Fix and suppress some warnings (Exawind#627)

.github/workflows/ci.yml

@@ -13,12 +13,12 @@ jobs:
     - name: Clone
       uses: actions/checkout@v3
     - name: Check formatting
-      uses: DoozyX/clang-format-lint-action@v0.11
+      uses: DoozyX/clang-format-lint-action@v0.13
       with:
         source: './amr-wind ./unit_tests ./tools/utilities'
         exclude: '.'
         extensions: 'H,h,cpp'
-        clangFormatVersion: 11
+        clangFormatVersion: 13
   CPU:
     needs: Formatting
     runs-on: ${{matrix.os}}

amr-wind/core/SimTime.H

@@ -126,7 +126,7 @@ public:
 
 private:
     //! Timestep sizes
-    amrex::Real m_dt[max_time_states];
+    amrex::Real m_dt[max_time_states]{0.0};
 
     //! Current simulation time
     amrex::Real m_cur_time{0.0};

amr-wind/equation_systems/AdvOp_Godunov.H

@@ -79,7 +79,7 @@ struct AdvectionOp<
         const auto& src_term = fields.src_term;
         // cppcheck-suppress constVariable
         auto& conv_term = fields.conv_term;
-        auto& dof_field = fields.field.state(fstate);
+        const auto& dof_field = fields.field.state(fstate);
 
         auto flux_x =
             repo.create_scratch_field(PDE::ndim, 0, amr_wind::FieldLoc::XFACE);

amr-wind/equation_systems/AdvOp_MOL.H

@@ -43,7 +43,7 @@ struct AdvectionOp<
         static_assert(
             PDE::ndim == 1, "Invalid number of components for scalar");
 
-        auto& repo = fields.repo;
+        const auto& repo = fields.repo;
         const auto& geom = repo.mesh().Geom();
 
         // cppcheck-suppress constVariable

amr-wind/equation_systems/icns/icns_advection.H

@@ -102,7 +102,7 @@ struct AdvectionOp<ICNS, fvm::Godunov>
     void preadvect(const FieldState fstate, const amrex::Real dt)
     {
 
-        auto& repo = fields.repo;
+        const auto& repo = fields.repo;
         const auto& geom = repo.mesh().Geom();
 
         const auto& src_term = fields.src_term;
@@ -262,7 +262,7 @@ struct AdvectionOp<ICNS, fvm::Godunov>
         const auto& src_term = fields.src_term;
         // cppcheck-suppress constVariable
         auto& conv_term = fields.conv_term;
-        auto& dof_field = fields.field.state(fstate);
+        const auto& dof_field = fields.field.state(fstate);
 
         auto flux_x =
             repo.create_scratch_field(ICNS::ndim, 0, amr_wind::FieldLoc::XFACE);
@@ -375,6 +375,7 @@ struct AdvectionOp<ICNS, fvm::MOL>
     void preadvect(const FieldState fstate, const amrex::Real dt)
     {
 
+        // cppcheck-suppress constVariable
         auto& repo = fields.repo;
         auto& dof_field = fields.field.state(fstate);
 
@@ -406,7 +407,7 @@ struct AdvectionOp<ICNS, fvm::MOL>
     void operator()(const FieldState fstate, const amrex::Real /*unused*/)
     {
 
-        auto& repo = fields.repo;
+        const auto& repo = fields.repo;
         const auto& geom = repo.mesh().Geom();
         // cppcheck-suppress constVariable
         auto& conv_term = fields.conv_term.state(fstate);

amr-wind/equation_systems/icns/icns_diffusion.H

@@ -203,7 +203,7 @@ public:
         const FieldState fstate = FieldState::New;
         auto& repo = m_pdefields.repo;
         const auto& geom = repo.mesh().Geom();
-        auto& field = m_pdefields.field;
+        const auto& field = m_pdefields.field;
         const auto& density = m_density.state(fstate);
         const int nlevels = repo.num_active_levels();
         const int ndim = field.num_comp();

amr-wind/equation_systems/vof/vof_advection.H

@@ -36,6 +36,7 @@ struct AdvectionOp<VOF, fvm::Godunov>
         auto& repo = fields.repo;
         const auto& geom = repo.mesh().Geom();
 
