Direct numerical simulation of electrokinetic transport phenomena: variational multi-scale stabilization and octree-based mesh refinement

Finite element modeling of charged species transport has enabled the analysis, design, and optimization of a diverse array of electrochemical and electrokinetic devices. These systems are represented by the Poisson-Nernst-Planck (PNP) equations coupled with the Navier-Stokes (NS) equation. Direct numerical simulation (DNS) to accurately capture the spatio-temporal variation of ion concentration and current flux remains challenging due to the (a) small critical dimension of the electric double layer (EDL), (b) stiff coupling, large advective effects, and steep gradients close to boundaries, and (c) complex geometries exhibited by electrochemical devices. In the current study, we address these challenges by presenting a direct numerical simulation framework that incorporates: (a) a variational multiscale (VMS) treatment, (b) a block-iterative strategy in conjunction with semi-implicit (for NS) and implicit (for PNP) time integrators, and (c) octree based adaptive mesh refinement. The VMS formulation provides numerical stabilization critical for capturing the electro-convective instabilities often observed in engineered devices. The block-iterative strategy decouples the difficulty of non-linear coupling between the NS and PNP equations and allows using tailored numerical schemes separately for NS and PNP equations. The carefully designed second-order, hybrid implicit methods circumvent the harsh timestep requirements of explicit time steppers, thus enabling simulations over longer time horizons. Finally, the octree-based meshing allows efficient and targeted spatial resolution of the EDL. These features are incorporated into a massively parallel computational framework, enabling the simulation of realistic engineering electrochemical devices. The numerical framework is illustrated using several challenging canonical examples

Assessment of an energy-based surface tension model for simulation of two-phase flows using second-order phase field methods

Second-order phase field models have emerged as an attractive option for capturing the advection of interfaces in two-phase flows. Prior to these, state-of-the-art models based on the Cahn-Hilliard equation, which is a fourth-order equation, allowed for the derivation of surface tension models through thermodynamic arguments. In contrast, the second-order phase field models do not follow a known energy law, and deriving a surface tension term for these models using thermodynamic arguments is not straightforward. In this work, we justify that the energy-based surface tension model from the Cahn-Hilliard context can be adopted for second-order phase field models as well and assess its performance. We test the surface tension model on three different second-order phase field equations; the conservative diffuse interface model of Chiu and Lin [1], and two models based on the modified Allen-Cahn equation introduced by Sun and Beckermann [2]. Additionally, we draw the connection between the energy-based model with a localized variation of the continuum surface force (CSF) model. Using canonical tests, we illustrate the lower magnitude of spurious currents, better accuracy, and superior convergence properties of the energy-based surface tension model compared to the CSF model, which is a popular choice used in conjunction with second-order phase field methods, and the localized CSF model. Importantly, in terms of computational expense and parallel efficiency, the energy-based model incurs no penalty compared to the CSF models.Comment: 13 pages, 5 figures, Revision submitted to Journal of Computational Physic

Inverse asymptotic treatment: capturing discontinuities in fluid flows via equation modification

A major challenge in developing accurate and robust numerical solutions to multi-physics problems is to correctly model evolving discontinuities in field quantities, which manifest themselves as interfaces between different phases in multi-phase flows, or as shock and contact discontinuities in compressible flows. When a quick response is required to rapidly emerging challenges, the complexity of bespoke discretization schemes impedes a swift transition from problem formulation to computation, which is exacerbated by the need to compose multiple interacting physics. We introduce "inverse asymptotic treatment" (IAT) as a unified framework for capturing discontinuities in fluid flows that enables building directly computable models based on off-the-shelf numerics. By capturing discontinuities through modifications at the level of the governing equations, IAT can seamlessly handle additional physics and thus enable novice end users to quickly obtain numerical results for various multi-physics scenarios. We outline IAT in the context of phase-field modeling of two-phase incompressible flows, and then demonstrate its generality by showing how localized artificial diffusivity (LAD) methods for single-phase compressible flows can be viewed as instances of IAT. Through the real-world example of a laminar hypersonic compression corner, we illustrate IAT's ability to, within just a few months, generate a directly computable model whose wall metrics predictions for sufficiently small corner angles come close to that of NASA's VULKAN-CFD solver. Finally, we propose a novel LAD approach via "reverse-engineered" PDE modifications, inspired by total variation diminishing (TVD) flux limiters, to eliminate the problem-dependent parameter tuning that plagues traditional LAD. We demonstrate that, when combined with second-order central differencing, it can robustly and accurately model compressible flows

Simulating two-phase flows with thermodynamically consistent energy stable Cahn-Hilliard Navier-Stokes equations on parallel adaptive octree based meshes

We report on simulations of two-phase flows with deforming interfaces at various density contrasts by solving thermodynamically consistent Cahn-Hilliard Navier-Stokes equations. An (essentially) unconditionally energy-stable Crank-Nicolson-type time integration scheme is used. Detailed proofs of energy stability of the semi-discrete scheme and for the existence of solutions of the advective-diffusive Cahn-Hilliard operator are provided. In space we discretize with a conforming continuous Galerkin finite element method in conjunction with a residual-based variational multi-scale (VMS) approach in order to provide pressure stabilization. We deploy this approach on a massively parallel numerical implementation using fast octree-based adaptive meshes. A detailed scaling analysis of the solver is presented. Numerical experiments showing convergence and validation with experimental results from the literature are presented for a large range of density ratios.This is a pre-print of the article Khanwale, Makrand A., Alec D. Lofquist, Hari Sundar, James A. Rossmanith, and Baskar Ganapathysubramanian. "Simulating two-phase flows with thermodynamically consistent energy stable Cahn-Hilliard Navier-Stokes equations on parallel adaptive octree based meshes." arXiv preprint arXiv:1912.12453 (2019). Posted with permission.</p

