Refactor code according to static analyzers

src/Chemistry/ChemistryModule.cpp

@@ -13,8 +13,6 @@
 #include <string>
 #include <vector>
 
-constexpr uint32_t MB_FACTOR = 1E6;
-
 std::vector<double>
 inverseDistanceWeighting(const std::vector<std::int32_t> &to_calc,
                          const std::vector<double> &from,
@@ -22,20 +20,21 @@ inverseDistanceWeighting(const std::vector<std::int32_t> &to_calc,
                          const std::vector<std::vector<double>> &output) {
   std::vector<double> results = from;
 
-  const std::uint32_t buffer_size = input.size() + 1;
+  // const std::uint32_t buffer_size = input.size() + 1;
-  double buffer[buffer_size];
+  // double buffer[buffer_size];
-  double from_rescaled;
+  // double from_rescaled;
 
   const std::uint32_t data_set_n = input.size();
   double rescaled[to_calc.size()][data_set_n + 1];
   double weights[data_set_n];
 
   // rescaling over all key elements
-  for (int key_comp_i = 0; key_comp_i < to_calc.size(); key_comp_i++) {
+  for (std::uint32_t key_comp_i = 0; key_comp_i < to_calc.size();
+       key_comp_i++) {
     const auto output_comp_i = to_calc[key_comp_i];
 
     // rescale input between 0 and 1
-    for (int point_i = 0; point_i < data_set_n; point_i++) {
+    for (std::uint32_t point_i = 0; point_i < data_set_n; point_i++) {
       rescaled[key_comp_i][point_i] = input[point_i][key_comp_i];
     }
 
@@ -46,7 +45,7 @@ inverseDistanceWeighting(const std::vector<std::int32_t> &to_calc,
     const double max = *std::max_element(rescaled[key_comp_i],
                                          rescaled[key_comp_i] + data_set_n + 1);
 
-    for (int point_i = 0; point_i < data_set_n; point_i++) {
+    for (std::uint32_t point_i = 0; point_i < data_set_n; point_i++) {
       rescaled[key_comp_i][point_i] =
           ((max - min) != 0
                ? (rescaled[key_comp_i][point_i] - min) / (max - min)
@@ -58,9 +57,10 @@ inverseDistanceWeighting(const std::vector<std::int32_t> &to_calc,
 
   // calculate distances for each data set
   double inv_sum = 0;
-  for (int point_i = 0; point_i < data_set_n; point_i++) {
+  for (std::uint32_t point_i = 0; point_i < data_set_n; point_i++) {
     double distance = 0;
-    for (int key_comp_i = 0; key_comp_i < to_calc.size(); key_comp_i++) {
+    for (std::uint32_t key_comp_i = 0; key_comp_i < to_calc.size();
+         key_comp_i++) {
       distance += std::pow(
           rescaled[key_comp_i][point_i] - rescaled[key_comp_i][data_set_n], 2);
     }
@@ -75,7 +75,8 @@ inverseDistanceWeighting(const std::vector<std::int32_t> &to_calc,
   // bool has_h = false;
   // bool has_o = false;
 
-  for (int key_comp_i = 0; key_comp_i < to_calc.size(); key_comp_i++) {
+  for (std::uint32_t key_comp_i = 0; key_comp_i < to_calc.size();
+       key_comp_i++) {
     const auto output_comp_i = to_calc[key_comp_i];
     double key_delta = 0;
 
@@ -87,7 +88,7 @@ inverseDistanceWeighting(const std::vector<std::int32_t> &to_calc,
     //   has_o = true;
     // }
 
-    for (int j = 0; j < data_set_n; j++) {
+    for (std::uint32_t j = 0; j < data_set_n; j++) {
       key_delta += weights[j] * output[j][output_comp_i];
     }
 
@@ -157,7 +158,7 @@ inverseDistanceWeighting(const std::vector<std::int32_t> &to_calc,
 poet::ChemistryModule::ChemistryModule(
     uint32_t wp_size_, const InitialList::ChemistryInit chem_params,
     MPI_Comm communicator)
-    : params(chem_params), wp_size(wp_size_), group_comm(communicator) {
+    : group_comm(communicator), wp_size(wp_size_), params(chem_params) {
   MPI_Comm_rank(communicator, &comm_rank);
   MPI_Comm_size(communicator, &comm_size);
 
@@ -306,9 +307,9 @@ void poet::ChemistryModule::initializeInterp(
 
     if (key_species.empty()) {
       map_copy = this->dht->getKeySpecies();
-      for (std::size_t i = 0; i < map_copy.size(); i++) {
+      for (auto i = 0; i < map_copy.size(); i++) {
         const std::uint32_t signif =
-            map_copy[i] - (map_copy[i] > InterpolationModule::COARSE_DIFF
+            static_cast<std::uint32_t>(map_copy[i]) - (map_copy[i] > InterpolationModule::COARSE_DIFF
                                ? InterpolationModule::COARSE_DIFF
                                : 0);
         map_copy[i] = signif;

src/Chemistry/ChemistryModule.hpp

@@ -69,7 +69,8 @@ public:
   auto GetChemistryTime() const { return this->chem_t; }
 
   void setFilePadding(std::uint32_t maxiter) {
-    this->file_pad = std::ceil(std::log10(maxiter + 1));
+    this->file_pad =
+        static_cast<std::uint8_t>(std::ceil(std::log10(maxiter + 1)));
   }
 
   struct SurrogateSetup {
@@ -365,7 +366,7 @@ protected:
 
   bool print_progessbar{false};
 
