Fix codeql warnings

CONTRIBUTING.md

@@ -14,7 +14,7 @@ Then step into the *PeleLMeX* folder and add the main *PeleLMeX* repository as t
 
        git add remote upstream https://github.com/AMReX-Combustion/PeleLMeX
 
-At any point, you can update the `developement` branch of your local repository with changes implemented in the main *PeleLMeX* repo by pulling from `upstream` : 
+At any point, you can update the `development` branch of your local repository with changes implemented in the main *PeleLMeX* repo by pulling from `upstream` : 
 
         git checkout development
         git pull upstream development

Docs/sphinx/manual/Tutorials_TripleFlame.rst

@@ -410,7 +410,7 @@ control the relaxation of the inlet velocity to the steady state velocity of the
 that should be of the order of ten times the simulation time-step. ``height`` is the user-defined location where the
 triple flame should settle, ``changeMax`` and ``velMax`` control the maximum velocity increment and maximum inlet velocity, respectively.
 The user is referred to [CAMCS2006]_ for an overview of the method and corresponding parameters.
-The ``pseudo_gravity`` triggers a manufactured force added to the momemtum equation to compensate for the acceleration of different density gases.
+The ``pseudo_gravity`` triggers a manufactured force added to the momentum equation to compensate for the acceleration of different density gases.
 
 Once these parameters are set, you continue the previous simulation by uncommenting the first line of the ``IO CONTROL`` block in the input file: ::
 

Exec/RegTests/EnclosedFlame/pelelmex_prob.H

@@ -41,8 +41,6 @@ pelelmex_initdata(
                , const amrex::Real yc = prob_lo[1] + 0.5 * Ly;
                , const amrex::Real zc = prob_lo[2] + 0.5 * Lz;);
 
-  // constexpr amrex::Real Pi = 3.14159265358979323846264338327950288;
-
   auto eos = pele::physics::PhysicsType::eos();
   amrex::GpuArray<amrex::Real, NUM_SPECIES + 4> pmf_vals = {0.0};
   amrex::Real molefrac[NUM_SPECIES] = {0.0};

Exec/RegTests/EnclosedInjection/pelelmex_prob.H

@@ -24,20 +24,6 @@ pelelmex_initdata(
   ProbParm const& prob_parm,
   pele::physics::PMF::PmfData::DataContainer const* /*pmf_data*/)
 {
-  // const amrex::Real* prob_lo = geomdata.ProbLo();
-  // const amrex::Real* prob_hi = geomdata.ProbHi();
-  // const amrex::Real* dx = geomdata.CellSize();
-  /*
-    AMREX_D_TERM(const amrex::Real x = prob_lo[0] + (i + 0.5) * dx[0];
-                 , const amrex::Real y = prob_lo[1] + (j + 0.5) * dx[1];
-                 , const amrex::Real z = prob_lo[2] + (k + 0.5) * dx[2];);
-
-    AMREX_D_TERM(const amrex::Real Lx = prob_hi[0] - prob_lo[0];
-                 , const amrex::Real Ly = prob_hi[1] - prob_lo[1];
-                 , const amrex::Real Lz = prob_hi[2] - prob_lo[2]);
-
-    constexpr amrex::Real Pi = 3.14159265358979323846264338327950288;
-  */
   auto eos = pele::physics::PhysicsType::eos();
   amrex::Real massfrac[NUM_SPECIES] = {0.0};
 
@@ -89,10 +75,6 @@ bcnormal(
   amrex::Real Y_jet[NUM_SPECIES] = {0.0};
   amrex::Real eta = 0.0;
 
