Fix FillPatchNLevels

This fixes periodic boundary bugs in FillPatchNLevels. The issue is
FillPatchNLevels calls FillPatchTwoLevels, which does not work if the
destination MultiFab's valid region is outside periodic boundaries. So we
need to make sure that that does not happen by shifting the boxes into valid
domain.

Src/AmrCore/AMReX_FillPatchUtil.H

@@ -24,6 +24,7 @@
 
 #include <cmath>
 #include <limits>
+#include <map>
 
 namespace amrex
 {

Src/AmrCore/AMReX_FillPatchUtil_I.H

@@ -1223,6 +1223,61 @@ FillPatchNLevels (MF& mf, int level, const IntVect& nghost, Real time,
 {
  BL_PROFILE("FillPatchNLevels");
 
+ // FillPatchTwolevels relies on that mf's valid region is inside the
+ // domain at periodic boundaries. But when we create coarsen boxarray
+ // using mapper->CoarseBox, the resulting boxarray might violate the
+ // requirement. If that happens, we need to create a second version of
+ // the boxarray that is safe for FillPatchTwolevels.
+
+ auto get_clayout = [&] () -> std::tuple<BoxArray,BoxArray,DistributionMapping>
+ {
+ if (level == 0) {
+ return std::make_tuple(BoxArray(),BoxArray(),DistributionMapping());
+ } else {
+ BoxArray const& ba = mf.boxArray();
+ auto const& typ = ba.ixType();
+ std::map<int,Vector<Box>> extra_boxes_map;
+ BoxList cbl(typ);
+ cbl.reserve(ba.size());
+ for (int i = 0, N = int(ba.size()); i < N; ++i) {
+ Box const& cbox = mapper->CoarseBox(amrex::grow(ba[i],nghost),ratio[level-1]);
+ cbl.push_back(cbox);
+ Box gdomain = geom[level-1].growNonPeriodicDomain(cbox.length());
+ gdomain.convert(typ);
+ if (!gdomain.contains(cbox)) {
+ auto& extra_boxes = extra_boxes_map[i];
+ auto const& pshift = geom[level-1].periodicity().shiftIntVect();
+ for (auto const& piv : pshift) {
+ auto const& ibox = amrex::shift(cbox,piv) & gdomain;
+ if (ibox.ok()) {
+ extra_boxes.push_back(ibox);
+ }
+ }
+ }
+ }
+
+ BoxArray cba2;
+ DistributionMapping dm2;
+ if (!extra_boxes_map.empty()) {
+ BoxList cbl2 = cbl;
+ auto& lbox = cbl2.data();
+ DistributionMapping const& dm = mf.DistributionMap();
+ Vector<int> procmap2 = dm.ProcessorMap();
+ for (auto const& [i, vb] : extra_boxes_map) {
+ lbox[i] = vb[0];
+ for (int j = 1, nj = int(vb.size()); j < nj; ++j) {
+ lbox.push_back(vb[j]);
+ procmap2.push_back(dm[i]);
+ }
+ }
+ cba2 = BoxArray(std::move(cbl2));
+ dm2 = DistributionMapping(std::move(procmap2));
+ }
+
+ return std::make_tuple(BoxArray(std::move(cbl)), cba2, dm2);
+ }
+ };
+
 #ifdef AMREX_USE_EB
  EB2::IndexSpace const* index_space = EB2::TopIndexSpaceIfPresent();
 #else
@@ -1235,35 +1290,40 @@ FillPatchNLevels (MF& mf, int level, const IntVect& nghost, Real time,
  if (level == 0) {
  FillPatchSingleLevel(mf, nghost, time, smf[0], st[0], scomp, dcomp, ncomp, geom[0],
  bc[0], bccomp);
- } else if (level >= int(smf.size())) {
- BoxArray const& ba = mf.boxArray();
- auto const& typ = ba.ixType();
- Box domain_g = geom[level].growPeriodicDomain(nghost);
- domain_g.convert(typ);
- BoxArray cba;
- {
- BoxList cbl(typ);
- cbl.reserve(ba.size());
- for (int i = 0, N = int(ba.size()); i < N; ++i) {
- cbl.push_back(mapper->CoarseBox(amrex::grow(ba[i],nghost), ratio[level-1]));
- }
- cba = BoxArray(std::move(cbl));
- }
- MultiFab cmf_tmp;
+ } else if (level >= int(smf.size()))
+ {
+ auto const& [ba1, ba2, dm2] = get_clayout();
+ MF cmf1, cmf2;
 #ifdef AMREX_USE_EB
  if (index_space) {
- auto factory = makeEBFabFactory(index_space, geom[level-1], cba,
+ auto factory = makeEBFabFactory(index_space, geom[level-1], ba1,
  mf.DistributionMap(), {0,0,0},
  EBSupport::basic);
- cmf_tmp.define(cba, mf.DistributionMap(), ncomp, 0, MFInfo(), *factory);
+ cmf1.define(ba1, mf.DistributionMap(), ncomp, 0, MFInfo(), *factory);
+ if (!ba2.empty()) {
+ auto factory2 = makeEBFabFactory(index_space, geom[level-1], ba2,
+ dm2, {0,0,0},
+ EBSupport::basic);
+ cmf2.define(ba2, dm2, ncomp, 0, MFInfo(), *factory2);
+ }
  } else
 #endif
  {
- cmf_tmp.define(cba, mf.DistributionMap(), ncomp, 0);
+ cmf1.define(ba1, mf.DistributionMap(), ncomp, 0);
+ if (!ba2.empty()) {
+ cmf2.define(ba2, dm2, ncomp, 0);
+ }
  }
- FillPatchNLevels(cmf_tmp, level-1, IntVect(0), time, smf, st, scomp, 0, ncomp,
+
+ MF* p_mf_inside = (ba2.empty()) ? &cmf1 : &cmf2;
+ FillPatchNLevels(*p_mf_inside, level-1, IntVect(0), time, smf, st, scomp, 0, ncomp,
  geom, bc, bccomp, ratio, mapper, bcr, bcrcomp);
- FillPatchInterp(mf, dcomp, cmf_tmp, 0, ncomp, nghost, geom[level-1], geom[level],
+ if (&cmf1 != p_mf_inside) {
+ cmf1.ParallelCopy(*p_mf_inside, geom[level-1].periodicity());
+ }
+ Box domain_g = geom[level].growPeriodicDomain(nghost);
+ domain_g.convert(mf.ixType());
+ FillPatchInterp(mf, dcomp, cmf1, 0, ncomp, nghost, geom[level-1], geom[level],
  domain_g, ratio[level-1], mapper, bcr, bcrcomp);
  } else {
  NullInterpHook<typename MF::FABType::value_type> hook{};
@@ -1278,30 +1338,34 @@ FillPatchNLevels (MF& mf, int level, const IntVect& nghost, Real time,
  hook, hook, index_space, true);
  if (error_code == 0) { return; }
 
