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AMReX-Combustion · Sep 19, 2023 · 441aafe · 441aafe
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Showing 8 changed files with 54 additions and 37 deletions.
diff --git a/Source/DiffusionOp.cpp b/Source/DiffusionOp.cpp
@@ -1108,7 +1108,8 @@ DiffusionTensorOp::compute_divtau(
 #else
   m_apply_op->setScalars(0.0, -scale);
   for (int lev = 0; lev <= finest_level; ++lev) {
-    if (have_density != 0) { // alpha being zero, not sure that this does anything.
+    if (have_density != 0) { // alpha being zero, not sure that this does
+                             // anything.
       m_apply_op->setACoeffs(lev, *a_density[lev]);
     }
     int doZeroVisc = 0;
@@ -1194,7 +1195,7 @@ DiffusionTensorOp::diffuse_velocity(
       auto const& rhs_a = rhs[lev].array(mfi);
       auto const& vel_a = a_vel[lev]->const_array(mfi);
       auto const& rho_a = (have_density) != 0 ? a_density[lev]->const_array(mfi)
-                                         : Array4<const Real>{};
+                                              : Array4<const Real>{};
       amrex::ParallelFor(
         bx, AMREX_SPACEDIM,
         [=, rho_incomp = m_pelelm->m_rho,

diff --git a/Source/PeleLMBC.cpp b/Source/PeleLMBC.cpp
@@ -339,7 +339,8 @@ PeleLM::fillpatch_state(
     PhysBCFunct<GpuBndryFuncFab<PeleLMCCFillExtDirState>> bndry_func(
       geom[lev], fetchBCRecArray(0, nCompState),
       PeleLMCCFillExtDirState{
-        lprobparm, lpmfdata, m_nAux, static_cast<int>(turb_inflow.is_initialized())});
+        lprobparm, lpmfdata, m_nAux,
+        static_cast<int>(turb_inflow.is_initialized())});
     FillPatchSingleLevel(
       a_state, IntVect(nGhost), a_time,
       {&(m_leveldata_old[lev]->state), &(m_leveldata_new[lev]->state)},
@@ -352,11 +353,13 @@ PeleLM::fillpatch_state(
     PhysBCFunct<GpuBndryFuncFab<PeleLMCCFillExtDirState>> crse_bndry_func(
       geom[lev - 1], fetchBCRecArray(0, nCompState),
       PeleLMCCFillExtDirState{
-        lprobparm, lpmfdata, m_nAux, static_cast<int>(turb_inflow.is_initialized())});
+        lprobparm, lpmfdata, m_nAux,
+        static_cast<int>(turb_inflow.is_initialized())});
     PhysBCFunct<GpuBndryFuncFab<PeleLMCCFillExtDirState>> fine_bndry_func(
       geom[lev], fetchBCRecArray(0, nCompState),
       PeleLMCCFillExtDirState{
-        lprobparm, lpmfdata, m_nAux, static_cast<int>(turb_inflow.is_initialized())});
+        lprobparm, lpmfdata, m_nAux,
+        static_cast<int>(turb_inflow.is_initialized())});
     FillPatchTwoLevels(
       a_state, IntVect(nGhost), a_time,
       {&(m_leveldata_old[lev - 1]->state), &(m_leveldata_new[lev - 1]->state)},
@@ -734,11 +737,13 @@ PeleLM::fillcoarsepatch_state(
   PhysBCFunct<GpuBndryFuncFab<PeleLMCCFillExtDirState>> crse_bndry_func(
     geom[lev - 1], fetchBCRecArray(0, nCompState),
     PeleLMCCFillExtDirState{
-      lprobparm, lpmfdata, m_nAux, static_cast<int>(turb_inflow.is_initialized())});
+      lprobparm, lpmfdata, m_nAux,
+      static_cast<int>(turb_inflow.is_initialized())});
   PhysBCFunct<GpuBndryFuncFab<PeleLMCCFillExtDirState>> fine_bndry_func(
     geom[lev], fetchBCRecArray(0, nCompState),
     PeleLMCCFillExtDirState{
-      lprobparm, lpmfdata, m_nAux, static_cast<int>(turb_inflow.is_initialized())});
+      lprobparm, lpmfdata, m_nAux,
+      static_cast<int>(turb_inflow.is_initialized())});
   InterpFromCoarseLevel(
     a_state, IntVect(nGhost), a_time, m_leveldata_new[lev - 1]->state, 0, 0,
     nCompState, geom[lev - 1], geom[lev], crse_bndry_func, 0, fine_bndry_func,
@@ -861,7 +866,8 @@ PeleLM::setInflowBoundaryVel(MultiFab& a_vel, int lev, TimeStamp a_time)
   PhysBCFunct<GpuBndryFuncFab<PeleLMCCFillExtDirState>> bndry_func(
     geom[lev], dummyVelBCRec,
     PeleLMCCFillExtDirState{
-      lprobparm, lpmfdata, m_nAux, static_cast<int>(turb_inflow.is_initialized())});
+      lprobparm, lpmfdata, m_nAux,
+      static_cast<int>(turb_inflow.is_initialized())});
 
