Moving charged particles in lattice Boltzmann-based electrokinetics

The motion of ionic solutes and charged particles under the influence of an electric field and the ensuing hydrodynamic flow of the underlying solvent is ubiquitous in aqueous colloidal suspensions. The physics of such systems is described by a coupled set of differential equations, along with boundary conditions, collectively referred to as the electrokinetic equations. Capuani et al. [J. Chem. Phys. 121, 973 (2004)] introduced a lattice-based method for solving this system of equations, which builds upon the lattice Boltzmann algorithm for the simulation of hydrodynamic flow and exploits computational locality. However, thus far, a description of how to incorporate moving boundary conditions into the Capuani scheme has been lacking. Moving boundary conditions are needed to simulate multiple arbitrarily-moving colloids. In this paper, we detail how to introduce such a particle coupling scheme, based on an analogue to the moving boundary method for the pure LB solver. The key ingredients in our method are mass and charge conservation for the solute species and a partial-volume smoothing of the solute fluxes to minimize discretization artifacts. We demonstrate our algorithm's effectiveness by simulating the electrophoresis of charged spheres in an external field; for a single sphere we compare to the equivalent electro-osmotic (co-moving) problem. Our method's efficiency and ease of implementation should prove beneficial to future simulations of the dynamics in a wide range of complex nanoscopic and colloidal systems that was previously inaccessible to lattice-based continuum algorithms

A scalable and extensible checkpointing scheme for massively parallel simulations

Realistic simulations in engineering or in the materials sciences can consume enormous computing resources and thus require the use of massively parallel supercomputers. The probability of a failure increases both with the runtime and with the number of system components. For future exascale systems, it is therefore considered critical that strategies are developed to make software resilient against failures. In this article, we present a scalable, distributed, diskless, and resilient checkpointing scheme that can create and recover snapshots of a partitioned simulation domain. We demonstrate the efficiency and scalability of the checkpoint strategy for simulations with up to 40 billion computational cells executing on more than 400 billion floating point values. A checkpoint creation is shown to require only a few seconds and the new checkpointing scheme scales almost perfectly up to more than 260, 000 (218) processes. To recover from a diskless checkpoint during runtime, we realize the recovery algorithms using ULFM MPI. The checkpointing mechanism is fully integrated in a state-of-the-art high-performance multi-physics simulation framework. We demonstrate the efficiency and robustness of the method with a realistic phase-field simulation originating in the material sciences and with a lattice Boltzmann method implementation

Exploring the solid state and solution structural chemistry of the utility amide potassium hexamethyldisilazide (KHMDS)

The structural chemistry of eleven donor complexes of the important Brønsted base potassium 1,1,1,3,3,3-hexamethyldisilazide (KHMDS) has been studied. Depending on the donor, each complex adopted one of four general structural motifs. Specifically, in this study the donors employed were toluene (to give polymeric 1 and dimeric 2), THF (dimeric 3), N,N,N',N'-tetramethylethylenediamine (TMEDA) (dimeric 4), (R,R)-N,N,N',N'-tetramethyl-1,2-diaminocyclohexane [(R,R)-TMCDA] (dimeric 5), 12-crown-4 (dimeric 6), N,N,N',N'-tetramethyldiaminoethyl ether (TMDAE) (tetranuclear dimeric 8 and monomeric 10), N,N,N',N',N''-pentamethyldiethylentriamine (PMDETA) (tetranuclear dimeric 7), tris[2-dimethyl(amino)ethyl]amine (Me6TREN) (tetranuclear dimeric 9) and tris{2-(2-methoxyethoxy)ethyl}amine (TMEEA) (monomeric 11). The complexes were also studied in solution by 1H and 13C NMR spectroscopy as well as DOSY NMR spectroscopy

Optimum configuration for accurate simulations of chaotic porous media with Lattice Boltzmann Methods considering boundary conditions, lattice spacing and domain size

[EN] Simulations of the flow field through chaotic porous media are powerful numerical challenges of special interest in science and technology. The simulations are usually done over representative samples which summarise the properties of the material. Several factors affect the accuracy of the results. Firstly the spatial resolution has to be fine enough to be able to capture the smallest geometrical details. Secondly the domain size has to be large enough to contain the large characteristic scale of the porous media. And finally the effects induced by the boundary conditions have to be diluted when more realistic options are not available. This is the case when the geometry is obtained by tomography and the periodic boundary conditions cannot be applied to delimit the sample because its geometry is not periodic. Impermeable boundary conditions are usually chosen to enclose the domain, forcing mass conservation. As a result, the flow field is over-restricted and the total pressure drop can be over-estimated. In this paper a new strategy is presented to optimise the computational resources consumption keeping the restrictions imposed by the accuracy criteria. The effects of the domain size, discretisation thickness and boundary condition disturbances are studied in detail. The study starts with the procedural generation of chaotic porous walls which mimics acicular mullite filters. An advantage of this process is the possibility to create periodic geometries. Periodicity permits the application of advanced techniques such as cyclic cross-correlations between the phase field and the velocity component fields without aliasing. From cross-correlation operations the large characteristic scale is obtained. The result is a lower threshold for the domain size. In second place a mesh independent study is done to find the upper threshold for the lattice spacing. The Minkowski-Bouligand fractal dimension of the fluid-solid interface corroborates the results. It has been demonstrated how the fractal dimension is a good candidate to replace the mesh independent study with lower computational cost for this type of problems. The last step is to compare the results obtained for a periodic geometry applying periodicity and symmetry as boundary conditions. Considering the periodic case as reference the resultant error is analysed. The explanation of the analysis includes how the intensity of the error changes in space and the limitations of symmetric boundary conditions.J.P.G. Galache was supported by a research grant from Generalitat Valenciana (Programa VALI+d, ACIF/2014/020 and BEFPI/2015/006). This work has been supported by the PAID-06-14 program (Primeros Proyectos de Investigacion UPV) of Universitat Politecnica de Valencia. "ESTUDIO DEL FLUJO EN MEDIOS POROSOS MEDIANTE METODOS LATTICE-BOLTZMANN". The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time on the GCS Supercomputer SuperMUC at Leibniz Supercomputing Centre (LRZ, www.lrz.de).Gil, A.; García Galache, JP.; Godenschwager, C.; Rüde. U. (2017). Optimum configuration for accurate simulations of chaotic porous media with Lattice Boltzmann Methods considering boundary conditions, lattice spacing and domain size. Computers & Mathematics with Applications. 73(12):2515-2528. doi:10.1016/j.camwa.2017.03.017S25152528731

Numerical simulation of pore fluid flow and fine sediment infiltration into the riverbed

The riverbed embodies an important ecotone for many organisms. It is also an interface between groundwater and surface water, two systems that feature numerous distinctions. The riverbed therefore exhibits many physical and biochemical gradients e.g. flow velocity, temperature, oxygen or nutrient concentration. If the riverbed however becomes clogged through input and deposition of fine sediments, its porosity and permeability decrease leads to reduced interconnectivity between both neighboring systems and eventually reduction of the suitability of the riverbed as a habitat for organisms. Reasons for fine sediment infiltration are high inputs of fine sediments from surface runoff or rainwater retention basins and continuous unnatural low flow velocities typically found in regulated rivers. The objective of our current research is to develop a model for the determination of the factors controlling fine sediment infiltration into the riverbed and their quantitative impact on fine sediment infiltration rates, reduction of riverbed porosity, and permeability. To do so, we use several numerical modeling techniques including the popular lattice Boltzmann method