-  // const amrex::Real* prob_lo = geomdata.ProbLo();
-  // const amrex::Real* prob_hi = geomdata.ProbHi();
-  // const amrex::Real* dx = geomdata.CellSize();
-
   // Simple, air into air injection
   X_air[O2_ID] = 0.21;
   X_air[N2_ID] = 1.0 - X_air[O2_ID];
@@ -160,9 +142,6 @@ zero_visc(
   // velocity, ...)
   if (beta_comp == 0 && nComp == NUM_SPECIES) {
     if (dir == 2 && k <= domainBox.smallEnd(dir)) {
-      // const amrex::Real* prob_lo = geomdata.ProbLo();
-      // const amrex::Real* prob_hi = geomdata.ProbHi();
-      // const amrex::Real* dx = geomdata.CellSize();
 
       // Just over whole inlet
       for (int n = 0; n < nComp; n++) {

Exec/RegTests/HITDecay/pelelmex_prob.cpp

@@ -126,9 +126,9 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
   ofs.close();
 
   // Read initial velocity field
-  const int nx = local_prob_parm.input_resolution;
-  const int ny = local_prob_parm.input_resolution;
-  const int nz = local_prob_parm.input_resolution;
+  const size_t nx = local_prob_parm.input_resolution;
+  const size_t ny = local_prob_parm.input_resolution;
+  const size_t nz = local_prob_parm.input_resolution;
   amrex::Vector<amrex::Real> data(
     nx * ny * nz * 6); /* this needs to be double */
   if (binfmt != 0) {
@@ -138,17 +138,12 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
   }
 
   // Extract position and velocities
-  amrex::Vector<amrex::Real> xinput;
-  amrex::Vector<amrex::Real> uinput;
-  amrex::Vector<amrex::Real> vinput;
-  amrex::Vector<amrex::Real> winput;
-  amrex::Vector<amrex::Real> xdiff;
-  amrex::Vector<amrex::Real> xarray;
-
-  xinput.resize(nx * ny * nz);
-  uinput.resize(nx * ny * nz);
-  vinput.resize(nx * ny * nz);
-  winput.resize(nx * ny * nz);
+  amrex::Vector<amrex::Real> xinput(nx * ny * nz);
+  amrex::Vector<amrex::Real> uinput(nx * ny * nz);
+  amrex::Vector<amrex::Real> vinput(nx * ny * nz);
+  amrex::Vector<amrex::Real> winput(nx * ny * nz);
+  amrex::Vector<amrex::Real> xdiff(nx);
+  amrex::Vector<amrex::Real> xarray(nx);
 
   for (long i = 0; i < xinput.size(); i++) {
     xinput[i] = data[0 + i * 6];
@@ -161,11 +156,9 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
   }
 
   // Get the xarray table and the differences.
-  xarray.resize(nx);
   for (long i = 0; i < xarray.size(); i++) {
     xarray[i] = xinput[i];
   }
-  xdiff.resize(nx);
   std::adjacent_difference(xarray.begin(), xarray.end(), xdiff.begin());
   xdiff[0] = xdiff[1];
 
@@ -188,11 +181,11 @@ PeleLM::readProbParm() // NOLINT(readability-make-member-function-const)
   local_prob_parm.d_winput =
     (amrex::Real*)amrex::The_Arena()->alloc(nx * ny * nz * sizeof(amrex::Real));
 
-  for (int i = 0; i < nx; i++) {
+  for (unsigned long i = 0; i < nx; i++) {
     local_prob_parm.d_xarray[i] = xarray[i];
     local_prob_parm.d_xdiff[i] = xdiff[i];
   }
-  for (int i = 0; i < nx * ny * nz; i++) {
+  for (unsigned long i = 0; i < nx * ny * nz; i++) {
     local_prob_parm.d_uinput[i] = uinput[i];
     local_prob_parm.d_vinput[i] = vinput[i];
     local_prob_parm.d_winput[i] = winput[i];

Exec/RegTests/HotBubble/pelelmex_prob.H

@@ -33,8 +33,7 @@ pelelmex_initdata(
                , const amrex::Real z = prob_lo[2] + (k + 0.5) * dx[2];);
 
