifab(iv,0).type == Node::VALID)
{
if (ifab(iv,0).level != lev)
std::cout << "bad level: " << ifab(iv,0) << std::endl;
nodeMap[ifab(iv,0)] = cnt++;
}
}
}
}
std::cerr << "After nodeMap built, size=" << nodeMap.size() << endl;
typedef std::set<Element> EltSet;
EltSet elements;
for (int lev=0; lev<Nlev; ++lev)
{
for (MFIter fai(nodes[lev]); fai.isValid(); ++fai)
{
NodeFab& ifab = nodes[lev][fai];
Box box = ifab.box() & subboxArray[lev];
for (int dir=0; dir<BL_SPACEDIM; ++dir)
box.growHi(dir,-1);
for (IntVect iv(box.smallEnd()); iv<=box.bigEnd(); box.next(iv))
{
#if (BL_SPACEDIM == 2)
const Node& n1 = ifab(iv,0);
const Node& n2 = ifab(IntVect(iv).shift(BoxLib::BASISV(0)),0);
const Node& n3 = ifab(IntVect(iv).shift(IntVect::TheUnitVector()),0);
const Node& n4 = ifab(IntVect(iv).shift(BoxLib::BASISV(1)),0);
if (n1.type==Node::VALID && n2.type==Node::VALID &&
n3.type==Node::VALID && n4.type==Node::VALID )
elements.insert(Element(n1,n2,n3,n4));
#else
const IntVect& ivu = IntVect(iv).shift(BoxLib::BASISV(2));
const Node& n1 = ifab(iv ,0);
const Node& n2 = ifab(IntVect(iv ).shift(BoxLib::BASISV(0)),0);
const Node& n3 = ifab(IntVect(iv ).shift(BoxLib::BASISV(0)).shift(BoxLib::BASISV(1)),0);
const Node& n4 = ifab(IntVect(iv ).shift(BoxLib::BASISV(1)),0);
const Node& n5 = ifab(ivu,0);
const Node& n6 = ifab(IntVect(ivu).shift(BoxLib::BASISV(0)),0);
const Node& n7 = ifab(IntVect(ivu).shift(BoxLib::BASISV(0)).shift(BoxLib::BASISV(1)),0);
const Node& n8 = ifab(IntVect(ivu).shift(BoxLib::BASISV(1)),0);
if (n1.type==Node::VALID && n2.type==Node::VALID &&
n3.type==Node::VALID && n4.type==Node::VALID &&
n5.type==Node::VALID && n6.type==Node::VALID &&
n7.type==Node::VALID && n8.type==Node::VALID )
elements.insert(Element(n1,n2,n3,n4,n5,n6,n7,n8));
#endif
}
}
}
int nElts = (connect_cc ? elements.size() : nodeMap.size());
std::cerr << "Before connData allocated " << elements.size() << " elements" << endl;
Array<int> connData(MYLEN*nElts);
std::cerr << "After connData allocated " << elements.size() << " elements" << endl;
if (connect_cc) {
cnt = 0;
for (EltSet::const_iterator it = elements.begin(); it!=elements.end(); ++it)
{
for (int j=0; j<MYLEN; ++j)
{
const NodeMap::const_iterator noit = nodeMap.find(*((*it).n[j]));
if (noit == nodeMap.end())
{
std::cout << "Node not found in node map" << std::endl;
std::cout << *((*it).n[j]) << std::endl;
}
else
{
connData[cnt++] = noit->second+1;
}
}
}
} else {
cnt = 1;
for (int i=0; i<nElts; ++i) {
for (int j=0; j<MYLEN; ++j) {
connData[i*MYLEN+j] = cnt++;
}
}
}
std::cerr << "Final elements built" << endl;
// Invert the map
std::vector<Node> nodeVect(nodeMap.size());
for (NodeMap::const_iterator it=nodeMap.begin(); it!=nodeMap.end(); ++it)
{
if (it->second>=nodeVect.size() || it->second<0)
std::cout << "Bad id: " << it->second << " bad node: " << it->first << std::endl;
BL_ASSERT(it->second>=0);
BL_ASSERT(it->second<nodeVect.size());
nodeVect[it->second] = (*it).first;
}
std::cerr << "Final nodeVect built (" << nodeVect.size() << " nodes)" << endl;
nodeMap.clear();
elements.clear();
nodes.clear();
std::cerr << "Temp nodes, elements cleared" << endl;
PArray<MultiFab> fileData(Nlev);
int ng = nGrowPer;
for (int lev=0; lev<Nlev; ++lev)
{
if (lev!=0)
ng *= amrData.RefRatio()[lev-1];
const BoxArray& ba = gridArray[lev];
fileData.set(lev,new MultiFab(ba,comps.size(),0));
fileData[lev].setVal(1.e30);
std::cerr << "My data set alloc'd at lev=" << lev << endl;
MultiFab pData, pDataNG;
if (ng>0 && geom[lev].isAnyPeriodic())
{
