David Trebotich

An investigation of the effect of pore scale flow on average geochemical reaction rates using direct numerical simulation

An Investigation of the Effect of Pore Scale Flow on Average Geochemical Reaction Rates Using Direct Numerical Simulation Sergi Molins 1 David Trebotich 2 Carl I. Steefel 1 Chaopeng Shen 2 Earth Sciences Division Lawrence Berkeley National Laboratory One Cyclotron Road, Mail Stop 90R1116, Berkeley, California 94720, USA Computational Research Division Lawrence Berkeley National Laboratory One Cyclotron Road, Mail Stop 50A-1148, Berkeley, California 94720, USA

Pore-scale controls on calcite dissolution rates from flow-through laboratory and numerical experiments.

A combination of experimental, imaging, and modeling techniques were applied to investigate the pore-scale transport and surface reaction controls on calcite dissolution under elevated pCO2 conditions. The laboratory experiment consisted of the injection of a solution at 4 bar pCO2 into a capillary tube packed with crushed calcite. A high resolution pore-scale numerical model was used to simulate the experiment based on a computational domain consisting of reactive calcite, pore space, and the capillary wall constructed from volumetric X-ray microtomography images. Simulated pore-scale effluent concentrations were higher than those measured by a factor of 1.8, with the largest component of the discrepancy related to uncertainties in the reaction rate model and its parameters. However, part of the discrepancy was apparently due to mass transport limitations to reactive surfaces, which were most pronounced near the inlet where larger diffusive boundary layers formed around grains and in slow-flowing pore spaces that exchanged mass by diffusion with fast flow paths. Although minor, the difference between pore- and continuum-scale results due to transport controls was discernible with the highly accurate methods employed and is expected to be more significant where heterogeneity is greater, as in natural subsurface materials.

High-Resolution Simulation of Pore-Scale Reactive Transport Processes Associated with Carbon Sequestration

New investigative tools, combined with experiments and computational methods, are being developed to build a next-generation understanding of molecular-to-pore-scale processes in fluid-rock systems and to demonstrate the ability to control critical aspects of flow and transport in porous rock media, in particular, as applied to geologic sequestration of CO2. Of scientific interest is to establish the rules governing emergent behavior at the porous-continuum macroscale under far from equilibrium conditions by carefully understanding the behavior at the underlying pore microscale. To this end, the authors present a direct numerical simulation modeling capability that can resolve flow and transport processes in geometric features obtained from the image data of realistic pore space at unprecedented scale and resolution. Here, they focus on scaling a new algorithmic approach based on embedded boundary, finite-volume methods and algebraic multigrid. They demonstrate the scalability of this new capability, known as Chombo-Crunch, to more than 100,000 processor cores and show results from pore-scale flow and transport in the realistic pore space obtained from image data.

Microfabricated microdialysis microneedles for continuous medical monitoring

Enzyme based biosensors suffer from loss of activity and sensitivity through a variety of processes. One major reason for the loss is through large molecular weight proteins settling onto the sensor and affecting sensor signal stability and disrupting enzyme function. One way to minimize loss of sensor activity is to filter out large molecular weight compounds before sensing small biochemicals such as glucose. A novel microdialysis microneedle is introduced that is capable of excluding large MW compounds based on size. Preliminary experimental evidence of membrane permeability is shown, as well as diffusion and permeability modeling. Solutions should be able to equilibrate across the microdialysis membrane in a few seconds, as opposed to a few minutes with existing technologies. Microdialysis microneedles present an attractive first step towards decreasing size, patient discomfort and energy consumption of portable medical monitors over existing technologies.

Performance of embedded boundary methods for CFD with complex geometry

In this paper, we discuss some of the issues in obtaining high performance for block-structured adaptive mesh refinement software for partial differential equations in complex geometry using embedded boundary/volume-of-fluid methods. We present the design of an adaptive embedded boundary multigrid algorithm for elliptic problems. We show examples in which this new elliptic solver scales to 1000 processors. We also apply this technology to more complex mathematical and physical algorithms for incompressible fluid dynamics and demonstrate similar scaling.

Embedded boundary algorithms and software for partial differential equations

In this paper, we give an overview of a set of methods being developed for solving classical PDEs in irregular geometries, or in the presence of free boundaries. In this approach, the irregular geometry is represented on a rectangular grid by specifying the intersection of each grid cell with the region on one or the other side of the boundary. This leads to a natural conservative discretization of the solution to the PDE on either side of the boundary. Stable and robust hyperbolic and linear elliptic/parabolic solvers have been designed and implemented. Example applications of this approach are shown for compressible and incompressible gas dynamics problems in complex geometries, and for surface diffusion in a cell membrane.

Toward a Mesoscale Model for the Dynamics of Polymer Solutions

Toward a Mesoscale Model for the Dynamics of Polymer Solutions G. H. Miller1 and D. Trebotich2 ∗ 1Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616, USA and Applied Numerical Algorithms Group, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA 2Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, P.O. Box 808, L-560, Livermore, CA 94551, USA

Short Note: An efficient solver for the equations of resistive MHD with spatially-varying resistivity

We regularize the variable coefficient Helmholtz equations arising from implicit time discretizations for resistive MHD, in a way that leads to a symmetric positive-definite system uniformly in the time step. Standard centered-difference discretizations in space of the resulting PDE leads to a method that is second-order accurate, and that can be used with multigrid iteration to obtain efficient solvers.

Scientific workflows at datawarp-speed: accelerated data-intensive science using NERSC's burst buffer

Emerging exascale systems have the ability to accelerate the time-to-discovery for scientific workflows. However, as these workflows become more complex, their generated data has grown at an unprecedented rate, making I/O constraints challenging. To address this problem advanced memory hierarchies, such as burst buffers, have been proposed as intermediate layers between the compute nodes and the parallel file system. In this paper, we utilize Cray DataWarp burst buffer coupled with in-transit processing mechanisms, to demonstrate the advantages of advanced memory hierarchies in preserving traditional coupled scientific workflows. We consider in-transit workflow which couples simulation of subsurface flows with on-the-fly flow visualization. With respect to the proposed workflow, we study the performance of the Cray DataWarp Burst Buffer and provide a comparison with the Lustre parallel file system.

A Second-Order Accurate Conservative Front-Tracking Method in One Dimension

This paper presents a conservative front-tracking method for shocks and contact discontinuities that is second-order accurate. It is based on a volume-of-fluid method that treats the moving front with concepts similar to those of an embedded-boundary method. Special care is taken in the centering of the data to ensure the right order of accuracy at the front, and a redistribution step guarantees conservation. A suite of test problems, for tracking both shocks and contact discontinuities, is presented that confirms that the method is second-order accurate.