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Two forced shallow-water flow scenarios are explored in a 2D fourth-order finite-volume dynamical core with adaptive mesh refinement (AMR) to investigate AMR’s ability to track and resolve complex evolving features. Traditional shallow-water test cases are mainly characterized by large-scale smooth flows that do not effectively test the multiscale abilities of variable-resolution and AMR models to resolve sharp gradients and small-scale flow filaments. Therefore, adding forcing mechanisms to the shallow-water system to model key atmospheric processes adds complexity and creates small-scale phenomena. These can serve as foci for dynamic grid refinement while remaining simple enough to study the numerical design of a model’s dynamical core. The first shallow-water flow scenario represents a strengthening, tropical cyclone–like, vortex that is driven by a Betts–Miller-like convection scheme. The second shallow-water test is built upon a barotropically unstable jet with an added Kessler-like warm rain scheme that leads to precipitating frontal zones. The key feature of both tests is that there is significant sensitivity to the model grid while converging (structurally) at high resolution. Both test cases are investigated for a series of uniform resolutions and a variety of AMR tagging criteria. The AMR simulations demonstrate that grid refinement can resolve local features without requiring global high-resolution meshes. However, the results are sensitive to the refinement criteria. Criteria that trigger refinement early in a simulation reproduce the uniform-resolution reference solutions most reliably. In contrast, AMR criteria that delay refinement for several days require careful tuning of the AMR thresholds to improve results compared with uniform-resolution simulations.

Mountains are natural dams that impede atmospheric moisture transport and water towers that cool, condense, and store precipitation. They are essential in the western United States where precipitation is seasonal, and snowpack is needed to meet water demand. With anthropogenic climate change increasingly threatening mountain snowpack, there is a pressing need to better understand the driving climatological processes. However, the coarse resolution typical of modern global climate models renders them largely insufficient for this task, and signals a need for an advanced strategy. This paper continues the assessment of variable-resolution in the Community Earth System Model (VR-CESM) in modeling mountain hydroclimatology to understand the role of grid-spacing at 55, 28, 14, and 7 km and microphysics, specifically the Morrison and Gettelman (, MG1, https://doi.org/10.1175/2008JCLI2105.1) scheme versus the Gettelman and Morrison (, MG2, https://doi.org/10.1175/JCLI-D-14-00102.1) scheme. Eight VR-CESM simulations were performed from 1999 to 2015 with the F_AMIP_CAM5 component set, which couples the atmosphere-land models and prescribes ocean data. Refining horizontal grid-spacing from 28 to 7 km with the MG1 scheme did not improve the simulated mountain hydroclimatology. Substantial improvements occurred with the use of MG2 at grid-spacings ≤28 km compared to MG1 as shown with subsequent statistics. Average SWE bias diminished by 9.4X, 4.9X, and 3.5X from 55 to 7 km. The range in minimum (maximum) DJF spatial correlations increased by 0.1–0.2 in both precipitation and SWE. Mountain windward/leeward distributions and elevation profiles improved across hydroclimate variables, however not always with model resolution alone. Disconcertingly, all VR-CESM simulations exhibited a systemic mountain cold bias that worsened with elevation and will require further examination.

Numerical weather, climate, or Earth system models involve the coupling of components. At a broad level, these components can be classified as the resolved fluid dynamics, unresolved fluid dynamical aspects (i.e., those represented by physical parameterizations such as subgrid-scale mixing), and nonfluid dynamical aspects such as radiation and microphysical processes. Typically, each component is developed, at least initially, independently.Once development ismature, the components are coupled to deliver a model of the required complexity. The implementation of the coupling can have a significant impact on the model.As the error associated with each component decreases, the errors introduced by the coupling will eventually dominate. Hence, any improvement in one of the components is unlikely to improve the performance of the overall system. The challenges associated with combining the components to create a coherentmodel are here termed physics-dynamics coupling. The issue goes beyond the coupling between the parameterizations and the resolved fluid dynamics. This paper highlights recent progress and some of the current challenges. It focuses on three objectives: to illustrate the phenomenology of the coupling problemwith references to examples in the literature, to show howthe problem can be analyzed, and to create awareness of the issue across the disciplines and specializations. The topics addressed are different ways of advancing full models in time, approaches to understanding the role of the coupling and evaluation of approaches, coupling ocean and atmosphere models, thermodynamic compatibility between model components, and emerging issues such as those that arise as model resolutions increase and/ormodels use variable resolutions.