const Box& pd = amrData.ProbDomain()[lev];
//const BoxArray& vba = amrData.boxArray(lev);
Box shrunkenDomain = pd;
for (int i=0; i<BL_SPACEDIM; ++i)
if (geom[lev].isPeriodic(i))
shrunkenDomain.grow(i,-ng);
const BoxArray edgeVBoxes = BoxLib::boxComplement(pd,shrunkenDomain);
pData.define(edgeVBoxes,1,ng,Fab_allocate);
pDataNG.define(BoxArray(edgeVBoxes).grow(ng),1,0,Fab_allocate);
}
for (int i=0; i<comps.size(); ++i)
{
BoxArray tmpBA = BoxLib::intersect(fileData[lev].boxArray(),amrData.ProbDomain()[lev]);
MultiFab tmpMF(tmpBA,1,0);
tmpMF.setVal(2.e30);
amrData.FillVar(tmpMF,lev,names[comps[i]],0);
fileData[lev].copy(tmpMF,0,i,1);
if (ng>0 && geom[lev].isAnyPeriodic())
{
pData.setVal(3.e30);
pDataNG.copy(tmpMF);
for (MFIter mfi(pData); mfi.isValid(); ++mfi)
pData[mfi].copy(pDataNG[mfi]);
amrData.FillVar(pData,lev,names[comps[i]],0);
geom[lev].FillPeriodicBoundary(pData);
for (MFIter mfi(pData); mfi.isValid(); ++mfi)
pDataNG[mfi].copy(pData[mfi]);
fileData[lev].copy(pDataNG,0,i,1);
}
}
if (fileData[lev].max(0) > 1.e29)
{
std::cerr << "Bad mf data" << std::endl;
VisMF::Write(fileData[lev],"out.mfab");
BoxLib::Abort();
}
}
std::cerr << "File data loaded" << endl;
int nNodesFINAL = (connect_cc ? nodeVect.size() : nElts*MYLEN );
int nCompsFINAL = BL_SPACEDIM+comps.size();
FABdata tmpData(nNodesFINAL,nCompsFINAL);
int tmpDatLen = nCompsFINAL*nNodesFINAL;
std::cerr << "Final node data allocated (size=" << tmpDatLen << ")" << endl;
//const Array<Array<Real> >& dxLevel = amrData.DxLevel(); // Do not trust dx from file...compute our own
Array<Array<Real> > dxLevel(Nlev);
for (int i=0; i<Nlev; ++i)
{
dxLevel[i].resize(BL_SPACEDIM);
for (int j=0; j<BL_SPACEDIM; ++j)
dxLevel[i][j] = amrData.ProbSize()[j]/amrData.ProbDomain()[i].length(j);
}
const Array<Real>& plo = amrData.ProbLo();
// Handy structures for loading data in usual fab ordering (transpose of mef/flt ordering)
#define BIN_POINT
#undef BIN_POINT
#ifdef BIN_POINT
Real* data = tmpData.dataPtr();
#else /* BLOCK ordering */
Array<Real*> fdat(comps.size()+BL_SPACEDIM);
for (int i=0; i<fdat.size(); ++i)
fdat[i] = tmpData.dataPtr(i);
#endif
cnt = 0;
int Nnodes = nodeVect.size();
int jGridPrev = 0;
int levPrev = -1;
for (int i=0; i<Nnodes; ++i)
{
const Node& node = nodeVect[i];
const Array<Real>& dx = dxLevel[node.level];
const IntVect& iv = node.iv;
const BoxArray& grids = fileData[node.level].boxArray();
int jGrid = node.grid;
if (jGrid<0)
{
bool found_it = false;
// Try same grid as last time, otherwise search list
if (node.level==levPrev && grids[jGridPrev].contains(iv))
{
found_it = true;
jGrid = jGridPrev;
}
for (int j=0; j<grids.size() && !found_it; ++j)
{
if (grids[j].contains(iv))
{
found_it = true;
jGrid = j;
}
}
BL_ASSERT(found_it);
}
// Remember these for next time
levPrev = node.level;
jGridPrev = jGrid;
Array<IntVect> ivt;
if (connect_cc) {
ivt.resize(1,iv);
} else {
ivt.resize(D_PICK(1,4,8),iv);
ivt[1] += BoxLib::BASISV(0);
ivt[2] = ivt[1] + BoxLib::BASISV(1);
ivt[3] += BoxLib::BASISV(1);
#if BLSPACEDIM==3
for (int n=0; n<4; ++n) {
ivt[4+n] = iv[n] + BoxLib::BASISV(2);
}
#endif
}
for (int j=0; j<ivt.size(); ++j) {
Real offset = (connect_cc ? 0.5 : 0);
#ifdef BIN_POINT
for (int dir=0; dir<BL_SPACEDIM; ++dir)
data[cnt++] = plo[dir] + (ivt[j][dir] + offset) * dx[dir];
#else /* BLOCK ordering */
for (int dir=0; dir<BL_SPACEDIM; ++dir)
fdat[dir][cnt] = plo[dir] + (ivt[j][dir] + offset) * dx[dir];
#endif /* BIN_POINT */
#ifdef BIN_POINT
for (int n=0; n<comps.size(); ++n) {
data[cnt++] = fileData[node.level][jGrid](iv,n);
