Tidy and fixes

.github/workflows/codeql.yml

@@ -52,6 +52,7 @@ jobs:
             -**/Submodules/sundials/**
             -**/Submodules/amrex/**
             -**/Submodules/AMReX-Hydro/**
+            -**/pelelmex/**
           input: sarif-results/cpp.sarif
           output: sarif-results/cpp.sarif
       - name: Upload CodeQL sarif

Source/PeleLMBCfill.H

@@ -1,3 +1,5 @@
+#ifndef PELE_BCFILL
+#define PELE_BCFILL
 #include <PeleLM_Index.H>
 #include <pelelm_prob.H>
 #include <PMFData.H>
@@ -530,3 +532,4 @@ struct umacFill
         }
     }
 };
+#endif

Source/PeleLMDerive.H

@@ -150,8 +150,6 @@ protected:
                     DeriveBoxMap               box_map,
                     amrex::Interpolater*       interp = &amrex::pc_interp);
 
-   //void buildBC (const DescriptorList& d_list);
-
 private:
 
    //! Name of derived quantity.

Source/PeleLMDiffusion.cpp

@@ -202,6 +202,8 @@ void PeleLM::computeDifferentialDiffusionFluxes(const TimeStamp &a_time,
 
 #ifdef AMREX_USE_EB
    int have_EBfluxes = (a_EBfluxes.empty()) ? 0 : 1;
+#else
+   amrex::ignore_unused(a_EBfluxes);
 #endif
 
    //----------------------------------------------------------------
@@ -1215,6 +1217,9 @@ void PeleLM::deltaTIter_update(int a_dtiter,
                                std::unique_ptr<AdvanceDiffData> &diffData,
                                Real &a_deltaT_norm)
 {
+#ifndef AMREX_USE_EB
+    amrex::ignore_unused(a_ebfluxes);
+#endif
 
    //------------------------------------------------------------------------
    // Evaluate deltaT norm and add Tsave back into the new LevelData

Source/PeleLMPlot.cpp

@@ -545,9 +545,6 @@ void PeleLM::ReadCheckPointFile()
    is >> m_prev_dt;
    GotoNextLine(is);
 
-   //is >> m_prev_prev_dt;
-   //GotoNextLine(is);
-
    // Low coordinates of domain bounding box
    std::getline(is, line);
    {

Source/PeleLMProjection.cpp

@@ -500,6 +500,8 @@ PeleLM::scaleProj_RZ(int a_lev,
         });
         Gpu::streamSynchronize();
     }
+#else
+    amrex::ignore_unused(a_lev,a_mf);
 #endif
 }
 
@@ -528,5 +530,7 @@ PeleLM::unscaleProj_RZ(int a_lev,
             }
         });
     }
+#else
+    amrex::ignore_unused(a_lev,a_mf);
 #endif
 }

Source/PeleLMSetup.cpp

@@ -17,7 +17,6 @@
 using namespace amrex;
 
 static Box the_same_box (const Box& b)    { return b;                }
-static Box grow_box_by_one (const Box& b) { return amrex::grow(b,1); }
 static Box grow_box_by_two (const Box& b) { return amrex::grow(b,2); }
 
 void PeleLM::Setup() {

Source/PeleLMTagging.cpp

@@ -56,15 +56,13 @@ PeleLM::ErrorEst( int lev,
       // Get distance function at current level
       MultiFab signDist(grids[lev],dmap[lev],1,0,MFInfo(),EBFactory(lev));
       getEBDistance(lev, signDist);
-      //VisMF::Write(signDist,"signDistLev"+std::to_string(lev));
 
       // Estimate how far I need to derefine
       Real diagFac = std::sqrt(2.0) * m_derefineEBBuffer;
       Real clearTagDist = Geom(m_EB_refine_LevMax).CellSize(0) * static_cast<Real>(nErrorBuf(m_EB_refine_LevMax)) * diagFac;
       for (int ilev = m_EB_refine_LevMax+1; ilev <= finest_level; ++ilev) {
           clearTagDist += static_cast<Real>(nErrorBuf(ilev)) * Geom(m_EB_refine_LevMax).CellSize(0) * diagFac;
       }
-      //Print() << " clearTagDist " <<  clearTagDist << "\n";
 
