Make some changes

- Add new programs
- Add command line args
- Add Usage to guide user on how to use programs

include/monte_carlo.hpp

@@ -31,8 +31,8 @@ namespace montecarlo {
  *  @param cycles The amount of Monte Carlo cycles to do
  *  @param filename The file to write to
  * */
-void progression(double T, int L, int cycles,
-                                    const std::string filename);
+void progression(double T, int L, int cycles, const std::string filename,
+                 int burn_in_time = BURN_IN_TIME);
 
 /** @brief Write the expected values for each Monte Carlo cycles to file.
  *
@@ -43,7 +43,7 @@ void progression(double T, int L, int cycles,
  *  @param filename The file to write to
  * */
 void progression(double T, int L, int cycles, int value,
-                                    const std::string filename);
+                 const std::string filename, int burn_in_time = BURN_IN_TIME);
 
 /** @brief Estimate the probability distribution for the energy.
  *
@@ -52,8 +52,8 @@ void progression(double T, int L, int cycles, int value,
  *  @param cycles The amount of Monte Carlo cycles to do
  *  @param filename The file to write to
  * */
-void pd_estimate(double T, int L, int cycles,
-                        const std::string filename);
+void pd_estimate(double T, int L, int cycles, const std::string filename,
+                 int burn_in_time = BURN_IN_TIME);
 
 /** @brief Execute the Metropolis algorithm for a certain amount of Monte
  *  Carlo cycles.
@@ -64,7 +64,8 @@ void pd_estimate(double T, int L, int cycles,
  *
  *  @return data_t
  * */
-data_t mcmc_serial(int L, double T, int cycles, int burn_in_time = BURN_IN_TIME);
+data_t mcmc_serial(int L, double T, int cycles,
+                   int burn_in_time = BURN_IN_TIME);
 
 /** @brief Execute the Metropolis algorithm for a certain amount of Monte
  *  Carlo cycles in parallel.
@@ -75,7 +76,8 @@ data_t mcmc_serial(int L, double T, int cycles, int burn_in_time = BURN_IN_TIME)
  *
  *  @return data_t
  * */
-data_t mcmc_parallel(int L, double T, int cycles, int burn_in_time = BURN_IN_TIME);
+data_t mcmc_parallel(int L, double T, int cycles,
+                     int burn_in_time = BURN_IN_TIME);
 
 /** @brief Perform the MCMC algorithm using a range of temperatures.
  *
@@ -86,10 +88,10 @@ data_t mcmc_parallel(int L, double T, int cycles, int burn_in_time = BURN_IN_TIM
  *  @param monte_carlo Which Monte Carlo implementation to use
  *  @param outfile The file to write the data to
  * */
-void
-phase_transition(int L, double start_T, double end_T, int points_T, int cycles,
-                 std::function<data_t(int, double, int, int)> monte_carlo,
-                 std::string outfile, int burn_in_time = BURN_IN_TIME);
+void phase_transition(int L, double start_T, double end_T, int points_T,
+                      int cycles,
+                      std::function<data_t(int, double, int, int)> monte_carlo,
+                      std::string outfile, int burn_in_time = BURN_IN_TIME);
 }; // namespace montecarlo
 
 #endif