Create dynamics interface to combine motion and dist

src/sims.cpp

@@ -1,5 +1,6 @@
 #include "sims.h"
 #include "utils/functions.h"
+#include "utils/io.h"
 
 #include <iostream>
 #include <chrono>
@@ -10,14 +11,12 @@ void run_simulation(
     Experiment& experiment,
     std::unordered_map<std::string, double>& parameter,
     std::unordered_map<std::string, double>& optional,
-    motions::BaseMotion& motion,
-    times::BaseDistribution& dist,
+    Dynamics& dynamics,
     std::mt19937_64& rng
     ) {
     const int num_walker = static_cast<int>(parameter["num_walker"]);
 
-    dist.setParameters(parameter);
-    motion.setParameters(parameter);
+    dynamics.setParameters(parameter);
     experiment.setup(parameter, optional);
 
     const auto start = printStart(optional);
@@ -31,13 +30,11 @@ void run_simulation(
         thread_rngs.emplace_back(rng());
     }
 
-    // Create per-thread clones of motion, distribution, and experiment
-    std::vector<std::unique_ptr<motions::BaseMotion>> thread_motions;
-    std::vector<std::unique_ptr<times::BaseDistribution>> thread_dists;
+    // Create per-thread clones of dynamics and experiment
+    std::vector<std::unique_ptr<Dynamics>> thread_dynamics;
     std::vector<std::unique_ptr<Experiment>> thread_experiments;
     for (int i = 0; i < num_threads; i++) {
-        thread_motions.push_back(motion.clone());
-        thread_dists.push_back(dist.clone());
+        thread_dynamics.push_back(dynamics.clone());
         thread_experiments.push_back(experiment.clone());
     }
 
@@ -48,14 +45,13 @@ void run_simulation(
     {
         const int tid = omp_get_thread_num();
         auto& local_rng = thread_rngs[tid];
-        auto& local_motion = *thread_motions[tid];
-        auto& local_dist = *thread_dists[tid];
+        auto& local_dynamics = *thread_dynamics[tid];
         auto& local_experiment = *thread_experiments[tid];
 
         #pragma omp for schedule(static)
         for (int mol_i = 0; mol_i < num_walker; mol_i++) {
-            auto traj = make_trajectory(local_motion, local_dist, experiment.tmax(), local_rng);
-            local_experiment.accumulate(traj, local_motion.getInitOmega(), num_walker);
+            auto traj = make_trajectory(local_dynamics, experiment.tmax(), local_rng);
+            local_experiment.accumulate(traj, local_dynamics.getInitOmega(), num_walker);
 
             if (tid == 0) {
                 #pragma omp atomic
@@ -73,24 +69,23 @@ void run_simulation(
         experiment.merge(*thread_experiments[i]);
     }
 
-    experiment.save(motion, dist);
+    const auto directory = make_directory(dynamics.toString());
+    experiment.save(directory);
     printEnd(start);
 }
 
 
 Trajectory make_trajectory(
-    motions::BaseMotion& motion,
-    times::BaseDistribution& dist,
+    Dynamics& dynamics,
     const double t_max,
     std::mt19937_64& rng
     ) {
     double t_passed = 0;
     double phase = 0;
 
-    motion.initialize(rng);
-    dist.initialize(rng);
+    dynamics.initialize(rng);
 
-    double omega = motion.getInitOmega();
+    double omega = dynamics.getInitOmega();
 
     Trajectory traj;
     traj.time.emplace_back(t_passed);
@@ -98,10 +93,10 @@ Trajectory make_trajectory(
     traj.omega.emplace_back(omega);
 
     while (t_passed < t_max) {
-        const double t = dist.tau_wait(rng);
-        t_passed += t;
-        omega = motion.jump(rng);
-        phase += omega * t;
+        auto [dt, new_omega] = dynamics.next(rng);
+        phase += omega * dt;
+        t_passed += dt;
+        omega = new_omega;
 
         traj.time.emplace_back(t_passed);
         traj.phase.emplace_back(phase);