}
#else /* BLOCK ordering */
for (int n=0; n<comps.size(); ++n) {
fdat[n+BL_SPACEDIM][cnt] = fileData[node.level][jGrid](iv,n);
}
cnt++;
#endif /* BIN_POINT */
}
}
//Collate(tmpData,connData,MYLEN);
//
// Write output
//
const int nState = BL_SPACEDIM + comps.size();
std::string vars = D_TERM("X"," Y"," Z");
for (int j=0; j<comps.size(); ++j)
vars += " " + amrData.PlotVarNames()[comps[j]];
if (outType == "tec")
{
#ifdef BIN_POINT
string block_or_point = "FEPOINT";
#else /* BLOCK ordering */
string block_or_point = "FEBLOCK";
#endif
if (doBin)
{
#ifdef USE_TEC_BIN_IO
INTEGER4 Debug = 0;
INTEGER4 VIsDouble = 1;
INTEGER4 EltID = D_PICK(0,1,3);
TECINI((char*)"Pltfile data", (char*)vars.c_str(), (char*)outfile.c_str(), (char*)".", &Debug, &VIsDouble);
INTEGER4 nPts = nNodesFINAL;
TECZNE((char*)infile.c_str(), &nPts, &nElts, &EltID, (char*)block_or_point.c_str(), NULL);
TECDAT(&tmpDatLen,tmpData.fab.dataPtr(),&VIsDouble);
TECNOD(connData.dataPtr());
TECEND();
#else
BoxLib::Abort("Need to recompile with USE_TEC_BIN_IO defined");
#endif
}
else
{
std::ofstream osf(outfile.c_str(),std::ios::out);
osf << D_TERM("VARIABLES= \"X\"", " \"Y\"", " \"Z\"");
for (int j=0; j<comps.size(); ++j)
osf << " \"" << amrData.PlotVarNames()[comps[j]] << "\"";
char buf[100];
sprintf(buf,"%g",amrData.Time());
osf << endl << "ZONE T=\"" << infile << " time = " << buf
<< "\", N=" << nNodesFINAL << ", E=" << nElts << ", F=" << "FEPOINT" << " ET="
//<< "\", N=" << nPts << ", E=" << nElts << ", F=" << block_or_point << " ET="
<< D_PICK("POINT","QUADRILATERAL","BRICK") << endl;
for (int i=0; i<nNodesFINAL; ++i)
{
for (int j=0; j<nState; ++j)
osf << tmpData.dataPtr(j)[i] << " ";
osf << endl;
}
for (int i=0; i<nElts; ++i)
{
for (int j=0; j<MYLEN; ++j)
osf << connData[i*MYLEN+j] << " ";
osf << endl;
}
osf << endl;
osf.close();
}
}
else
{
std::ofstream ofs;
std::ostream* os =
(outfile=="-" ? (std::ostream*)(&std::cout) : (std::ostream*)(&ofs) );
if (outfile!="-")
ofs.open(outfile.c_str(),std::ios::out|std::ios::trunc|std::ios::binary);
(*os) << infile << " time = " << amrData.Time() << endl;
(*os) << vars << endl;
(*os) << nElts << " " << MYLEN << endl;
tmpData.fab.writeOn(*os);
(*os).write((char*)connData.dataPtr(),sizeof(int)*connData.size());
if (outfile!="-")
ofs.close();
}
BoxLib::Finalize();
return 0;
}
void main_main ()
{
// What time is it now? We'll use this to compute total run time.
Real strt_time = ParallelDescriptor::second();
// AMREX_SPACEDIM: number of dimensions
int n_cell, max_grid_size;
Vector<int> bc_lo(AMREX_SPACEDIM,0);
Vector<int> bc_hi(AMREX_SPACEDIM,0);
// inputs parameters
{
// ParmParse is way of reading inputs from the inputs file
ParmParse pp;
// We need to get n_cell from the inputs file - this is the
// number of cells on each side of a square (or cubic) domain.
pp.get("n_cell", n_cell);
// The domain is broken into boxes of size max_grid_size
max_grid_size = 32;
pp.query("max_grid_size", max_grid_size);
}
Vector<int> is_periodic(AMREX_SPACEDIM,0);
for (int idim=0; idim < AMREX_SPACEDIM; ++idim) {
is_periodic[idim] = 1;
}
// make BoxArray and Geometry
BoxArray ba;
Geometry geom;
{
IntVect dom_lo(AMREX_D_DECL( 0, 0, 0));
IntVect dom_hi(AMREX_D_DECL(n_cell-1, n_cell-1, n_cell-1));
Box domain(dom_lo, dom_hi);
// Initialize the boxarray "ba" from the single box "bx"
ba.define(domain);
// Break up boxarray "ba" into chunks no larger than
// "max_grid_size" along a direction
ba.maxSize(max_grid_size);
// This defines the physical box, [0, 1] in each direction.
