Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Carbon capture and storage (CCS) is broadly recognised as having the potential to play a key role in meeting climate change targets, delivering low carbon heat and power, decarbonising industry and, more recently, its ability to facilitate the net removal of CO2 from the atmosphere. However, despite this broad consensus and its technical maturity, CCS has not yet been deployed on a scale commensurate with the ambitions articulated a decade ago. Thus, in this paper we review the current state-of-the-art of CO2 capture, transport, utilisation and storage from a multi-scale perspective, moving from the global to molecular scales. In light of the COP21 commitments to limit warming to less than 2 °C, we extend the remit of this study to include the key negative emissions technologies (NETs) of bioenergy with CCS (BECCS), and direct air capture (DAC). Cognisant of the non-technical barriers to deploying CCS, we reflect on recent experience from the UK's CCS commercialisation programme and consider the commercial and political barriers to the large-scale deployment of CCS. In all areas, we focus on identifying and clearly articulating the key research challenges that could usefully be addressed in the coming decade.

/pdf/carbon-capture-and-storage-ccs-the-way-forward-11rgsqyer0.pdf

Carbon capture and storage (CCS): the way forward

Knowledge of temperature and pressure, however qualitative, has been central to our views of geology since at least the early 19th century. In 1822, for example, Charles Daubeny presented what may be the very first “Geological Thermometer,” comparing temperatures of various geologic processes (Torrens 2006). Daubeny (1835) may even have been the first to measure the temperature of a lava flow, by laying a thermometer on the top of a flow at Vesuvius—albeit several months following the eruption, after intervening rain (his estimate was 390°F). In any case, pressure ( P ) and temperature ( T ) estimation lie at the heart of fundamental questions: How hot is Earth, and at what rate has the planet cooled. Are volcanoes the products of thermally driven mantle plumes? Where are magmas stored, and how are they transported to the surface—and how do storage and transport relate to plate tectonics? Well-calibrated thermometers and barometers are essential tools if we are to fully appreciate the driving forces and inner workings of volcanic systems.

This chapter presents methods to estimate the P-T conditions of volcanic and other igneous processes. The coverage includes a review of existing geothermometers and geobarometers, and a presentation of approximately 30 new models, including a new plagioclase-liquid hygrometer. Our emphasis is on experimentally calibrated “thermobarometers,” based on analytic expressions using P or T as dependent variables. For numerical reasons (touched on below) such expressions will always provide the most accurate means of P-T estimation, and are also most easily employed. Analytical expressions also allow error to be ascertained; in the absence of estimates of error, P-T estimates are nearly meaningless. This chapter is intended to complement the chapters by Anderson et al. (2008), who cover granitic systems, and by Blundy and Cashman (2008) and Hansteen and Klugel (2008), who consider additional methods …

Thermometers and Barometers for Volcanic Systems

The validity of the cubic law for laminar flow of fluids through open fractures consisting of parallel planar plates has been established by others over a wide range of conditions with apertures ranging down to a minimum of 0.2 µm. The law may be given in simplified form by Q/Δh = C(2b)3, where Q is the flow rate, Δh is the difference in hydraulic head, C is a constant that depends on the flow geometry and fluid properties, and 2b is the fracture aperture. The validity of this law for flow in a closed fracture where the surfaces are in contact and the aperture is being decreased under stress has been investigated at room temperature by using homogeneous samples of granite, basalt, and marble. Tension fractures were artificially induced, and the laboratory setup used radial as well as straight flow geometries. Apertures ranged from 250 down to 4µm, which was the minimum size that could be attained under a normal stress of 20 MPa. The cubic law was found to be valid whether the fracture surfaces were held open or were being closed under stress, and the results are not dependent on rock type. Permeability was uniquely defined by fracture aperture and was independent of the stress history used in these investigations. The effects of deviations from the ideal parallel plate concept only cause an apparent reduction in flow and may be incorporated into the cubic law by replacing C by C/ƒ. The factor ƒ varied from 1.04 to 1.65 in these investigations. The model of a fracture that is being closed under normal stress is visualized as being controlled by the strength of the asperities that are in contact. These contact areas are able to withstand significant stresses while maintaining space for fluids to continue to flow as the fracture aperture decreases. The controlling factor is the magnitude of the aperture, and since flow depends on (2b)3, a slight change in aperture evidently can easily dominate any other change in the geometry of the flow field. Thus one does not see any noticeable shift in the correlations of our experimental results in passing from a condition where the fracture surfaces were held open to one where the surfaces were being closed under stress.

