Make changes

include/WaveSimulation.hpp

@@ -18,19 +18,20 @@
 #include <armadillo>
 #include <cstdint>
 
+/** @brief Simulate the evolution of a wave packet in 2 + 1 domensions.*/
 class WaveSimulation {
-protected:
+private:
-    uint32_t M;
+    int32_t M;     ///< The size
-    int32_t N;
+    int32_t N;     ///< The size of the inner part
-    arma::cx_mat V;
+    arma::cx_mat V; ///< The potential matrix
-    arma::cx_mat U;
+    arma::cx_mat U; ///< The particle wave matrix
-    arma::sp_cx_mat B;
+    arma::sp_cx_mat B; ///< The B matrix
-    arma::sp_cx_mat A;
+    arma::sp_cx_mat A; ///< The A matrix
-    double h;
+    double h; ///< The step size in both x and y direction
-    double dt;
+    double dt; ///< The step size int the time direction
-    double T;
+    double T; ///< The end time
 
-    /*  @brief Initialize the U matrix using an unormalized Gaussian wave
+    /**  @brief Initialize the U matrix using an unormalized Gaussian wave
      * packet.
      *
      *  @param x_c The center of the packet in the x direction.
@@ -39,36 +40,41 @@ protected:
      *  @param sigma_y The The initial width in the y direction.
      *  @param p_x The wave packet momentum in the x direction.
      *  @param p_y The wave packet momentum in the y direction.
-     * **/
+     * */
     void initialize_U(double x_c, double y_c, double sigma_x, double sigma_y,
                       double p_x, double p_y);
 
-    /*  @brief Initialize the V matrix.
+    /** @brief Initialize the V matrix.
      *
      *  @param thickness The thickness of the wall in the x direction.
      *  @param pos_x The center of the wall in the x direction.
      *  @param ap_sep The separation between each aperture.
      *  @param ap The aperture width.
      *  @param slits The number of slits.
-     * **/
+     * */
     void initialize_V(double thickness, double pos_x,
                       double aperture_separation, double aperture,
                       uint32_t slits);
 
-    /*  @brief Initialize the V matrix with no wall.
+    /** @brief Initialize the V matrix with no wall.
-     * **/
+     * */
     void initialize_V();
 
-    /*  @brief Initialize the A matrix according to the Crank-Nicolson method
+    /** @brief Initialize the A matrix according to the Crank-Nicolson method
-     * **/
+     * */
     void initialize_A();
 
-    /*  @brief Initialize the B matrix according to the Crank-Nicolson method
+    /** @brief Initialize the B matrix according to the Crank-Nicolson method
-     * **/
+     * */
     void initialize_B();
 
+    /** @brief Write the U matrix in a single line to the file buffer given
+     *
+     *  @param ofile The file buffer to write to
+     * */
+    void write_U(std::ofstream &ofile);
 public:
-    /*  @brief Constructor for the WaveSimulation class.
+    /** @brief Constructor for the WaveSimulation class.
      *
      *  @param h The step size in the x and y direction.
      *  @param dt The step size in the temporal dimension.
@@ -84,13 +90,13 @@ public:
      *  @param ap_sep The separation between each aperture.
      *  @param ap The aperture width.
      *  @param slits The number of slits.
-     * **/
+     * */
     WaveSimulation(double h, double dt, double T, double x_c, double y_c,
                    double sigma_x, double sigma_y, double p_x, double p_y,
                    double thickness, double pos_x, double ap_sep, double ap,
                    uint32_t slits);
 
-    /*  @brief Constructor for the WaveSimulation class with no wall.
+    /** @brief Constructor for the WaveSimulation class with no wall.
      *
      *  @param h The step size in the x and y direction.
      *  @param dt The step size in the temporal dimension.
@@ -101,16 +107,37 @@ public:
      *  @param sigma_y The The initial width in the y direction.
      *  @param p_x The wave packet momentum in the x direction.
      *  @param p_y The wave packet momentum in the y direction.
-     * **/
+     * */
     WaveSimulation(double h, double dt, double T, double x_c, double y_c,
                    double sigma_x, double sigma_y, double p_x, double p_y);
 
+    /** @brief Evolve a step forward in time
+     * */
     void step();
-    void solve(std::string outfile, bool write_each_step = false);
+
-    void solve(std::string outfile, std::vector<double> &steps);
+    /** @brief Evolve the wave packet until the time T has been reached and 
+     *  write U to file.
+     *
+     *  @param outfile The name of the file to write to
+     *  @param write_each_step Boolean for deciding to write each step to file 
+     *  or just the last step
+     * */
+    void simulate(std::string outfile, bool write_each_step = false);
+    
+    /** @brief Evolve the wave packet and write U to fileto file at each time step in
+     *  the vector given.
+     *
+     *  @param outfile The name of the file to write to
+     *  @param steps What time steps to write U to file.
+     * */
+    void simulate(std::string outfile, std::vector<double> &steps);
+
+    /** @brief Write the deviation of the sum of the probability of U from 1
+     *
+     *  @param outfile The name of the file to write to
+     *  to file*/
     void probability_deviation(std::string outfile,
                                bool write_each_step = false);
-    void write_U(std::ofstream &ofile);
 };
 
 #endif

include/utils.hpp

@@ -131,6 +131,26 @@ std::string concatpath(const std::string &left, const std::string &right);
 
 // A function that prints the structure of a sparse matrix to screen.
 void print_sp_matrix_structure(const arma::sp_cx_mat &A);
+
+// A function that splits a string using a delimiter
+std::vector<std::string> split(const std::string &s, char delim);
+
+// trim from left
+std::string &ltrim(std::string &s, const char *t = " \t\n\r\f\v");
+
+// trim from right
+std::string &rtrim(std::string &s, const char *t = " \t\n\r\f\v");
+
+// trim from left & right
+std::string &trim(std::string &s, const char *t = " \t\n\r\f\v");
+
+// copying versions
+
+std::string ltrim_copy(std::string s, const char *t = " \t\n\r\f\v");
+
+std::string rtrim_copy(std::string s, const char *t = " \t\n\r\f\v");
+
+std::string trim_copy(std::string s, const char *t = " \t\n\r\f\v");
 } // namespace utils
 
 #endif