RealBox real_box({AMREX_D_DECL(0.0, 0.0, 0.0)},
{AMREX_D_DECL(1.0, 1.0, 1.0)});
// This defines a Geometry object
geom.define(domain, &real_box,
CoordSys::cartesian, is_periodic.data());
}
// Nghost = number of ghost cells for each array
int Nghost = 0;
// do the runtime parameter initializations and microphysics inits
if (ParallelDescriptor::IOProcessor()) {
std::cout << "reading extern runtime parameters ..." << std::endl;
}
ParmParse ppa("amr");
std::string probin_file = "probin";
ppa.query("probin_file", probin_file);
const int probin_file_length = probin_file.length();
Vector<int> probin_file_name(probin_file_length);
for (int i = 0; i < probin_file_length; i++)
probin_file_name[i] = probin_file[i];
init_unit_test(probin_file_name.dataPtr(), &probin_file_length);
// Ncomp = number of components for each array
int Ncomp = -1;
init_variables();
get_ncomp(&Ncomp);
int name_len = -1;
get_name_len(&name_len);
// get the variable names
Vector<std::string> varnames;
for (int i=0; i<Ncomp; i++) {
char* cstring[name_len+1];
get_var_name(cstring, &i);
std::string name(*cstring);
varnames.push_back(name);
}
// time = starting time in the simulation
Real time = 0.0;
// How Boxes are distrubuted among MPI processes
DistributionMapping dm(ba);
// we allocate our main multifabs
MultiFab state(ba, dm, Ncomp, Nghost);
// Initialize the state and compute the different thermodynamics
// by inverting the EOS
for ( MFIter mfi(state); mfi.isValid(); ++mfi )
{
const Box& bx = mfi.validbox();
#pragma gpu
do_eos(AMREX_INT_ANYD(bx.loVect()), AMREX_INT_ANYD(bx.hiVect()),
BL_TO_FORTRAN_ANYD(state[mfi]), n_cell);
}
std::string name = "test_eos.";
// get the name of the EOS
int eos_len = -1;
get_eos_len(&eos_len);
char* eos_string[eos_len+1];
get_eos_name(eos_string);
std::string eos(*eos_string);
// Write a plotfile
WriteSingleLevelPlotfile(name + eos, state, varnames, geom, time, 0);
// Call the timer again and compute the maximum difference between
// the start time and stop time over all processors
Real stop_time = ParallelDescriptor::second() - strt_time;
const int IOProc = ParallelDescriptor::IOProcessorNumber();
ParallelDescriptor::ReduceRealMax(stop_time, IOProc);
// Tell the I/O Processor to write out the "run time"
amrex::Print() << "Run time = " << stop_time << std::endl;
}
int
main (int argc,
char* argv[])
{
BoxLib::Initialize(argc,argv);
std::cout << std::setprecision(10);
if (argc < 2)
{
std::cerr << "usage: " << argv[0] << " inputsfile [options]" << '\n';
exit(-1);
}
ParmParse pp;
int n;
BoxArray bs;
#if BL_SPACEDIM == 2
Box domain(IntVect(0,0),IntVect(11,11));
std::string boxfile("gr.2_small_a") ;
#elif BL_SPACEDIM == 3
Box domain(IntVect(0,0,0),IntVect(11,11,11));
std::string boxfile("grids/gr.3_2x3x4") ;
#endif
pp.query("boxes", boxfile);
std::ifstream ifs(boxfile.c_str(), std::ios::in);
if (!ifs)
{
std::string msg = "problem opening grids file: ";
msg += boxfile.c_str();
BoxLib::Abort(msg.c_str());
}
ifs >> domain;
if (ParallelDescriptor::IOProcessor())
std::cout << "domain: " << domain << std::endl;
bs.readFrom(ifs);
if (ParallelDescriptor::IOProcessor())
std::cout << "grids:\n" << bs << std::endl;
Geometry geom(domain);
const Real* H = geom.CellSize();
int ratio=2; pp.query("ratio", ratio);
// allocate/init soln and rhs
int Ncomp=BL_SPACEDIM;
int Nghost=0;
int Ngrids=bs.size();
MultiFab soln(bs, Ncomp, Nghost, Fab_allocate); soln.setVal(0.0);
MultiFab out(bs, Ncomp, Nghost, Fab_allocate);
MultiFab rhs(bs, Ncomp, Nghost, Fab_allocate); rhs.setVal(0.0);
for(MFIter rhsmfi(rhs); rhsmfi.isValid(); ++rhsmfi)
{
FORT_FILLRHS(rhs[rhsmfi].dataPtr(),
ARLIM(rhs[rhsmfi].loVect()),ARLIM(rhs[rhsmfi].hiVect()),
H,&Ncomp);
}
// Create the boundary object
MCViscBndry vbd(bs,geom);
BCRec phys_bc;
Array<int> lo_bc(BL_SPACEDIM), hi_bc(BL_SPACEDIM);
pp.getarr("lo_bc",lo_bc,0,BL_SPACEDIM);
pp.getarr("hi_bc",hi_bc,0,BL_SPACEDIM);
for (int i = 0; i < BL_SPACEDIM; i++)
{
phys_bc.setLo(i,lo_bc[i]);
phys_bc.setHi(i,hi_bc[i]);
}
