void
AuxBoundaryData::initialize (const BoxArray& ba,
int n_grow,
int n_comp,
const Geometry& geom)
{
BL_ASSERT(!m_initialized);
const bool verbose = false;
const int NProcs = ParallelDescriptor::NProcs();
const Real strt_time = ParallelDescriptor::second();
m_ngrow = n_grow;
BoxList gcells = BoxLib::GetBndryCells(ba,n_grow);
//
// Remove any intersections with periodically shifted valid region.
//
if (geom.isAnyPeriodic())
{
Box dmn = geom.Domain();
for (int d = 0; d < BL_SPACEDIM; d++)
if (!geom.isPeriodic(d))
dmn.grow(d,n_grow);
for (BoxList::iterator it = gcells.begin(); it != gcells.end(); )
{
const Box& isect = *it & dmn;
if (isect.ok())
{
*it++ = isect;
}
else
{
gcells.remove(it++);
}
}
}
gcells.simplify();
if (gcells.size() < NProcs)
{
gcells.maxSize(BL_SPACEDIM == 3 ? 64 : 128);
}
BoxArray nba(gcells);
gcells.clear();
if (nba.size() > 0)
{
m_fabs.define(nba, n_comp, 0, Fab_allocate);
}
else
{
m_empty = true;
}
if (verbose)
{
const int IOProc = ParallelDescriptor::IOProcessorNumber();
Real run_time = ParallelDescriptor::second() - strt_time;
const int sz = nba.size();
#ifdef BL_LAZY
Lazy::QueueReduction( [=] () mutable {
#endif
ParallelDescriptor::ReduceRealMax(run_time,IOProc);
if (ParallelDescriptor::IOProcessor())
std::cout << "AuxBoundaryData::initialize() size = " << sz << ", time = " << run_time << '\n';
#ifdef BL_LAZY
});
#endif
}
m_initialized = true;
}
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;
}