MURPHY -- A scalable multiresolution framework for scientific computing on 3D block-structured collocated grids

We present the derivation, implementation, and analysis of a multiresolution adaptive grid framework for numerical simulations on octree-based 3D block-structured collocated grids with distributed computational architectures. Our approach provides a consistent handling of non-lifted and lifted interpolating wavelets of arbitrary order demonstrated using second, fourth, and sixth order wavelets, combined with standard finite-difference based discretization operators. We first validate that the wavelet family used provides strict and explicit error control when coarsening the grid, and show that lifting wavelets increase the grid compression rate while conserving discrete moments across levels. Further, we demonstrate that high-order PDE discretization schemes combined with sufficiently high order wavelets retain the expected convergence order even at resolution jumps. We then simulate the advection of a scalar to analyze convergence for the temporal evolution of a PDE. The results shows that our wavelet-based refinement criterion is successful at controlling the overall error while the coarsening criterion is effective at retaining the relevant information on a compressed grid. Our software exploits a block-structured grid data structure for efficient multi-level operations, combined with a parallelization strategy that relies on a one-sided MPI-RMA communication approach with active PSCW synchronization. Using performance tests up to 16,384 cores, we demonstrate that this leads to a highly scalable performance. The associated code is available under a BSD-3 license at https://github.com/vanreeslab/murphy.Comment: submitted to SIAM Journal of Scientific Computing (SISC) on Dec 1

Lattice Green's Functions for High Order Finite Difference Stencils

Lattice Green's Functions (LGFs) are fundamental solutions to discretized linear operators, and as such they are a useful tool for solving discretized elliptic PDEs on domains that are unbounded in one or more directions. The majority of existing numerical solvers that make use of LGFs rely on a second-order discretization and operate on domains with free-space boundary conditions in all directions. Under these conditions, fast expansion methods are available that enable precomputation of 2D or 3D LGFs in linear time, avoiding the need for brute-force multi-dimensional quadrature of numerically unstable integrals. Here we focus on higher-order discretizations of the Laplace operator on domains with more general boundary conditions, by (1) providing an algorithm for fast and accurate evaluation of the LGFs associated with high-order dimension-split centered finite differences on unbounded domains, and (2) deriving closed-form expressions for the LGFs associated with both dimension-split and Mehrstellen discretizations on domains with one unbounded dimension. Through numerical experiments we demonstrate that these techniques provide LGF evaluations with near machine-precision accuracy, and that the resulting LGFs allow for numerically consistent solutions to high-order discretizations of the Poisson's equation on fully or partially unbounded 3D domains

Optimal shapes for anguilliform swimmers at intermediate Reynolds numbers

We investigate the optimal morphologies for fast and efficient anguilliform swimmers at intermediate Reynolds numbers, by combining an evolution strategy with three-dimensional viscous vortex methods. We show that anguilliform swimmer shapes enable the trapping and subsequent acceleration of regions of fluid transported along the entire body by the midline travelling wave. A sensitivity analysis of the optimal morphological traits identifies that the width thickness in the anterior of the body and the height of the caudal fin are critical factors for both speed and efficiency. The fastest swimmer without a caudal fin, however, still retains 80 % of its speed, showing that the entire body is used to generate thrust. The optimal shapes share several features with naturally occurring morphologies, but their overall appearances differ. This demonstrates that engineered swimmers can outperform biomimetic swimmers for the criteria considered her

An immersed interface method for the 2D vorticity-velocity Navier-Stokes equations with multiple bodies

We present an immersed interface method for the vorticity-velocity form of the 2D Navier Stokes equations that directly addresses challenges posed by multiply connected domains, nonconvex obstacles, and the calculation of force distributions on immersed surfaces. The immersed interface method is re-interpreted as a polynomial extrapolation of flow quantities and boundary conditions into the obstacle, reducing its computational and implementation complexity. In the flow, the vorticity transport equation is discretized using a conservative finite difference scheme and explicit Runge-Kutta time integration. The velocity reconstruction problem is transformed to a scalar Poisson equation that is discretized with conservative finite differences, and solved using an FFT-accelerated iterative algorithm. The use of conservative differencing throughout leads to exact enforcement of a discrete Kelvin's theorem, which provides the key to simulations with multiply connected domains and outflow boundaries. The method achieves second order spatial accuracy and third order temporal accuracy, and is validated on a variety of 2D flows in internal and free-space domains