A fully-coupled framework for solving Cahn-Hilliard Navier-Stokes equations: Second-order, energy-stable numerical methods on adaptive octree based meshes

We present a fully-coupled, implicit-in-time framework for solving a thermodynamically-consistent Cahn-Hilliard Navier-Stokes system that models two-phase flows. In this work, we extend the block iterative method presented in Khanwale et al. [{\it Simulating two-phase flows with thermodynamically consistent energy stable Cahn-Hilliard Navier-Stokes equations on parallel adaptive octree based meshes}, J. Comput. Phys. (2020)], to a fully-coupled, provably second-order accurate scheme in time, while maintaining energy-stability. The new method requires fewer matrix assemblies in each Newton iteration resulting in faster solution time. The method is based on a fully-implicit Crank-Nicolson scheme in time and a pressure stabilization for an equal order Galerkin formulation. That is, we use a conforming continuous Galerkin (cG) finite element method in space equipped with a residual-based variational multiscale (RBVMS) procedure to stabilize the pressure. We deploy this approach on a massively parallel numerical implementation using parallel octree-based adaptive meshes. We present comprehensive numerical experiments showing detailed comparisons with results from the literature for canonical cases, including the single bubble rise, Rayleigh-Taylor instability, and lid-driven cavity flow problems. We analyze in detail the scaling of our numerical implementation.This is a pre-print of the article Khanwale, Makrand A., Kumar Saurabh, Milinda Fernando, Victor M. Calo, James A. Rossmanith, Hari Sundar, and Baskar Ganapathysubramanian. "A fully-coupled framework for solving Cahn-Hilliard Navier-Stokes equations: Second-order, energy-stable numerical methods on adaptive octree based meshes." arXiv preprint arXiv:2009.06628 (2020). Posted with permission.</p

Approximation of phase-field models with meshfree methods: exploring biomembrane dynamics

Las biomembranas constituyen la estructura de separación fundamental en las celulas animales, y son importantes en el diseño de sistemas bioinspirados. Su simulación presenta desafíos, especialmente cuando ésta implica dinámica y grandes cambios de forma o se estudian sistemas micrométricos, impidiendo el uso de modelos atomísticos y de grano grueso. El objetivo principal de esta tesis es el desarrollo de un marco computacional para entender la dinámica de biomembranas inmersas en fluido viscoso usando modelos de campo de fase. Los modelos de campo de fase introducen un campo escalar contínuo que define una interfase difusa, cuya física está codificada en las ecuaciones en derivadas parciales que la gobiernan. Estos modelos son capaces de soportar cambios dramáticos de forma y topología, y facilitan el acoplamiento de distintos fenómenos físicos. No obstante, presentan desafíos numéricos significativos, como el alto orden de las ecuaciones, la resolución de frentes móviles y abruptos, o una eficiente integración en el tiempo. En esta disertación abordamos estos puntos mediante la combinación de una discretización espacial con métodos sin malla usando las funciones base locales de máxima entropía, y una formulación variacional Lagrangiana para acoplamiento elástico-hidrodinámico. La suavidad del método sin malla genera una aproximación precisa del campo de fase y puede lidiar fácilmente con adaptatividad local, la aproximación Lagrangiana extiende de manera natural esta adaptividad a la dinámica, y la formulación variacional permite una integración variacional temporal no linealmente estable y robusta. La implementación numérica de estos métodos en un entorno de computación de alto rendimiento ha motivado el desarrollo de un nuevo código computacional. Este código integra el estado del arte de las librerías en paralelo e incorpora importantes contribuciones técnicas para solventar cuellos de botella que aparecen con el uso de métodos sin malla en computación a gran escala. El código resultante es flexible y ha sido aplicado a otros problemas científicos en varias colaboraciones que incluyen flexoelectricidad, conformado metálico, fluidos viscosos o fractura en materiales con energía de superficie altamente anisotrópica.Biomembranes are the fundamental separation structure in animal cells, and are also used in engineered bioinspired systems. Their simulation is challenging, particularly when large shape changes and dynamics are involved, or micrometer systems are considered, ruling out atomistic or coarse-grained molecular modeling. The main goal of this thesis is to develop a computational framework to understand the dynamics of biomembranes embedded in a viscous fluid using phase-field models. Phase-field models introduce a scalar continuous field to define a diffuse moving interface, whose physics is encoded in partial differential equations governing it. These models can deal with dramatic shape and topological transformations and are amenable to multiphysics coupling. However, they present significant numerical challenges, such as the high-order character of the equations, the resolution of sharp and moving fronts, or the efficient time-integration. We address all these issues through a combination of meshfree spacial discretization using local maximum-entropy basis functions, and a Lagrangian variational formulation of the coupled elasticity-hydrodynamics. The smooth meshfree approach provides accurate approximations of the phase-field and can easily deal with local adaptivity, the Lagrangian approach naturally extend adaptivity to dynamics, and the variational formulation enables nonlinearly-stable robust variational time integration. The numerical implementation of these methods in a high-performance computing framework has motivated the development of a new computer code, which integrates state-of-the-art parallel libraries and incorporates important technical contributions to overcome bottlenecks that arise in meshfree methods for large-scale problems. The resulting code is flexible and has been applied to other scientific problems in a number of collaborations dealing with flexoelectricity, metal forming, creeping flows, or fracture in materials with strongly anisotropic surface energy