static void Boxes (const std::string& file, const std::string& name, BoxArray& boxes, int& boxesLevel) { const std::string TheDflt = "default:"; const std::string TheName = name + ":"; std::ifstream is(file.c_str(),std::ios::in); if (!is.good()) BoxLib::FileOpenFailed(file); #define STRIP while( is.get() != '\n' ) BoxArray ba_dflt; BoxArray ba_name; int bxLvl_dflt = -1; int bxLvl_name = -1; std::string line; while (std::getline(is,line)) { if (line.empty() || line[0] == '#') continue; if (line == TheDflt || line == TheName) { bool dflt = (line == TheDflt) ? true : false; int N; int lvl; Box bx; BoxList bl; is >> N; STRIP; is >> lvl; STRIP; BL_ASSERT(N > 0); for (int i = 0; i < N; i++) { is >> bx; STRIP; bl.push_back(bx); } if (dflt) { ba_dflt = BoxArray(bl); bxLvl_dflt = lvl; } else { ba_name = BoxArray(bl); bxLvl_name = lvl; } } }
BoxList Box::LoadBoxesFromFile(const string& fileName) { FILE* fin = fopen(fileName.c_str(), "r"); BoxList boxes; int n; if (!fin) { printf("ERROR: NO such file '%s'\n", fileName.c_str()); return boxes; } fscanf(fin, "%d", &n); for (int i = 0; i < n; i++) { int l, w, h; fscanf(fin, "%d%d%d", &l, &w, &h); boxes.push_back(Box(l, w, h)); } fclose(fin); return boxes; }
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; }
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); }