   bndry_func(a_vel, 0, AMREX_SPACEDIM, a_vel.nGrowVect(), time, 0);
 

diff --git a/Source/PeleLMDiffusion.cpp b/Source/PeleLMDiffusion.cpp
@@ -88,11 +88,12 @@ PeleLM::computeDifferentialDiffusionTerms(
   // wbar term During initialization, don't bother getting the wbar fluxes
   // separately
   Vector<std::array<MultiFab*, AMREX_SPACEDIM>> wbarFluxVec =
-    ((is_init != 0) || (m_use_wbar == 0)) ? Vector<std::array<MultiFab*, AMREX_SPACEDIM>>{}
-                             : GetVecOfArrOfPtrs(diffData->wbar_fluxes);
+    ((is_init != 0) || (m_use_wbar == 0))
+      ? Vector<std::array<MultiFab*, AMREX_SPACEDIM>>{}
+      : GetVecOfArrOfPtrs(diffData->wbar_fluxes);
   Vector<std::array<MultiFab*, AMREX_SPACEDIM>> soretFluxVec =
     (m_use_soret) != 0 ? GetVecOfArrOfPtrs(diffData->soret_fluxes)
-                  : Vector<std::array<MultiFab*, AMREX_SPACEDIM>>{};
+                       : Vector<std::array<MultiFab*, AMREX_SPACEDIM>>{};
 #ifdef AMREX_USE_EB
   if (m_isothermalEB) {
     computeDifferentialDiffusionFluxes(
@@ -108,7 +109,8 @@ PeleLM::computeDifferentialDiffusionTerms(
   // If doing species balances, compute face domain integrals
   // using level 0 since we've averaged down the fluxes already
   // Factor for SDC is 0.5 is for Dn and -0.5 for Dnp1
-  if ((m_sdcIter == 0 || m_sdcIter == m_nSDCmax) && (m_do_speciesBalance != 0)) {
+  if (
+    (m_sdcIter == 0 || m_sdcIter == m_nSDCmax) && (m_do_speciesBalance != 0)) {
     Real sdc_weight = (a_time == AmrOldTime) ? 0.5 : -0.5;
     addRhoYFluxes(GetArrOfConstPtrs(fluxes[0]), geom[0], sdc_weight);
   }
@@ -1040,8 +1042,9 @@ PeleLM::differentialDiffusionUpdate(
         (m_use_wbar) != 0
           ? diffData->Dwbar[lev].const_array(mfi)
           : diffData->Dhat[lev].const_array(mfi); // Dummy unused Array4
-      auto const& dT = (m_use_soret) != 0 ? diffData->DT[lev].const_array(mfi)
-                                     : diffData->Dhat[lev].const_array(mfi);
+      auto const& dT = (m_use_soret) != 0
+                         ? diffData->DT[lev].const_array(mfi)
+                         : diffData->Dhat[lev].const_array(mfi);
 