Dynamical downscaling is a widely used technique to properly capture regional surface heterogeneities that shape the local hydroclimatology. However, in the context of dynamical downscaling, the impacts on simulation fidelity have not been comprehensively evaluated across many user-specified factors, including the refinements of model horizontal resolution, large-scale forcing datasets, and dynamical cores. Two global-to-regional downscaling methods are used to assess these: specifically, the variable-resolution Community Earth System Model (VR-CESM) and the Weather Research and Forecasting (WRF) Model with horizontal resolutions of 28, 14, and 7 km. The modeling strategies are assessed by comparing the VR-CESM and WRF simulations with consistent physical parameterizations and grid domains. Two groups of WRF Models are driven by either the NCEP reanalysis dataset (WRF_NCEP) or VR-CESM7 results (WRF_VRCESM) to evaluate the effects of large-scale forcing datasets. The simulated hydroclimatologies are compared with reference datasets for key properties including total precipitation, snow cover, snow water equivalent (SWE), and surface temperature. The large-scale forcing datasets are critical to the WRF simulations of total precipitation but not surface temperature, controlled by the wind field and atmospheric moisture transport at the ocean boundary. No significant benefit is found in the regional average simulated hydroclimatology by increasing horizontal resolution refinement from 28 to 7 km, probably due to the systematic biases from the diagnostic treatment of rainfall and snowfall in the microphysics scheme. The choice of dynamical core has little impact on total precipitation but significantly determines simulated surface temperature, which is affected by the snow-albedo feedback in winter and soil moisture estimations in summer.

We present a moving control volume (CV) approach to computing hydrodynamic forces and torques on complex geometries. The method requires surface and volumetric integrals over a simple and regular Cartesian box that moves with an arbitrary velocity to enclose the body at all times. The moving box is aligned with Cartesian grid faces, which makes the integral evaluation straightforward in an immersed boundary (IB) framework. Discontinuous and noisy derivatives of velocity and pressure at the fluid–structure interface are avoided and far-field (smooth) velocity and pressure information is used. We re-visit the approach to compute hydrodynamic forces and torques through force/torque balance equations in a Lagrangian frame that some of us took in a prior work (Bhalla et al., 2013 [13]). We prove the equivalence of the two approaches for IB methods, thanks to the use of Peskin's delta functions. Both approaches are able to suppress spurious force oscillations and are in excellent agreement, as expected theoretically. Test cases ranging from Stokes to high Reynolds number regimes are considered. We discuss regridding issues for the moving CV method in an adaptive mesh refinement (AMR) context. The proposed moving CV method is not limited to a specific IB method and can also be used, for example, with embedded boundary methods.

In this paper, we present a fourth-order algorithm to solve Poisson's equation in two and three dimensions. We use a Cartesian grid, embedded boundary method to resolve complex boundaries. We use a weighted least squares algorithm to solve for our stencils. We use convergence tests to demonstrate accuracy and we show the eigenvalues of the operator to demonstrate stability. We compare accuracy and performance with an established second-order algorithm. We also discuss in depth strategies for retaining higher-order accuracy in the presence of nonsmooth geometries.

Modernizing SW4 for massively parallel time-domain simulations of earthquake ground motions in 3D earth models increases resolution and provides ground motion estimates for critical infrastructure risk evaluations. Simulations of ground motions from large (M ≥ 7.0) earthquakes require domains on the order of 100 to500 km and spatial granularity on the order of 1 to5 m resulting in hundreds of billions of grid points. Surface-focused structured mesh refinement (SMR) allows for more constant grid point per wavelength scaling in typical Earth models, where wavespeeds increase with depth. In fact, MR allows for simulations to double the frequency content relative to a fixed grid calculation on a given resource. The authors report improvements to the SW4 algorithm developed while porting the code to the Cori Phase 2 (Intel Xeon Phi) systems at the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Investigations of the performance of the innermost loop of the calculations found that reorganizing the order of operations can improve performance for massive problems.

This paper extends on the first part of this series by describing four examples of 2D linear maps that can be constructed in accordance with the theory of the earlier work. The focus is again on spherical geometry, although these techniques can be readily extended to arbitrary manifolds. The four maps include conservative, consistent, and (optionally) monotone linear maps (i) between two finite-volume meshes, (ii) from finite-volume to finite-element meshes using a projection-type approach, (iii) from finite-volume to finite-element meshes using volumetric integration, and (iv) between two finite-element meshes. Arbitrary order of accuracy is supported for each of the described nonmonotone maps.

