Verification of BOUT++ by the method of manufactured solutions

BOUT++ is a software package designed for solving plasma fluid models. It has been used to simulate a wide range of plasma phenomena ranging from linear stability analysis to 3D plasma turbulence and is capable of simulating a wide range of drift-reduced plasma fluid and gyro-fluid models. A verification exercise has been performed as part of a EUROfusion Enabling Research project, to rigorously test the correctness of the algorithms implemented in BOUT++, by testing order-of-accuracy convergence rates using the Method of Manufactured Solutions (MMS). We present tests of individual components including time-integration and advection schemes, non-orthogonal toroidal field-aligned coordinate systems and the shifted metric procedure which is used to handle highly sheared grids. The flux coordinate independent approach to differencing along magnetic field-lines has been implemented in BOUT++ and is here verified using the MMS in a sheared slab configuration. Finally, we show tests of three complete models: 2-field Hasegawa-Wakatani in 2D slab, 3-field reduced magnetohydrodynamics (MHD) in 3D field-aligned toroidal coordinates, and 5-field reduced MHD in slab geometry

The effects of non-uniform drive on plasma filaments

Wendelstein 7-X core fueling is primarily achieved through pellet injection. The trajectory of plasmoids from an ablating pellet is an ongoing research question, which is complicated by the complex magnetic geometry of W7-X; curvature drive varies significantly toroidally, including a change in the drift drive direction. Here we use the Hermes model in BOUT++ to simulate cold plasma filaments in slab geometries where the magnetic drift drive is non-uniform along the field line. It is shown that if the field-line-averaged curvature drive is non-zero, a filament will propagate coherently in the direction of average drive. It is also shown that a non-uniform drive will provide a non-uniform propagation; an effect which is reduced at higher temperatures due to an increased sound speed along the field line. Finally, simulations with curvature similar to that found in Wendelstein 7-X are performed which indicate a slow radial propagation of plasma filaments despite a highly non-uniform drive profile

BOUT++ : Recent and current developments

BOUT++ is a 3D nonlinear finite-difference plasma simulation code, capable of solving quite general systems of PDEs, but targeted particularly on studies of the edge region of tokamak plasmas. BOUT++ is publicly available, and has been adopted by a growing number of researchers worldwide. Here we present improvements which have been made to the code since its original release, both in terms of structure and its capabilities. Some recent applications of these methods are reviewed, and areas of active development are discussed. We also present algorithms and tools which have been developed to enable creation of inputs from analytic expressions and experimental data, and for processing and visualisation of output results. This includes a new tool Hypnotoad for the creation of meshes from experimental equilibria. Algorithms have been implemented in BOUT++ to solve a range of linear algebraic problems encountered in the simulation of reduced MHD and gyro-fluid models: A preconditioning scheme is presented which enables the plasma potential to be calculated efficiently using iterative methods supplied by the PETSc library, without invoking the Boussinesq approximation. Scaling studies are also performed of a linear solver used as part of physics-based preconditioning to accelerate the convergence of implicit time-integration schemes

Overview of recent physics results from MAST

New results from MAST are presented that focus on validating models in order to extrapolate to future devices. Measurements during start-up experiments have shown how the bulk ion temperature rise scales with the square of the reconnecting field. During the current ramp-up, models are not able to correctly predict the current diffusion. Experiments have been performed looking at edge and core turbulence. At the edge, detailed studies have revealed how filament characteristics are responsible for determining the near and far scrape off layer density profiles. In the core the intrinsic rotation and electron scale turbulence have been measured. The role that the fast ion gradient has on redistributing fast ions through fishbone modes has led to a redesign of the neutral beam injector on MAST Upgrade. In H-mode the turbulence at the pedestal top has been shown to be consistent with being due to electron temperature gradient modes. A reconnection process appears to occur during edge localized modes (ELMs) and the number of filaments released determines the power profile at the divertor. Resonant magnetic perturbations can mitigate ELMs provided the edge peeling response is maximised and the core kink response minimised. The mitigation of intrinsic error fields with toroidal mode number n  >  1 has been shown to be important for plasma performance

Blob dynamics in the TORPEX experiment:a multi-code validation

Three-dimensional and two-dimensional seeded blob simulations are performed with five different fluid models, all based on the drift-reduced Braginskii equations, and the numerical results are compared among themselves and validated against experimental measurements provided by the TORPEX device (Fasoli et al 2006 Phys. Plasmas 13 055902). The five models are implemented in four simulation codes, typically used to simulate the plasma dynamics in the tokamak scrape-off layer, namely BOUT++ (Dudson et al 2009 Comput. Phys. Commun. 180 1467), GBS (Ricci et al 2012 Plasma Phys. Control. Fusion 54 124047), HESEL (Nielsen et al 2015 Phys. Lett. A 379 3097), and TOKAM3X (Tamain et al 2014 Contrib. Plasma Phys. 54 555). Three blobs with different velocities and different stability properties are simulated. The differences observed among the simulation results and the different levels of agreement with experimental measurements are investigated, increasing our confidence in our simulation tools and shedding light on the blob dynamics. The comparisons demonstrate that the radial blob dynamics observed in the three-dimensional simulations is in good agreement with experimental measurements and that, in the present experimental scenario, the two-dimensional model derived under the assumption of ${{k}_{\parallel}}=0$ is able to recover the blob dynamics observed in the three-dimensional simulations. Moreover, it is found that an accurate measurement of the blob temperature is important to perform reliable seeded blob simulations

Proteomics of Buccal Cavity Mucus in Female Tilapia Fish (Oreochromis spp.): A Comparison between Parental and Non-Parental Fish

Mouthbrooding is an elaborate form of parental care displayed by many teleost species. While the direct benefits of mouthbrooding such as protection and transportation of offsprings are known, it is unclear if mouthbrooding offers additional benefits to embryos during incubation. In addition, mouthbrooding could incur negative costs on parental fish, due to limited feeding opportunities. Parental tilapia fish (Oreochromis spp.) display an elaborated form of parental care by incubating newly hatched embryos in oral buccal cavity until the complete adsorption of yolk sac. In order to understand the functional aspects of mouthbrooding, we undertake a proteomics approach to compare oral mucus sampled from mouthbrooders and non-mouthbrooders, respectively. Majority of the identified proteins have also been previously identified in other biological fluids or mucus-rich organs in different organisms. We also showed the upregulation of 22 proteins and down regulation of 3 proteins in mucus collected from mouthbrooders. Anterior gradient protein, hemoglobin beta-A chain and alpha-2 globin levels were lower in mouthbrooder samples. Mouthbrooder oral mucus collectively showed increase levels of proteins related to cytoskeletal properties, glycolytic pathway and mediation of oxidative stress. Overall the findings suggest cellular stress response, probably to support production of mucus during mouthbrooding phase

A beer a minute in Texas football: Heavy drinking and the heroizing of the antihero in Friday Night Lights

This article applies a qualitative framing analysis to the first three seasons of the television series Friday Night Lights, focusing particularly on its incorporation of heavy drinking into narrative representations of the player whose character is most consistently central to the game of football as fictionally mediated in small-town Texas over the course of those three seasons. The analysis suggests that over the course of that period Friday Night Lights embeds nuanced social meanings in its framing of alcohol use by that player and other characters so as to associate it with multiple potential outcomes. Yet among those outcomes, the most dominant framing works to, in effect, reverse a progression through which media representations historically evolved from a heroic model toward an antihero model, with heavy drinking central to that narrative process of meaning-making in such messages.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline