add more motions
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@ -35,6 +35,18 @@ for fit_files in pathlib.Path('.').glob(f'IsotropicAngle/angle=*/Delta/tau=*/ste
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tau_cc.append(fit_values[nearest_idx, 1])
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tau_ss.append(fit_values[nearest_idx, 4])
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angles = np.array(angles)
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tau_cc = np.array(tau_cc)
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tau_ss = np.array(tau_ss)
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tau2 = np.array(tau2)
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sortidx = np.argsort(angles)
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angles = angles[sortidx]
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tau_cc = tau_cc[sortidx]
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tau_ss = tau_ss[sortidx]
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tau2 = tau2[sortidx]
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plt.semilogy(angles, tau_cc, '-.')
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plt.semilogy(angles, tau_ss, '--')
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41
process_spectrum.py
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41
process_spectrum.py
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@ -0,0 +1,41 @@
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import pathlib
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import matplotlib.pyplot as plt
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from python.spectrum import *
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tpulse = 3e-6
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gb = 4e3
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fig_spec, ax_spec = plt.subplots()
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# for conf_file in pathlib.Path('.').glob(f'SixSiteOctahedral/angle=59/Delta/tau=*/timesignal_*_parameter.txt'):
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for conf_file in pathlib.Path('.').glob(f'RandomJumpOnCone/angle=128.*/Delta/tau=*/timesignal_*_parameter.txt'):
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vary_string = post_process_spectrum(conf_file, tpulse=tpulse, apod=gb)
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print(conf_file)
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# ax_spec
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#
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# ax_tau_cc.semilogy(tau_cc[:, 0], tau_cc[:, 1], label=vary_string)
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# ax_tau_cc.axhline(tau_2[:, 1], color='k', linestyle='--')
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# ax_beta_cc.plot(*beta_cc.T, label=vary_string)
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# ax_finfty_cc.plot(*finfty_cc.T, label=vary_string)
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# ax_tau_ss.semilogy(tau_ss[:, 0], tau_ss[:, 1], label=vary_string)
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# ax_tau_ss.axhline(tau_2[:, 1], color='k', linestyle='--')
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# ax_beta_ss.plot(*beta_ss.T, label=vary_string)
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# ax_finfty_ss.plot(*finfty_ss.T, label=vary_string)
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#
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# np.savetxt(
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# conf_file.with_name(f'ste_fit_{vary_string}.dat'),
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# np.c_[
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# tau_cc, beta_cc[:, 1], finfty_cc[:, 1],
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# tau_ss[:, 1], beta_ss[:, 1], finfty_ss[:, 1],
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# ],
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# header=f'Fit STE {vary_string}\n'
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# f'F2: tau={tau_2[0, 1]} beta={beta_2[0, 1]} finfty={finfty_2[0, 1]}\n'
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# f'tevo\ttaucc\tbetacc\tfinftycc\ttauss\tbetass\tfinftyss',
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# )
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#
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# for ax in [ax_tau_cc, ax_beta_cc, ax_finfty_cc, ax_tau_ss, ax_beta_ss, ax_finfty_ss]:
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# ax.legend()
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# plt.show()
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@ -1,7 +1,3 @@
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import pathlib
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import matplotlib.pyplot as plt
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from python.ste import *
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fig_tau_cc, ax_tau_cc = plt.subplots()
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@ -1,7 +1,6 @@
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from __future__ import annotations
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import pathlib
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import re
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import subprocess
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from itertools import product
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@ -1,8 +1,7 @@
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import numpy
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import numpy as np
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from matplotlib import pyplot