+        // cppcheck-suppress constVariable
         auto& dof_field = fields.field;
         //
         // Advect volume using either the Explicit Lagrangian onto-cell or

amr-wind/immersed_boundary/bluff_body/bluff_body_ops.cpp

@@ -33,6 +33,7 @@ void apply_mms_vel(CFDSim& sim)
     const int nlevels = sim.repo().num_active_levels();
 
     const auto& levelset = sim.repo().get_field("ib_levelset");
+    // cppcheck-suppress constVariable
     auto& velocity = sim.repo().get_field("velocity");
     auto& m_conv_taylor_green =
         sim.physics_manager().get<ctv::ConvectingTaylorVortex>();
@@ -78,6 +79,7 @@ void apply_dirichlet_vel(CFDSim& sim, const amrex::Vector<amrex::Real>& vel_bc)
 {
     const int nlevels = sim.repo().num_active_levels();
     auto& geom = sim.mesh().Geom();
+    // cppcheck-suppress constVariable
     auto& velocity = sim.repo().get_field("velocity");
     auto& levelset = sim.repo().get_field("ib_levelset");
     levelset.fillpatch(sim.time().current_time());

amr-wind/main.cpp

@@ -17,6 +17,7 @@ int main(int argc, char* argv[])
         return 1;
     }
 
+    // cppcheck-suppress knownConditionTrueFalse
     if (argc >= 2) {
         // Look for "-h" or "--help" flag and print usage
         for (auto i = 1; i < argc; i++) {

amr-wind/physics/SyntheticTurbulence.cpp

@@ -546,7 +546,7 @@ void SyntheticTurbulence::update_impl(
     const InterpWeights& weights,
     const T& velfunc)
 {
-    auto& repo = m_turb_force.repo();
+    const auto& repo = m_turb_force.repo();
     const auto& geom_vec = repo.mesh().Geom();
 
     const int sdir = (*m_wind_profile).shear_dir();

amr-wind/physics/multiphase/MultiPhase.H

@@ -91,7 +91,10 @@ private:
     // sum of volume fractions (for vof only)
     amrex::Real m_total_volfrac{0.0};
 
-    amrex::Real q0, q1, q2, sumvof0;
+    amrex::Real q0{0.0};
+    amrex::Real q1{0.0};
+    amrex::Real q2{0.0};
+    amrex::Real sumvof0{0.0};
 };
 
 } // namespace amr_wind

amr-wind/physics/multiphase/MultiPhase.cpp

@@ -240,8 +240,8 @@ void MultiPhase::set_density_via_levelset()
             const amrex::Array4<amrex::Real>& phi = levelset.array(mfi);
             const amrex::Array4<amrex::Real>& rho = density.array(mfi);
             const amrex::Real eps = std::cbrt(2. * dx[0] * dx[1] * dx[2]);
-            const amrex::Real rho1 = m_rho1;
-            const amrex::Real rho2 = m_rho2;
+            const amrex::Real captured_rho1 = m_rho1;
+            const amrex::Real captured_rho2 = m_rho2;
             amrex::ParallelFor(
                 vbx, [=] AMREX_GPU_DEVICE(int i, int j, int k) noexcept {
                     amrex::Real smooth_heaviside;
@@ -255,8 +255,8 @@ void MultiPhase::set_density_via_levelset()
                             (1.0 + phi(i, j, k) / eps +
                              1.0 / M_PI * std::sin(phi(i, j, k) * M_PI / eps));
                     }
-                    rho(i, j, k) = rho1 * smooth_heaviside +
-                                   rho2 * (1.0 - smooth_heaviside);
+                    rho(i, j, k) = captured_rho1 * smooth_heaviside +
+                                   captured_rho2 * (1.0 - smooth_heaviside);
                 });
         }
     }
@@ -275,12 +275,12 @@ void MultiPhase::set_density_via_vof()
             const auto& vbx = mfi.validbox();
             const amrex::Array4<amrex::Real>& F = vof.array(mfi);
             const amrex::Array4<amrex::Real>& rho = density.array(mfi);
-            const amrex::Real rho1 = m_rho1;
-            const amrex::Real rho2 = m_rho2;
+            const amrex::Real captured_rho1 = m_rho1;
+            const amrex::Real captured_rho2 = m_rho2;
             amrex::ParallelFor(
                 vbx, [=] AMREX_GPU_DEVICE(int i, int j, int k) noexcept {
-                    rho(i, j, k) =
-                        rho1 * F(i, j, k) + rho2 * (1.0 - F(i, j, k));
+                    rho(i, j, k) = captured_rho1 * F(i, j, k) +
+                                   captured_rho2 * (1.0 - F(i, j, k));
                 });
         }
     }

