93 lines
2.7 KiB
Python
93 lines
2.7 KiB
Python
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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from python.helpers import read_parameter_file
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def ste_decay(x: np.ndarray, m0: float, t: float, beta: float, finfty: float) -> np.ndarray:
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"""
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Calculate stimulated-echo decay.
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:param x: Mixing times in seconds.
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:param m0: Amplitude
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:param t: Correlation time in seconds
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:param beta: Stretching parameter
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:param finfty: Final plateau
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:return: Stimulated-echo decay
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"""
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return m0 * ((1-finfty) * np.exp(-(x/t)**beta) + finfty)
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def fit_decay(x: np.ndarray, y: np.ndarray, tevo: np.ndarray, verbose: bool = True) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
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num_evo = y.shape[1]
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if num_evo != tevo.size:
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tevo = np.arange(num_evo)
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tau_fit = np.empty((num_evo, 2))
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tau_fit[:, 0] = tevo
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beta_fit = np.empty((num_evo, 2))
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beta_fit[:, 0] = tevo
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finfty_fit = np.empty((num_evo, 2))
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finfty_fit[:, 0] = tevo
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scaled_y = (y-y[-1, :]) / (y[0, :]-y[-1, :])
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for j in range(num_evo):
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p0 = [y[0, 0], x[np.argmin(np.abs(scaled_y[:, j]-np.exp(-1)))], 0.8, 0.1]
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try:
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res = curve_fit(ste_decay, x, y[:, j], p0, bounds=[(0, 0, 0., 0), (np.inf, np.inf, 1, 1)])
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except RuntimeError as e:
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print(f'Fit {j+1} of {num_evo} failed with {e.args}')
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continue
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m0, tauc, beta, finfty = res[0]
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if verbose:
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print(f'Fit {j+1} of {num_evo}: tau_c = {tauc:.6e}, beta={beta:.4e}, amplitude = {m0: .4e}, f_infty={finfty:.4e}')
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tau_fit[j, 1] = tauc
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beta_fit[j, 1] = beta
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finfty_fit[j, 1] = finfty
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return tau_fit, beta_fit, finfty_fit
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def fit_ste(
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parameter_file: pathlib.Path,
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prefix: str,
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plot_decays: bool = True,
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verbose: bool = True,
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) -> tuple[str, np.ndarray, np.ndarray, np.ndarray]:
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# read simulation parameters
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parameter = read_parameter_file(parameter_file)
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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['tevo_start'], parameter['tevo_stop'], num=int(parameter['tevo_steps']))
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raw_data = np.loadtxt(parameter_file.with_name(f'{prefix}_{varied_string}.dat'))
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t_mix = raw_data[:, 0]
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decay = raw_data[:, 1:]
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if plot_decays:
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fig, ax = plt.subplots()
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ax.set_title(prefix)
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ax.semilogx(t_mix, decay, '.')
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fig.show()
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print(f'Fit {prefix}')
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tau, beta, finfty = fit_decay(t_mix, decay, tevo, verbose=verbose)
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return varied_string, tau, beta, finfty
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