use struct for coordinates

CMakeLists.txt

@@ -26,6 +26,10 @@ add_executable(rwsim main.cpp
         motions/isosmallangle.h
         motions/coordinates.cpp
         motions/coordinates.h
+        motions/bimodalangle.cpp
+        motions/bimodalangle.h
+        times/lognormal.cpp
+        times/lognormal.h
 )
 
 target_compile_options(rwsim PUBLIC -Werror -Wall -Wextra -Wconversion -O2)

config.txt

@@ -12,9 +12,26 @@ techo_start=0e-6
 techo_stop=40e-6
 techo_steps=5
 # STE part
-tevo_start=0e-6
+tevo_start=1e-6
 tevo_stop=60e-6
 tevo_steps=121
-tmix_start=1e-6
+tmix_start=1e-5
-tmix_stop=1e0
+tmix_stop=1e1
-tmix_steps=51
+tmix_steps=61
+tau=0.001
+tau=0.001
+tau=0.001
+tau=0.001
+tau=0.001
+tau=0.001
+tau=0.01
+tau=0.0031622776601683794
+tau=0.001
+tau=0.00031622776601683794
+tau=0.0001
+tau=3.1622776601683795e-05
+tau=1e-05
+tau=3.162277660168379e-06
+tau=1e-06
+tau=3.162277660168379e-07
+tau=1e-07

main.cpp

@@ -4,10 +4,12 @@
 
 #include "io.h"
 #include "sims.h"
+#include "motions/bimodalangle.h"
 #include "motions/isosmallangle.h"
 #include "motions/random.h"
 #include "motions/tetrahedral.h"
 #include "times/delta.h"
+#include "times/lognormal.h"
 
 
 int main (const int argc, char *argv[]) {
@@ -19,15 +21,22 @@ int main (const int argc, char *argv[]) {
         return 1;
     }
 
+
     std::unordered_map parameter { read_parameter(args.parameter_file) };
 
+
+
     std::random_device rd;
     std::mt19937_64 rng(rd());
 
-    auto motion = TetrahedralJump(rng);
+    // auto motion = BimodalAngle(1, 1, 2, 30, 0.98, rng);
+    // auto motion = TetrahedralJump(rng);
     // auto motion = RandomJump(rng);
-    // auto motion = SmallAngle(1, 1, 123, rng);
+    auto motion = SmallAngle(1, 1, 1, rng);
-    auto dist = DeltaDistribution(rng);
+
+    // auto dist = DeltaDistribution(rng);
+    auto dist = LogNormalDistribution(1, 2, rng);
+
 
     if (args.spectrum) {
        run_spectrum(parameter, motion, dist);

motions/base.cpp

@@ -9,7 +9,7 @@
 #include "base.h"
 #include "coordinates.h"
 
-#include <iostream>
+#include <unordered_map>
 
 Motion::Motion(const double delta, const double eta, std::mt19937_64& rng) : m_delta(delta), m_eta(eta), m_rng(rng) {
     m_uni_dist = std::uniform_real_distribution(0., 1.);
@@ -38,4 +38,4 @@ SphericalPos Motion::draw_position() {
     const double phi = 2.0 * M_PI * m_uni_dist(m_rng);
 
     return {cos_theta, phi};
-}
+}

motions/base.h

@@ -7,7 +7,7 @@
 
 #include "coordinates.h"
 #include <random>
-
+#include <unordered_map>
 
 
 class Motion {
@@ -36,4 +36,5 @@ protected:
     std::uniform_real_distribution<> m_uni_dist;
 };
 
+
 #endif //RWSIM_MOTIONBASE_H

motions/bimodalangle.cpp

@@ -0,0 +1,25 @@
+//
+// Created by dominik on 8/23/24.
+//
+
+#include "bimodalangle.h"
+#include "base.h"
+
+BimodalAngle::BimodalAngle(const double delta, const double eta, const double angle1, const double angle2, const double prob, std::mt19937_64 &rng) :
+    Motion(delta, eta, rng),
+    m_angle1(angle1 * M_PI / 180.0),
+    m_angle2(angle2 * M_PI / 180.0),
+    m_prob(prob) {};
+BimodalAngle::BimodalAngle(std::mt19937_64 &rng) : Motion(rng) {}
+
+void BimodalAngle::initialize() {
+    m_prev_pos = draw_position();
+};
+
+double BimodalAngle::jump() {
+    const double angle = m_uni_dist(m_rng) < m_prob ? m_angle1 : m_angle2;
+    const double gamma{2 * M_PI * m_uni_dist(m_rng)};
+    m_prev_pos = rotate(m_prev_pos, angle, gamma);
+
+    return omega_q(m_prev_pos);
+}

