31 lines
937 B
Python
31 lines
937 B
Python
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"""
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Calculating the ISF of Water
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=======================================================
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In this example the ISF of water oxygens is calculated for a bulk simulation.
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Additionally a KWW function is fitted to the results.
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"""
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from functools import partial
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import matplotlib.pyplot as plt
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from scipy.optimize import curve_fit
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import mdevaluate as md
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import tudplot
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OW = md.open('/data/niels/sim/water/bulk/260K', trajectory='out/*.xtc').subset(atom_name='OW')
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t, S = md.correlation.shifted_correlation(
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partial(md.correlation.isf, q=22.7),
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OW,
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average=True
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)
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# Only include data-points of the alpha-relaxation for the fit
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mask = t > 3e-1
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fit, cov = curve_fit(md.functions.kww, t[mask], S[mask])
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tau = md.functions.kww_1e(*fit)
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tudplot.activate()
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plt.figure()
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plt.plot(t, S, '.', label='ISF of Bulk Water')
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plt.plot(t, md.functions.kww(t, *fit), '-', label=r'KWW, $\tau$={:.2f}ps'.format(tau))
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plt.xscale('log')
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plt.legend()
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