       amrex::ParallelFor(
         bx, NUM_SPECIES,
@@ -1421,8 +1424,9 @@ PeleLM::getScalarDiffForce(
         (m_use_wbar) != 0
           ? diffData->Dwbar[lev].const_array(mfi, 0)
           : diffData->Dn[lev].const_array(mfi, 0); // Dummy unsed Array4
-      auto const& dT = (m_use_soret) != 0 ? diffData->DT[lev].const_array(mfi, 0)
-                                     : diffData->Dn[lev].const_array(mfi, 0);
+      auto const& dT = (m_use_soret) != 0
+                         ? diffData->DT[lev].const_array(mfi, 0)
+                         : diffData->Dn[lev].const_array(mfi, 0);
 
       amrex::ParallelFor(
         bx,

diff --git a/Source/PeleLMEos.cpp b/Source/PeleLMEos.cpp
@@ -63,7 +63,7 @@ PeleLM::calcDivU(
 
     MultiFab RhoYdot;
     if ((m_do_react != 0) && (m_skipInstantRR == 0)) {
-      if (is_init != 0) {      // Either pre-divU, divU or press initial iterations
+      if (is_init != 0) { // Either pre-divU, divU or press initial iterations
         if (m_dt > 0.0) { // divU ite   -> use I_R
           auto* ldataR_p = getLevelDataReactPtr(lev);
           RhoYdot.define(grids[lev], dmap[lev], nCompIR(), 0);

diff --git a/Source/PeleLMEvolve.cpp b/Source/PeleLMEvolve.cpp
@@ -111,7 +111,9 @@ PeleLM::Evolve()
     (plt_justDidIt == 0) && m_nstep > 0) {
     WritePlotFile();
   }
-  if ((m_check_int > 0 || m_check_per > 0.) && (chk_justDidIt == 0) && m_nstep > 0) {
+  if (
+    (m_check_int > 0 || m_check_per > 0.) && (chk_justDidIt == 0) &&
+    m_nstep > 0) {
     WriteCheckPointFile();
   }
 }

diff --git a/Source/PeleLMRegrid.cpp b/Source/PeleLMRegrid.cpp
@@ -56,9 +56,10 @@ PeleLM::regrid(int lbase, amrex::Real time, bool initial)
         (m_loadBalanceEffRatioThreshold > 0.0) &&
         (ParallelDescriptor::MyProc() ==
          ParallelDescriptor::IOProcessorNumber())) {
-        remakeLevel =
-          (static_cast<int>(remakeLevel != 0) ||
-          (testEfficiency > m_loadBalanceEffRatioThreshold * currentEfficiency));
+        remakeLevel = static_cast<int>(
+          (remakeLevel != 0) ||
+          (testEfficiency >
+           m_loadBalanceEffRatioThreshold * currentEfficiency));
       }
       ParallelDescriptor::Bcast(
         &remakeLevel, 1, ParallelDescriptor::IOProcessorNumber());
@@ -220,9 +221,10 @@ PeleLM::regrid(int lbase, amrex::Real time, bool initial)
               (m_loadBalanceEffRatioThreshold > 0.0) &&
               (ParallelDescriptor::MyProc() ==
                ParallelDescriptor::IOProcessorNumber())) {
-              remakeLevel = (static_cast<int>(remakeLevel != 0) ||
-                            (testEfficiency > m_loadBalanceEffRatioThreshold *
-                                                currentEfficiency));
+              remakeLevel = static_cast<int>(
+                (remakeLevel != 0) ||
+                (testEfficiency >
+                 m_loadBalanceEffRatioThreshold * currentEfficiency));
             }
             ParallelDescriptor::Bcast(
               &remakeLevel, 1, ParallelDescriptor::IOProcessorNumber());

diff --git a/Source/PeleLMUtils.cpp b/Source/PeleLMUtils.cpp
@@ -18,7 +18,8 @@ PeleLM::fluxDivergence(
   Real scale)
 {
   BL_PROFILE("PeleLMeX::fluxDivergence()");
-  if (intensiveFluxes != 0) { // Fluxes are intensive -> need area scaling in div
+  if (intensiveFluxes != 0) { // Fluxes are intensive -> need area scaling in
+                              // div
     for (int lev = 0; lev <= finest_level; ++lev) {
       intFluxDivergenceLevel(
         lev, *a_divergence[lev], div_comp, a_fluxes[lev], flux_comp, ncomp,
@@ -47,7 +48,8 @@ PeleLM::fluxDivergence(
 {
 