motions/bimodalangle.h

@@ -0,0 +1,25 @@
+//
+// Created by dominik on 8/23/24.
+//
+
+#ifndef BIMODALANGLE_H
+#define BIMODALANGLE_H
+
+#include "base.h"
+
+class BimodalAngle : public Motion {
+public:
+    BimodalAngle(double, double, double, double, double, std::mt19937_64& );
+    explicit BimodalAngle(std::mt19937_64&);
+
+    void initialize() override;
+    double jump() override;
+
+protected:
+    double m_angle1{0};
+    double m_angle2{0};
+    double m_prob{0};
+    SphericalPos m_prev_pos{0., 0.};
+};
+
+#endif //BIMODALANGLE_H

motions/isosmallangle.cpp

@@ -3,12 +3,11 @@
 //
 
 #include "isosmallangle.h"
+#include "coordinates.h"
 
-#include <algorithm>
 
-SmallAngle::SmallAngle(const double delta, const double eta, const double chi, std::mt19937_64 &rng) : Motion(delta, eta, rng), m_chi(chi) {};
+SmallAngle::SmallAngle(const double delta, const double eta, const double chi, std::mt19937_64 &rng) : Motion(delta, eta, rng), m_chi(chi * M_PI / 180.0) {};
-SmallAngle::SmallAngle(std::mt19937_64 &rng) : Motion(rng) {
+SmallAngle::SmallAngle(std::mt19937_64 &rng) : Motion(rng) {}
-}
 
 void SmallAngle::initialize() {
     m_prev_pos = draw_position();
@@ -16,7 +15,7 @@ void SmallAngle::initialize() {
 
 double SmallAngle::jump() {
     const double gamma{2 * M_PI * m_uni_dist(m_rng)};
-    m_prev_pos = rotate(m_prev_pos, gamma, m_chi);
+    m_prev_pos = rotate(m_prev_pos, m_chi, gamma);
 
     return omega_q(m_prev_pos);
 }

motions/tetrahedral.cpp

@@ -9,12 +9,10 @@ TetrahedralJump::TetrahedralJump(const double delta, const double eta, std::mt19
 TetrahedralJump::TetrahedralJump(std::mt19937_64& rng) : Motion(rng) {}
 
 void TetrahedralJump::initialize() {
-    // const auto pos = SphericalPos{0., 0};
     const auto pos = draw_position();
     m_corners[0] = omega_q(pos);
 
     const double alpha = 2. * M_PI * m_uni_dist(m_rng);
-    // const double alpha = 0.;
 
     for (int i = 1; i<4; i++) {
         auto corner_pos = rotate(pos, m_beta, alpha + (i-1) * 2*M_PI/3.);

sims.cpp

@@ -112,6 +112,7 @@ void run_ste(std::unordered_map<std::string, double>& parameter, Motion& motion,
     motion.setEta(parameter["eta"]);
 
     const auto start = std::chrono::system_clock::now();
+    auto last_print_out = std::chrono::system_clock::now();
     const time_t start_time = std::chrono::system_clock::to_time_t(start);
     std::cout << "Start tau = " << tau << "s : " << ctime(&start_time);
 
@@ -148,6 +149,7 @@ void run_ste(std::unordered_map<std::string, double>& parameter, Motion& motion,
                 ss_j[mix_idx] += ss_tevo * std::sin(rephased) / num_walker;
             }
         }
+        last_print_out = printSteps(last_print_out, start, num_walker, mol_i);
     }
 
     // write to files
@@ -164,12 +166,13 @@ void run_ste(std::unordered_map<std::string, double>& parameter, Motion& motion,
 }
 
