create Motion classes on runtime instead of compile

io.cpp

@@ -25,22 +25,28 @@ Arguments parse_args(const int argc, char **argv) {
 
     for (int i=1; i<argc; i++) {
         if (std::string arg = argv[i]; arg[0] == '-') {
-            if (arg == "-ste") {
+            if (arg == "--ste") {
                 args.ste = true;
-            } else if (arg == "-spectrum") {
+            } else if (arg == "--spectrum") {
                 args.spectrum = true;
             } else {
                 throw std::runtime_error("Unrecognized option: " + arg);
             }
         } else if (args.parameter_file.empty()) {
             args.parameter_file = arg;
+        } else if (args.motion_type.empty()) {
+            args.motion_type = arg;
         } else {
-            throw std::runtime_error("Too many options for parameter file");
+            throw std::invalid_argument("Too many options for parameter file");
         }
     }
 
     if (args.parameter_file.empty()) {
-        throw std::runtime_error("Missing parameter file");
+        throw std::invalid_argument("Missing parameter file");
+    }
+
+    if (args.motion_type.empty()) {
+        throw std::invalid_argument("Missing motion model");
     }
 
     return args;

io.h

@@ -12,6 +12,7 @@ struct Arguments {
     std::string parameter_file{};
     bool ste = false;
     bool spectrum = false;
+    std::string motion_type{};
 };
 
 Arguments parse_args(int argc, char **argv);

main.cpp

@@ -4,6 +4,7 @@
 
 #include "io.h"
 #include "sims.h"
+#include "motions/base.h"
 #include "motions/bimodalangle.h"
 #include "motions/isosmallangle.h"
 #include "motions/random.h"
@@ -12,6 +13,7 @@
 #include "times/lognormal.h"
 
 
+
 int main (const int argc, char *argv[]) {
     Arguments args;
     try {
@@ -26,18 +28,15 @@ int main (const int argc, char *argv[]) {
     std::random_device rd;
     std::mt19937_64 rng(rd());
 
-    // auto motion = BimodalAngle(1, 1, 2, 30, 0.98, rng); // arguments: delta, eta, angle1, angle2, probability of angle1
-    auto motion = TetrahedralJump(rng);
-    // auto motion = RandomJump(rng);
-    // auto motion = SmallAngle(1, 1, 4, rng);  // arguments: delta, eta, angle
+    Motion *motion = Motion::createFromInput(args.motion_type, rng);
 
     auto dist = DeltaDistribution(rng);
     // auto dist = LogNormalDistribution(1, 2, rng);  // arguments: tau_max, sigma
 
     if (args.spectrum) {
-       run_spectrum(parameter, motion, dist);
+       run_spectrum(parameter, *motion, dist);
     }
     if (args.ste) {
-        run_ste(parameter, motion, dist);
+        run_ste(parameter, *motion, dist);
     }
 }

motions/base.cpp

@@ -2,20 +2,25 @@
 // Created by dominik on 8/12/24.
 //
 
-// #include <cmath>
 #include <random>
 #include <cmath>
 
 #include "base.h"
+
+#include <stdexcept>
+#include <utility>
+
 #include "coordinates.h"
+#include "bimodalangle.h"
+#include "isosmallangle.h"
+#include "random.h"
+#include "tetrahedral.h"
 
-#include <unordered_map>
-
-Motion::Motion(const double delta, const double eta, std::mt19937_64& rng) : m_delta(delta), m_eta(eta), m_rng(rng) {
+Motion::Motion(std::string name, const double delta, const double eta, std::mt19937_64& rng) : m_name(std::move(name)), m_delta(delta), m_eta(eta), m_rng(rng) {
     m_uni_dist = std::uniform_real_distribution(0., 1.);
 }
 
-Motion::Motion(std::mt19937_64& rng) : m_rng(rng) {
+Motion::Motion(std::string name, std::mt19937_64& rng) : m_name(std::move(name)), m_rng(rng) {
     m_uni_dist = std::uniform_real_distribution(0., 1.);
 }
 
