Update formatting

include/Particle.hpp

@@ -14,12 +14,13 @@
 
 #include <armadillo>
 
-#include "typedefs.hpp"
 #include "constants.hpp"
+#include "typedefs.hpp"
 
 /** @brief A class that holds attributes of a particle
  * */
-class Particle {
+class Particle
+{
 private:
     vec_3d r_vec; ///< position
     vec_3d v_vec; ///< velocity
@@ -37,7 +38,8 @@ public:
      *  @param r_vec The initial position of the particle
      *  @param v_vec The initial velocity of the particle
      * */
-    Particle(vec_3d r_vec, vec_3d v_vec, double q = CA_CHARGE, double m = CA_MASS);
+    Particle(vec_3d r_vec, vec_3d v_vec, double q = CA_CHARGE,
+             double m = CA_MASS);
 
     /** @brief Make private attributes available for PenningTrap.
      * */

include/constants.hpp

@@ -12,14 +12,24 @@
 #ifndef __CONST__
 #define __CONST__
 
-#define K_E 1.38935333*1e5 ///< Coulomb constant. unit: \f$\frac{u(\mu m)^3}{(\mu s)^2 e^2}\f$
+/** @brief Coulomb constant. unit: \f$\frac{u(\mu m)^3}{(\mu s)^2 e^2}\f$
+ * */
+#define K_E 1.38935333 * 1e5
 
-#define T 9.64852558*1e1 ///< 1 Tesla. unit: \f$ \frac{u}{(\mu s) e} \f$
+/** @brief 1 Tesla. unit: \f$ \frac{u}{(\mu s) e} \f$
+ * */
+#define T 9.64852558 * 1e1
 
-#define V 9.64852558*1e7 ///< 1 Volt. unit: \f$ \frac{u (\mu m)^2}{(\mu s)^2 e} \f$
+/** @brief 1 Volt. unit: \f$ \frac{u (\mu m)^2}{(\mu s)^2 e} \f$
+ * */
+#define V 9.64852558 * 1e7
 
-#define CA_MASS 40.078 ///< Mass of a single calcium ion. unit: amu
+/** @brief Mass of a single calcium ion. unit: amu
+ * */
+#define CA_MASS 40.078
 
-#define CA_CHARGE 1. ///< Charge of a singly charged calcium ion. unit: e
+/** @brief Charge of a singly charged calcium ion. unit: e
+ * */
+#define CA_CHARGE 1.
 
 #endif

include/typedefs.hpp

@@ -7,7 +7,7 @@
  *
  *  @brief Useful typedefs for cleaner code.
  *
- *  @details These typedefs make the code more readable and easy to follow 
+ *  @details These typedefs make the code more readable and easy to follow
  *  along.
  *
  *  @bug No known bugs
@@ -18,7 +18,7 @@
 #include <armadillo>
 #include <vector>
 
-/** @brief Typedef for the column of the result vector from simulating 
+/** @brief Typedef for the column of the result vector from simulating
  *  particles.
  * */
 typedef std::vector<arma::vec::fixed<3>> sim_cols;

include/utils.hpp

@@ -27,14 +27,14 @@
  *
  *  This macro writes a debug message that includes the filename,
  *  line number, and a custom message. The function is wrapped in an ifdef
- *  that checks if DBG is defined, so one can choose to display the debug 
+ *  that checks if DBG is defined, so one can choose to display the debug
  *  messages by adding the -DDBG flag when compiling.
  * */
 #ifdef DBG
-    #define DEBUG(msg) std::cout << __FILE__ << " " << __LINE__ << ": " \
-        << msg << std::endl
+#define DEBUG(msg)                                                            \
+    std::cout << __FILE__ << " " << __LINE__ << ": " << msg << std::endl
 #else
-    #define DEBUG(msg)
+#define DEBUG(msg)
 #endif
 
