added flexibility

This commit is contained in:
Dominik Demuth 2024-11-28 14:50:26 +01:00
parent 1c8befac3f
commit d844aac0e8
16 changed files with 121 additions and 52 deletions

1
.gitignore vendored
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@ -1,2 +1,3 @@
/cmake-build-debug/ /cmake-build-debug/
.idea .idea
/build/

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@ -5,8 +5,6 @@
# Build # Build
This
# Running # Running
## Command line ## Command line

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@ -5,3 +5,4 @@ cmake ..
cmake --build . cmake --build .
cp ./src/rwsim ../rwsim cp ./src/rwsim ../rwsim
cd ..

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@ -4,7 +4,7 @@ num_walker=20000
delta=126e3 delta=126e3
eta=0.0 eta=0.0
# Distribution part # Distribution part
tau=1e-2 tau=1e-3
angle1=2 angle1=2
angle2=30 angle2=30
probability1=0 probability1=0

26
main.py
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@ -1,11 +1,14 @@
import matplotlib.pyplot as plt
from python.ste import * from python.ste import *
from python.helpers import * from python.helpers import *
# Simulation parameter # Simulation parameter
motion = 'IsotropicAngle' motion = 'IsotropicAngle'
distribution = 'Delta' distribution = 'Delta'
# parameter = {}
parameter = { parameter = {
"angle": [3, 10, 30, 109.4], "angle": [10, 109.47],
} }
parameter = prepare_rw_parameter(parameter) parameter = prepare_rw_parameter(parameter)
@ -20,27 +23,30 @@ fig_finfty_cc, ax_finfty_cc = plt.subplots()
ax_finfty_cc.set_title('f_infty_cc') ax_finfty_cc.set_title('f_infty_cc')
fig_tau_ss, ax_tau_ss = plt.subplots() fig_tau_ss, ax_tau_ss = plt.subplots()
ax_tau_ss.set_title('tau_cc') ax_tau_ss.set_title('tau_ss')
fig_beta_ss, ax_beta_ss = plt.subplots() fig_beta_ss, ax_beta_ss = plt.subplots()
ax_beta_ss.set_title('beta_cc') ax_beta_ss.set_title('beta_ss')
fig_finfty_ss, ax_finfty_ss = plt.subplots() fig_finfty_ss, ax_finfty_ss = plt.subplots()
ax_finfty_ss.set_title('f_infty_cc') ax_finfty_ss.set_title('f_infty_ss')
for variation in parameter: for variation in parameter:
print(f"\nRun RW for {motion}/{distribution} with arguments {variation}\n") print(f"\nRun RW for {motion}/{distribution} with arguments {variation}\n")
run_sims(motion, distribution, ste=True, spectrum=True, **variation) run_sims(motion, distribution, ste=True, spectrum=False, **variation)
conf_file = find_config_file(variation) conf_file = find_config_file(motion, distribution, variation)
print(conf_file)
vary_string, tau_cc, beta_cc, finfty_cc, tau_ss, beta_ss, finfty_ss = fit_and_save_ste(conf_file, plot_decays=False, verbose=False) vary_string, tau_cc, beta_cc, finfty_cc = fit_and_save_ste(conf_file, 'coscos', plot_decays=False, verbose=False)
_, tau_ss, beta_ss, finfty_ss = fit_and_save_ste(conf_file, 'sinsin', plot_decays=False, verbose=False)
_, tau_2, beta_2, finfty_2 = fit_and_save_ste(conf_file, 'f2', plot_decays=True, verbose=True)
ax_tau_cc.semilogy(*tau_cc.T, label=vary_string) ax_tau_cc.semilogy(tau_cc[:, 0], tau_cc[:, 1], label=vary_string)
ax_tau_cc.axhline(tau_2[:, 1], color='k', linestyle='--')
ax_beta_cc.plot(*beta_cc.T, label=vary_string) ax_beta_cc.plot(*beta_cc.T, label=vary_string)
ax_finfty_cc.plot(*finfty_cc.T, label=vary_string) ax_finfty_cc.plot(*finfty_cc.T, label=vary_string)
ax_tau_ss.semilogy(*tau_ss.T, label=vary_string) ax_tau_ss.semilogy(tau_ss[:, 0], tau_ss[:, 1], label=vary_string)
ax_tau_ss.axhline(tau_2[:, 1], color='k', linestyle='--')
ax_beta_ss.plot(*beta_ss.T, label=vary_string) ax_beta_ss.plot(*beta_ss.T, label=vary_string)
ax_finfty_ss.plot(*finfty_ss.T, label=vary_string) ax_finfty_ss.plot(*finfty_ss.T, label=vary_string)