   AMREX_D_TERM(const amrex::Real Lx = prob_hi[0] - prob_lo[0];
-               , /*const amrex::Real Ly = prob_hi[1] - prob_lo[1];*/
-               , const amrex::Real Lz = prob_hi[2] - prob_lo[2]);
+               , , const amrex::Real Lz = prob_hi[2] - prob_lo[2]);
 
   auto eos = pele::physics::PhysicsType::eos();
   amrex::Real massfrac[NUM_SPECIES] = {0.0};

Exec/RegTests/PeriodicCases/pelelmex_prob.H

@@ -25,19 +25,9 @@ pelelmex_initdata(
   pele::physics::PMF::PmfData::DataContainer const* /*pmf_data*/)
 {
   const amrex::Real* prob_lo = geomdata.ProbLo();
-  // const amrex::Real* prob_hi = geomdata.ProbHi();
   const amrex::Real* dx = geomdata.CellSize();
   AMREX_D_TERM(const amrex::Real x = prob_lo[0] + (i + 0.5) * dx[0];
-               , const amrex::Real y = prob_lo[1] + (j + 0.5) * dx[1];,
-               /*const amrex::Real z = prob_lo[2] + (k + 0.5) * dx[2];*/);
-  /*
-    AMREX_D_TERM(const amrex::Real Lx = prob_hi[0] - prob_lo[0];
-                 , const amrex::Real Ly = prob_hi[1] - prob_lo[1];
-                 , const amrex::Real Lz = prob_hi[2] - prob_lo[2]);
-    AMREX_D_TERM(const amrex::Real x_c = prob_lo[0] + 0.5 * Lx;
-                 , const amrex::Real y_c = prob_lo[1] + 0.5 * Ly;
-                 , const amrex::Real z_c = prob_lo[2] + 0.5 * Lz);
-  */
+               , const amrex::Real y = prob_lo[1] + (j + 0.5) * dx[1];, );
   auto eos = pele::physics::PhysicsType::eos();
   constexpr amrex::Real Pi = 3.14159265358979323846264338327950288;
 
@@ -224,7 +214,6 @@ pelelmex_initdata(
     // constant diffusion coeff. gaussDiff. Use ampgauss to avoid
     // undershoot/overshoot of the 2-species mixture.
     const amrex::Real deltax = x - prob_parm.xgauss;
-    // const amrex::Real deltay = y - prob_parm.ygauss;
     amrex::Real denom_inv =
       prob_parm.ampgauss /
       std::sqrt(4 * Pi * prob_parm.gaussTime * prob_parm.gaussDiff);

Exec/RegTests/TaylorGreen/pelelmex_prob.H

@@ -25,17 +25,11 @@ pelelmex_initdata(
   pele::physics::PMF::PmfData::DataContainer const* /*pmf_data*/)
 {
   const amrex::Real* prob_lo = geomdata.ProbLo();
-  // const amrex::Real* prob_hi = geomdata.ProbHi();
   const amrex::Real* dx = geomdata.CellSize();
 
   AMREX_D_TERM(const amrex::Real x = prob_lo[0] + (i + 0.5) * dx[0];
                , const amrex::Real y = prob_lo[1] + (j + 0.5) * dx[1];
                , const amrex::Real z = prob_lo[2] + (k + 0.5) * dx[2];);
-  /*
-    AMREX_D_TERM(const amrex::Real Lx = prob_hi[0] - prob_lo[0];
-                 , const amrex::Real Ly = prob_hi[1] - prob_lo[1];
-                 , const amrex::Real Lz = prob_hi[2] - prob_lo[2]);
-  */
   auto eos = pele::physics::PhysicsType::eos();
 
   amrex::Real massfrac[NUM_SPECIES] = {0.0};