amr-wind/projection/incflo_apply_nodal_projection.cpp

@@ -11,15 +11,15 @@ using namespace amrex;
 void incflo::set_inflow_velocity(
     int lev, amrex::Real time, MultiFab& vel, int nghost)
 {
-    auto& velocity = icns().fields().field;
-    velocity.set_inflow(lev, time, vel, nghost);
+    auto& lvelocity = icns().fields().field;
+    lvelocity.set_inflow(lev, time, vel, nghost);
 
     // TODO fix hack for ABL
     auto& phy_mgr = m_sim.physics_manager();
     if (phy_mgr.contains("ABL")) {
         auto& abl = phy_mgr.get<amr_wind::ABL>();
         const auto& bndry_plane = abl.bndry_plane();
-        bndry_plane.populate_data(lev, time, velocity, vel);
+        bndry_plane.populate_data(lev, time, lvelocity, vel);
     }
 }
 

amr-wind/turbulence/LES/OneEqKsgs.cpp

@@ -104,7 +104,7 @@ void OneEqKsgsM84<Transport>::update_turbulent_viscosity(
     auto& mu_turb = this->mu_turb();
     const amrex::Real Ce = this->m_Ce;
     const auto& den = this->m_rho.state(fstate);
-    auto& repo = mu_turb.repo();
+    const auto& repo = mu_turb.repo();
     const auto& geom_vec = repo.mesh().Geom();
 
     const int nlevels = repo.num_active_levels();
@@ -231,6 +231,7 @@ void OneEqKsgsM84<Transport>::post_advance_work()
     // Update sdr field based on sfs ke
 
     auto& tke = *(this->m_tke);
+    // cppcheck-suppress constVariable
     auto& sdr = *(this->m_sdr);
     const amrex::Real Ce = this->m_Ce;
 

amr-wind/turbulence/LES/Smagorinsky.cpp

@@ -24,7 +24,7 @@ void Smagorinsky<Transport>::update_turbulent_viscosity(const FieldState fstate)
         "amr-wind::" + this->identifier() + "::update_turbulent_viscosity");
 
     auto& mu_turb = this->mu_turb();
-    auto& repo = mu_turb.repo();
+    const auto& repo = mu_turb.repo();
     const auto& vel = m_vel.state(fstate);
     const auto& den = m_rho.state(fstate);
     const auto& geom_vec = repo.mesh().Geom();

amr-wind/turbulence/RANS/KOmegaSST.cpp

@@ -64,6 +64,7 @@ void KOmegaSST<Transport>::update_turbulent_viscosity(const FieldState fstate)
     const auto& den = this->m_rho.state(fstate);
     const auto& tke = (*this->m_tke).state(fstate);
     const auto& sdr = (*this->m_sdr).state(fstate);
+    // cppcheck-suppress constVariable
     auto& repo = mu_turb.repo();
 
     const int nlevels = repo.num_active_levels();
@@ -80,6 +81,7 @@ void KOmegaSST<Transport>::update_turbulent_viscosity(const FieldState fstate)
 
