Analysis of a parallelized nonlinear elliptic boundary value problem solver with application to reacting flows

A parallelized finite difference code based on the Newton method for systems of nonlinear elliptic boundary value problems in two dimensions is analyzed in terms of computational complexity and parallel efficiency. An approximate cost function depending on 15 dimensionless parameters is derived for algorithms based on stripwise and boxwise decompositions of the domain and a one-to-one assignment of the strip or box subdomains to processors. The sensitivity of the cost functions to the parameters is explored in regions of parameter space corresponding to model small-order systems with inexpensive function evaluations and also a coupled system of nineteen equations with very expensive function evaluations. The algorithm was implemented on the Intel Hypercube, and some experimental results for the model problems with stripwise decompositions are presented and compared with the theory. In the context of computational combustion problems, multiprocessors of either message-passing or shared-memory type may be employed with stripwise decompositions to realize speedup of O(n), where n is mesh resolution in one direction, for reasonable n

On the definition of a moist-air potential vorticity

A new potential vorticity is derived by using a specific entropy formulation expressed in terms of a moist-air entropy potential temperature. The new formulation is compared with Ertel's version and with others based on virtual and equivalent potential temperatures. The new potential vorticity is subject to conservative properties ensured by the Second Law applied to the moist-air material derivatives. It is shown that the upper tropospheric and stratospheric (dry) structures are nearly the same as those obtained with Ertel's component. Moreover, new structures are observed in the low troposphere, with negative values associated with moist frontal regions. The negative values are observed in the frontal regions where slantwise convection instabilities may take place, but they are smaller than those observed with the equivalent potential vorticity. The main purpose of the article is to diagnose the behaviour of the new potential vorticity from numerical output generated by the ARPEGE NWP model, with the help of isobaric charts and vertical cross-sections. Two inversion methods are suggested. The first method could be based on the invertibility principle verified by the virtual potential vorticity, with a possibility to control and modify separately potential vorticity components in the (dry) upper and (moist) lower atmospheric levels. The other method may consist of an inversion process directly applied to the new moist-air entropy potential vorticity, because the negative values and the solenoidal term are smaller than those observed with equivalent potential vorticity, as shown by numerical evaluations.Comment: Submitted to the Q. J. R. Meteorol. Soc. in August 2012. Accepted in April 2013. Early view on the QJRMS site http://onlinelibrary.wiley.com/doi/10.1002/qj.2182/abstract. 24 pages, 10 color figures. V2: add the arXiv links of Marquet (2011), Geleyn and Marquet (2012) and Marquet and Geleyn (2013

The HPx software for multicomponent reactive transport during variably-saturated flow: Recent developments and applications

Abstract HPx is a multicomponent reactive transport model which uses HYDRUS as the flow and transport solver and PHREEQC-3 as the biogeochemical solver. Some recent adaptations have significantly increased the flexibility of the software for different environmental and engineering applications. This paper gives an overview of the most significant changes of HPx, such as coupling transport properties to geochemical state variables, gas diffusion, and transport in two and three dimensions. OpenMP allows for parallel computing using shared memory. Enhancements for scripting may eventually simplify input definitions and create possibilities for defining templates for generic (sub)problems. We included a discussion of root solute uptake and colloid-affected solute transport to show that most or all of the comprehensive features of HYDRUS can be extended with geochemical information. Finally, an example is used to demonstrate how HPx, and similar reactive transport models, can be helpful in implementing different factors relevant for soil organic matter dynamics in soils. HPx offers a unique framework to couple spatial-temporal variations in water contents, temperatures, and water fluxes, with dissolved organic matter and CO2 transport, as well as bioturbation processes

Ensemble evaluation of hydrological model hypotheses

It is demonstrated for the first time how model parameter, structural and data uncertainties can be accounted for explicitly and simultaneously within the Generalized Likelihood Uncertainty Estimation (GLUE) methodology. As an example application, 72 variants of a single soil moisture accounting store are tested as simplified hypotheses of runoff generation at six experimental grassland field-scale lysimeters through model rejection and a novel diagnostic scheme. The fields, designed as replicates, exhibit different hydrological behaviors which yield different model performances. For fields with low initial discharge levels at the beginning of events, the conceptual stores considered reach their limit of applicability. Conversely, one of the fields yielding more discharge than the others, but having larger data gaps, allows for greater flexibility in the choice of model structures. As a model learning exercise, the study points to a “leaking” of the fields not evident from previous field experiments. It is discussed how understanding observational uncertainties and incorporating these into model diagnostics can help appreciate the scale of model structural error

Statistical inference of the mechanisms driving collective cell movement

Numerous biological processes, many impacting on human health, rely on collective cell movement. We develop nine candidate models, based on advection-diffusion partial differential equations, to describe various alternative mechanisms that may drive cell movement. The parameters of these models were inferred from one-dimensional projections of laboratory observations of Dictyostelium discoideum cells by sampling from the posterior distribution using the delayed rejection adaptive Metropolis algorithm (DRAM). The best model was selected using the Widely Applicable Information Criterion (WAIC). We conclude that cell movement in our study system was driven both by a self-generated gradient in an attractant that the cells could deplete locally, and by chemical interactions between the cells

Galactic and Accretion Disk Dynamos

Dynamos in astrophysical disks are usually explained in terms of the standard alpha-omega mean field dynamo model where the local helicity generates a radial field component from an azimuthal field. The subsequent shearing of the radial field gives rise to exponentially growing dynamo modes. There are several problems with this model. The exponentiation time for the galactic dynamo is hard to calculate, but is probably uncomfortably long. Moreover, numerical simulations of magnetic fields in shearing flows indicate that the presence of a dynamo does not depend on a non-zero average helicity. However, these difficulties can be overcome by including a fluctuating helicity driven by hydrodynamic or magnetic instabilities. Unlike traditional disk dynamo models, this `incoherent' dynamo does not depend on the presence of systematic fluid helicity or any kind of vertical symmetry breaking. It will depend on geometry, in the sense that the dynamo growth rate becomes smaller for very thin disks, in agreement with constraints taken from the study of X-ray novae. In this picture the galactic dynamo will operate efficiently, but the resulting field will have a radial coherence length which is a fraction of the galactic radius.Comment: 16 pages, in Proceedings of the Chapman Conference on Magnetic Helicit

A review of the theoretical basis for bulk mass flux convective parameterization

Most parameterizations for precipitating convection in use today are bulk schemes, in which an ensemble of cumulus elements with different properties is modelled as a single, representative entraining-detraining plume. We review the underpinning mathematical model for such parameterizations, in particular by comparing it with spectral models in which elements are not combined into the representative plume. The chief merit of a bulk model is that the representative plume can be described by an equation set with the same structure as that which describes each element in a spectral model. The equivalence relies on an ansatz for detrained condensate introduced by Yanai et al. (1973) and on a simplified microphysics. There are also conceptual differences in the closure of bulk and spectral parameterizations. In particular, we show that the convective quasi-equilibrium closure of Arakawa and Schubert (1974) for spectral parameterizations cannot be carried over to a bulk parameterization in a straightforward way. Quasi-equilibrium of the cloud work function assumes a timescale separation between a slow forcing process and a rapid convective response. But, for the natural bulk analogue to the cloud-work function (the dilute CAPE), the relevant forcing is characterised by a different timescale, and so its quasi-equilibrium entails a different physical constraint. Closures of bulk parameterization that use the non-entraining parcel value of CAPE do not suffer from this timescale issue. However, the Yanai et al. (1973) ansatz must be invoked as a necessary ingredient of those closures