Exec/RegTests/TurbInflow/pelelmex_prob.H

@@ -24,22 +24,6 @@ pelelmex_initdata(
   ProbParm const& prob_parm,
   pele::physics::PMF::PmfData::DataContainer const* /*pmf_data*/)
 {
-  // const amrex::Real* prob_lo = geomdata.ProbLo();
-  // const amrex::Real* prob_hi = geomdata.ProbHi();
-  // const amrex::Real* dx = geomdata.CellSize();
-  /*
-    AMREX_D_TERM(const amrex::Real x = prob_lo[0] + (i + 0.5) * dx[0];
-                 , const amrex::Real y = prob_lo[1] + (j + 0.5) * dx[1];
-                 , const amrex::Real z = prob_lo[2] + (k + 0.5) * dx[2];);
-  */
-  /*  AMREX_D_TERM(const amrex::Real Lx = prob_hi[0] - prob_lo[0];
-                 , const amrex::Real Ly = prob_hi[1] - prob_lo[1];
-                 , const amrex::Real Lz = prob_hi[2] - prob_lo[2]);*/
-  /*
-    AMREX_D_TERM(const amrex::Real x_c = prob_lo[0] + 0.5 * Lx;
-                 , const amrex::Real y_c = prob_lo[1] + 0.5 * Ly;
-                 , const amrex::Real z_c = prob_lo[2] + 0.5 * Lz);
-  */
   auto eos = pele::physics::PhysicsType::eos();
 
   amrex::Real massfrac[NUM_SPECIES] = {0.0};

Source/PeleLMeX.cpp

@@ -52,13 +52,6 @@ PeleLM::getLevelDataPtr(
     m_nAux, m_nGrowState, m_use_soret, static_cast<int>(m_do_les));
   Real time = getTime(lev, a_time);
   fillpatch_state(lev, time, m_leveldata_floating->state, m_nGrowState);
-  // if (useUMac) {
-  //    // TODO: find a way to get U^{n+1/2} from Umac
-  //    // For now get old time
-  //    Real oldtime = getTime(lev,AmrOldTime);
-  //    fillpatch_velocity(lev, oldtime, m_leveldata_floating->state, VELX,
-  //    m_nGrowState);
-  // }
   return m_leveldata_floating.get();
 }
 

Source/PeleLMeX_DeriveUserDefined.cpp

@@ -13,7 +13,6 @@ using namespace amrex;
 Vector<std::string>
 pelelmex_setuserderives()
 {
-  // Vector<std::string> var_names({"derUserDefine_null"});
   return {"derUserDefine_null"}; // var_names;
 }
 

Source/PeleLMeX_Diffusion.cpp

@@ -604,7 +604,6 @@ PeleLM::addSoretTerm(
                 Ted_arr);
             });
 
-          // auto const& rhoY = rhoY_ed.const_array(0);
           auto const& T = T_ed.const_array(0);
           auto const& gradT_ar = gradT[lev][idim].const_array(mfi);
           auto const& beta_ar = beta_ec[idim].const_array(mfi);

Source/PeleLMeX_Setup.cpp

@@ -1001,11 +1001,6 @@ PeleLM::derivedSetup()
     grow_box_by_one);
 #endif
 #endif
-#endif
-#ifdef PELELM_USE_SOOT
-  // if (do_soot_solve) {
-  //   addSootDerivePlotVars(derive_lst);
-  // }
 #endif
   auto it = m_derivePlotVars.begin();
   while (it != m_derivePlotVars.end()) {

Source/PeleLMeX_Temporals.cpp

@@ -534,7 +534,7 @@ PeleLM::writeTemporals()
   if (fuelID >= 0 && !(m_chem_integrator == "ReactorNull")) {
     fuelConsumptionInt = MFSum(GetVecOfConstPtrs(getIRVect()), fuelID);
     for (int lev = 0; lev <= finest_level; ++lev) {
-      getHeatRelease(lev, kinEnergy[lev].get()); // Re-use kinEnergy container
+      getHeatRelease(lev, kinEnergy[lev].get()); // Reuse kinEnergy container
     }
     heatReleaseRateInt = MFSum(GetVecOfConstPtrs(kinEnergy), 0);
   }