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import matplotlib.pyplot as plt
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from python.helpers import read_parameter_file
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# parameter for spectrum simulations
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lb = 2e3
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@ -41,14 +40,19 @@ def pulse_attn(freq: np.ndarray, t_pulse: float) -> np.ndarray:
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return np.pi * numerator / denominator / 2
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def post_process_spectrum(taus, apod, tpulse):
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reduction_factor = np.zeros((taus.size, 5)) # hard-coded t_echo :(
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def post_process_spectrum(parameter_file, apod, tpulse):
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parameter = read_parameter_file(parameter_file)
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for i, tau in enumerate(taus):
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try:
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raw_data = np.loadtxt(f'fid_tau={tau:.6e}.dat')
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except OSError:
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continue
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# files have form ste_arg=0.000000e+01_parameter.txt, first remove ste part then parameter.txt to get variables
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varied_string = str(parameter_file).partition('_')[-1].rpartition('_')[0]
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# make evolution times
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tevo = np.linspace(parameter['techo_start'], parameter['techo_stop'], num=int(parameter['techo_steps']))
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if varied_string:
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raw_data = np.loadtxt(parameter_file.with_name(f'timesignal_{varied_string}.dat'))
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else:
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raw_data = np.loadtxt(parameter_file.with_name(f'timesignal.dat'))
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t = raw_data[:, 0]
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timesignal = raw_data[:, 1:]
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@ -57,14 +61,18 @@ def post_process_spectrum(taus, apod, tpulse):
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timesignal[0, :] /= 2
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# FT to spectrum
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freq = np.fft.fftshift(np.fft.fftfreq(t.size, d=1e-6))
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freq = np.fft.fftshift(np.fft.fftfreq(t.size, d=parameter['dwell_time']))
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spec = np.fft.fftshift(np.fft.fft(timesignal, axis=0), axes=0).real
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spec *= pulse_attn(freq, t_pulse=tpulse)[:, None]
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reduction_factor[i, :] = 2*timesignal[0, :]
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#
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#
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# reduction_factor[i, :] = 2*timesignal[0, :]
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plt.plot(freq, spec)
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plt.gca().set_title(varied_string)
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plt.show()
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plt.semilogx(taus, reduction_factor, '.')
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plt.show()
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#
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# plt.semilogx(taus, reduction_factor, '.')
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# plt.show()
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@ -1,6 +1,5 @@
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import pathlib
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import numpy
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import numpy as np
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from matplotlib import pyplot as plt
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from scipy.optimize import curve_fit
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@ -74,7 +73,10 @@ def fit_ste(
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# make evolution times
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tevo = np.linspace(parameter['tevo_start'], parameter['tevo_stop'], num=int(parameter['tevo_steps']))
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if varied_string:
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raw_data = np.loadtxt(parameter_file.with_name(f'{prefix}_{varied_string}.dat'))
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else:
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raw_data = np.loadtxt(parameter_file.with_name(f'{prefix}.dat'))
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t_mix = raw_data[:, 0]
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decay = raw_data[:, 1:]
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@ -6,7 +6,6 @@ add_subdirectory(utils)
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add_library(simulation STATIC sims.cpp sims.h)
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target_link_libraries(simulation PRIVATE utils)
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add_executable(
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rwsim
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main.cpp