     auto& tke_lhs = (this->m_sim).repo().get_field("tke_lhs_src_term");
     tke_lhs.setVal(0.0);
+    // cppcheck-suppress constVariable
     auto& sdr_lhs = (this->m_sim).repo().get_field("sdr_lhs_src_term");
 
     const amrex::Real deltaT = (this->m_sim).time().deltaT();

amr-wind/turbulence/RANS/KOmegaSSTIDDES.cpp

@@ -88,6 +88,7 @@ void KOmegaSSTIDDES<Transport>::update_turbulent_viscosity(
     const auto& geom_vec = repo.mesh().Geom();
     auto& tke_lhs = (this->m_sim).repo().get_field("tke_lhs_src_term");
     tke_lhs.setVal(0.0);
+    // cppcheck-suppress constVariable
     auto& sdr_lhs = (this->m_sim).repo().get_field("sdr_lhs_src_term");
 
     auto gradK = (this->m_sim.repo()).create_scratch_field(3, 0);

amr-wind/utilities/FieldPlaneAveraging.H

@@ -58,8 +58,8 @@ public:
      */
     amrex::Real line_derivative_of_average_cell(int ind, int comp) const;
 
-    void
-    output_line_average_ascii(std::string filename, int step, amrex::Real time);
+    void output_line_average_ascii(
+        const std::string& filename, int step, amrex::Real time);
     void output_line_average_ascii(int step, amrex::Real time);
 
     /** change precision of text file output */
@@ -179,8 +179,8 @@ public: // public for GPU
        velocity magnitude */
     amrex::Real line_hvelmag_derivative_of_average_cell(int ind) const;
 
-    void
-    output_line_average_ascii(std::string filename, int step, amrex::Real time);
+    void output_line_average_ascii(
+        const std::string& filename, int step, amrex::Real time);
     void output_line_average_ascii(int step, amrex::Real time);
 };
 

amr-wind/utilities/FieldPlaneAveraging.cpp

@@ -52,7 +52,7 @@ FPlaneAveraging<FType>::FPlaneAveraging(
 
 template <typename FType>
 void FPlaneAveraging<FType>::output_line_average_ascii(
-    std::string filename, int step, amrex::Real time)
+    const std::string& filename, int step, amrex::Real time)
 {
     BL_PROFILE("amr-wind::FPlaneAveraging::output_line_average_ascii");
 
@@ -97,7 +97,7 @@ template <typename FType>
 void FPlaneAveraging<FType>::output_line_average_ascii(
     int step, amrex::Real time)
 {
-    std::string filename = "plane_average_" + m_field.name() + ".txt";
+    const std::string filename = "plane_average_" + m_field.name() + ".txt";
     output_line_average_ascii(filename, step, time);
 }
 
@@ -265,7 +265,7 @@ void FPlaneAveraging<FType>::compute_averages(
         m_line_average.data(), m_line_average.size());
 
     amrex::Real* line_avg = lavg.data();
-    const int ncomp = m_ncomp;
+    const int captured_ncomp = m_ncomp;
 
 #ifdef _OPENMP
 #pragma omp parallel if (amrex::Gpu::notInLaunchRegion())
@@ -296,9 +296,9 @@ void FPlaneAveraging<FType>::compute_averages(
 
                             const int ind = idxOp(i, j, k);
 
-                            for (int n = 0; n < ncomp; ++n) {
+                            for (int n = 0; n < captured_ncomp; ++n) {
                                 amrex::Gpu::deviceReduceSum(
-                                    &line_avg[ncomp * ind + n],
+                                    &line_avg[captured_ncomp * ind + n],
                                     fab_arr(i, j, k, n) * denom, handler);
                             }
                         }
@@ -491,7 +491,7 @@ amrex::Real VelPlaneAveraging::line_hvelmag_average_cell(int ind) const
 }
 
 void VelPlaneAveraging::output_line_average_ascii(
-    std::string filename, int step, amrex::Real time)
+    const std::string& filename, int step, amrex::Real time)
 {
     BL_PROFILE("amr-wind::VelPlaneAveraging::output_line_average_ascii");
 