@@ -27,7 +32,6 @@ double Motion::omega_q(const double cos_theta, const double phi) const {
 }
 
 double Motion::omega_q(const SphericalPos& pos) const {
-    // std::cout << pos.cos_theta << " " << pos.phi << std::endl;
     auto [cos_theta, phi] = pos;
 
     return omega_q(cos_theta, phi);
@@ -39,3 +43,24 @@ SphericalPos Motion::draw_position() {
 
     return {cos_theta, phi};
 }
+
+Motion* Motion::createFromInput(const std::string& input, std::mt19937_64& rng) {
+    if (input == "TetrahedralJump")
+        return new TetrahedralJump(rng);
+
+    if (input == "IsotropicAngle")
+        return new SmallAngle(rng);
+
+    if (input == "RandomJump")
+        return new RandomJump(rng);
+
+    if (input == "BimodalAngle")
+        return new BimodalAngle(rng);
+
+    throw std::invalid_argument("Invalid input " + input);
+}
+
+std::ostream& operator<<(std::ostream& os, const Motion& m) {
+    os << m.getName();
+    return os;
+}

motions/base.h

@@ -7,15 +7,13 @@
 
 #include "coordinates.h"
 #include <random>
-#include <unordered_map>
-
 
 class Motion {
 public:
     virtual ~Motion() = default;
 
-    Motion(double, double, std::mt19937_64&);
-    explicit Motion(std::mt19937_64&);
+    Motion(std::string, double, double, std::mt19937_64&);
+    explicit Motion(std::string, std::mt19937_64&);
 
     SphericalPos draw_position();
     [[nodiscard]] double omega_q(double, double) const;
@@ -28,13 +26,18 @@ public:
     void setDelta(const double delta) { m_delta = delta; }
     [[nodiscard]] double getEta() const { return m_eta; }
     void setEta(const double eta) { m_eta = eta; }
+    [[nodiscard]] std::string getName() const { return m_name; }
+
+    static Motion* createFromInput(const std::string& input, std::mt19937_64& rng);
 
 protected:
+    std::string m_name{"Base motion"};
     double m_delta{1.};
     double m_eta{0.};
     std::mt19937_64& m_rng;
     std::uniform_real_distribution<> m_uni_dist;
 };
 
+std::ostream& operator<<(std::ostream& os, const Motion& m);
 
 #endif //RWSIM_MOTIONBASE_H

motions/bimodalangle.cpp

@@ -6,11 +6,11 @@
 #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),
+    Motion(std::string("Bimodal Angle Jump"), 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) {}
+BimodalAngle::BimodalAngle(std::mt19937_64 &rng) : Motion(std::string("Bimodal Angle Jump"), rng) {}
 
 void BimodalAngle::initialize() {
     m_prev_pos = draw_position();

motions/isosmallangle.cpp

@@ -6,8 +6,9 @@
 #include "coordinates.h"
 
 
-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(const double delta, const double eta, const double chi, std::mt19937_64 &rng) :
+    Motion(std::string("Isotropic Angle Jump"), delta, eta, rng), m_chi(chi * M_PI / 180.0) {};
+SmallAngle::SmallAngle(std::mt19937_64 &rng) : Motion(std::string("Isotropic Angle Jump"), rng) {}
 
 void SmallAngle::initialize() {
     m_prev_pos = draw_position();

motions/random.cpp

@@ -5,9 +5,9 @@
 #include "random.h"
 
 
-RandomJump::RandomJump(const double delta, const double eta, std::mt19937_64 &rng) : Motion(delta, eta, rng) {}
+RandomJump::RandomJump(const double delta, const double eta, std::mt19937_64 &rng) : Motion(std::string("Random Jump"), delta, eta, rng) {}
 
-RandomJump::RandomJump(std::mt19937_64 &rng) : Motion(rng) {}
+RandomJump::RandomJump(std::mt19937_64 &rng) : Motion(std::string("Random Jump"), rng) {}
 
 void RandomJump::initialize() {}
 

motions/tetrahedral.cpp

@@ -2,11 +2,13 @@
 // Created by dominik on 8/16/24.
 //
 #include <random>
+
 #include "tetrahedral.h"
 
