add comments, docs, removed all TODOS

src/debug/debug_print.h

@@ -22,9 +22,15 @@
 #define INFO(msg) SpdWrapper::get()->info(msg);
 #define INFO_FMT(msg, ...) SpdWrapper::get()->info(msg, __VA_ARGS__);
 
-// TODO: move or rename
+/**
+ * @brief Info prints any vector of type T and length 3
+ * @tparam T any type that's in vector (double and int here)
+ * @param msg The message in front of the vector, or the debug information
+ * @param vec the vector to be printed
+ */
 template <typename T>
-inline void InfoVec(std::string msg, std::array<T, 3> vec) {
+void InfoVec(std::string msg, std::array<T, 3> vec) {
   INFO_FMT("{} -- [{},{},{}]", msg, vec[0], vec[1], vec[2]);
 }
+
 #endif  // DEBUG_H

src/defs/Generators/MembraneGenerator.h

@@ -45,7 +45,8 @@ class MembraneGenerator final : public ParticleGenerator {
    * @param mv temperature of our system
    * @param type type of the particle in the system
    * @param two_d dimension of velocity vector of brownian motion
-   * @param indices Grid coordinates TODO
+   * @param indices Grid coordinates, so the dimension of the cuboids (not
+   * spatial)
    */
   MembraneGenerator(const dvec3 &corner, const std::array<int, 3> &dimensions,
                     double h, double m,

src/defs/Generators/SpheroidGenerator.h

@@ -42,7 +42,7 @@ class SpheroidGenerator final : public ParticleGenerator {
    */
   const int type_;
   /**
-   * TODO
+   * Mean velocity for brownian motion
    */
   double mv_;
   /**
@@ -61,7 +61,7 @@ class SpheroidGenerator final : public ParticleGenerator {
    * @param epsilon epsilon of generated particles
    * @param sigma sigma of generated particles
    * @param type type of generated particles
-   * @param mv TODO of generated particles
+   * @param mv brownian mean velocity
    * @param two_d whether generator is 2D or 3D
    */
   SpheroidGenerator(const dvec3 &origin, int radius, double h, double m,

src/defs/Particle.h

@@ -176,7 +176,9 @@ class Particle final {
   [[nodiscard]] std::string toString() const;
 
   /**
-   * TODO
+   * @brief Copy assignment operator for the Particle class.
+   * @param other The Particle instance to copy from
+   * @return a reference to the current particle
    */
   Particle &operator=(const Particle &other) {
     if (this != &other) {
@@ -195,7 +197,10 @@ class Particle final {
   }
 
   /**
-   * TODO
+   * @brief Move assignment operator for Particle. Transfers the ownership of
+   * the neighbours vector
+   *
+   * @param other The Particle instance to move from
    */
   Particle &operator=(Particle &&other) noexcept {
     if (this != &other) {

src/defs/Simulation.h

@@ -183,7 +183,7 @@ struct ThermostatConfig {
  */
 struct StatisticsConfig {
   /**
-   * TODO ?
+   * Inicates whether to write statistics to a file
    */
   bool calc_stats{};
   /**
@@ -195,70 +195,28 @@ struct StatisticsConfig {
    */
   int y_bins{};
   /**
-   * TODO ?
+   * Periodicity of outputting to files
    */
   int output_interval{};
   /**
-   * TODO ?
+   * Path to the csv containing the velocity information
    */
   std::string velocity_output_location{};
   /**
-   * TODO ?
+   * Path to the csv containing the density information
    */
   std::string density_output_location{};
 };
 
