add namespaces and cmakelists for sub-dirs

src/sims.h

@@ -0,0 +1,46 @@
+#ifndef RWSIM_SIMS_H
+#define RWSIM_SIMS_H
+
+#include "motions/base.h"
+#include "times/base.h"
+
+#include <unordered_map>
+#include <string>
+#include <chrono>
+
+/**
+ * @brief Run simulation for spectra
+ *
+ * @param parameter Dictionary of parameter for simulation
+ * @param optional Dictionary of parameter set via command line
+ * @param motion Motion model
+ * @param dist Distribution of correlation times
+ */
+void run_spectrum(std::unordered_map<std::string, double>& parameter, std::unordered_map<std::string, double> optional, motions::BaseMotion& motion, times::BaseDistribution& dist);
+
+/**
+ * @brief Run simulation for stimulated echoes
+ *
+ * @param parameter Dictionary of parameter for simulation
+ * @param optional Dictionary of parameter set via command line
+ * @param motion Motion model
+ * @param dist Distribution of correlation times
+ */
+void run_ste(std::unordered_map<std::string, double>& parameter, std::unordered_map<std::string, double> optional, motions::BaseMotion& motion, times::BaseDistribution& dist);
+
+/**
+ * @brief Create trajectory of a single walker
+ *
+ * @param motion Motion model
+ * @param dist Distribution of correlation times
+ * @param t_max Double that defines maximum time of trajectory
+ * @param out_time Vector of waiting times
+ * @param out_phase Vector of phase between waiting times
+ * @param out_omega Vector of omega at jump time
+ */
+void make_trajectory(motions::BaseMotion& motion, times::BaseDistribution& dist, double t_max, std::vector<double>& out_time, std::vector<double>& out_phase, std::vector<double>& out_omega);
+
+std::chrono::system_clock::time_point printStart(std::unordered_map<std::string, double> &optional);
+void printEnd(std::chrono::system_clock::time_point start);
+
+#endif //RWSIM_SIMS_H