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@ -19,5 +19,7 @@ add_library(
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bimodalangle.h
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sixsitejump.cpp
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sixsitejump.h
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nsiteconejump.cpp
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nsiteconejump.h
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)
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@ -1,14 +1,20 @@
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#include "base.h"
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#include <iostream>
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#include "coordinates.h"
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#include "bimodalangle.h"
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#include "isosmallangle.h"
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#include "random.h"
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#include "foursitejump.h"
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#include "nsiteconejump.h"
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#include "sixsitejump.h"
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#include "rjoac.h"
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#include <stdexcept>
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#include "sixsitejump.h"
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namespace motions {
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BaseMotion::BaseMotion(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) {
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@ -43,8 +49,8 @@ namespace motions {
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if (input == "FourSiteTetrahedral")
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return new FourSiteTetrahedron(rng);
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if (input == "SixSiteOctahedral")
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return new SixSiteOctahedron(rng);
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if (input == "SixSiteOctahedralC3")
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return new SixSiteOctahedronC3(rng);
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if (input == "IsotropicAngle")
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return new SmallAngle(rng);
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@ -55,6 +61,12 @@ namespace motions {
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if (input == "BimodalAngle")
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return new BimodalAngle(rng);
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if (input == "NSiteConeJump")
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return new NSiteJumpOnCone(rng);
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if (input == "RandomJumpOnCone")
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return new RandomJumpOnCone(rng);
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throw std::invalid_argument("Invalid input " + input);
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}
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@ -28,7 +28,7 @@ namespace motions {
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[[nodiscard]] double getEta() const { return m_eta; }
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void setEta(const double eta) { m_eta = eta; }
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[[nodiscard]] std::string getName() const { return m_name; }
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[[nodiscard]] double getInitOmega() const { return m_initial_omega; };
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[[nodiscard]] double getInitOmega() const { return m_initial_omega; }
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[[nodiscard]] virtual std::string toString() const = 0;
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@ -8,18 +8,18 @@ namespace motions {
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BaseMotion(std::string("BimodalAngle"), delta, eta, rng),
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m_angle1(angle1 * M_PI / 180.0),
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m_angle2(angle2 * M_PI / 180.0),
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m_prob(prob) {};
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m_prob(prob) {}
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BimodalAngle::BimodalAngle(std::mt19937_64 &rng) : BaseMotion(std::string("BimodalAngle"), rng) {}
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void BimodalAngle::initialize() {
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m_prev_pos = draw_position();
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m_initial_omega = omega_q(m_prev_pos);
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};
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}
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double BimodalAngle::jump() {
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const double angle = m_uni_dist(m_rng) < m_prob ? m_angle1 : m_angle2;
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const double gamma{2 * M_PI * m_uni_dist(m_rng)};
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m_prev_pos = coordinates::rotate(m_prev_pos, angle, gamma);
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m_prev_pos = rotate(m_prev_pos, angle, gamma);
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return omega_q(m_prev_pos);
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}
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@ -6,7 +6,7 @@
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#include "coordinates.h"