// Create the BCRec's interpreted by ViscBndry objects
#if BL_SPACEDIM==2
Array<BCRec> pbcarray(4);
pbcarray[0] = BCRec(D_DECL(REFLECT_ODD,REFLECT_EVEN,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[1] = BCRec(D_DECL(REFLECT_EVEN,REFLECT_ODD,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[2] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[3] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
#elif BL_SPACEDIM==3
Array<BCRec> pbcarray(12);
#if 1
pbcarray[0] = BCRec(EXT_DIR,EXT_DIR,EXT_DIR,EXT_DIR,EXT_DIR,EXT_DIR);
pbcarray[1] = BCRec(EXT_DIR,EXT_DIR,EXT_DIR,EXT_DIR,EXT_DIR,EXT_DIR);
pbcarray[2] = BCRec(EXT_DIR,EXT_DIR,EXT_DIR,EXT_DIR,EXT_DIR,EXT_DIR);
pbcarray[3] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[4] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[5] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[6] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[7] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[8] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[9] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[10] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
pbcarray[11] = BCRec(D_DECL(EXT_DIR,EXT_DIR,EXT_DIR),
D_DECL(EXT_DIR,EXT_DIR,EXT_DIR));
#else
for (int i = 0; i < 12; i++)
pbcarray[i] = phys_bc;
#endif
#endif
Nghost = 1; // need space for bc info
MultiFab fine(bs,Ncomp,Nghost,Fab_allocate);
for(MFIter finemfi(fine); finemfi.isValid(); ++finemfi)
{
FORT_FILLFINE(fine[finemfi].dataPtr(),
ARLIM(fine[finemfi].loVect()),ARLIM(fine[finemfi].hiVect()),
H,&Ncomp);
}
// Create "background coarse data"
Box crse_bx = Box(domain).coarsen(ratio).grow(1);
BoxArray cba(crse_bx);
cba.maxSize(32);
Real h_crse[BL_SPACEDIM];
for (n=0; n<BL_SPACEDIM; n++) h_crse[n] = H[n]*ratio;
MultiFab crse_mf(cba, Ncomp, 0);
// FArrayBox crse_fab(crse_bx,Ncomp);
for (MFIter mfi(crse_mf); mfi.isValid(); ++mfi)
{
FORT_FILLCRSE(crse_mf[mfi].dataPtr(),
ARLIM(crse_mf[mfi].loVect()),ARLIM(crse_mf[mfi].hiVect()),
h_crse,&Ncomp);
}
// Create coarse boundary register, fill w/data from coarse FAB
int bndry_InRad=0;
int bndry_OutRad=1;
int bndry_Extent=1;
BoxArray cbs = BoxArray(bs).coarsen(ratio);
BndryRegister cbr(cbs,bndry_InRad,bndry_OutRad,bndry_Extent,Ncomp);
for (OrientationIter face; face; ++face)
{
Orientation f = face();
FabSet& bnd_fs(cbr[f]);
bnd_fs.copyFrom(crse_mf, 0, 0, 0, Ncomp);
}
// Interpolate crse data to fine boundary, where applicable
int cbr_Nstart=0;
int fine_Nstart=0;
int bndry_Nstart=0;
vbd.setBndryValues(cbr,cbr_Nstart,fine,fine_Nstart,
bndry_Nstart,Ncomp,ratio,pbcarray);
Nghost = 1; // other variables don't need extra space
DivVis lp(vbd,H);
Real a = 0.0;
Real b[BL_SPACEDIM];
b[0] = 1.0;
b[1] = 1.0;
#if BL_SPACEDIM>2
b[2] = 1.0;
#endif
MultiFab acoefs;
int NcompA = (BL_SPACEDIM == 2 ? 2 : 1);
acoefs.define(bs, NcompA, Nghost, Fab_allocate);
acoefs.setVal(a);
MultiFab bcoefs[BL_SPACEDIM];
for (n=0; n<BL_SPACEDIM; ++n)
{
BoxArray bsC(bs);
bcoefs[n].define(bsC.surroundingNodes(n), 1,
Nghost, Fab_allocate);
#if 1
for(MFIter bmfi(bcoefs[n]); bmfi.isValid(); ++bmfi)
{
FORT_MAKEMU(bcoefs[n][bmfi].dataPtr(),
ARLIM(bcoefs[n][bmfi].loVect()),ARLIM(bcoefs[n][bmfi].hiVect()),H,n);
}
#else
bcoefs[n].setVal(b[n]);
#endif
} // -->> over dimension
lp.setCoefficients(acoefs, bcoefs);
#if 1
lp.maxOrder(4);
#endif
Nghost = 1;
MultiFab tsoln(bs, Ncomp, Nghost, Fab_allocate);
tsoln.setVal(0.0);
#if 1
tsoln.copy(fine);
#endif
#if 0
// testing apply
lp.apply(out,tsoln);
Box subbox = out[0].box();
Real n1 = out[0].norm(subbox,1,0,BL_SPACEDIM)*pow(H[0],BL_SPACEDIM);
ParallelDescriptor::ReduceRealSum(n1);
if (ParallelDescriptor::IOProcessor())
{
cout << "n1 output is "<<n1<<std::endl;
}
out.minus(rhs,0,BL_SPACEDIM,0);
// special to single grid prob
Real n2 = out[0].norm(subbox,1,0,BL_SPACEDIM)*pow(H[0],BL_SPACEDIM);
ParallelDescriptor::ReduceRealSum(n2);
if (ParallelDescriptor::IOProcessor())
{
cout << "n2 difference is "<<n2<<std::endl;
}
#if 0
subbox.grow(-1);
Real n3 = out[0].norm(subbox,0,0,BL_SPACEDIM)*pow(H[0],BL_SPACEDIM);
