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Fix issues #186, #191-#193, #195-#200 #205

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Merged
asalmgren merged 1 commit into from
Sep 28, 2026
Merged

Fix issues #186, #191-#193, #195-#200 #205

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2 changes: 2 additions & 0 deletions Source/Diffusion.H
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Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,7 @@ public:
const amrex::MultiFab& rho_half,
int rho_flag,
const amrex::MultiFab* const* beta,
const amrex::MultiFab* betaCC,
int betaComp = 0,
bool update_fluxreg = true);

Expand All @@ -127,6 +128,7 @@ public:
const amrex::MultiFab& rho_half,
int rho_flag,
const amrex::MultiFab* const* beta,
const amrex::MultiFab* betaCC,
int betaComp,
bool update_fluxreg);

Expand Down
51 changes: 31 additions & 20 deletions Source/Diffusion.cpp
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Expand Up @@ -394,6 +394,14 @@ Diffusion::diffuse_scalar (const Vector<MultiFab*>& S_old,
}
opn.setCoarseFineBC(Solnc.get(), cratio[0]);
}
else if (level > 0) {
//
// No coarse data supplied, but this is a level > 0 solve, so
// we still must tell MLMG the true refinement ratio for the
// homogeneous Dirichlet coarse-fine boundary condition.
//
opn.setCoarseFineBC(nullptr, cratio[0]);
}
MultiFab::Copy(Soln,*S_old[0],sigma,0,nComp,ng);
if (rho_flag == 2) {
#ifdef AMREX_USE_OMP
Expand Down Expand Up @@ -517,6 +525,9 @@ Diffusion::diffuse_scalar (const Vector<MultiFab*>& S_old,
}
opnp1.setCoarseFineBC(Solnc.get(), cratio[0]);
}
else if (level > 0) {
opnp1.setCoarseFineBC(nullptr, cratio[0]);
}
#ifdef AMREX_USE_OMP
#pragma omp parallel if (Gpu::notInLaunchRegion())
#endif
Expand Down Expand Up @@ -847,7 +858,6 @@ Diffusion::diffuse_tensor_velocity (Real dt,
// const Real tol_abs = 0.0;
// cribbing from scalar
const Real tol_rel = visc_tol;
const Real tol_abs = get_scaled_abs_tol(Rhs, visc_tol);

LPInfo info;
info.setAgglomeration(agglomeration);
Expand Down Expand Up @@ -889,10 +899,10 @@ Diffusion::diffuse_tensor_velocity (Real dt,
tensorop.setLevelBC(0, &Soln);
}

Real rhsscale = 1.0;
{
MultiFab acoef;
std::pair<Real,Real> scalars;
Real rhsscale = 1.0;
const MultiFab& rho = (rho_flag == 1) ? rho_half : navier_stokes->get_new_data(State_Type);
const int rho_comp = (rho_flag == 1) ? 0 : Density;
computeAlpha(acoef, scalars, a, b,
Expand All @@ -901,6 +911,12 @@ Diffusion::diffuse_tensor_velocity (Real dt,
tensorop.setScalars(scalars.first, scalars.second);
tensorop.setACoeffs(0, acoef);
}
//
// computeAlpha scaled the operator scalars by rhsscale; the RHS must be
// scaled to match (cf. diffuse_scalar and diffuse_Ssync).
//
Rhs.mult(rhsscale,0,AMREX_SPACEDIM);
const Real tol_abs = get_scaled_abs_tol(Rhs, visc_tol);

#ifdef AMREX_USE_EB
setViscosity(tensorop, betanp1, betaComp, *betanp1CC);
Expand Down Expand Up @@ -966,6 +982,7 @@ Diffusion::diffuse_Vsync (MultiFab& Vsync,
const MultiFab& rho_half,
int rho_flag,
const MultiFab* const* beta,
const MultiFab* betaCC,
int betaComp,
bool update_fluxreg)
{
Expand All @@ -979,7 +996,7 @@ Diffusion::diffuse_Vsync (MultiFab& Vsync,
AMREX_ASSERT(beta[d]->min(0,0) >= 0.0);
#endif

diffuse_tensor_Vsync(Vsync,dt,be_cn_theta,rho_half,rho_flag,beta,betaComp,update_fluxreg);
diffuse_tensor_Vsync(Vsync,dt,be_cn_theta,rho_half,rho_flag,beta,betaCC,betaComp,update_fluxreg);
//
// applyBC has put "incorrect" values in the ghost cells
// outside external Dirichlet boundaries. Reset these to zero
Expand Down Expand Up @@ -1017,8 +1034,9 @@ Diffusion::diffuse_tensor_Vsync (MultiFab& Vsync,
Real be_cn_theta,
const MultiFab& rho_half,
int rho_flag,
const MultiFab* const* /*beta*/,
int /*betaComp*/,
const MultiFab* const* beta,
const MultiFab* betaCC,
int betaComp,
bool update_fluxreg)
{
AMREX_ASSERT(rho_flag == 1 || rho_flag == 3);
Expand All @@ -1045,7 +1063,9 @@ Diffusion::diffuse_tensor_Vsync (MultiFab& Vsync,
{
const Box& bx = mfi.tilebox();
auto const& rhs = Rhs.array(mfi);
auto const& rho = (rho_flag == 1) ? rho_half.array(mfi) : navier_stokes->get_old_data(State_Type).array(mfi,Density);
// NOTE: must use the new-time density here to match the acoef built
// below and mac_sync's normalization of Vsync by rho^{n+1}.
auto const& rho = (rho_flag == 1) ? rho_half.array(mfi) : navier_stokes->get_new_data(State_Type).array(mfi,Density);

amrex::ParallelFor(bx, [rhs, rho]
AMREX_GPU_DEVICE (int i, int j, int k) noexcept
Expand Down Expand Up @@ -1113,22 +1133,13 @@ Diffusion::diffuse_tensor_Vsync (MultiFab& Vsync,
tensorop.setACoeffs(0, acoef);
}