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namespace motions {
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class BimodalAngle : public BaseMotion {
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class BimodalAngle final : public BaseMotion {
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public:
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BimodalAngle(double, double, double, double, double, std::mt19937_64& );
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explicit BimodalAngle(std::mt19937_64&);
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@ -16,7 +16,7 @@ namespace motions {
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double WobbleCone::jump() {
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const double real_angle = m_uni_dist(m_rng) * m_angle;
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const double phi = 2 * M_PI * m_uni_dist(m_rng);
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return omega_q(coordinates::rotate(m_axis, real_angle, phi));
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return omega_q(rotate(m_axis, real_angle, phi));
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}
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void WobbleCone::setParameters(const std::unordered_map<std::string, double> ¶meters) {
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@ -7,7 +7,7 @@
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#include <random>
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namespace motions {
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class WobbleCone: public BaseMotion {
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class WobbleCone final: public BaseMotion {
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public:
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WobbleCone(double, double, double, std::mt19937_64&);
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explicit WobbleCone(std::mt19937_64&);
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@ -22,9 +22,9 @@ namespace coordinates {
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auto [x, y , z] = spherical_to_xyz(old_pos);
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const auto new_pos = CartesianPos{
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cos_alpha * x + sin_alpha * (-x * z * sin_beta - y * cos_beta) / norm,
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cos_alpha * y + sin_alpha * (-y * z * sin_beta + x * cos_beta) / norm,
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cos_alpha * z + sin_alpha * norm * sin_beta
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cos_alpha * x + sin_alpha * (-cos_beta * y - sin_beta * x * z) / norm,
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cos_alpha * y + sin_alpha * (cos_beta * x - sin_beta * y * z) / norm,
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cos_alpha * z + sin_alpha * sin_beta * norm,
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};
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return xyz_to_spherical(new_pos);
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@ -16,7 +16,7 @@ namespace motions {
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const double alpha = 2. * M_PI * m_uni_dist(m_rng);
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for (int i = 1; i<4; i++) {
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auto corner_pos = coordinates::rotate(pos, m_beta, alpha + (i-1) * 2*M_PI/3.);
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auto corner_pos = rotate(pos, m_beta, alpha + (i-1) * 2*M_PI/3.);
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m_corners[i] = omega_q(corner_pos);
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}
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m_initial_omega = FourSiteTetrahedron::jump();
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@ -6,17 +6,17 @@
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namespace motions {
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SmallAngle::SmallAngle(const double delta, const double eta, const double chi, std::mt19937_64 &rng) :
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BaseMotion(std::string("IsotropicAngle"), delta, eta, rng), m_chi(chi * M_PI / 180.0) {};
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BaseMotion(std::string("IsotropicAngle"), delta, eta, rng), m_chi(chi * M_PI / 180.0) {}
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SmallAngle::SmallAngle(std::mt19937_64 &rng) : BaseMotion(std::string("IsotropicAngle"), rng) {}
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void SmallAngle::initialize() {
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m_prev_pos = draw_position();
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m_initial_omega = omega_q(m_prev_pos);
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};
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}
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double SmallAngle::jump() {
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const double gamma{2 * M_PI * m_uni_dist(m_rng)};
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m_prev_pos = coordinates::rotate(m_prev_pos, m_chi, gamma);
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m_prev_pos = rotate(m_prev_pos, m_chi, gamma);
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return omega_q(m_prev_pos);
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}
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59
src/motions/nsiteconejump.cpp
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59
src/motions/nsiteconejump.cpp
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//
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// Created by dominik on 12/14/24.
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//