 /** @def ASSERT(expr)
@@ -43,15 +43,14 @@
  *  This macro calls the m_assert function which is a more informative
  *  assertion function than the regular assert function from cassert.
  * */
-#define ASSERT(expr, msg) m_assert(expr, #expr, __METHOD_NAME__, __FILE__, \
-                                   __LINE__, msg)
+#define ASSERT(expr, msg)                                                     \
+    m_assert(expr, #expr, __METHOD_NAME__, __FILE__, __LINE__, msg)
 
 /** @def __METHOD_NAME__
  *  @brief Get the name of the current method/function without the return type.
  * */
 #define __METHOD_NAME__ methodName(__PRETTY_FUNCTION__)
 
-
 /** @brief Turns a double into a string written in scientific format.
  *
  *  @details The code is stolen from https://github.com/anderkve/FYS3150.
@@ -62,11 +61,11 @@
  *
  *  @return std::string
  * */
-std::string scientific_format(double d, int width=20, int prec=10);
+std::string scientific_format(double d, int width = 20, int prec = 10);
 
-
-/** @brief Turns a vector of doubles into a string written in scientific format.
- *  
+/** @brief Turns a vector of doubles into a string written in scientific
+ * format.
+ *
  *  @details The code is stolen from https://github.com/anderkve/FYS3150.
  *
  *  @param v The vector to stringify
@@ -75,14 +74,12 @@ std::string scientific_format(double d, int width=20, int prec=10);
  *
  *  @return std::string
  * */
-std::string scientific_format(const std::vector<double>& v, 
-                              int width=20, 
-                              int prec=10);
-
+std::string scientific_format(const std::vector<double> &v, int width = 20,
+                              int prec = 10);
 
 /** @brief Test an expression, confirm that test is ok, or abort execution.
  *
- *  @details This function takes in an expression and prints an OK message if 
+ *  @details This function takes in an expression and prints an OK message if
  *  it's true, or it prints a fail message and aborts execution if it fails.
  *
  *  @param expr The expression to be evaluated
@@ -92,17 +89,12 @@ std::string scientific_format(const std::vector<double>& v,
  *  @param line The line number where this function is called from
  *  @param msg The message to be displayed
  * */
-void m_assert(bool expr, 
-              std::string expr_str, 
-              std::string func, 
-              std::string file, 
-              int line,
-              std::string msg);
-
+void m_assert(bool expr, std::string expr_str, std::string func,
+              std::string file, int line, std::string msg);
 
 /** @brief Test if two armadillo vectors are close to each other.
  *
- *  @details This function takes in 2 vectors and checks if they are 
+ *  @details This function takes in 2 vectors and checks if they are
  *  approximately equal to each other given a tolerance.
  *
  *  @param a Vector a
@@ -111,8 +103,7 @@ void m_assert(bool expr,
  *
  *  @return bool
  * */
-bool close_to(arma::vec &a, arma::vec &b, double tol=1e-8);
-
+bool close_to(arma::vec &a, arma::vec &b, double tol = 1e-8);
 
 /** @brief Takes in the __PRETTY_FUNCTION__ string and removes the return type.
  *
@@ -124,16 +115,15 @@ bool close_to(arma::vec &a, arma::vec &b, double tol=1e-8);
  *
  *  @return std::string
  * */
-static inline std::string methodName(const std::string& pretty_function)
+static inline std::string methodName(const std::string &pretty_function)
 {
     size_t colons = pretty_function.find("::");
-    size_t begin = pretty_function.substr(0,colons).rfind(" ") + 1;
+    size_t begin = pretty_function.substr(0, colons).rfind(" ") + 1;
     size_t end = pretty_function.rfind("(") - begin;
 
-    return pretty_function.substr(begin,end) + "()";
+    return pretty_function.substr(begin, end) + "()";
 }
 
-
 /** @brief Make path given.
  *
  *  @details This tries to be the equivalent to "mkdir -p" and creates a new