STable AutoCorrelation Integral Estimator (STACIE): Robust and accurate transport properties from molecular dynamics simulations
arXiv:2506.20438 · doi:10.1021/acs.jcim.5c01475
Abstract
STACIE (STable AutoCorrelation Integral Estimator) is a novel algorithm and Python package that delivers robust, uncertainty-aware estimates of autocorrelation integrals from time-correlated data. While its primary application is deriving transport properties from equilibrium molecular dynamics simulations, STACIE is equally applicable to time-correlated data in other scientific fields. A key feature of STACIE is its ability to provide robust and accurate estimates without requiring manual adjustment of hyperparameters. Additionally, one can follow a simple protocol to prepare sufficient simulation data to achieve a desired relative error of the transport property. We demonstrate its application by estimating the ionic electrical conductivity of a NaCl-water electrolyte solution. We also present a massive synthetic benchmark dataset to rigorously validate STACIE, comprising 15360 sets of time-correlated inputs generated with diverse covariance kernels with known autocorrelation integrals. STACIE is open source and available on GitHub and PyPI, with comprehensive documentation and examples.
Minor corrections, in particular the outer product in Eq. 30, and a small update of the software overview in the supporting information, for consistency with the final publication
References in corpus (14)
- SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python
- Array Programming with NumPy
- emcee: The MCMC Hammer
- QuantumATK: An integrated platform of electronic and atomic-scale modelling tools
- Fast and scalable Gaussian process modeling with applications to astronomical time series
- Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS
- Shear Viscosity Coefficient from Microscopic Models
- Transport phenomena in electrolyte solutions: Non-equilibrium thermodynamics and statistical mechanics
- Accurate thermal conductivities from optimally short molecular dynamics simulations
- Transport and Helfand moments in the Lennard-Jones fluid. I. Shear viscosity
- Selecting likelihood weights by cross-validation
- Theory and numerical simulation of heat transport in multi-component systems
- Ab initio Green-Kubo simulations of heat transport in solids: Method and implementation
- Heat transport in insulators from ab initio Green-Kubo theory