Adaptive mesh refinement (AMR) is a technique that has been featured only sporadically in atmospheric science literature. This paper aims to demonstrate the utility of AMR for simulating atmospheric flows. Several test cases are implemented in a 2D shallow-water model on the sphere using the Chombo-AMR dynamical core. This high-order finite-volume model implements adaptive refinement in both space and time on a cubed-sphere grid using a mapped-multiblock mesh technique. The tests consist of the passive advection of a tracer around moving vortices, a steady-state geostrophic flow, an unsteady solid-body rotation, a gravity wave impinging on a mountain, and the interaction of binary vortices. Both static and dynamic refinements are analyzed to determine the strengths and weaknesses of AMR in both complex flows with small-scale features and large-scale smooth flows. The different test cases required different AMR criteria, such as vorticity or height-gradient based thresholds, in order to achieve the best accuracy for cost. The simulations show that the model can accurately resolve key local features without requiring global high-resolution grids. The adaptive grids are able to track features of interest reliably without inducing noise or visible distortions at the coarse-fine interfaces. Furthermore, the AMR grids keep any degradations of the large-scale smooth flows to a minimum.

We present a survey of physical and computational techniques that have the potential to contribute to the next generation of high-fidelity, multi-scale climate simulations. Examples of the climate science problems that can be investigated with more depth with these computational improvements include the capture of remote forcings of localized hydrological extreme events, an accurate representation of cloud features over a range of spatial and temporal scales, and parallel, large ensembles of simulations to more effectively explore model sensitivities and uncertainties. Numerical techniques, such as adaptive mesh refinement, implicit time integration, and separate treatment of fast physical time scales are enabling improved accuracy and fidelity in simulation of dynamics and allowing more complete representations of climate features at the global scale. At the same time, partnerships with computer science teams have focused on taking advantage of evolving computer architectures such as many-core processors and GPUs. As a result, approaches which were previously considered prohibitively costly have become both more efficient and scalable. In combination, progress in these three critical areas is poised to transform climate modeling in the coming decades. These topics have been presented within a workshop titled, "Numerical and Computational Developments to Advance Multiscale Earth System Models (MSESM'15)," as part of the International Conference on Computational Sciences, Reykjavik, Iceland, June 1-3, 2015.

We present a high-order finite-volume approach for solving the shallow-water equations on the sphere, using multiblock grids on the cubed sphere. This approach combines a Runge-Kutta time discretization with a fourth-order-accurate spatial discretization and includes adaptive mesh refinement and refinement in time. Results of tests show fourth-order convergence for the shallow-water equations as well as for advection in a highly deformational flow. Hierarchical adaptive mesh refinement allows solution error to be achieved that is comparable to that obtained with uniform resolution of the most refined level of the hierarchy but with many fewer operations.

Maggot debridement therapy (MDT) is widely used for debridement of chronic infected wounds; however, for wounds harbouring specific bacteria limited effect or failure of the treatment has been described. Here we studied the survival of Lucilia sericata maggots encountering Pseudomonas aeruginosa PAO1 in a simple assay with emphasis on the quorum-sensing (QS)-regulated virulence. The maggots were challenged with GFP-tagged P. aeruginosa wild-type (WT) PAO1 and a GFP-tagged P. aeruginosa [DELTA]lasR rhlR ([DELTA]RR) QS-deficient mutant in different concentrations. Maggots were killed in the presence of WT PAO1 whereas the challenge with the QS mutant showed a survival reduction of ~25% compared to negative controls. Furthermore, bacterial intake by the maggots was lower in the presence of WT PAO1 compared to the PAO1 [DELTA]RR mutant. Maggot excretions/secretions (ES) were assayed for the presence of QS inhibitors; only high doses of ES showed inhibition of QS in P. aeruginosa. Thus P. aeruginosa was shown to be toxic to L. sericata maggots. This, coupled to the preferential feeding by the maggots and reduced ingestion of P. aeruginosa, could explain MDT failure in wounds colonized by P. aeruginosa. Wounds heavily colonized with P. aeruginosa should be a counterindication for MDT unless used in combination with a pre-treatment with other topical therapeutics targeting P. aeruginosa. DOI 10.1099/mic.0.032730-0