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Dominik Demuth
183
simulation/sims.cpp
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183
simulation/sims.cpp
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#include "sims.h"
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#include "../motions/base.h"
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#include "../times/base.h"
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#include "../utils/functions.h"
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#include "../utils/ranges.h"
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#include "../utils/io.h"
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#include <iostream>
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#include <algorithm>
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#include <unordered_map>
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#include <map>
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#include <string>
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#include <vector>
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#include <cmath>
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#include <chrono>
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void run_spectrum(std::unordered_map<std::string, double>& parameter, Motion& motion, Distribution& dist) {
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const int num_walker = static_cast<int>(parameter["num_walker"]);
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// time axis for all time signals
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const int num_acq = static_cast<int>(parameter["num_acq"]);
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const std::vector<double> t_fid = arange(num_acq, parameter["dwell_time"]);
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const std::vector<double> echo_times = linspace(parameter["techo_start"], parameter["techo_stop"], static_cast<int>(parameter["techo_steps"]));
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// make timesignal vectors and set them to zero
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std::map<double, std::vector<double>> fid_dict;
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for (auto t_evo_i: echo_times) {
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fid_dict[t_evo_i] = std::vector<double>(num_acq);
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std::fill(fid_dict[t_evo_i].begin(), fid_dict[t_evo_i].end(), 0.);
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}
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// calculate min length of a trajectory
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const double tmax = *std::max_element(echo_times.begin(), echo_times.end()) * 2 + t_fid.back();
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// set parameter in distribution and motion model
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const double tau = parameter.at("tau");
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dist.setTau(tau);
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motion.setParameters(parameter);
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const auto start = std::chrono::system_clock::now();
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auto last_print_out = std::chrono::system_clock::now();
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const time_t start_time = std::chrono::system_clock::to_time_t(start);
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std::cout << "Start tau = " << tau << "s : " << ctime(&start_time);
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// let the walker walk
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for (int mol_i = 0; mol_i < num_walker; mol_i++){
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std::vector<double> traj_time{};
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std::vector<double> traj_phase{};
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make_trajectory(motion, dist, tmax, traj_time, traj_phase);
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for (auto& [t_echo_j, fid_j] : fid_dict) {
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// get phase at echo pulse
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int current_pos = nearest_index(traj_time, t_echo_j, 0);
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const double phase_techo = lerp(traj_time, traj_phase, t_echo_j, current_pos);
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for (int acq_idx = 0; acq_idx < num_acq; acq_idx++) {
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const double real_time = t_fid[acq_idx] + 2 * t_echo_j;
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current_pos = nearest_index(traj_time, real_time, current_pos);
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const double phase_acq = lerp(traj_time, traj_phase, real_time, current_pos);
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fid_j[acq_idx] += std::cos(phase_acq - 2 * phase_techo) / num_walker;
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}
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last_print_out = printSteps(last_print_out, start, num_walker, mol_i);
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}
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}
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// write fid to files
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fid_write_out("fid", t_fid, fid_dict, tau);
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const auto end = std::chrono::system_clock::now();
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std::chrono::duration<float> duration = end - start;
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const time_t end_time = std::chrono::system_clock::to_time_t(end);
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std::cout << "End tau = " << tau << "s : " << ctime(&end_time);
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std::cout << "Duration: " << duration.count() << "s\n" << std::endl;
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}
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void run_ste(std::unordered_map<std::string, double>& parameter, Motion& motion, Distribution& dist) {
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const int num_walker = static_cast<int>(parameter[std::string("num_walker")]);
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const int num_mix_times = static_cast<int>(parameter[std::string("tmix_steps")]);
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const std::vector<double> evolution_times = linspace(parameter["tevo_start"], parameter["tevo_stop"], static_cast<int>(parameter["tevo_steps"]));
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const std::vector<double> mixing_times = logspace(parameter["tmix_start"], parameter["tmix_stop"], num_mix_times);
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// make ste decay vectors and set them to zero
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std::map<double, std::vector<double>> cc_dict;
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std::map<double, std::vector<double>> ss_dict;
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for (auto t_evo_i: evolution_times) {
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cc_dict[t_evo_i] = std::vector<double>(num_mix_times);
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ss_dict[t_evo_i] = std::vector<double>(num_mix_times);
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std::fill(ss_dict[t_evo_i].begin(), ss_dict[t_evo_i].end(), 0.);
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}
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// each trajectory must have a duration of at least tmax
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const double tmax = *std::max_element(evolution_times.begin(), evolution_times.end()) * 2 + *std::max_element(mixing_times.begin(), mixing_times.end());
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// set parameter in distribution and motion model
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const double tau = parameter.at("tau");
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dist.setTau(tau);
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motion.setParameters(parameter);
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const auto start = std::chrono::system_clock::now();
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auto last_print_out = std::chrono::system_clock::now();
