SporTran is a Python utility designed to estimate generic transport coefficients in extended systems, based on the Green-Kubo theory of linear response and the recently introduced cepstral analysis of the current time series generated by molecular dynamics simulations. SporTran can be applied to univariate as well as multivariate time series. Cepstral analysis requires minimum discretion from the user, in that it weakly depends on two parameters, one of which is automatically estimated by a statistical model-selection criterion that univocally determines the resulting accuracy. In order to facilitate the optimal refinement of these parameters, SporTran features an easy-to-use graphical user interface. A command-line interface and a Python API, easy to embed in complex data-analysis workflows, are also provided. Program summaryProgram Title:SporTranCPC Library link to program files:https://doi.org/10.17632/hm48f8kgj9.1Licensing provisions: GPLv3Programming language: PythonNature of problem: Given an M-variate time series, Jj(t), j=0,…M−1, typically describing a number of currents resulting from a molecular-dynamics simulation, SporTran estimates the transport coefficient κ=1/(Λ−1)00, where Λij=∫0∞〈Jj(t)Jk(0)〉dt is the matrix of the Onsager linear-response coefficients, and 〈⋅〉 indicates an equilibrium average over initial conditions.Solution method:i)It is first observed that the Onsager transport coefficients are the zero-frequency values of the cross power spectra of the currents under scrutiny: Λij=12Sij(ω=0), where Sij(ω)=∫−∞∞〈Ji(t)Jj(0)〉eiωtdt.ii)We next define the (cross) periodogram as the product of pairs of Fourier transforms of the current time series: Skij=ϵNJ˜kiJ˜kj⁎, where ϵ is the time step of the time series, N the number of their terms, and J˜kj=∑n=0N−1Jnje2πiknN their discrete Fourier transforms, and Jnj=Jj(ϵn).iii)As the current time series are realisations of a Gaussian process, in the long-time limit and for k≠k′ the Skij are uncorrelated complex Wishart random matrices (a matrix generalisation of the χ2 distribution) whose expectation, according to the Wiener-Khintchine theorem, is the cross power spectrum we are after. It follows that (Sk−1)00 is proportional to a set of uncorrelated χ2 deviates;iv)A consistent estimator for log(κ)=−log((Λ−1)00) is finally obtained by applying a low-pass filter to the process log((Sk−1)00). The theoretical background of the methodology implemented in SporTran is thoroughly presented in Refs. [1-3].
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