ParallelDescriptor::ReduceRealMax(n3);
if (ParallelDescriptor::IOProcessor())
{
cout << "n3 difference is "<<n3<<std::endl;
}
#endif
#endif
const IntVect refRatio(D_DECL(2,2,2));
const Real bgVal = 1.0;
#if 1
#ifndef NDEBUG
// testing flux computation
BoxArray xfluxbox(bs);
xfluxbox.surroundingNodes(0);
MultiFab xflux(xfluxbox,Ncomp,Nghost,Fab_allocate);
xflux.setVal(1.e30);
BoxArray yfluxbox(bs);
yfluxbox.surroundingNodes(1);
MultiFab yflux(yfluxbox,Ncomp,Nghost,Fab_allocate);
yflux.setVal(1.e30);
#if BL_SPACEDIM>2
BoxArray zfluxbox(bs);
zfluxbox.surroundingNodes(2);
MultiFab zflux(zfluxbox,Ncomp,Nghost,Fab_allocate);
zflux.setVal(1.e30);
#endif
lp.compFlux(xflux,
yflux,
#if BL_SPACEDIM>2
zflux,
#endif
tsoln);
// Write fluxes
//writeMF(&xflux,"xflux.mfab");
//writeMF(&yflux,"yflux.mfab");
#if BL_SPACEDIM>2
//writeMF(&zflux,"zflux.mfab");
#endif
#endif
#endif
Real tolerance = 1.0e-10; pp.query("tol", tolerance);
Real tolerance_abs = 1.0e-10; pp.query("tol_abs", tolerance_abs);
#if 0
cout << "Bndry Data object:" << std::endl;
cout << lp.bndryData() << std::endl;
#endif
#if 0
bool use_mg_pre = false;
MCCGSolver cg(lp,use_mg_pre);
cg.solve(soln,rhs,tolerance,tolerance_abs);
#else
MCMultiGrid mg(lp);
mg.solve(soln,rhs,tolerance,tolerance_abs);
#endif
#if 0
cout << "MCLinOp object:" << std::endl;
cout << lp << std::endl;
#endif
VisMF::Write(soln,"soln");
#if 0
// apply operator to soln to see if really satisfies eqn
tsoln.copy(soln);
lp.apply(out,tsoln);
soln.copy(out);
// Output "apply" results on soln
VisMF::Write(soln,"apply");
// Compute truncation
for (MFIter smfi(soln); smfi.isValid(); ++smfi)
{
soln[smfi] -= fine[smfi];
}
for( int icomp=0; icomp < BL_SPACEDIM ; icomp++ )
{
Real solnMin = soln.min(icomp);
Real solnMax = soln.max(icomp);
ParallelDescriptor::ReduceRealMin(solnMin);
ParallelDescriptor::ReduceRealMax(solnMax);
if (ParallelDescriptor::IOProcessor())
{
cout << icomp << " "<<solnMin << " " << solnMax <<std::endl;
}
}
// Output truncation
VisMF::Write(soln,"trunc");
#endif
int dumpLp=0; pp.query("dumpLp",dumpLp);
bool write_lp = (dumpLp == 1 ? true : false);
if (write_lp)
std::cout << lp << std::endl;
// Output trunc
ParallelDescriptor::EndParallel();
}
bool
ParticleBase::CrseToFine (const BoxArray& cfba,
const Array<IntVect>& cells,
Array<IntVect>& cfshifts,
const Geometry& gm,
Array<int>& which,
Array<IntVect>& pshifts)
{
//
// We're in AssignDensity(). We want to know whether or not updating
// with a particle, will we cross a crse->fine boundary of the level
// with coarsened fine BoxArray "cfba". "cells" are as calculated from
// CIC_Cells_Fracs().
//
const int M = cells.size();
which.resize(M);
cfshifts.resize(M);
for (int i = 0; i < M; i++)
which[i] = 0;
bool result = false;
for (int i = 0; i < M; i++)
{
if (cfba.contains(cells[i]))
{
result = true;
which[i] = 1;
cfshifts[i] = IntVect::TheZeroVector();
}
else if (!gm.Domain().contains(cells[i]))
{
BL_ASSERT(gm.isAnyPeriodic());
//
// Can the cell be shifted into cfba?
//
const Box bx(cells[i],cells[i]);
gm.periodicShift(bx, gm.Domain(), pshifts);
if (!pshifts.empty())
{
BL_ASSERT(pshifts.size() == 1);
const Box& dbx = bx - pshifts[0];
BL_ASSERT(dbx.ok());
if (cfba.contains(dbx))
{
//
// Note that pshifts[0] is from the coarse perspective.
// We'll later need to multiply it by ref ratio to use
// at the fine level.
//
result = true;
which[i] = 1;
cfshifts[i] = pshifts[0];
}
}
}
}
return result;
}
void main_main ()
{
// What time is it now? We'll use this to compute total run time.
Real strt_time = ParallelDescriptor::second();
std::cout << std::setprecision(15);
int n_cell, max_grid_size, nsteps, plot_int, is_periodic[BL_SPACEDIM];
// Boundary conditions
Array<int> lo_bc(BL_SPACEDIM), hi_bc(BL_SPACEDIM);
// inputs parameters
{
// ParmParse is way of reading inputs from the inputs file
ParmParse pp;
// We need to get n_cell from the inputs file - this is the number of cells on each side of
// a square (or cubic) domain.