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#include "nsiteconejump.h"
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#include "coordinates.h"
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#include <cmath>
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#include <iostream>
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#include <ostream>
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#include <vector>
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namespace motions {
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NSiteJumpOnCone::NSiteJumpOnCone(const double delta, const double eta, const int num_sites, const double chi, std::mt19937_64 &rng) :
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BaseMotion("NSiteJumpOnCone", delta, eta, rng),
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m_num_sites(num_sites),
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m_chi(chi*M_PI/180.) {}
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NSiteJumpOnCone::NSiteJumpOnCone(std::mt19937_64 &rng) : BaseMotion("NSiteJumpOnCone", rng) { }
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void NSiteJumpOnCone::initialize() {
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m_sites = std::vector<double>(m_num_sites);
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m_chooser = std::uniform_int_distribution<>{1, m_num_sites - 1};
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m_axis = draw_position();
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const double alpha = m_uni_dist(m_rng) * 2 * M_PI;
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const double steps = 2*M_PI / m_num_sites;
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for (int i = 0; i < m_num_sites; i++) {
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m_sites[i] = omega_q(rotate(m_axis, m_chi, i * steps + alpha));
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}
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}
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double NSiteJumpOnCone::jump() {
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m_cone_idx += m_chooser(m_rng);
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m_cone_idx %= m_num_sites;
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return m_sites[m_cone_idx];
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}
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void NSiteJumpOnCone::setParameters(const std::unordered_map<std::string, double> ¶meters) {
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BaseMotion::setParameters(parameters);
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m_num_sites = static_cast<int>(parameters.at("num_sites"));
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m_chi = parameters.at("chi") * M_PI/180.;
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}
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std::unordered_map<std::string, double> NSiteJumpOnCone::getParameters() const {
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auto parameter = BaseMotion::getParameters();
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parameter["num_sites"] = m_num_sites;
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parameter["chi"] = m_chi * 180. / M_PI;
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return parameter;
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}
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std::string NSiteJumpOnCone::toString() const {
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return std::to_string(m_num_sites) + "SiteJumpOnCone/angle=" + std::to_string(m_chi*180/M_PI);
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}
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} // motions
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33
src/motions/nsiteconejump.h
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33
src/motions/nsiteconejump.h
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#ifndef NSITEJUMPONCONE_H
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#define NSITEJUMPONCONE_H
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#include "base.h"
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#include <random>
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#include <vector>
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namespace motions {
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class NSiteJumpOnCone final : public BaseMotion {
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public:
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NSiteJumpOnCone(double, double, int, double, std::mt19937_64&);
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explicit NSiteJumpOnCone(std::mt19937_64&);
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void initialize() override;
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double jump() override;
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[[nodiscard]] std::string toString() const override;
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void setParameters(const std::unordered_map<std::string, double> &) override;
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[[nodiscard]] std::unordered_map<std::string, double> getParameters() const override;
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private:
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int m_num_sites{2};
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std::vector<double> m_sites{};
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double m_chi{1./2.};
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int m_cone_idx = 0;
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coordinates::SphericalPos m_axis{1, 0};
