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Qmoist ptr (#1337)
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* Make qmoist a unique_ptr and size it based upon the microphysics model.

* Merge develop and adhere to formatting.
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@AMLattanzi
AMLattanzi authored Dec 11, 2023
1 parent f83644c commit 59c4ca9
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Showing 24 changed files with 906 additions and 855 deletions.
2 changes: 1 addition & 1 deletion Source/ERF.H
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Expand Up @@ -530,7 +530,7 @@ private:
amrex::Vector<amrex::MultiFab> rW_new;

Microphysics micro;
amrex::Vector<amrex::MultiFab> qmoist; // This has 6 components: qv, qc, qi, qr, qs, qg
amrex::Vector<std::unique_ptr<amrex::MultiFab>> qmoist; // This has up to 6 components: qv, qc, qi, qr, qs, qg

#if defined(ERF_USE_RRTMGP)
Radiation rad;
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12 changes: 6 additions & 6 deletions Source/ERF.cpp
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Expand Up @@ -548,7 +548,7 @@ ERF::InitData ()
if (solverChoice.moisture_type != MoistureType::None)
{
for (int lev = 0; lev <= finest_level; lev++) {
FillPatchMoistVars(lev, qmoist[lev]);
FillPatchMoistVars(lev, *(qmoist[lev]));
}
}
}
Expand Down Expand Up @@ -587,9 +587,9 @@ ERF::InitData ()
{
// If not restarting we need to fill qmoist given qt and qp.
if (restart_chkfile.empty()) {
micro.Init(vars_new[lev][Vars::cons], qmoist[lev],
micro.Init(vars_new[lev][Vars::cons], *(qmoist[lev]),
grids[lev], Geom(lev), 0.0); // dummy value, not needed just to diagnose
micro.Update(vars_new[lev][Vars::cons], qmoist[lev]);
micro.Update(vars_new[lev][Vars::cons], *(qmoist[lev]));
}
}
}
Expand Down Expand Up @@ -856,6 +856,8 @@ ERF::init_only (int lev, Real time)
lev_new[Vars::yvel].setVal(0.0); lev_old[Vars::yvel].setVal(0.0);
lev_new[Vars::zvel].setVal(0.0); lev_old[Vars::zvel].setVal(0.0);

qmoist[lev]->setVal(0.);

// Initialize background flow (optional)
if (init_type == "input_sounding") {
// The base state is initialized by integrating vertically through the
Expand Down Expand Up @@ -889,8 +891,6 @@ ERF::init_only (int lev, Real time)
init_from_hse(lev);
}

qmoist[lev].setVal(0.);

// Add problem-specific flow features
//
// Notes:
Expand Down Expand Up @@ -1172,7 +1172,7 @@ ERF::MakeHorizontalAverages ()

if (use_moisture)
{
MultiFab qv(qmoist[lev], make_alias, 0, 1);
MultiFab qv(*(qmoist[lev]), make_alias, 0, 1);

for (MFIter mfi(mf); mfi.isValid(); ++mfi) {
const Box& bx = mfi.validbox();
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12 changes: 9 additions & 3 deletions Source/ERF_make_new_level.cpp
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Expand Up @@ -59,7 +59,8 @@ void ERF::MakeNewLevelFromScratch (int lev, Real time, const BoxArray& ba,
//********************************************************************************************
// Microphysics
// *******************************************************************************************
qmoist[lev].define(ba, dm, 6, ngrow_state); // qv, qc, qi, qr, qs, qg
int q_size = micro.Get_Qmoist_Size();
qmoist[lev] = std::make_unique<MultiFab>(ba, dm, q_size, ngrow_state); // qv, qc, qi, qr, qs, qg

// ********************************************************************************************
// Build the data structures for calculating diffusive/turbulent terms
Expand Down Expand Up @@ -194,7 +195,8 @@ ERF::MakeNewLevelFromCoarse (int lev, Real time, const BoxArray& ba,
// Microphysics
// *******************************************************************************************
int ngrow_state = ComputeGhostCells(solverChoice.advChoice, solverChoice.use_NumDiff) + 1;
qmoist[lev].define(ba, dm, 6, ngrow_state); // qv, qc, qi, qr, qs, qg
int q_size = micro.Get_Qmoist_Size();
qmoist[lev] = std::make_unique<MultiFab>(ba, dm, q_size, ngrow_state);

init_stuff(lev, ba, dm);