{
FluxBoxes fb_bcoef;
MultiFab** face_bcoef = nullptr;
face_bcoef = fb_bcoef.define(navier_stokes);
for (int dir=0; dir<AMREX_SPACEDIM; dir++) {
face_bcoef[dir]->setVal(1.0);
}

#ifdef AMREX_USE_EB
MultiFab bcoefCC(grids,dmap,1,0,MFInfo(),navier_stokes->Factory());
bcoefCC.setVal(1.0);
setViscosity(tensorop, face_bcoef, 0, bcoefCC);
AMREX_ALWAYS_ASSERT(betaCC != nullptr);
setViscosity(tensorop, beta, betaComp, *betaCC);
#else
setViscosity(tensorop, face_bcoef, 0);
amrex::ignore_unused(betaCC);
setViscosity(tensorop, beta, betaComp);
#endif
}

MLMG mlmg(tensorop);
if (max_iter > 0) {
Expand All @@ -1144,7 +1155,7 @@ Diffusion::diffuse_tensor_Vsync (MultiFab& Vsync,
mlmg.setMaxFmgIter(max_fmg_iter);
mlmg.setVerbose(verbose);

Rhs.mult(rhsscale,0,1);
Rhs.mult(rhsscale,0,AMREX_SPACEDIM);

mlmg.setFinalFillBC(true);
mlmg.solve({&Soln}, {&Rhs}, tol_rel, tol_abs);
Expand Down
8 changes: 7 additions & 1 deletion Source/NS_LES.cpp
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Expand Up @@ -125,7 +125,13 @@ NavierStokesBase::calc_mut_LES(MultiFab* mu_LES[AMREX_SPACEDIM], const Real time
Real smag = 0;
for (int i_symij = 0; i_symij < dim_fluxes; ++i_symij)
{
Real symij = src(i,j,k,i_symij) + src(i,j,k,i_symij);
// compVelGrad stores du_m/dx_n in component AMREX_SPACEDIM*n+m,
// so the transpose of flat index c is
// (c%AMREX_SPACEDIM)*AMREX_SPACEDIM + c/AMREX_SPACEDIM. Pairing
// each component with its transpose gives symij = 2*S_mn, so
// smag below is 2*S:S and mu_t = (Cs*dx)^2*sqrt(2 S_ij S_ij).
int i_symji = (i_symij%AMREX_SPACEDIM)*AMREX_SPACEDIM + i_symij/AMREX_SPACEDIM;
Real symij = src(i,j,k,i_symij) + src(i,j,k,i_symji);
smag += symij * symij;
}

Expand Down
10 changes: 10 additions & 0 deletions Source/NS_average.cpp
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Expand Up @@ -26,6 +26,16 @@ NavierStokesBase::time_average(amrex::Real& a_time_avg, amrex::Real& a_time_av
{
MultiFab& Sstate = get_new_data(State_Type);
MultiFab& Savg = get_new_data(Average_Type);
//
// Old data may not have been allocated yet, e.g. when this is called from
// post_init and no advance has taken place (ns.init_iter <= 0).
// Zero is the right seed: the kernel below copies S_avg back into
// S_avg_old on every sample, so both time levels agree by construction.
//
if (! state[Average_Type].hasOldData()) {
state[Average_Type].allocOldData();
state[Average_Type].oldData().setVal(0.);
}
MultiFab& Savg_old = get_old_data(Average_Type);

#ifdef _OPENMP
Expand Down
4 changes: 3 additions & 1 deletion Source/NavierStokes.cpp
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Expand Up @@ -1561,7 +1561,9 @@ NavierStokes::mac_sync ()
loc_viscn = fb_viscn.define(this);
getViscosity(loc_viscn, viscTime);

diffusion->diffuse_Vsync(Vsync,dt,be_cn_theta,Rh,rho_flag,loc_viscn,0);
// viscn_cc holds the cell-centered viscosity at prevTime; needed by
// MLEBTensorOp::setEBShearViscosity in EB builds.
diffusion->diffuse_Vsync(Vsync,dt,be_cn_theta,Rh,rho_flag,loc_viscn,viscn_cc,0);
}

FluxBoxes fb_SC;
Expand Down
6 changes: 6 additions & 0 deletions Source/NavierStokesBase.H
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Expand Up @@ -787,6 +787,12 @@ public:
static amrex::Vector<amrex::Real> time_avg;
static amrex::Vector<amrex::Real> time_avg_fluct;
static amrex::Vector<amrex::Real> dt_avg;
//
// Grow time_avg/time_avg_fluct/dt_avg so that every level up to
// a_finest_level has an entry. New entries are zero-filled; existing
// accumulations are preserved.
//
static void grow_avg_vectors (int a_finest_level);
static int avg_interval;
static int compute_fluctuations;
//
Expand Down
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