Annotate bad ptr arithm

Author: vgvassilev

src/diffusion_thomas_algorithm.cc

@@ -88,9 +88,10 @@ void DiffusionThomasAlgorithm::InitializeThomasAlgorithmVectors(
 
 // Apply Dirichlet boundary conditions to the grid
 void DiffusionThomasAlgorithm::ApplyDirichletBoundaryConditions() {
+  // FIXME: Fix BioDynaMo by returning a view or c++20 std::span.
   const auto* dimensions_ptr = GetDimensionsPtr();
-  const real_t origin = dimensions_ptr
-      [0];  // NOLINT(cppcoreguidelines-pro-bounds-pointer-arithmetic)
+  // NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
+  const real_t origin = dimensions_ptr[0];
   const real_t simulated_time = GetSimulatedTime();
 #pragma omp parallel
   {
@@ -166,10 +167,12 @@ void DiffusionThomasAlgorithm::ApplyDirichletBoundaryConditions() {
 
 // Sets the concentration at a specific voxel
 void DiffusionThomasAlgorithm::SetConcentration(size_t idx, real_t amount) {
+  // NOLINTBEGIN(cppcoreguidelines-pro-bounds-pointer-arithmetic)
   const auto* all_concentrations = GetAllConcentrations();
   const real_t current_concentration = all_concentrations[idx];
   ChangeConcentrationBy(idx, amount - current_concentration,
                         InteractionMode::kAdditive, false);
+  // NOLINTEND(cppcoreguidelines-pro-bounds-pointer-arithmetic)
 }
 
 // Flattens the 3D coordinates (x, y, z) into a 1D index
@@ -270,6 +273,7 @@ void DiffusionThomasAlgorithm::ForwardElimination(
     const std::vector<real_t>& thomas_denom, unsigned int jump) {
   // Get initial index based on direction
   size_t ind = GetLoopIndex(direction, outer, middle, 0);
+  // NOLINTBEGIN(cppcoreguidelines-pro-bounds-pointer-arithmetic)
   const auto* all_concentrations = GetAllConcentrations();
   const real_t initial_concentration = all_concentrations[ind];
   SetConcentration(ind, initial_concentration / thomas_denom[0]);
@@ -283,11 +287,13 @@ void DiffusionThomasAlgorithm::ForwardElimination(
                      (current_concentration + constant1_ * prev_concentration) /
                          thomas_denom[inner]);
   }
+  // NOLINTEND(cppcoreguidelines-pro-bounds-pointer-arithmetic)
 }
 
 void DiffusionThomasAlgorithm::BackSubstitution(
     unsigned int direction, unsigned int outer, unsigned int middle,
     const std::vector<real_t>& thomas_c, unsigned int jump) {
+  // NOLINTBEGIN(cppcoreguidelines-pro-bounds-pointer-arithmetic)
   const auto* all_concentrations = GetAllConcentrations();
 
   // Back substitution loop
@@ -300,6 +306,7 @@ void DiffusionThomasAlgorithm::BackSubstitution(
         ind, current_concentration -
                  thomas_c[static_cast<size_t>(inner)] * next_concentration);
   }
+  // NOLINTEND(cppcoreguidelines-pro-bounds-pointer-arithmetic)
 }
 
 size_t DiffusionThomasAlgorithm::GetLoopIndex(unsigned int direction,