-//TODO: delete?
-struct SphereoidGeneratorConfig {
-  dvec3 origin{};
-  const int radius{};
-  double h{};
-  double m{};
-  const dvec3 initial_velocity{};
-  double epsilon{};
-  double sigma{};
-  const int type{};
-  double mv{};
-  const bool two_d{};
-  SphereoidGeneratorConfig() = default;
-};
-
-//TODO: delete?
-struct CuboidGeneratorConfig {
-  dvec3 corner{};
-  ivec3 dimensions{};
-  double h{};
-  double m{};
-  const dvec3 initial_velocity{};
-  double mv{};
-  double epsilon{};
-  double sigma{};
-  const int type{};
-  const bool two_d{};
-  CuboidGeneratorConfig() = default;
-};
-
-//TODO: delete?
-struct MembraneGeneratorConfig {
-  dvec3 corner{};
-  ivec3 dimensions{};
-  double h{};
-  double m{};
-  const dvec3 initial_velocity{};
-  double mv{};
-  double epsilon{};
-  double sigma{};
-  const int type{};
-  const bool two_d{};
-  std::vector<int> ids{};
-  std::vector<ivec3> indeces{};
-};
-
 /**
- * @brief struct to hold command line arguments
+ * @brief Supertype for all Singular Forces
  */
 using SingularForceTypes =
     std::variant<SingularGravityConfig, HarmonicForceConfig>;
+
+/**
+ * @brief Supertype for all Interactive Forces
+ */
 using InteractiveForceTypes = std::variant<LennardJonesConfig, GravityConfig,
                                            TruncatedLennardJonesConfig>;
 
@@ -303,13 +261,6 @@ struct Arguments {
    */
   StatisticsConfig statistics_config;
 
-  //TODO
-  SphereoidGeneratorConfig spheroid_generator_config;
-  //TODO
-  CuboidGeneratorConfig cuboid_generator_config;
-  //TODO
-  MembraneGeneratorConfig membrane_generator_config;
-
   /**
    * Parallelization strategy
    */

src/defs/containers/DirectSumContainer.h

@@ -119,9 +119,9 @@ class DirectSumContainer final : public ParticleContainer {
   double getKineticEnergy() override;
 
   /**
-   * TODO: this is giga redundant because size exists
    * @brief Get particle count
    * @return particle in the container
+   * @note this is technically unnecessary as its just size
    */
   size_t getParticleCount() override { return particles_.size(); }
 

src/defs/containers/LinkedCellsContainer.cpp

@@ -246,7 +246,6 @@ void LinkedCellsContainer::singleIterator(
   }
 }
 
-// TODO: this is now unused => could be removed, are we allowed to? I guess
 void LinkedCellsContainer::pairIterator(
     const std::function<void(Particle &, Particle &)> &f) {
   // - as x, y, z are all increasing offsets point to all neighbours in
@@ -724,7 +723,7 @@ void LinkedCellsContainer::applyPeriodicBoundary(const size_t dimension) {
   // the right place
   const std::size_t problematic_dimension = dimension / 2;
   const std::size_t problematic_dimension_direction = dimension % 2;
-  // TODO #pragma omp parallel for schedule(static)
+
   for (const std::size_t cell_index : halo_direction_cells_[dimension]) {
     int counter = 0;
     for (auto it = cells_[cell_index].begin(); it < cells_[cell_index].end();
@@ -737,10 +736,8 @@ void LinkedCellsContainer::applyPeriodicBoundary(const size_t dimension) {
       const std::size_t should_be_index = dvec3ToCellIndex(new_pos);
 
       (*it)->setX(new_pos);
-      // TODO #pragma omp critical
       cells_[should_be_index].push_back(*it);
     }
-    // TODO #pragma omp critical
     {
       cells_[cell_index].clear();
       cells_[cell_index].shrink_to_fit();
@@ -753,7 +750,6 @@ void LinkedCellsContainer::applyPeriodicBoundary(const size_t dimension) {
   }
 
   // iterate over all 9 / 3 cells on the other end
-  // TODO #pragma omp parallel for schedule(static)
   for (const std::size_t cell_index : boundary_direction_cells_[dimension]) {
     ivec3 cell_coordinates = cellIndexToCoord(cell_index);
 
@@ -795,10 +791,8 @@ void LinkedCellsContainer::applyPeriodicBoundary(const size_t dimension) {
 
           const dvec3 applied_force = LennardJones::directionalForceWithOffset(
               *p, *q, accounted_particle_distance);
-          // TODO #pragma omp critical
           p->addF(applied_force);
 
-          // TODO #pragma omp critical
           q->subF(applied_force);
         }
       }

src/defs/containers/LinkedCellsContainer.h

@@ -35,7 +35,7 @@ class LinkedCellsContainer final : public ParticleContainer {
   std::vector<std::vector<Particle*>> cells_;
 