 
-void make_trajectory(Motion& motion, const Distribution& dist, const double t_max, std::vector<double>& out_time, std::vector<double>& out_phase) {
+void make_trajectory(Motion& motion, Distribution& dist, const double t_max, std::vector<double>& out_time, std::vector<double>& out_phase) {
     // Starting position
     double t_passed = 0;
     double phase = 0;
 
     motion.initialize();
+    dist.initialize();
 
     out_time.emplace_back(t_passed);
     out_phase.emplace_back(0);

sims.h

@@ -13,6 +13,6 @@
 
 void run_spectrum(std::unordered_map<std::string, double>& parameter, Motion& motion, Distribution& dist);
 void run_ste(std::unordered_map<std::string, double>& parameter, Motion& motion, Distribution& dist);
-void make_trajectory(Motion&, const Distribution&, double, std::vector<double>&, std::vector<double>&);
+void make_trajectory(Motion&, Distribution&, double, std::vector<double>&, std::vector<double>&);
 
 #endif //RWSIM_SIMS_H

test.py

@@ -58,7 +58,7 @@ def post_process_spectrum(taus, apod, tpulse):
 
 
 def post_process_ste(taus):
-    for i, tau in enumerate(tau_values):
+    for i, tau in enumerate(taus):
 
         try:
             raw_data_cc = np.loadtxt(f'coscos_tau={tau:.6e}.dat')

times/base.cpp

@@ -3,11 +3,11 @@
 //
 #include "base.h"
 
-Distribution::Distribution(const double tau, std::mt19937_64 &rng) : m_tau(tau), m_rng(rng) {}
+Distribution::Distribution(const double tau, std::mt19937_64 &rng) : m_tau(tau), m_tau_jump(tau), m_rng(rng) {}
 
 Distribution::Distribution(std::mt19937_64 &rng) : m_rng(rng) {}
 
 double Distribution::tau_wait() const {
-    return std::exponential_distribution(1./m_tau)(m_rng);
+    return std::exponential_distribution(1./m_tau_jump)(m_rng);
 }
 

times/base.h

@@ -17,11 +17,13 @@ public:
     [[nodiscard]] double getTau() const { return m_tau; }
     void setTau(const double tau) { m_tau = tau;}
 
+    virtual void initialize() = 0;
     virtual void draw_tau() = 0;
     [[nodiscard]] double tau_wait() const;
 
-private:
+protected:
     double m_tau{1.};
+    double m_tau_jump{1.};
     std::mt19937_64& m_rng;
 };
 

times/delta.cpp

@@ -6,5 +6,9 @@
 DeltaDistribution::DeltaDistribution(const double tau, std::mt19937_64& rng) : Distribution(tau, rng) {}
 DeltaDistribution::DeltaDistribution(std::mt19937_64& rng) : Distribution(rng) {}
 
+void DeltaDistribution::initialize() {
+    m_tau_jump = m_tau;
+}
+
 void DeltaDistribution::draw_tau() {}
 

times/delta.h

@@ -12,6 +12,7 @@ public:
     DeltaDistribution(double, std::mt19937_64&);
     explicit DeltaDistribution(std::mt19937_64 &rng);
 
+    void initialize() override;
     void draw_tau() override;
 };
 

times/lognormal.cpp

@@ -0,0 +1,18 @@
+//
+// Created by dominik on 8/24/24.
+//
+
+#include "lognormal.h"
+#include <cmath>
+
+LogNormalDistribution::LogNormalDistribution(const double tau, const double sigma, std::mt19937_64& rng) : Distribution(tau, rng), m_sigma(sigma), m_distribution(std::log(tau), sigma) {}
+LogNormalDistribution::LogNormalDistribution(std::mt19937_64& rng) : Distribution(rng) {}
+
+void LogNormalDistribution::initialize() {
+    m_distribution = std::lognormal_distribution(std::log(m_tau), m_sigma);
+    m_tau_jump = m_distribution(m_rng);
+}
+
+void LogNormalDistribution::draw_tau() {
+    m_tau_jump = m_distribution(m_rng);
+}

times/lognormal.h

@@ -0,0 +1,21 @@
+
+#ifndef LOGNORMAL_H
+#define LOGNORMAL_H
+
+#include "base.h"
+#include <random>
+
+class LogNormalDistribution final : public Distribution {
+public:
+    LogNormalDistribution(double, double, std::mt19937_64&);
+    explicit LogNormalDistribution(std::mt19937_64 &rng);
+
+    void initialize() override;
+    void draw_tau() override;
+
+private:
+    double m_sigma{1};
+    std::lognormal_distribution<> m_distribution;
+};
+
+#endif //LOGNORMAL_H