@@ -536,7 +536,7 @@ void VelPlaneAveraging::output_line_average_ascii(
 
 void VelPlaneAveraging::output_line_average_ascii(int step, amrex::Real time)
 {
-    std::string filename = "plane_average_" + m_field.name() + ".txt";
+    const std::string filename = "plane_average_" + m_field.name() + ".txt";
     output_line_average_ascii(filename, step, time);
 }
 

amr-wind/utilities/SecondMomentAveraging.H

@@ -47,8 +47,8 @@ public:
     };
     void line_moment(int comp, amrex::Vector<amrex::Real>& l_vec);
 
-    void
-    output_line_average_ascii(std::string filename, int step, amrex::Real time);
+    void output_line_average_ascii(
+        const std::string& filename, int step, amrex::Real time);
     void output_line_average_ascii(int step, amrex::Real time);
 
     /** change precision of text file output */

amr-wind/utilities/SecondMomentAveraging.cpp

@@ -3,7 +3,7 @@
 namespace amr_wind {
 
 void SecondMomentAveraging::output_line_average_ascii(
-    std::string filename, int step, amrex::Real time)
+    const std::string& filename, int step, amrex::Real time)
 {
     BL_PROFILE("amr-wind::SecondMomentAveraging::output_line_average_ascii");
 

amr-wind/utilities/ThirdMomentAveraging.H

@@ -41,8 +41,8 @@ public:
     };
     void line_moment(int comp, amrex::Vector<amrex::Real>& l_vec);
 
-    void
-    output_line_average_ascii(std::string filename, int step, amrex::Real time);
+    void output_line_average_ascii(
+        const std::string& filename, int step, amrex::Real time);
     void output_line_average_ascii(int step, amrex::Real time);
 
     /** change precision of text file output */

amr-wind/utilities/ThirdMomentAveraging.cpp

@@ -3,7 +3,7 @@
 namespace amr_wind {
 
 void ThirdMomentAveraging::output_line_average_ascii(
-    std::string filename, int step, amrex::Real time)
+    const std::string& filename, int step, amrex::Real time)
 {
     BL_PROFILE("amr-wind::ThirdMomentAveraging::output_line_average_ascii");
 

amr-wind/utilities/io.cpp

@@ -25,8 +25,8 @@ void incflo::ReadCheckpointFile()
     amrex::Print() << "Restarting from checkpoint " << restart_file
                    << std::endl;
 
-    Real prob_lo[AMREX_SPACEDIM];
-    Real prob_hi[AMREX_SPACEDIM];
+    Real prob_lo[AMREX_SPACEDIM] = {0.0};
+    Real prob_hi[AMREX_SPACEDIM] = {0.0};
 
     /***************************************************************************
      * Load header: set up problem domain (including BoxArray)                 *

amr-wind/wind_energy/ABLBoundaryPlane.cpp

@@ -236,8 +236,8 @@ void InletData::interpolate(const amrex::Real time)
             continue;
         }
 
-        const int nlevels = m_data_n[ori]->size();
-        for (int lev = 0; lev < nlevels; ++lev) {
+        const int lnlevels = m_data_n[ori]->size();
+        for (int lev = 0; lev < lnlevels; ++lev) {
 
             const auto& datn = (*m_data_n[ori])[lev];
             const auto& datnp1 = (*m_data_np1[ori])[lev];

amr-wind/wind_energy/ABLWallFunction.cpp

@@ -153,7 +153,7 @@ void ABLVelWallFunc::wall_model(
     BL_PROFILE("amr-wind::ABLVelWallFunc");
 
     constexpr int idim = 2;
-    auto& repo = velocity.repo();
+    const auto& repo = velocity.repo();
     const auto& density = repo.get_field("density", rho_state);
     const auto& viscosity = repo.get_field("velocity_mueff");
     const int nlevels = repo.num_active_levels();