The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent ...rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only ∼1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional ∼119,000 nearly full-length sequences and 28,000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life.
A well-balanced discontinuous Galerkin (DG) flux-form shallow-water (SW) model on the sphere is developed and compared with a nodal DG SW model cast in the vector-invariant form for accuracy and ...conservation properties. A second-order diffusion scheme based on the local discontinuous Galerkin (LDG) method is added to the viscous version of the SW model and tested for conservation behaviors. The inviscid flux-form SW model is found to have better conservation of total energy and zonal angular momentum while the vector-invariant form provides better ability of conserving potential enstrophy. The inviscid flux-form tends to generate spurious vorticity but the LDG scheme combined with a well-balanced treatment can effectively eliminate the small-scale noise and generate smooth and accurate results.
Abstract
It is the purpose of this short article to analyze mass conservation in high-order rigorous remapping schemes, which contrary to flux-based methods, relies on elaborate integral constraints ...over overlap areas and reconstruction functions. For applications on the sphere these integral constraints may be violated primarily as a result of inexact or ill-conditioned integration and the authors propose a generic, local, and multitracer efficient method that guarantees that the integral constraints are satisfied in discrete space irrespective of the accuracy of the numerical integration method and slight inaccuracies in the computation of overlap areas. The authors refer to this method as
enforcement of consistency
as it is based on integral constraints valid in continuous space. The consistency enforcement method is illustrated in idealized transport tests with the Conservative Semi-Lagrangian Multitracer scheme (CSLAM) in the High Order Method Modeling Environment (HOMME) where the analytic integrals, which were found to be ill conditioned at certain resolutions and flow conditions, have been replaced with robust quadrature. This violates mass conservation; however, with the consistency enforcement method, mass conservation is inherent even with low-order quadrature and renders rigorous remap schemes such as CSLAM (which was previously limited to gnomonic cubed-sphere grids) mass conservative on any spherical grid.
Abstract
In an effort to study the applicability of adaptive mesh refinement (AMR) techniques to atmospheric models, an interpolation-based spectral element shallow-water model on a cubed-sphere grid ...is compared to a block-structured finite-volume method in latitude–longitude geometry. Both models utilize a nonconforming adaptation approach that doubles the resolution at fine–coarse mesh interfaces. The underlying AMR libraries are quad-tree based and ensure that neighboring regions can only differ by one refinement level. The models are compared via selected test cases from a standard test suite for the shallow-water equations, and via a barotropic instability test. These tests comprise the passive advection of a cosine bell and slotted cylinder, a steady-state geostrophic flow, a flow over an idealized mountain, a Rossby–Haurwitz wave, and the evolution of a growing barotropic wave. Both static and dynamics adaptations are evaluated, which reveal the strengths and weaknesses of the AMR techniques. Overall, the AMR simulations show that both models successfully place static and dynamic adaptations in local regions without requiring a fine grid in the global domain. The adaptive grids reliably track features of interests without visible distortions or noise at mesh interfaces. Simple threshold adaptation criteria for the geopotential height and the relative vorticity are assessed.
The Dynamical Core Model Intercomparison Project (DCMIP) provides a set of tests and procedures designed to facilitate development and intercomparison of atmospheric dynamical cores in general ...circulation models (GCMs). Test category 1 examines the advective transport of passive tracers by three‐dimensional prescribed wind velocity fields, on the sphere. These tests are applied to the Spectral Element (SE) dynamical core of the Community Atmosphere Model (CAM), the default for high‐resolution simulations in the Community Earth System Model (CESM). Test case results are compared with results from the CAM‐FV (Finite Volume) and MCore models where possible. This analysis serves both to evaluate the performance of CAM‐SE's spectral‐element tracer transport routines as well as to provide a baseline for comparison with other atmospheric dynamical cores and f or future improvements to CAM‐SE itself.
The NCAR Community Climate System Model, version 4 (CCSM4), includes a new dynamical core option based on NCAR’s High-Order Method Modeling Environment (HOMME). HOMME is a petascale-capable ...high-order element-based conservative dynamical core developed on the cubed-sphere grid. Initial simulations have been completed in an aquaplanet configuration of the Community Atmosphere Model, version 4 (CAM4), the atmospheric component of CCSM4. The authors examined the results of this simulation and assessed its fidelity in simulating rainfall, which is one of the most important components of the earth’s climate system. For this they compared the results from two other dynamical cores of CAM4: the finite volume (FV) and Eulerian (EUL).
Instantaneous features of rainfall in HOMME are similar to FV and EUL. Similar to EUL and FV, HOMME simulates a single-peak intertropical convergence zone (ITCZ) over the equator. The strength of the ITCZ is found to be almost the same in HOMME and EUL but more in FV. It is observed that in HOMME and EUL, there is higher surface evaporation, which supplies more moisture to the deep tropics and gives more rainfall over the ITCZ. The altitude of maximum precipitation is found to be at almost the same level in all three dynamical cores. The eastward propagation of rainfall bands is organized and more prominent in FV and HOMME than in EUL. The phase speed of the eastward propagation in HOMME is found to be higher than in FV. The results show that, in general, the rainfall simulated by HOMME falls in a regime between that of FV and EUL. Hence, they conclude that the key aspects of rainfall simulation with HOMME falls into an acceptable range, as compared to the existing dynamical cores used in the model.
Three different high-order finite element methods are used to solve the advection problem—two implementations of a discontinuous Galerkin and a spectral element (high-order continuous Galerkin) ...method. The three methods are tested using a 2D Gaussian hill as a test function, and the relative
L
2
errors are compared. Using an explicit Runge–Kutta time stepping scheme, all three methods can be parallelized using a straightforward domain decomposition and are shown to be easily and efficiently scaled across multiple-processor distributed memory machines. The effect of a monotonic limiter on a DG scheme is demonstrated for a non-smooth solution. Additionally, the necessary geometry for implementing these methods on the surface of a sphere is discussed.
We lay out the ramifications of the 2020 pandemic for all people in geosciences, especially the young, and argue for significant changes on training and career development. We focus primarily on its ...devastating impact in USA and compare with that in other countries especially China. We review the potential effect for the next four years or so on the aspirations of an academic career versus more realistic career goals. We urge people in mid-career about the need to reassess previous goals. We stress the need for students or researchers to acquire technical skills in high-performance computing (HPC), data analytics, artificial intelligence, and/or visualization along with a broad set of technical skills in applied computer science and mathematics. We give advice about hot prospects in several areas that have great potential for advancement in the coming decade, such as visualization, deep learning, quantum computing and information, and cloud computing, all of which lie within the aegis of HPC. Our forecast is that the pandemic will significantly reshape the job landscape and career paths for both young and established researchers and we discuss bluntly the dire situation facing junior people in geosciences in the aftermath of the pandemic around the world until 2024.
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