Minkowski's Object: A Starburst Triggered by a Radio Jet, Revisited

We present neutral hydrogen, ultraviolet, optical and near-infrared imaging, and optical spectroscopy, of Minkowski's Object (MO), a star forming peculiar galaxy near NGC 541. The observations strengthen evidence that star formation in MO was triggered by the radio jet from NGC 541. Key new results are the discovery of a 4.9E8 solar mass double HI cloud straddling the radio jet downstream from MO, where the jet changes direction and decollimates; strong detections of MO, also showing double structure, in UV and H-alpha; and numerous HII regions and associated clusters in MO. In UV, MO resembles the radio-aligned, rest-frame UV morphologies in many high redshift radio galaxies (HzRGs), also thought to be caused by jet-induced star formation. MO's stellar population is dominated by a 7.5 Myr-old, 1.9E7 solar mass instantaneous burst, with current star formation rate 0.52 solar masses per year (concentrated upstream from where the HI column density is high). This is unlike the jet-induced star formation in Centaurus A, where the jet interacts with pre-existing cold gas; in MO the HI may have cooled out of a warmer, clumpy intergalactic or interstellar medium as a result of jet interaction, followed by collapse of the cooling clouds and subsequent star formation (consistent with numerical simulations). Since the radio source that triggered star formation in MO is much less luminous, and therefore more common, than powerful HzRGs, and because the environment around MO is not particularly special in terms of abundant dense, cold gas, jet-induced star formation in the early universe might be even more prevalent than previously thought.Comment: 52 pages, 15 figures, accepted for publication in Ap

Endovascular Treatment for Acute Ischemic Stroke in Patients on Oral Anticoagulants: Results from the MR CLEAN Registry

Background and Purpose - The use of oral anticoagulants (OAC) is considered a contra-indication for intravenous thrombolytics as acute treatment of ischemic stroke. However, little is known about the risks and benefits of endovascular treatment in patients on prior OAC. We aim to compare outcomes after endovascular treatment between patients with and without prior use of OAC. Methods - Data of patients with acute ischemic stroke caused by an intracranial anterior circulation occlusion, included in the nationwide, prospective, MR CLEAN Registry between March 2014 and November 2017, were analyzed. Outcomes of interest included symptomatic intracranial hemorrhage and functional outcome at 90 days (modified Rankin Scale score). Outcomes between groups were compared with (ordinal) logistic regression analyses, adjusted for prognostic factors. Results - Three thousand one hundred sixty-two patients were included in this study, of whom 502 (16%) used OAC. There was no significant difference in the occurrence of symptomatic intracranial hemorrhage between patients with and without prior OACs (5% versus 6%; adjusted odds ratio, 0.63 [95% CI, 0.38-1.06]). Patients on OACs had worse functional outcomes than patients without OACs (common odds ratio, 0.57 [95% CI, 0.47-0.66]). However, this observed difference in functional outcome disappeared after adjustment for prognostic factors (adjusted common odds ratio, 0.91 [95% CI, 0.74-1.13]). Conclusions - Prior OAC use in patients treated with endovascular treatment for ischemic stroke is not associated with an increased risk of symptomatic intracranial hemorrhage or worse functional outcome compared with no prior OAC use. Therefore, prior OAC use should not be a contra-indication for endovascular treatment

Quantifying nitrogen fluxes and their influence on the greenhouse gas balance: recent findings of the NitroEurope Integrated Project

The generation of reactive nitrogen (Nr) by human activities to stimulate agricultural productivity and the unintended formation of Nr in combustion processes both have major impacts on the global environment. Effects of excess Nr include the deterioration of air quality, water quality, soil quality and a decline in biodiversity. One of the most controversial impacts of nitrogen, however, is on the greenhouse gas balance. While recent papers have highlighted a possible benefit of nitrogen in enhancing rates of carbon sequestration, there remain many trade-offs between nitrogen and greenhouse gas exchange. The result is that the net effect of Nr on the global radiative balance has yet to be fully quantified. To better understand these relationships requires intense measurement and modelling of Nr fluxes at various temporal and spatial scales in order to make the link between different nitrogen forms and their fate in the environment. It is essential to measure fluxes for a wide range of ecosystems considering the biosphere-atmosphere exchange of the Nr components and greenhouse gases, as well as the fixation of di-nitrogen and its creation by denitrification. Long-term observations are needed for representative ecosystems, together with results from experiments addressing the responses of the key nitrogen and greenhouse gas fluxes to different global change drivers. The NitroEurope Integrated Project (in short NEU IP), funded under the 6th Framework Programme of the European Commission, has developed and applied a strategy for quantifying these different terms on multiple scales. With the project nearing completion, this presentation reports selected preliminary findings. It highlights the first estimates of Nr inputs and net green-house gas exchange for a series of 13 flux ‘supersites’, complemented by the emerging results of Nr concentrations and related N inputs at a network of 58 ‘inferential sites’, which extend the European representativity of the results. In addition, new low cost methods to measure nitrogen fluxes will be reported, which have been extensively tested at those sites. Results from this 3-tier flux network are underpinned by emerging findings from an extensive network of manipulation sites. A combination of modelling at plot, landscape and European scales is used to upscale the results. Finally the talk will illustrate how nitrogen mitigation techniques are being considered at the European scale, including an estimation of the scale of costs involved in simultaneously mitigating nitrous oxide, ammonia and nitrate losse