   /**
-   * TODO
+   * saves the index that we have to locate in particles, so e.g. left or top
    */
   std::vector<std::vector<std::size_t>> c18_colours_;
 
@@ -523,7 +523,6 @@ class LinkedCellsContainer final : public ParticleContainer {
    */
   void initializeC18Schema() {
     for (auto start_offset : c_18_schema_) {
-
       std::vector<std::size_t> iterators;
       for (int cx = start_offset[0]; cx <= cell_count_[0]; cx += 2) {
         for (int cy = start_offset[1]; cy <= cell_count_[1]; cy += 3) {
@@ -541,7 +540,6 @@ class LinkedCellsContainer final : public ParticleContainer {
   }
 };
 
-
 /**
  * @brief directions for better readability; implicitly cast
  */

src/io/file/in/xml/XmlReader.h

@@ -38,17 +38,18 @@ class XmlReader {
   /**
    * @brief Reads a xml checkpoint file as specified in
    * MolSim/src/io/file/out/checkpoint-schema.xsd
-   * @param filepath path pointing to checkpoint // TODO default location
+   * @param filepath path pointing to checkpoint
    * @param particles particles to which the checkpoint is read
    */
   static void loadCheckpoint(const std::string& filepath,
                              std::vector<Particle>& particles);
 
   /**
-   * @brief TODO
-   * @param filepath TODO
-   * @param dimensions TODO
-   * @param particles TODO
+   * @brief Reads a checkpoint file
+   * @param filepath path pointing to checkpoint containing membrane
+   * @param dimensions the dimensions of the original membrane cuboid / membrane
+   * generator
+   * @param particles particles to which the checkpoint is read
    */
   static void loadCheckpointMembrane(const std::string& filepath,
                                      const ivec3& dimensions,
@@ -58,7 +59,7 @@ class XmlReader {
 /**
  * @brief validates that the number of bins are correct and not smaller than 1
  * and the output time is larger than 0
- * @param stats TODO
+ * @param stats Statistics config to validate
  */
 inline void validateStatisticsInput(const StatisticsConfig& stats) {
   if (stats.x_bins < 1 || stats.y_bins < 1) {
@@ -83,8 +84,8 @@ inline void validateStatisticsInput(const StatisticsConfig& stats) {
  * @param type the type of file you are checking (Input, checkpoint, etc)
  */
 inline void validatePath(const std::filesystem::path& path,
-                          const std::string& extension,
-                          const std::string& type) {
+                         const std::string& extension,
+                         const std::string& type) {
   if (!exists(path)) {
     throw std::runtime_error(type + " file not found: " + path.string());
   }

src/utils/ArrayUtils.h

@@ -185,7 +185,12 @@ auto L2InnerProduct(const Container &c) {
                          [](auto a, auto b) { return a + b * b; });
 }
 
-// TODO
+/**
+ * @brief returns the signs of the vectors
+ * @tparam Container
+ * @param c
+ * @return vector of length of c containing the sings of the elements
+ */
 template <class Container>
 auto getSigns(const Container &c) {
   std::vector<int> signs;

src/utils/Statistics.h

@@ -25,11 +25,11 @@ class Statistics {
  public:
   /**
    * @brief Initialize Statistics object
-   * @param x_bins TODO
-   * @param y_bins TODO
-   * @param container TODO
-   * @param density_profile_output_location TODO
-   * @param velocity_profile_output_location TODO
+   * @param x_bins amount of x_bins
+   * @param y_bins amount of y_bins
+   * @param container holds the particles
+   * @param density_profile_output_location path to density csv
+   * @param velocity_profile_output_location path to velocity csv
    */
   Statistics(const int x_bins, const int y_bins, ParticleContainer& container,
              const std::string& density_profile_output_location,
@@ -50,7 +50,7 @@ class Statistics {
    * The bins can also be along the y axis at the same time for a checkerboard
    * pattern. The bins are from left to right (x-axis), and for the lines from
    * down to up (y-axis)
-   * @param time TODO
+   * @param time current time for indexing
    */
   void writeStatistics(const double time) {
     std::vector<std::vector<Particle*>> bins(x_bins_ * y_bins_);