- BoxArray cba;
- {
- BoxArray const& ba = mf.boxArray();
- BoxList cbl(mf.ixType());
- cbl.reserve(ba.size());
- for (int i = 0; i < int(ba.size()); ++i) {
- cbl.push_back(mapper->CoarseBox(amrex::grow(ba[i], nghost), ratio[level-1]));
- }
- cba = BoxArray(std::move(cbl));
- }
- MultiFab cmf_tmp;
+ auto const& [ba1, ba2, dm2] = get_clayout();
+ MF cmf_tmp;
 #ifdef AMREX_USE_EB
  if (index_space) {
- auto factory = makeEBFabFactory(index_space, geom[level-1], cba,
- mf.DistributionMap(), {0,0,0},
- EBSupport::basic);
- cmf_tmp.define(cba, mf.DistributionMap(), ncomp, 0, MFInfo(), *factory);
+ if (ba2.empty()) {
+ auto factory = makeEBFabFactory(index_space, geom[level-1], ba1,
+ mf.DistributionMap(), {0,0,0},
+ EBSupport::basic);
+ cmf_tmp.define(ba1, mf.DistributionMap(), ncomp, 0, MFInfo(), *factory);
+ } else {
+ auto factory = makeEBFabFactory(index_space, geom[level-1], ba2,
+ dm2, {0,0,0},
+ EBSupport::basic);
+ cmf_tmp.define(ba2, dm2, ncomp, 0, MFInfo(), *factory);
+ }
  } else
 #endif
  {
- cmf_tmp.define(cba, mf.DistributionMap(), ncomp, 0);
+ if (ba2.empty()) {
+ cmf_tmp.define(ba1, mf.DistributionMap(), ncomp, 0);
+ } else {
+ cmf_tmp.define(ba2, dm2, ncomp, 0);
+ }
  }
+
  FillPatchNLevels(cmf_tmp, level-1, IntVect(0), time, smf, st, scomp, 0, ncomp,
  geom, bc, bccomp, ratio, mapper, bcr, bcrcomp);
+
  Vector<MF*> cmf{&cmf_tmp};
  Vector<MF*> fmf = smf[level];
  Vector<MF> fmf_raii;
@@ -1310,6 +1374,7 @@ FillPatchNLevels (MF& mf, int level, const IntVect& nghost, Real time,
  fmf_raii.emplace_back(*p, amrex::make_alias, scomp, ncomp);
  }
  }
+
  detail::FillPatchTwoLevels_doit(mf, nghost, time,
  cmf, {time},
  fmf, st[level],