Add doxygen

.gitignore

@@ -1 +1,2 @@
 build/
+doc/

src/md/Atom.hpp

@@ -15,19 +15,18 @@
 #include <vector>
 
 /**
- * @brief Atom class
+ * @brief Basic atom class
  *
  */
 class Atom {
 public:
-  double      x, y, z;    ///< Positions
+  double x, y, z;        ///< Positions
-  double      vx, vy, vz; ///< Velocities
+  double vx, vy, vz;     ///< Velocities
-  double      m    = 1;   ///< Mass
+  double m = 1;          ///< Mass
-  std::string name = "";  ///< Name
+  std::string name = ""; ///< Name
 
   Atom(double x, double y, double z, std::string name, double mass)
-      : x(x), y(y), z(z), vx(0), vy(0), vz(0), m(mass), name(name) {
+      : x(x), y(y), z(z), vx(0), vy(0), vz(0), m(mass), name(name) {}
-  }
 };
 
 /**

src/md/Potentials.hpp

@@ -13,12 +13,20 @@
 
 #include <cmath>
 
+/**
+ * @brief Potential generator base class
+ *
+ */
 class Potential {
 public:
   virtual double potential(double r) = 0;
-  virtual double force(double r)     = 0;
+  virtual double force(double r) = 0;
 };
 
+/**
+ * @brief Lennard Jones potential generator
+ *
+ */
 class LennardJones : public Potential {
 public:
   double potential(double r) override {

src/md/System.hpp

@@ -17,6 +17,10 @@
 #include "Atom.hpp"
 #include "Potentials.hpp"
 
+/**
+ * @brief System class that aggregates functions and data related to the system
+ *
+ */
 class System {
 private:
   std::vector<Atom> atoms;    ///< Atoms in the system
@@ -57,9 +61,7 @@ private:
   void buildGrid();
 
 public:
-  explicit System(double      timeDelta,
+  explicit System(double timeDelta, double rcut, Potential *potential,
-                  double      rcut,
-                  Potential  *potential,
                   std::size_t tableResolution = 1000);
 
   void step();

src/md/mpi/Worker.hpp

@@ -13,6 +13,10 @@
 
 #include <boost/mpi.hpp>
 
+/**
+ * @brief MPI worker class
+ * 
+ */
 class Worker {
 public:
   Worker(boost::mpi::communicator &comm) : m_comm(comm) {}