/pdf/validity-of-cubic-law-for-fluid-flow-in-a-deformable-rock-2ynq4id3hq.pdf

VALIDITY OF CUBIC LAW FOR FLUID FLOW IN A DEFORMABLE ROCK FRACTURE - eScholarship

https://cyberleninka.org/article/n/22310.pdf

Pore-scale imaging and modelling

We present a linear stability analysis of density-driven miscible flow in porous media in the context of carbon dioxide sequestration in saline aquifers. Carbon dioxide dissolution into the underlying brine leads to a local density increase that results in a gravitational instability. The physical phenomenon is analogous to the thermal convective instability in a semi-infinite domain, owing to a step change in temperature at the boundary. The critical time for the onset of convection in such problems has not been determined accurately by previous studies. We present a solution, based on the dominant mode of the self-similar diffusion operator, which can accurately predict the critical time and the associated unstable wavenumber. This approach is used to explain the instability mechanisms of the critical time and the long-wave cutoff in a semi-infinite domain. The dominant mode solution, however, is valid only for a small parameter range. We extend the analysis by employing the quasi-steady-state approximation (QSSA) which provides accurate solutions in the self-similar coordinate system. For large times, both the maximum growth rate and the most dangerous mode decay as , respectively. The instability problem is also analysed in the nonlinear regime by high-accuracy direct numerical simulations. The nonlinear simulations at short times show good agreement with the linear stability predictions. At later times, macroscopic fingers display intense nonlinear interactions that significantly influence both the front propagation speed and the overall mixing rate. A dimensional analysis for typical aquifers shows that for a permeability variation of 1—3000 mD, the critical time can vary from 2000 yrs to about 10 days while the critical wavelength can be between 200 m and 0.3 m.

Onset of convection in a gravitationally unstable diffusive boundary layer in porous media

[1] Geological carbon dioxide (CO2) storage is a means of reducing anthropogenic emissions. Dissolution of CO2 into the brine, resulting in stable stratification, increases storage security. The dissolution rate is determined by convection in the brine driven by the increase of brine density with CO2 saturation. We present a new analogue fluid system that reproduces the convective behaviour of CO2‐enriched brine. Laboratory experiments and high‐resolution numerical simulations show that the convective flux scales with the Rayleigh number to the 4/5 power, in contrast with a classical linear relationship. A scaling argument for the convective flux incorporating lateral diffusion from downwelling plumes explains this nonlinear relationship for the convective flux, provides a physical picture of high Rayleigh number convection in a porous medium, and predicts the CO2 dissolution rates in CO2 accumulations. These estimates of the dissolution rate show that convective dissolution can play an important role in enhancing storage security. Citation: Neufeld,J.A.,M.A .Hesse,A.Riaz,M. A.H allworth, H. A. Tchelepi, and H. E. Huppert (2010), Convective dissolution of carbon dioxide in saline aquifers, Geophys. Res. Lett., 37, L22404, doi:10.1029/2010GL044728.

/pdf/convective-dissolution-of-carbon-dioxide-in-saline-aquifers-4kjo4ecyj8.pdf

Convective dissolution of carbon dioxide in saline aquifers

Motivated by geological carbon dioxide (CO2) storage, we present a vertical-equilibrium sharp-interface model for the migration of immiscible gravity currents with constant residual trapping in a two-dimensional confined aquifer. The residual acts as a loss term that reduces the current volume continuously. In the limit of a horizontal aquifer, the interface shape is self-similar at early and at late times. The spreading of the current and the decay of its volume are governed by power-laws. At early times the exponent of the scaling law is independent of the residual, but at late times it decreases with increasing loss. Owing to the self-similar nature of the current the volume does not become zero, and the current continues to spread. In the hyperbolic limit, the leading edge of the current is given by a rarefaction and the trailing edge by a shock. In the presence of residual trapping, the current volume is reduced to zero in finite time. Expressions for the up-dip migration distance and the final migration time are obtained. Comparison with numerical results shows that the hyperbolic limit is a good approximation for currents with large mobility ratios even far from the hyperbolic limit. In gently sloping aquifers, the current evolution is divided into an initial near-parabolic stage, with power-law decrease of volume, and a later near-hyperbolic stage, characterized by a rapid decay of the plume volume. Our results suggest that the efficient residual trapping in dipping aquifers may allow CO2 storage in aquifers lacking structural closure, if CO2 is injected far enough from the outcrop of the aquifer.

Gravity currents with residual trapping

Iterative multiscale finite-volume method

We investigate the evolution of a finite release of fluid into an infinite, two-dimensional, horizontal, porous slab saturated with a fluid of different density and viscosity. The vertical boundaries of the slab are impermeable and the released fluid spreads as a gravity current along a horizontal boundary. At early times the released fluid fills the entire height of the layer, and the governing equation admits a self-similar solution that is a function of the viscosity ratio between the two fluids. This early similarity solution describes a tilting interface with tips propagating as x ∝ t 1/2 . At late times the released fluid has spread along the boundary and the height of the current is much smaller than the thickness of the layer. The governing equation simplifies and admits a different similarity solution that is independent of the viscosity ratio. This late similarity solution describes a point release of fluid in a semi-infinite porous half-space, where the tip of the interface propagates as x ∝ t 1/3 . The same simplification of the governing equation occurs if the viscosity of the released fluid is much higher than the viscosity of the ambient fluid. We have obtained an expression for the time when the solution transitions from the early to the late self-similar regime. The transition time increases monotonically with increasing viscosity ratio. The transition period during which the solution is not self-similar also increases monotonically with increasing viscosity ratio, for mobility ratios larger than unity. Numerical computations describing the full evolution of the governing equation show good agreement with the theoretical results. Estimates of the spreading of injected fluids over long times are important for geological storage of CO 2 , and for the migration of pollutants in aquifers. In all cases it is important to be able to anticipate when the spreading regime transitions from x ∝ t 1/2 to Χ ∝ t 1/3 .

Marc A. Hesse

Papers

Onset of convection in a gravitationally unstable diffusive boundary layer in porous media

Convective dissolution of carbon dioxide in saline aquifers

Gravity currents with residual trapping

Iterative multiscale finite-volume method

Gravity currents in horizontal porous layers: transition from early to late self-similarity