-TetrahedralJump::TetrahedralJump(const double delta, const double eta, std::mt19937_64& rng) : Motion(delta, eta, rng) {}
+TetrahedralJump::TetrahedralJump(const double delta, const double eta, std::mt19937_64& rng) :
+    Motion(std::string{"TetrahedralJump"}, delta, eta, rng) {}
 
-TetrahedralJump::TetrahedralJump(std::mt19937_64& rng) : Motion(rng) {}
+TetrahedralJump::TetrahedralJump(std::mt19937_64& rng) : Motion(std::string{"TetrahedralJump"}, rng) {}
 
 void TetrahedralJump::initialize() {
     const auto pos = draw_position();

sims.h

@@ -11,8 +11,33 @@
 #include "motions/base.h"
 #include "times/base.h"
 
+/**
+ * @brief Run simulation for spectra
+ *
+ * @param parameter Dictionary of parameter for simulation
+ * @param motion Motion model
+ * @param dist Distribution of correlation times
+ */
 void run_spectrum(std::unordered_map<std::string, double>& parameter, Motion& motion, Distribution& dist);
+
+/**
+ * @brief Run simulation for stimulated echoes
+ *
+ * @param parameter Dictionary of parameter for simulation
+ * @param motion Motion model
+ * @param dist Distribution of correlation times
+ */
 void run_ste(std::unordered_map<std::string, double>& parameter, Motion& motion, Distribution& dist);
-void make_trajectory(Motion&, Distribution&, double, std::vector<double>&, std::vector<double>&);
+
+/**
+ * @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
+ */
+void make_trajectory(Motion& motion, Distribution& dist, double t_max, std::vector<double>& out_time, std::vector<double>& out_phase);
 
 #endif //RWSIM_SIMS_H

test.py

@@ -7,11 +7,21 @@ import matplotlib.pyplot as plt
 
 
 
-def run_sims(taus):
+def run_sims(taus, ste: bool = True, spectrum: bool = False, exec_file: str = './build/rwsim', config_file: str = './config.txt'):
     for tau in taus:
-        with pathlib.Path('./config.txt').open('a') as f:
+        arguments = [exec_file, config_file]
+        if ste:
+            arguments += ['--ste']
+        if spectrum:
+            arguments += ['--spectrum']
+
+        arguments += ['IsotropicAngle']
+
+        with pathlib.Path(config_file).open('a') as f:
             f.write(f'tau={tau}\n')
-        subprocess.run(['./build/rwsim', '-ste', './config.txt'])
+
+        subprocess.run(arguments)
+
 
 
 def dampening(x: np.ndarray, apod: float) -> np.ndarray:
@@ -101,7 +111,7 @@ def post_process_ste(taus):
 
             res = curve_fit(ste, t_mix, raw_data_cc[:, j+1], p0, bounds=[(0, 0, 0, 0), (np.inf, np.inf, 1, 1)])
             m0, tauc, beta, finfty = res[0]
-            print(f'Cos-Cos-Fit for {tevo[j]}: tau_c = {tauc:.6e}, beta={beta:.4e}, amplitude = {m0: .4e}, f_infty={finfty:.4e}')
+            # print(f'Cos-Cos-Fit for {tevo[j]}: tau_c = {tauc:.6e}, beta={beta:.4e}, amplitude = {m0: .4e}, f_infty={finfty:.4e}')
 
             tau_cc_fit.append(res[0][1])
             beta_cc_fit.append(res[0][2])
@@ -116,7 +126,7 @@ def post_process_ste(taus):
 
             res = curve_fit(ste, t_mix, raw_data_ss[:, j+1], p0, bounds=[(0, 0, 0, 0), (np.inf, np.inf, 1, 1)])
             m0, tauc, beta, finfty = res[0]
-            print(f'Sin-Sin-Fit for {tevo[j]}: tau_c = {tauc:.6e}, beta={beta:.4e}, amplitude = {m0: .4e}, f_infty={finfty:.4e}')
+            # print(f'Sin-Sin-Fit for {tevo[j]}: tau_c = {tauc:.6e}, beta={beta:.4e}, amplitude = {m0: .4e}, f_infty={finfty:.4e}')
 
             tau_ss_fit.append(res[0][1])
             beta_ss_fit.append(res[0][2])