pp.get("n_cell",n_cell);
// Default nsteps to 0, allow us to set it to something else in the inputs file
pp.get("max_grid_size",max_grid_size);
// Default plot_int to 1, allow us to set it to something else in the inputs file
// If plot_int < 0 then no plot files will be written
plot_int = 1;
pp.query("plot_int",plot_int);
// Default nsteps to 0, allow us to set it to something else in the inputs file
nsteps = 0;
pp.query("nsteps",nsteps);
// Boundary conditions - default is periodic (INT_DIR)
for (int i = 0; i < BL_SPACEDIM; ++i)
{
lo_bc[i] = hi_bc[i] = INT_DIR; // periodic boundaries are interior boundaries
}
pp.queryarr("lo_bc",lo_bc,0,BL_SPACEDIM);
pp.queryarr("hi_bc",hi_bc,0,BL_SPACEDIM);
}
// make BoxArray and Geometry
BoxArray ba;
Geometry geom;
{
IntVect dom_lo(IntVect(D_DECL(0,0,0)));
IntVect dom_hi(IntVect(D_DECL(n_cell-1, n_cell-1, n_cell-1)));
Box domain(dom_lo, dom_hi);
// Initialize the boxarray "ba" from the single box "bx"
ba.define(domain);
// Break up boxarray "ba" into chunks no larger than "max_grid_size" along a direction
ba.maxSize(max_grid_size);
// This defines the physical size of the box. Right now the box is [-1,1] in each direction.
RealBox real_box;
for (int n = 0; n < BL_SPACEDIM; n++) {
real_box.setLo(n,-1.0);
real_box.setHi(n, 1.0);
}
// This says we are using Cartesian coordinates
int coord = 0;
// This sets the boundary conditions to be doubly or triply periodic
int is_periodic[BL_SPACEDIM];
for (int i = 0; i < BL_SPACEDIM; i++)
{
is_periodic[i] = 0;
if (lo_bc[i] == 0 && hi_bc[i] == 0) {
is_periodic[i] = 1;
}
}
// This defines a Geometry object
geom.define(domain,&real_box,coord,is_periodic);
}
// Boundary conditions
PhysBCFunct physbcf;
BCRec bcr(&lo_bc[0], &hi_bc[0]);
physbcf.define(geom, bcr, BndryFunctBase(phifill)); // phifill is a fortran function
// define dx[]
const Real* dx = geom.CellSize();
// Nghost = number of ghost cells for each array
int Nghost = 1;
// Ncomp = number of components for each array
int Ncomp = 1;
// time = starting time in the simulation
Real time = 0.0;
// we allocate two phi multifabs; one will store the old state, the other the new
// we swap the indices each time step to avoid copies of new into old
PArray<MultiFab> phi(2, PArrayManage);
phi.set(0, new MultiFab(ba, Ncomp, Nghost));
phi.set(1, new MultiFab(ba, Ncomp, Nghost));
// Initialize both to zero (just because)
phi[0].setVal(0.0);
phi[1].setVal(0.0);
// Initialize phi[init_index] by calling a Fortran routine.
// MFIter = MultiFab Iterator
int init_index = 0;
for ( MFIter mfi(phi[init_index]); mfi.isValid(); ++mfi )
{
const Box& bx = mfi.validbox();
init_phi(phi[init_index][mfi].dataPtr(),
bx.loVect(), bx.hiVect(), &Nghost,
geom.CellSize(), geom.ProbLo(), geom.ProbHi());
}
// compute the time step
Real dt = 0.9*dx[0]*dx[0] / (2.0*BL_SPACEDIM);
// Write a plotfile of the initial data if plot_int > 0 (plot_int was defined in the inputs file)
if (plot_int > 0)
{
int n = 0;
const std::string& pltfile = BoxLib::Concatenate("plt",n,5);
writePlotFile(pltfile, phi[init_index], geom, time);
}
// build the flux multifabs
PArray<MultiFab> flux(BL_SPACEDIM, PArrayManage);
for (int dir = 0; dir < BL_SPACEDIM; dir++)
{
// flux(dir) has one component, zero ghost cells, and is nodal in direction dir
BoxArray edge_ba = ba;
edge_ba.surroundingNodes(dir);
flux.set(dir, new MultiFab(edge_ba, 1, 0));
}
int old_index = init_index;
for (int n = 1; n <= nsteps; n++, old_index = 1 - old_index)
{
int new_index = 1 - old_index;
// new_phi = old_phi + dt * (something)
advance(phi[old_index], phi[new_index], flux, time, dt, geom, physbcf, bcr);
time = time + dt;
// Tell the I/O Processor to write out which step we're doing
if (ParallelDescriptor::IOProcessor())
std::cout << "Advanced step " << n << std::endl;
// Write a plotfile of the current data (plot_int was defined in the inputs file)
if (plot_int > 0 && n%plot_int == 0)
{
const std::string& pltfile = BoxLib::Concatenate("plt",n,5);
writePlotFile(pltfile, phi[new_index], geom, time);
}
}
// Call the timer again and compute the maximum difference between the start time and stop time
// over all processors
Real stop_time = ParallelDescriptor::second() - strt_time;
const int IOProc = ParallelDescriptor::IOProcessorNumber();
ParallelDescriptor::ReduceRealMax(stop_time,IOProc);
// Tell the I/O Processor to write out the "run time"