       // Untag cells too close to EB
 #ifdef AMREX_USE_OMP

Source/PeleLMTimestep.cpp

@@ -231,7 +231,6 @@ PeleLM::checkDt(const TimeStamp &a_time,
         auto ldata_p = getLevelDataPtr(lev, a_time);
 
         const auto dxinv = geom[lev].InvCellSizeArray();
-        const auto dx    = geom[lev].CellSize();
 
 #ifdef AMREX_USE_OMP
 #pragma omp parallel if (Gpu::notInLaunchRegion())

Source/PeleLMUserKeys.H

@@ -9,6 +9,7 @@
   * \brief struct holding PeleLMeX physical BC options
   */
 struct BoundaryCondition {
+    BoundaryCondition() = default;
     enum {
         BCInterior = 0,
         BCInflow,
@@ -38,6 +39,7 @@ const BoundaryCondition boundarycondition;
            default is LowMachNumber
   */
 struct NSSolver {
+    NSSolver() = default;
     enum {
         LowMachNumber = 0,
         Incompressible
@@ -56,6 +58,7 @@ const NSSolver nssolver;
            default is PiecewiseLinearConserv
   */
 struct Interpolator {
+    Interpolator() = default;
     enum {
         PiecewiseLinearConserv = 0,
         PiecewiseLinearConservMinMax,
@@ -76,6 +79,7 @@ const Interpolator interpolator;
            default is None
   */
 struct LESModel {
+    LESModel() = default;
     enum {
         None = 0,
         Smagorinsky,
@@ -98,6 +102,7 @@ const LESModel lesmodel;
            default is Godunov_PLM
   */
 struct AdvectionScheme {
+    AdvectionScheme() = default;
     enum {
         Godunov_PLM = 0,
         Godunov_PPM,
@@ -122,6 +127,7 @@ const AdvectionScheme advscheme;
            default is Ncell
   */
 struct LoadBalanceCost {
+    LoadBalanceCost() = default;
     enum {
         Ncell = 0,
         ChemFunctCallAvg,
@@ -150,6 +156,7 @@ const LoadBalanceCost lbcost;
            default is SFC
   */
 struct LoadBalanceMethod {
+    LoadBalanceMethod() = default;
     enum {
         SFC = 0,
         Knapsack,

Source/PeleLMUtils.cpp

@@ -103,6 +103,8 @@ void PeleLM::fluxDivergenceRD(const Vector<const MultiFab*> &a_state,
     amrex::ignore_unused(state_comp);
     amrex::ignore_unused(state_bc_d);
     amrex::ignore_unused(a_dt);
+    amrex::ignore_unused(a_EBfluxes);
+    amrex::ignore_unused(ebflux_comp);
     fluxDivergence(a_divergence, div_comp, a_fluxes, flux_comp, ncomp, intensiveFluxes, scale);
 #endif
 }
@@ -348,6 +350,8 @@ void PeleLM::intFluxDivergenceLevelEB(int lev,
    Array< const MultiCutFab*,AMREX_SPACEDIM> areafrac;
    areafrac  = ebfact.getAreaFrac();
    const auto* eb_area = &(ebfact.getBndryArea());
+#else
+   amrex::ignore_unused(a_EBfluxes,ebflux_comp);
 #endif
 
 #ifdef AMREX_USE_OMP
@@ -445,6 +449,8 @@ void PeleLM::advFluxDivergence(int a_lev,
         geom[a_lev].GetFaceArea(mf_ax, grids[a_lev], dmap[a_lev], 0, 0);
         geom[a_lev].GetFaceArea(mf_ay, grids[a_lev], dmap[a_lev], 1, 0);
     }
+#else
+    amrex::ignore_unused(a_lev);
 #endif
 
 #ifdef AMREX_USE_EB

Source/PeleLM_K.H

@@ -418,6 +418,7 @@ intFluxDivergence_K(int i, int j, int k,
    }
 }
 
+#if (AMREX_SPACEDIM == 2)
 AMREX_GPU_DEVICE
 AMREX_FORCE_INLINE
 void
@@ -444,6 +445,7 @@ intFluxDivergence_rz_K(int i, int j, int k,
       div(i,j,k,n) *= factor;
    }
 }
+#endif
 
 AMREX_GPU_DEVICE
 AMREX_FORCE_INLINE

Source/Utils.cpp

@@ -5,7 +5,6 @@ using namespace amrex;
 
 void writeBuildInfo ()
 {
-   std::string PrettyLine = std::string(78, '=') + "\n";
    std::string OtherLine = std::string(78, '-') + "\n";
    std::string SkipSpace = std::string(8, ' ');