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const time_t start_time = std::chrono::system_clock::to_time_t(start);
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std::cout << "Start tau = " << tau << "s : " << ctime(&start_time);
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// let the walker walk
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for (int mol_i = 0; mol_i < num_walker; mol_i++){
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std::vector<double> traj_time{};
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std::vector<double> traj_phase{};
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make_trajectory(motion, dist, tmax, traj_time, traj_phase);
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for (auto& [t_evo_j, _] : cc_dict) {
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auto& cc_j = cc_dict[t_evo_j];
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auto& ss_j = ss_dict[t_evo_j];
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// get phase at beginning of mixing time
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int current_pos = nearest_index(traj_time, t_evo_j, 0);
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const double dephased = lerp(traj_time, traj_phase, t_evo_j, current_pos);
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const double cc_tevo = std::cos(dephased);
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const double ss_tevo = std::sin(dephased);
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for (int mix_idx = 0; mix_idx < num_mix_times; mix_idx++) {
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// get phase at end of mixing time
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const double time_end_mix = mixing_times[mix_idx] + t_evo_j;
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current_pos = nearest_index(traj_time, time_end_mix, current_pos);
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const double phase_mix_end = lerp(traj_time, traj_phase, time_end_mix, current_pos);
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// get phase at echo position
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const double time_echo = mixing_times[mix_idx] + 2 * t_evo_j;
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current_pos = nearest_index(traj_time, time_echo, current_pos);
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const double rephased = lerp(traj_time, traj_phase, time_echo, current_pos) - phase_mix_end;
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cc_j[mix_idx] += cc_tevo * std::cos(rephased) / num_walker;
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ss_j[mix_idx] += ss_tevo * std::sin(rephased) / num_walker;
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}
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}
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last_print_out = printSteps(last_print_out, start, num_walker, mol_i);
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}
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// write to files
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fid_write_out("coscos", mixing_times, cc_dict, tau);
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fid_write_out("sinsin", mixing_times, ss_dict, tau);
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const auto end = std::chrono::system_clock::now();
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const std::chrono::duration<float> duration = end - start;
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const time_t end_time = std::chrono::system_clock::to_time_t(end);
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std::cout << "End tau = " << tau << "s : " << ctime(&end_time);
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std::cout << "Duration: " << duration.count() << "s\n" << std::endl;
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}
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void make_trajectory(Motion& motion, Distribution& dist, const double t_max, std::vector<double>& out_time, std::vector<double>& out_phase) {
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// Starting position
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double t_passed = 0;
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double phase = 0;
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motion.initialize();
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dist.initialize();
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out_time.emplace_back(t_passed);
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out_phase.emplace_back(0);
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while (t_passed < t_max) {
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const double t = dist.tau_wait();
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t_passed += t;
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phase += motion.jump() * t;
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out_time.emplace_back(t_passed);
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out_phase.emplace_back(phase);
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}
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}
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43
simulation/sims.h
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43
simulation/sims.h
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//
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// Created by dominik on 8/14/24.
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//
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#ifndef RWSIM_SIMS_H
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#define RWSIM_SIMS_H
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#include "../motions/base.h"
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#include "../times/base.h"
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#include <unordered_map>
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#include <string>
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/**
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* @brief Run simulation for spectra
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*
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* @param parameter Dictionary of parameter for simulation
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* @param motion Motion model
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* @param dist Distribution of correlation times
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*/
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void run_spectrum(std::unordered_map<std::string, double>& parameter, Motion& motion, Distribution& dist);
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/**
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* @brief Run simulation for stimulated echoes
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*
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* @param parameter Dictionary of parameter for simulation
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* @param motion Motion model
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* @param dist Distribution of correlation times
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*/
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void run_ste(std::unordered_map<std::string, double>& parameter, Motion& motion, Distribution& dist);
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/**
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* @brief Create trajectory of a single walker
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*
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* @param motion Motion model
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* @param dist Distribution of correlation times
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* @param t_max Double that defines maximum time of trajectory
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* @param out_time Vector of waiting times
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* @param out_phase Vector of phase between waiting times
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*/
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void make_trajectory(Motion& motion, Distribution& dist, double t_max, std::vector<double>& out_time, std::vector<double>& out_phase);
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#endif //RWSIM_SIMS_H
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