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@ -53,13 +53,23 @@ def run_sims(
subprocess.run(arguments) subprocess.run(arguments)
def find_config_file(var_params: dict) -> pathlib.Path: def find_config_file(motion: str, distribution: str, var_params: dict) -> pathlib.Path:
# TODO handle situation if multiple files fit # TODO handle situation if multiple files fit
pattern = re.compile('|'.join(([f'{k}={v:1.6e}' for (k, v) in var_params.items()])).replace('.', '\.').replace('+', '\+')) p_file = None
if var_params:
var_string = '|'.join(([f'{k}={v:1.6e}' for (k, v) in var_params.items()])).replace('.', '\.').replace('+', '\+')
pattern = re.compile(var_string)
for p_file in pathlib.Path('.').glob('*_parameter.txt'): for p_file in pathlib.Path('.').glob('*_parameter.txt'):
if len(re.findall(pattern, str(p_file))) == len(var_params): if len(re.findall(pattern, str(p_file))) == len(var_params) and re.search(f'{motion}_{distribution}', str(p_file)):
return p_file return p_file
raise ValueError(f'No parameter file found for {motion}, {distribution}, {var_params}')
else:
for p_file in pathlib.Path('.').glob('*_parameter.txt'):
if re.search(f'{motion}_{distribution}', str(p_file)):
return p_file
raise ValueError(f'No parameter file found for {motion}, {distribution}, {var_params}')
def read_parameter_file(path: str | pathlib.Path) -> dict[str, float]: def read_parameter_file(path: str | pathlib.Path) -> dict[str, float]:

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@ -24,6 +24,8 @@ def ste_decay(x: np.ndarray, m0: float, t: float, beta: float, finfty: float) ->
def fit_decay(x: np.ndarray, y: np.ndarray, tevo: np.ndarray, verbose: bool = True) -> tuple[np.ndarray, np.ndarray, np.ndarray]: def fit_decay(x: np.ndarray, y: np.ndarray, tevo: np.ndarray, verbose: bool = True) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
num_evo = y.shape[1] num_evo = y.shape[1]
if num_evo != tevo.size:
tevo = np.arange(num_evo)
tau_fit = np.empty((num_evo, 2)) tau_fit = np.empty((num_evo, 2))
tau_fit[:, 0] = tevo tau_fit[:, 0] = tevo
@ -37,7 +39,7 @@ def fit_decay(x: np.ndarray, y: np.ndarray, tevo: np.ndarray, verbose: bool = Tr
scaled_y = (y-y[-1, :]) / (y[0, :]-y[-1, :]) scaled_y = (y-y[-1, :]) / (y[0, :]-y[-1, :])
for j in range(num_evo): for j in range(num_evo):
p0 = [scaled_y[0, 1], x[np.argmin(np.abs(scaled_y[:, j]-np.exp(-1)))], 0.5, 0.1] p0 = [y[0, 0], x[np.argmin(np.abs(scaled_y[:, j]-np.exp(-1)))], 0.8, 0.1]
try: try:
res = curve_fit(ste_decay, x, y[:, j], p0, bounds=[(0, 0, 0., 0), (np.inf, np.inf, 1, 1)]) res = curve_fit(ste_decay, x, y[:, j], p0, bounds=[(0, 0, 0., 0), (np.inf, np.inf, 1, 1)])
@ -57,7 +59,12 @@ def fit_decay(x: np.ndarray, y: np.ndarray, tevo: np.ndarray, verbose: bool = Tr
return tau_fit, beta_fit, finfty_fit return tau_fit, beta_fit, finfty_fit
def fit_and_save_ste(parameter_file: pathlib.Path, plot_decays: bool = True, verbose: bool = True): def fit_and_save_ste(
parameter_file: pathlib.Path,
prefix: str,
plot_decays: bool = True,
verbose: bool = True,
) -> tuple[str, np.ndarray, np.ndarray, np.ndarray]:
# read simulation parameters # read simulation parameters
parameter = read_parameter_file(parameter_file) parameter = read_parameter_file(parameter_file)
@ -67,36 +74,24 @@ def fit_and_save_ste(parameter_file: pathlib.Path, plot_decays: bool = True, ver
# make evolution times # make evolution times
tevo = np.linspace(parameter['tevo_start'], parameter['tevo_stop'], num=int(parameter['tevo_steps'])) tevo = np.linspace(parameter['tevo_start'], parameter['tevo_stop'], num=int(parameter['tevo_steps']))
raw_data_cc = np.loadtxt(f'coscos_{varied_string}.dat') raw_data = np.loadtxt(f'{prefix}_{varied_string}.dat')
raw_data_ss = np.loadtxt(f'sinsin_{varied_string}.dat')
t_mix = raw_data_cc[:, 0] t_mix = raw_data[:, 0]
cc_decay = raw_data_cc[:, 1:] decay = raw_data[:, 1:]
ss_decay = raw_data_ss[:, 1:]
if plot_decays: if plot_decays:
fig_cc, ax_cc = plt.subplots() fig, ax = plt.subplots()
ax_cc.set_title('Cos-Cos') ax.set_title(prefix)
ax_cc.semilogx(t_mix, cc_decay, '.') ax.semilogx(t_mix, decay, '.')
fig_ss, ax_ss = plt.subplots() fig.show()
ax_ss.set_title('Sin-Sin')
ax_ss.semilogx(t_mix, ss_decay, '.')
plt.show() print(f'Fit {prefix}')
tau, beta, finfty = fit_decay(t_mix, decay, tevo, verbose=verbose)
print('Fit Cos-Cos')
tau_cc, beta_cc, finfty_cc = fit_decay(t_mix, cc_decay, tevo, verbose=verbose)
np.savetxt(f'tau_cc_{varied_string}.dat', tau_cc) np.savetxt(f'tau_{prefix}_{varied_string}.dat', tau)
np.savetxt(f'beta_cc_{varied_string}.dat', beta_cc) np.savetxt(f'beta_{prefix}_{varied_string}.dat', beta)
np.savetxt(f'finfty_cc_{varied_string}.dat', finfty_cc) np.savetxt(f'finfty_{prefix}_{varied_string}.dat', finfty)
print('Fit Sin-Sin') return varied_string, tau, beta, finfty
tau_ss, beta_ss, finfty_ss = fit_decay(t_mix, ss_decay, tevo, verbose=verbose)
np.savetxt(f'tau_ss_{varied_string}.dat', tau_ss)
np.savetxt(f'beta_ss_{varied_string}.dat', beta_ss)
np.savetxt(f'finfty_ss_{varied_string}.dat', finfty_ss)
return varied_string, tau_cc, beta_cc, finfty_cc, tau_ss, beta_ss, finfty_ss