if (ParallelDescriptor::IOProcessor()) {
std::cout << "Run time = " << stop_time << std::endl;
}
}
int
main (int argc,
char* argv[])
{
amrex::Initialize(argc,argv);
if (argc < 2)
print_usage(argc,argv);
ParmParse pp;
if (pp.contains("help"))
print_usage(argc,argv);
bool verbose = false;
if (pp.contains("verbose"))
{
verbose = true;
AmrData::SetVerbose(true);
}
std::string infile;
pp.get("infile",infile);
if (ParallelDescriptor::IOProcessor())
std::cout << "Reading " << infile << "...";
DataServices::SetBatchMode();
Amrvis::FileType fileType(Amrvis::NEWPLT);
DataServices dataServices(infile, fileType);
if( ! dataServices.AmrDataOk())
DataServices::Dispatch(DataServices::ExitRequest, NULL);
if (ParallelDescriptor::IOProcessor())
std::cout << "Done reading plot file" << std::endl;
AmrData& amrData = dataServices.AmrDataRef();
int finestLevel = amrData.FinestLevel();
pp.query("finestLevel",finestLevel); finestLevel=std::min(finestLevel,amrData.FinestLevel());
int Nlev = finestLevel + 1;
if (ParallelDescriptor::IOProcessor())
std::cout << "... finest level " << finestLevel << std::endl;
Vector<int> comps;
if (int nc = pp.countval("comps"))
{
comps.resize(nc);
pp.getarr("comps",comps,0,nc);
}
else
{
int sComp = 0;
pp.query("sComp",sComp);
int nComp = 1;
pp.query("nComp",nComp);
BL_ASSERT(sComp+nComp <= amrData.NComp());
comps.resize(nComp);
std::cout << "NCOMP NOW " << nComp << std::endl;
for (int i=0; i<nComp; ++i)
comps[i] = sComp + i;
}
int nComp = comps.size();
const Vector<string>& plotVarNames=amrData.PlotVarNames();
Vector<string> inVarNames(nComp);
Vector<int> destFillComps(nComp);
for (int i=0; i<nComp; ++i)
{
inVarNames[i] = plotVarNames[comps[i]];
std::cout << "plotVarNames " << plotVarNames[comps[i]] << std::endl;;
destFillComps[i] = i;
}
const int nGrow = 0;
if (ParallelDescriptor::IOProcessor() && verbose>0)
{
cerr << "Will read the following states: ";
for (int i=0; i<nComp; ++i)
cerr << " " << amrData.StateNumber(inVarNames[i]) << " (" << inVarNames[i] << ")" ;
cerr << '\n';
}
const Box& probDomain = amrData.ProbDomain()[finestLevel];
int dir=BL_SPACEDIM-1; pp.query("dir",dir);
const IntVect lo=probDomain.smallEnd();
IntVect hi=lo; hi[dir] = probDomain.bigEnd()[dir];
const Box resBox(lo,hi);
FArrayBox resFab(resBox,nComp); resFab.setVal(0.);
int accumFac = 1;
for (int lev=finestLevel; lev>=0; --lev)
{
const BoxArray& ba = amrData.boxArray(lev);
const DistributionMapping& dm = amrData.DistributionMap(lev);
MultiFab mf(ba,dm,nComp,nGrow);
if (ParallelDescriptor::IOProcessor() && verbose>0)
cerr << "...filling data at level " << lev << endl;
amrData.FillVar(mf,lev,inVarNames,destFillComps);
// Zero covered regions
if (lev < finestLevel)
{
const BoxArray baf = BoxArray(amrData.boxArray(lev+1)).coarsen(amrData.RefRatio()[lev]);
for (MFIter mfi(mf); mfi.isValid(); ++mfi)
{
FArrayBox& myFab = mf[mfi];
std::vector< std::pair<int,Box> > isects = baf.intersections(ba[mfi.index()]);
for (int ii = 0; ii < isects.size(); ii++)
myFab.setVal(0,isects[ii].second,0,nComp);
}
}
// Scale by "volume" (plane, 1 cell thick) of cells, normalized to volume of finest cells
mf.mult(accumFac*accumFac,0,nComp);
for (MFIter mfi(mf); mfi.isValid(); ++mfi)
{
const FArrayBox& fab = mf[mfi];
const Box& box = mfi.validbox();
IntVect ivlo = box.smallEnd();
IntVect ivhi = box.bigEnd(); ivhi[dir] = ivlo[dir];
for (int plane=box.smallEnd(dir); plane<=box.bigEnd(dir); ++plane)
{
ivlo[dir] = plane;
ivhi[dir] = plane;
Box subbox(ivlo,ivhi);
Vector<Real> thisSum(nComp);
for (int n=0; n<nComp; ++n)
thisSum[n] = fab.sum(subbox,n,1);
// Now, increment each sum affected by this coarse plane
for (int r=0; r<accumFac; ++r)
{
const int finePlane = plane*accumFac + r;
IntVect ivF=resBox.smallEnd(); ivF[dir] = finePlane;
for (int n=0; n<nComp; ++n)
resFab(ivF,n) += thisSum[n];
}
}
}
if (lev>0)
accumFac *= amrData.RefRatio()[lev-1];
}
// Accumulate sums from all processors to IOProc
ParallelDescriptor::ReduceRealSum(resFab.dataPtr(),nComp*resBox.numPts(),ParallelDescriptor::IOProcessorNumber());
if (ParallelDescriptor::IOProcessor())
{
// Scale result by total "volume" (plane, 1 cell thick) of slab at each plane
Real volume=1;
for (int d=0; d<BL_SPACEDIM; ++d)
if (d!=dir)
volume*=probDomain.length(d);
resFab.mult(1/volume);
std::cout << "RESFAB " << resFab << std::endl;
}
amrex::Finalize();
return 0;
}