   BL_PROFILE("PeleLMeX::fluxDivergence()");
-  if (intensiveFluxes != 0) { // Fluxes are intensive -> need area scaling in div
+  if (intensiveFluxes != 0) { // Fluxes are intensive -> need area scaling in
+                              // div
     for (int lev = 0; lev <= finest_level; ++lev) {
       intFluxDivergenceLevelEB(
         lev, *a_divergence[lev], div_comp, a_fluxes[lev], flux_comp,
@@ -777,8 +779,8 @@ PeleLM::loadBalanceChemLev(int a_lev)
   if (
     (m_loadBalanceEffRatioThreshold > 0.0) &&
     (ParallelDescriptor::MyProc() == ParallelDescriptor::IOProcessorNumber())) {
-    updateDmap =
-      static_cast<int>(testEfficiency > m_loadBalanceEffRatioThreshold * currentEfficiency);
+    updateDmap = static_cast<int>(
+      testEfficiency > m_loadBalanceEffRatioThreshold * currentEfficiency);
   }
   ParallelDescriptor::Bcast(
     &updateDmap, 1, ParallelDescriptor::IOProcessorNumber());
@@ -953,7 +955,7 @@ PeleLM::initProgressVariable()
   if (hasUserC != 0) {
     pp.query("progressVariable.format", Cformat);
     if (Cformat.compare("Cantera") == 0) { // use a Cantera-like format with
-                                       // <entry>:<weight>, default to 0.0
+                                           // <entry>:<weight>, default to 0.0
       // Weights
       Vector<std::string> stringIn;
       Vector<Real> weightsIn(NUM_SPECIES + 1, 0.0);
@@ -980,9 +982,9 @@ PeleLM::initProgressVariable()
         m_C0 += coldState[i] * m_Cweights[i];
         m_C1 += hotState[i] * m_Cweights[i];
       }
-    } else if (Cformat.compare(
-                 "RealList") == 0) { // use a list of Real. MUST contains an entry
-                                // for each species+Temp
+    } else if (Cformat.compare("RealList") == 0) { // use a list of Real. MUST
+                                                   // contains an entry
+                                                   // for each species+Temp
       // Weights
       Vector<Real> weightsIn;
       int entryCount = pp.countval("progressVariable.weights");
@@ -1655,7 +1657,7 @@ PeleLM::initMixtureFraction()
   if (hasUserMF != 0) {
     pp.query("mixtureFraction.format", MFformat);
     if (MFformat.compare("Cantera") == 0) { // use a Cantera-like format with
-                                        // <SpeciesName>:<Value>, default in 0.0
+      // <SpeciesName>:<Value>, default in 0.0
       std::string MFCompoType;
       pp.query("mixtureFraction.type", MFCompoType);
       Vector<std::string> compositionIn;
@@ -1667,9 +1669,9 @@ PeleLM::initMixtureFraction()
       compositionIn.resize(entryCount);
       pp.getarr("mixtureFraction.fuelTank", compositionIn, 0, entryCount);
       parseComposition(compositionIn, MFCompoType, YF);
-    } else if (MFformat.compare(
-                 "RealList") == 0) { // use a list of Real. MUST contains an entry
-                                // for each species in the mixture
+    } else if (MFformat.compare("RealList") == 0) { // use a list of Real. MUST
+                                                    // contains an entry
+      // for each species in the mixture
       std::string MFCompoType;
       pp.query("mixtureFraction.type", MFCompoType);
       if (MFCompoType.compare("mass") == 0) {

diff --git a/Source/PeleLM_K.H b/Source/PeleLM_K.H
@@ -847,7 +847,7 @@ buildAdvectionForcing(
   for (int n = 0; n < NUM_SPECIES; n++) {
     y[n] = rhoY(i, j, k, n) * rhoinv;    // get y
     forceY(i, j, k, n) = dn(i, j, k, n); // forceY = Dnk
-  if (do_react != 0) {
+    if (do_react != 0) {
       forceY(i, j, k, n) += r(i, j, k, n); //         + Rk
     }
     forceT(i, j, k) -= forceY(i, j, k, n) * hi_spec[n] *