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@ -27,6 +27,7 @@ public:
[[nodiscard]] double getEta() const { return m_eta; } [[nodiscard]] double getEta() const { return m_eta; }
void setEta(const double eta) { m_eta = eta; } void setEta(const double eta) { m_eta = eta; }
[[nodiscard]] std::string getName() const { return m_name; } [[nodiscard]] std::string getName() const { return m_name; }
[[nodiscard]] double getInitOmega() const { return m_initial_omega; };
static Motion* createFromInput(const std::string& input, std::mt19937_64& rng); static Motion* createFromInput(const std::string& input, std::mt19937_64& rng);
@ -36,6 +37,7 @@ protected:
double m_eta{0.}; double m_eta{0.};
std::mt19937_64& m_rng; std::mt19937_64& m_rng;
std::uniform_real_distribution<> m_uni_dist; std::uniform_real_distribution<> m_uni_dist;
double m_initial_omega{0.};
}; };
std::ostream& operator<<(std::ostream& os, const Motion& m); std::ostream& operator<<(std::ostream& os, const Motion& m);

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@ -11,6 +11,7 @@ BimodalAngle::BimodalAngle(std::mt19937_64 &rng) : Motion(std::string("BimodalAn
void BimodalAngle::initialize() { void BimodalAngle::initialize() {
m_prev_pos = draw_position(); m_prev_pos = draw_position();
m_initial_omega = omega_q(m_prev_pos);
}; };
double BimodalAngle::jump() { double BimodalAngle::jump() {

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@ -11,6 +11,7 @@ SmallAngle::SmallAngle(std::mt19937_64 &rng) : Motion(std::string("IsotropicAngl
void SmallAngle::initialize() { void SmallAngle::initialize() {
m_prev_pos = draw_position(); m_prev_pos = draw_position();
m_initial_omega = omega_q(m_prev_pos);
}; };
double SmallAngle::jump() { double SmallAngle::jump() {