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std::uniform_int_distribution<> m_chooser;
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};
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} // motions
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#endif //NSITEJUMPONCONE_H
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double RandomJumpOnCone::jump() {
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const double phi = 2 * M_PI * m_uni_dist(m_rng);
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return omega_q(coordinates::rotate(m_axis, m_angle, phi));
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return omega_q(rotate(m_axis, m_angle, phi));
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}
|
||||
|
||||
void RandomJumpOnCone::setParameters(const std::unordered_map<std::string, double> ¶meters) {
|
||||
|
@ -7,7 +7,7 @@
|
||||
#include <random>
|
||||
|
||||
namespace motions {
|
||||
class RandomJumpOnCone: public BaseMotion {
|
||||
class RandomJumpOnCone final: public BaseMotion {
|
||||
public:
|
||||
RandomJumpOnCone(double, double, double, std::mt19937_64&);
|
||||
explicit RandomJumpOnCone(std::mt19937_64&);
|
||||
|
@ -1,34 +1,41 @@
|
||||
#include "sixsitejump.h"
|
||||
|
||||
#include <iomanip>
|
||||
#include <iostream>
|
||||
|
||||
#include "coordinates.h"
|
||||
|
||||
namespace motions {
|
||||
SixSiteOctahedron::SixSiteOctahedron(const double delta, const double eta, std::mt19937_64& rng) :
|
||||
SixSiteOctahedronC3::SixSiteOctahedronC3(const double delta, const double eta, const double chi, std::mt19937_64& rng) :
|
||||
m_chi{chi*M_PI/180.},
|
||||
BaseMotion(std::string{"SixSiteOctahedral"}, delta, eta, rng) {}
|
||||
|
||||
SixSiteOctahedron::SixSiteOctahedron(std::mt19937_64& rng) : BaseMotion(std::string{"SixSiteOctahedral"}, rng) {}
|
||||
|
||||
void SixSiteOctahedron::initialize() {
|
||||
const auto pos = draw_position();
|
||||
m_corners[0] = omega_q(pos);
|
||||
m_corners[1] = omega_q(rotate(pos, M_PI, 0));
|
||||
SixSiteOctahedronC3::SixSiteOctahedronC3(std::mt19937_64& rng) : BaseMotion(std::string{"SixSiteOctahedralC3"}, rng) {}
|
||||
|
||||
void SixSiteOctahedronC3::initialize() {
|
||||
const coordinates::SphericalPos c3_axis = draw_position();
|
||||
const auto [x, y, z] = spherical_to_xyz(c3_axis);
|
||||
const double alpha = 2. * M_PI * m_uni_dist(m_rng);
|
||||
|
||||
for (int i = 2; i<6; i++) {
|
||||
auto corner_pos = coordinates::rotate(pos, M_PI_2, alpha + (i-2) * M_PI_2);
|
||||
m_corners[i] = omega_q(corner_pos);
|
||||
}
|
||||
m_initial_omega = SixSiteOctahedron::jump();
|
||||
const double m_chi_opposite = M_PI - m_chi;
|
||||
|
||||
for (int i = 0; i<3; i++) {
|
||||
m_corners[2*i] = omega_q(rotate(c3_axis, m_chi, alpha + i * 2./3.*M_PI));
|
||||
m_corners[2*i+1] = omega_q(rotate(c3_axis, m_chi_opposite, alpha + i * 2./3.*M_PI + M_PI/3.));
|
||||
}
|
||||
|
||||
double SixSiteOctahedron::jump() {
|
||||
m_initial_omega = SixSiteOctahedronC3::jump();
|
||||
}
|
||||
|
||||
|
||||
double SixSiteOctahedronC3::jump() {
|
||||
m_corner_idx += m_chooser(m_rng);
|
||||
m_corner_idx %= 6;
|
||||
|
||||
return m_corners[m_corner_idx];
|
||||
}
|
||||
|
||||
std::string SixSiteOctahedron::toString() const {
|
||||
return {"SixSiteOctahedral"};
|
||||
std::string SixSiteOctahedronC3::toString() const {
|
||||
return {"SixSiteOctahedral/angle=" + std::to_string(m_chi / M_PI * 180.)};
|
||||
}
|
||||
}
|
||||
|
@ -9,10 +9,10 @@
|
||||
#include <array>
|
||||
|
||||
namespace motions {
|
||||
class SixSiteOctahedron final : public BaseMotion {
|
||||
class SixSiteOctahedronC3 final : public BaseMotion {
|
||||
public:
|
||||
SixSiteOctahedron(double, double, std::mt19937_64&);
|
||||
explicit SixSiteOctahedron(std::mt19937_64&);
|
||||
SixSiteOctahedronC3(double, double, double, std::mt19937_64&);
|
||||
explicit SixSiteOctahedronC3(std::mt19937_64&);
|
||||
|
||||
void initialize() override;
|
||||
double jump() override;
|
||||
@ -20,7 +20,7 @@ namespace motions {
|
||||
[[nodiscard]] std::string toString() const override;
|
||||
|
||||
private:
|
||||
const double m_beta{std::acos(-1/3.)};
|
||||
const double m_chi{0.95531661812450927816385710251575775424341469501000549095969812932191204590}; // 54.74 deg
|
||||
|
||||
std::array<double, 6> m_corners{};
|
||||
int m_corner_idx{0};
|
||||
|
@ -14,7 +14,7 @@ namespace times {
|
||||
|
||||
[[nodiscard]] double getTau() const { return m_tau; }
|
||||
void setTau(const double tau) { m_tau = tau; }
|
||||
[[nodiscard]] std::string getName() const { return m_name; };
|
||||
[[nodiscard]] std::string getName() const { return m_name; }
|
||||
|
||||
virtual void setParameters(const std::unordered_map<std::string, double>&);
|
||||
[[nodiscard]] virtual std::unordered_map<std::string, double> getParameters() const;
|
||||
|
@ -25,7 +25,7 @@ std::pair<std::string, double> get_optional_parameter(std::vector<std::string>::
|
||||
stripped_arg = it->substr(1, it->size());
|
||||
}
|
||||
std::transform(stripped_arg.begin(), stripped_arg.end(), stripped_arg.begin(), [](unsigned char c) { return std::tolower(c); });
|
||||
const auto stripped_value = std::stod(*(++it), nullptr);
|
||||
const auto stripped_value = std::stod(*++it, nullptr);
|
||||
|
||||
return std::make_pair(stripped_arg, stripped_value);
|
||||
}
|
||||
@ -95,7 +95,7 @@ Arguments parse_args(const int argc, char* argv[]) {
|
||||
|
||||
|
||||
std::unordered_map<std::string, double> read_parameter(const std::filesystem::path& infile) {
|
||||
if (!std::filesystem::exists(infile)) {
|
||||
if (!exists(infile)) {
|
||||
std::cerr << "File " << infile << " does not exist" << std::endl;
|
||||
exit(1);
|
||||
}
|
||||
|
@ -1,3 +1,5 @@
|
||||
import numpy as np
|
||||
|
||||
from python.helpers import *
|
||||
|
||||
#Simulation parameter
|
||||
|
Loading…
Reference in New Issue
Block a user