Expand Down Expand Up @@ -296,7 +298,8 @@ ERF::RemakeLevel (int lev, Real time, const BoxArray& ba, const DistributionMapp
//********************************************************************************************
// Microphysics
// *******************************************************************************************
qmoist[lev].define(ba, dm, 6, ngrow_state); // qv, qc, qi, qr, qs, qg
int q_size = micro.Get_Qmoist_Size();
qmoist[lev]->define(ba, dm, q_size, ngrow_state); // qv, qc, qi, qr, qs, qg

init_stuff(lev,ba,dm);

Expand Down Expand Up @@ -544,6 +547,9 @@ ERF::ClearLevel (int lev)
rW_new[lev].clear();
rW_old[lev].clear();

// Clears the qmoist memory
qmoist[lev].reset();

// Clears the integrator memory
mri_integrator_mem[lev].reset();
physbcs[lev].reset();
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14 changes: 7 additions & 7 deletions Source/IO/Checkpoint.cpp
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Expand Up @@ -129,9 +129,9 @@ ERF::WriteCheckpointFile () const
IntVect ng;
if (solverChoice.moisture_type != MoistureType::None) {
// We must read and write qmoist with ghost cells because we don't directly impose BCs on these vars
ng = qmoist[lev].nGrowVect();
MultiFab moist_vars(grids[lev],dmap[lev],qmoist[lev].nComp(),ng);
MultiFab::Copy(moist_vars,qmoist[lev],0,0,qmoist[lev].nComp(),ng);
ng = qmoist[lev]->nGrowVect();
MultiFab moist_vars(grids[lev],dmap[lev],qmoist[lev]->nComp(),ng);
MultiFab::Copy(moist_vars,*(qmoist[lev]),0,0,qmoist[lev]->nComp(),ng);
VisMF::Write(moist_vars, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "MoistVars"));
}

Expand Down Expand Up @@ -346,12 +346,12 @@ ERF::ReadCheckpointFile ()

IntVect ng;
if (solverChoice.moisture_type == MoistureType::None) {
qmoist[lev].setVal(0.0);
qmoist[lev]->setVal(0.0);
} else {
ng = qmoist[lev].nGrowVect();
MultiFab moist_vars(grids[lev],dmap[lev],qmoist[lev].nComp(),ng);
ng = qmoist[lev]->nGrowVect();
MultiFab moist_vars(grids[lev],dmap[lev],qmoist[lev]->nComp(),ng);
VisMF::Read(moist_vars, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "MoistVars"));
MultiFab::Copy(qmoist[lev],moist_vars,0,0,qmoist[lev].nComp(),ng);
MultiFab::Copy(*(qmoist[lev]),moist_vars,0,0,qmoist[lev]->nComp(),ng);
}

// Note that we read the ghost cells of the base state (unlike above)
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2 changes: 1 addition & 1 deletion Source/IO/ERF_Write1DProfiles.cpp
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Expand Up @@ -246,7 +246,7 @@ ERF::derive_diag_profiles(Gpu::HostVector<Real>& h_avg_u , Gpu::HostVector<Rea

if (use_moisture)
{
MultiFab qv(qmoist[lev], make_alias, 0, 1);
MultiFab qv(*(qmoist[lev]), make_alias, 0, 1);

for ( MFIter mfi(mf_cons,TilingIfNotGPU()); mfi.isValid(); ++mfi)
{
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18 changes: 10 additions & 8 deletions Source/IO/Plotfile.cpp
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Expand Up @@ -205,7 +205,7 @@ ERF::WritePlotFile (int which, Vector<std::string> plot_var_names)
const Box& bx = mfi.tilebox();
const Array4<Real >& derdat = mf[lev].array(mfi);
const Array4<Real const>& S_arr = vars_new[lev][Vars::cons].const_array(mfi);
const Array4<Real const>& qv_arr = qmoist[0].const_array(mfi);
const Array4<Real const>& qv_arr = qmoist[0]->const_array(mfi);

ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k) noexcept
{
Expand All @@ -227,7 +227,7 @@ ERF::WritePlotFile (int which, Vector<std::string> plot_var_names)
const Array4<Real>& derdat = mf[lev].array(mfi);
const Array4<Real const>& p0_arr = p_hse.const_array(mfi);
const Array4<Real const>& S_arr = vars_new[lev][Vars::cons].const_array(mfi);
const Array4<Real const> & qv_arr = qmoist[0].const_array(mfi);
const Array4<Real const> & qv_arr = qmoist[0]->const_array(mfi);

ParallelFor(bx, [=] AMREX_GPU_DEVICE(int i, int j, int k) noexcept
{
Expand Down Expand Up @@ -593,12 +593,14 @@ ERF::WritePlotFile (int which, Vector<std::string> plot_var_names)
mf_comp ++;
}

MultiFab qv_mf(qmoist[lev], make_alias, 0, 1);
MultiFab qc_mf(qmoist[lev], make_alias, 1, 1);
MultiFab qi_mf(qmoist[lev], make_alias, 2, 1);
MultiFab qr_mf(qmoist[lev], make_alias, 3, 1);
MultiFab qs_mf(qmoist[lev], make_alias, 4, 1);
MultiFab qg_mf(qmoist[lev], make_alias, 5, 1);
// TODO: Protect against accessing non-existent data
int q_size = micro.Get_Qmoist_Size();
MultiFab qv_mf(*(qmoist[lev]), make_alias, 0, 1);
MultiFab qc_mf(*(qmoist[lev]), make_alias, 1, 1);
MultiFab qi_mf(*(qmoist[lev]), make_alias, 2, 1);
MultiFab qr_mf(*(qmoist[lev]), make_alias, 3, 1);
MultiFab qs_mf(*(qmoist[lev]), make_alias, 4, 1);
MultiFab qg_mf(*(qmoist[lev]), make_alias, 5, 1);

if (containerHasElement(plot_var_names, "qt"))
{
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4 changes: 2 additions & 2 deletions Source/Initialization/ERF_init_custom.cpp
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Expand Up @@ -25,7 +25,7 @@ void
ERF::init_custom (int lev)
{
auto& lev_new = vars_new[lev];
auto& qmoist_new = qmoist[lev];
auto& qmoist_new = *(qmoist[lev]);

MultiFab r_hse(base_state[lev], make_alias, 0, 1); // r_0 is first component
MultiFab p_hse(base_state[lev], make_alias, 1, 1); // p_0 is second component
Expand All @@ -42,7 +42,7 @@ ERF::init_custom (int lev)
yvel_pert.setVal(0.);
zvel_pert.setVal(0.);

MultiFab qmoist_pert(qmoist[lev].boxArray(), qmoist[lev].DistributionMap(), 3, qmoist[lev].nGrow());
MultiFab qmoist_pert(qmoist[lev]->boxArray(), qmoist[lev]->DistributionMap(), 3, qmoist[lev]->nGrow());
qmoist_pert.setVal(0.);

MultiFab qv_pert(qmoist_pert, amrex::make_alias, 0, 1);
Expand Down
2 changes: 1 addition & 1 deletion Source/Initialization/InputSoundingData.H
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Expand Up @@ -79,7 +79,7 @@ public:
iss_z >> z >> theta >> qv >> U >> V;
if (z == 0) {
AMREX_ALWAYS_ASSERT(theta == theta_inp_sound_tmp[0]);
AMREX_ALWAYS_ASSERT(qv == qv_inp_sound_tmp[0]);
AMREX_ALWAYS_ASSERT(qv*0.001 == qv_inp_sound_tmp[0]);
U_inp_sound_tmp[0] = U;
V_inp_sound_tmp[0] = V;
} else {
Expand Down
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