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@ -6,7 +6,9 @@ RandomJump::RandomJump(const double delta, const double eta, std::mt19937_64 &rn
RandomJump::RandomJump(std::mt19937_64 &rng) : Motion(std::string("RandomJump"), rng) {} RandomJump::RandomJump(std::mt19937_64 &rng) : Motion(std::string("RandomJump"), rng) {}
void RandomJump::initialize() {} void RandomJump::initialize() {
m_initial_omega = RandomJump::jump();
}
double RandomJump::jump() { double RandomJump::jump() {
return omega_q(draw_position()); return omega_q(draw_position());

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@ -19,6 +19,7 @@ void TetrahedralJump::initialize() {
auto corner_pos = rotate(pos, m_beta, alpha + (i-1) * 2*M_PI/3.); auto corner_pos = rotate(pos, m_beta, alpha + (i-1) * 2*M_PI/3.);
m_corners[i] = omega_q(corner_pos); m_corners[i] = omega_q(corner_pos);
} }
m_initial_omega = TetrahedralJump::jump();
} }
double TetrahedralJump::jump() { double TetrahedralJump::jump() {

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@ -49,8 +49,9 @@ void run_spectrum(
for (int mol_i = 0; mol_i < num_walker; mol_i++){ for (int mol_i = 0; mol_i < num_walker; mol_i++){
std::vector<double> traj_time{}; std::vector<double> traj_time{};
std::vector<double> traj_phase{}; std::vector<double> traj_phase{};
std::vector<double> traj_omega{};
make_trajectory(motion, dist, tmax, traj_time, traj_phase); make_trajectory(motion, dist, tmax, traj_time, traj_phase, traj_omega);
for (auto& [t_echo_j, fid_j] : fid_dict) { for (auto& [t_echo_j, fid_j] : fid_dict) {
// get phase at echo pulse // get phase at echo pulse
@ -96,8 +97,10 @@ void run_ste(
for (auto t_evo_i: evolution_times) { for (auto t_evo_i: evolution_times) {
cc_dict[t_evo_i] = std::vector<double>(num_mix_times); cc_dict[t_evo_i] = std::vector<double>(num_mix_times);
ss_dict[t_evo_i] = std::vector<double>(num_mix_times); ss_dict[t_evo_i] = std::vector<double>(num_mix_times);
std::fill(cc_dict[t_evo_i].begin(), cc_dict[t_evo_i].end(), 0.);
std::fill(ss_dict[t_evo_i].begin(), ss_dict[t_evo_i].end(), 0.); std::fill(ss_dict[t_evo_i].begin(), ss_dict[t_evo_i].end(), 0.);
} }
std::vector<double> f2(num_mix_times);
// each trajectory must have a duration of at least tmax // each trajectory must have a duration of at least tmax
const double tmax = *std::max_element(evolution_times.begin(), evolution_times.end()) * 2 + *std::max_element(mixing_times.begin(), mixing_times.end()); const double tmax = *std::max_element(evolution_times.begin(), evolution_times.end()) * 2 + *std::max_element(mixing_times.begin(), mixing_times.end());
@ -113,8 +116,16 @@ void run_ste(
for (int mol_i = 0; mol_i < num_walker; mol_i++){ for (int mol_i = 0; mol_i < num_walker; mol_i++){
std::vector<double> traj_time{}; std::vector<double> traj_time{};
std::vector<double> traj_phase{}; std::vector<double> traj_phase{};
std::vector<double> traj_omega{};
make_trajectory(motion, dist, tmax, traj_time, traj_phase); make_trajectory(motion, dist, tmax, traj_time, traj_phase, traj_omega);
int f2_pos = 0;
for (int f2_idx=0; f2_idx < num_mix_times; f2_idx++) {
const double t_mix_f2 = mixing_times[f2_idx];
f2_pos = nearest_index(traj_time, t_mix_f2, f2_pos);
f2[f2_idx] += traj_omega[f2_pos] * motion.getInitOmega() / num_walker;
}
for (auto& [t_evo_j, _] : cc_dict) { for (auto& [t_evo_j, _] : cc_dict) {
auto& cc_j = cc_dict[t_evo_j]; auto& cc_j = cc_dict[t_evo_j];
@ -149,6 +160,7 @@ void run_ste(
save_parameter_to_file("ste", motion.getName(), dist.getName(), parameter, optional); save_parameter_to_file("ste", motion.getName(), dist.getName(), parameter, optional);
save_data_to_file("coscos", motion.getName(), dist.getName(), mixing_times, cc_dict, optional); save_data_to_file("coscos", motion.getName(), dist.getName(), mixing_times, cc_dict, optional);
save_data_to_file("sinsin", motion.getName(), dist.getName(), mixing_times, ss_dict, optional); save_data_to_file("sinsin", motion.getName(), dist.getName(), mixing_times, ss_dict, optional);
save_data_to_file("f2", motion.getName(), dist.getName(), mixing_times, f2, optional);
printEnd(start); printEnd(start);
} }
@ -159,7 +171,8 @@ void make_trajectory(
Distribution& dist, Distribution& dist,
const double t_max, const double t_max,
std::vector<double>& out_time, std::vector<double>& out_time,
std::vector<double>& out_phase std::vector<double>& out_phase,
std::vector<double>& out_omega
) { ) {
// Starting position // Starting position
double t_passed = 0; double t_passed = 0;
@ -168,16 +181,21 @@ void make_trajectory(
motion.initialize(); motion.initialize();
dist.initialize(); dist.initialize();
double omega = motion.getInitOmega();
out_time.emplace_back(t_passed); out_time.emplace_back(t_passed);
out_phase.emplace_back(0); out_phase.emplace_back(phase);
out_omega.emplace_back(omega);
while (t_passed < t_max) { while (t_passed < t_max) {
const double t = dist.tau_wait(); const double t = dist.tau_wait();
t_passed += t; t_passed += t;
phase += motion.jump() * t; omega = motion.jump();
phase += omega * t;
out_time.emplace_back(t_passed); out_time.emplace_back(t_passed);
out_phase.emplace_back(phase); out_phase.emplace_back(phase);
out_omega.emplace_back(omega);
} }
} }

