Viscosity and stress autocorrelation function in supercooled water: a molecular dynamics study

Guo, Guang-Jun; Zhang, Yigang; Refson, Keith; Zhao, Yajuan

doi:10.1080/00268970210133477

Cited by 38 publications

(28 citation statements)

References 63 publications

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“…The primary difficulty is finding a model that can adequately match the autocorrelation function without introducing bias into the estimate of viscosity. A common function found in the literature is [2,55]…”

Section: Model Fit To Autocorrelation Functionmentioning

confidence: 99%

Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]

et al. 2020

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The ability to predict transport properties (e.g., diffusivity, viscosity, and conductivity) is one of the primary benefits of molecular simulation. Although most studies focus on the accuracy of the simulation output compared to experimental data, such a comparison primarily tests the adequacy of the force field (i.e., the model). By contrast, the reliability of different simulation methodologies for predicting transport properties is the focus of this manuscript. Unfortunately, obtaining reproducible estimates of transport properties from molecular simulation is not as straightforward as static properties. Therefore, this manuscript discusses the best practices that should be followed to ensure that the simulation output is reliable, i.e., is a valid representation of the force field implemented. We also discuss procedures to use so that the results are reproducible (i.e., can be obtained by other researchers following the same methods and procedures). There are two classes by which transport properties are predicted: equilibrium molecular dynamics (EMD) and non-equilibrium molecular dynamics (NEMD). This manuscript presents the best practices for EMD, leaving NEMD for a future publication. As self-diffusivity and shear viscosity are the most prevalent transport properties found in the literature, the discussion will also be limited to these properties with the expectation that future publications will discuss best practices for thermal conductivity, ionic conductivity, and multicomponent diffusivity.

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Section: Model Fit To Autocorrelation Functionmentioning

confidence: 99%

Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]

et al. 2020

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“…As we can see in Figure 2 this six-parameter function type fits quite well bulk and shear ACFs [29]. It is not the case for elongation ACF (not shown).…”

Section: Fitting the Acfs To An Analytical Formmentioning

confidence: 67%

“…It is not the case for elongation ACF (not shown). This one is not unexpected, it is a consequence of the linear dependence of elongation ACF from bulk and shear ACFs [14,[18][19][20]29]-while noise is not dominant. Because it is well checked numerically that E ACF (t) B ACF (t) + G ACF (t) we can write…”

Section: Fitting the Acfs To An Analytical Formmentioning

confidence: 95%

Filtered stress autocorrelation functions of liquid water models

Medina

Prosmiti

Villarreal

et al. 2010

Int J of Quantum Chemistry

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Pressure autocorrelation functions of two models, SPC/E and SPC/Fw, of pure liquid water are presented. Periodic boundary condition simulations, in the microcanonical ensemble (NVE), of 256 molecules at room temperature are accomplished for both models. Green-Kubo relations are used over the stress tensor time series to extract viscosity properties of the system. Filtering of noise and signal in the numerical data is considered. Three steps are discussed to reach relevant physical data pertaining to transport coefficients calculations: (1) removing noise via Savitzky-Golay filters to smooth signals, (2) fitting data by combining Kohlrausch type functions, (3) separating low frequency from high frequency behavior. On the latter resides the essential difference between rigid and flexible models. Considerations about the stress tensor structure in flexible case, and the physical meaning each part holds, are explained and used to show similarities in low frequency (librational/translational and cluster) motions present in both models.

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“…The same is true of shear relaxation times in viscosity calculations. For ionic liquids' calculations, authors have also fit the pressure tensor autocorrelation function to Kohlrausch's law [29,30] and/or applied weighing factors to their fits [31,32]. Fits to the frequency domain are also a solution, depending on the resulting ACF for given data [12,28].…”

Section: B Common Autocorrelation Function Integration Approachesmentioning

confidence: 99%

Method to manage integration error in the Green-Kubo method

Oliveira

Greaney

2017

Phys. Rev. E

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The Green-Kubo method is a commonly used approach for predicting transport properties in a system from equilibrium molecular dynamics simulations. The approach is founded on the fluctuation dissipation theorem and relates the property of interest to the lifetime of fluctuations in its thermodynamic driving potential. For heat transport, the lattice thermal conductivity is related to the integral of the autocorrelation of the instantaneous heat flux. A principal source of error in these calculations is that the autocorrelation function requires a long averaging time to reduce remnant noise. Integrating the noise in the tail of the autocorrelation function becomes conflated with physically important slow relaxation processes. In this paper we present a method to quantify the uncertainty on transport properties computed using the Green-Kubo formulation based on recognizing that the integrated noise is a random walk, with a growing envelope of uncertainty. By characterizing the noise we can choose integration conditions to best trade off systematic truncation error with unbiased integration noise, to minimize uncertainty for a given allocation of computational resources.

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Viscosity and stress autocorrelation function in supercooled water: a molecular dynamics study

Cited by 38 publications

References 63 publications

Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]

Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]

Filtered stress autocorrelation functions of liquid water models

Method to manage integration error in the Green-Kubo method

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