-  std::uint32_t file_pad{1};
+  std::uint8_t file_pad{1};
 
   double chem_t{0.};
 

src/Init/InitialList.cpp

@@ -20,8 +20,8 @@ void InitialList::importList(const Rcpp::List &setup) {
 
   Rcpp::NumericVector grid_specs =
       setup[static_cast<int>(ExportList::GRID_SPECS)];
-  this->n_rows = grid_specs[0];
+  this->n_rows = static_cast<std::uint32_t>(grid_specs[0]);
-  this->n_cols = grid_specs[1];
+  this->n_cols = static_cast<std::uint32_t>(grid_specs[1]);
 
   Rcpp::NumericVector spatial =
       setup[static_cast<int>(ExportList::GRID_SPATIAL)];

src/Init/InitialList.hpp

@@ -92,13 +92,13 @@ private:
 
   void prepareGrid(const Rcpp::List &grid_input);
 
-  std::uint8_t dim;
+  std::uint8_t dim{0};
 
-  std::uint32_t n_cols;
+  std::uint32_t n_cols{0};
-  std::uint32_t n_rows;
+  std::uint32_t n_rows{0};
 
-  double s_cols;
+  double s_cols{0};
-  double s_rows;
+  double s_rows{0};
 
   std::vector<std::uint32_t> constant_cells;
   std::vector<double> porosity;

src/Transport/DiffusionModule.hpp

@@ -85,7 +85,7 @@ private:
    * @brief time spent for transport
    *
    */
-  double transport_t = 0.f;
+  double transport_t = 0.;
 };
 } // namespace poet
 

src/initializer.cpp

@@ -25,10 +25,6 @@ int main(int argc, char **argv) {
 
   Rcpp::List setup = R["setup"];
 
-  //   Rcpp::List grid = R.parseEval("setup$grid");
-
-  //   Rcpp::List results;
-
   poet::InitialList init(R);
 
   init.initializeFromList(setup);

src/poet.cpp

@@ -76,8 +76,7 @@ void writeFieldsToR(RInside &R, const Field &trans, const Field &chem) {
 
 enum ParseRet { PARSER_OK, PARSER_ERROR, PARSER_HELP };
 
-ParseRet parseInitValues(char **argv, RInsidePOET &R,
+ParseRet parseInitValues(char **argv, RuntimeParameters &params) {
-                         RuntimeParameters &params) {
   // initialize argh object
   argh::parser cmdl(argv);
 
@@ -222,7 +221,7 @@ ParseRet parseInitValues(char **argv, RInsidePOET &R,
   return ParseRet::PARSER_OK;
 }
 
-static Rcpp::List RunMasterLoop(RInside &R, const RuntimeParameters &params,
+static Rcpp::List RunMasterLoop(const RuntimeParameters &params,
                                 DiffusionModule &diffusion,
                                 ChemistryModule &chem) {
 
@@ -230,8 +229,6 @@ static Rcpp::List RunMasterLoop(RInside &R, const RuntimeParameters &params,
    * master for the following loop) */
   uint32_t maxiter = params.timesteps.size();
 
-  double sim_time = .0;
-
   if (params.print_progressbar) {
     chem.setProgressBarPrintout(true);
   }
@@ -241,7 +238,6 @@ static Rcpp::List RunMasterLoop(RInside &R, const RuntimeParameters &params,
   double dSimTime{0};
   for (uint32_t iter = 1; iter < maxiter + 1; iter++) {
     double start_t = MPI_Wtime();
-    uint32_t tick = 0;
 
     const double &dt = params.timesteps[iter - 1];
 
@@ -325,8 +321,6 @@ static Rcpp::List RunMasterLoop(RInside &R, const RuntimeParameters &params,
 }
 
 int main(int argc, char *argv[]) {
-  double dSimTime, sim_end;
-
   int world_size;
 
   MPI_Init(&argc, &argv);
@@ -343,7 +337,7 @@ int main(int argc, char *argv[]) {
 
     RuntimeParameters run_params;
 
-    switch (parseInitValues(argv, R, run_params)) {
+    switch (parseInitValues(argv, run_params)) {
     case ParseRet::PARSER_ERROR:
     case ParseRet::PARSER_HELP:
       MPI_Finalize();
@@ -401,7 +395,7 @@ int main(int argc, char *argv[]) {
 
       chemistry.masterSetField(init_list.getInitialGrid());
 
-      Rcpp::List profiling = RunMasterLoop(R, run_params, diffusion, chemistry);
+      Rcpp::List profiling = RunMasterLoop(run_params, diffusion, chemistry);
 
       MSG("finished simulation loop");