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@ -36,8 +36,9 @@ void run_ste(std::unordered_map<std::string, double>& parameter, std::unordered_
* @param t_max Double that defines maximum time of trajectory * @param t_max Double that defines maximum time of trajectory
* @param out_time Vector of waiting times * @param out_time Vector of waiting times
* @param out_phase Vector of phase between waiting times * @param out_phase Vector of phase between waiting times
* @param out_omega Vector of omega at jump time
*/ */
void make_trajectory(Motion& motion, Distribution& dist, double t_max, std::vector<double>& out_time, std::vector<double>& out_phase); void make_trajectory(Motion& motion, Distribution& 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); std::chrono::system_clock::time_point printStart(std::unordered_map<std::string, double> &optional);
void printEnd(std::chrono::system_clock::time_point start); void printEnd(std::chrono::system_clock::time_point start);

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@ -193,3 +193,33 @@ void save_data_to_file(
} }
} }
} }
void save_data_to_file(
const std::string& resulttype,
const std::string& motiontype,
const std::string& disttype,
const std::vector<double>& x,
const std::vector<double>& y,
std::unordered_map<std::string, double>& optional
) {
// make file name
std::ostringstream datafile_name;
datafile_name << resulttype << "_" << motiontype << "_" << disttype;
datafile_name << std::setprecision(6) << std::scientific;
for (const auto& [key, value]: optional) {
datafile_name << "_" << key << "=" << value;
}
datafile_name << ".dat";
{
// write data to file, columns are secondary axis (echo delay, evolution times)
std::string datafile = datafile_name.str();
std::ofstream filestream(datafile, std::ios::out);
// write values to file
auto size = x.size();
for (unsigned int i = 0; i < size; i++) {
filestream << x[i] << "\t" << y[i] << "\n";
}
}
}

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@ -21,7 +21,9 @@ std::pair<std::string, double> get_optional_parameter(std::vector<std::string>::
std::unordered_map<std::string, double> read_parameter(const std::filesystem::path&); std::unordered_map<std::string, double> read_parameter(const std::filesystem::path&);
void save_parameter_to_file(const std::string&, const std::string&, const std::string&, std::unordered_map<std::string, double>&, std::unordered_map<std::string, double>&); void save_parameter_to_file(const std::string&, const std::string&, const std::string&, std::unordered_map<std::string, double>&, std::unordered_map<std::string, double>&);
void save_data_to_file(const std::string&, const std::string&, const std::string&, const std::vector<double>&, const std::map<double, std::vector<double>>&, std::unordered_map<std::string, double>&); void save_data_to_file(const std::string&, const std::string&, const std::string&, const std::vector<double>&, const std::map<double, std::vector<double>>&, std::unordered_map<std::string, double>&);
void save_data_to_file(const std::string&, const std::string&, const std::string&, const std::vector<double>&, const std::vector<double>&, std::unordered_map<std::string, double>&);
#endif #endif