Parallel grid library for rapid and flexible simulation development

We present an easy to use and flexible grid library for developing highly scalable parallel simulations. The distributed cartesian cell-refinable grid (dccrg) supports adaptive mesh refinement and allows an arbitrary C++ class to be used as cell data. The amount of data in grid cells can vary both in space and time allowing dccrg to be used in very different types of simulations, for example in fluid and particle codes. Dccrg transfers the data between neighboring cells on different processes transparently and asynchronously allowing one to overlap computation and communication. This enables excellent scalability at least up to 32 k cores in magnetohydrodynamic tests depending on the problem and hardware. In the version of dccrg presented here part of the mesh metadata is replicated between MPI processes reducing the scalability of adaptive mesh refinement (AMR) to between 200 and 600 processes. Dccrg is free software that anyone can use, study and modify and is available at [https://gitorious.org/dccrg]. Users are also kindly requested to cite this work when publishing results obtained with dccrg.Comment: Accepted to Computer Physics Communications, 36 pages, 13 figure

Energy conversion at the Earth's magnetopause using single and multispacecraft methods

We present a small statistical data set, where we investigate energy conversion at the magnetopause using Cluster measurements of magnetopause crossings. The Cluster observations of magnetic field, plasma velocity, current density and magnetopause orientation are needed to infer the energy conversion at the magnetopause. These parameters can be inferred either from accurate multispacecraft methods, or by using single-spacecraft methods. Our final aim is a large statistical study, for which only single-spacecraft methods can be applied. The Cluster mission provides an opportunity to examine and validate single-spacecraft methods against the multispacecraft methods. For single-spacecraft methods, we use the Generic Residue Analysis (GRA) and a standard one-dimensional current density method using magnetic field measurements. For multispacecraft methods, we use triangulation (Constant Velocity Approach - CVA) and the curlometer technique. We find that in some cases the single-spacecraft methods yield a different sign for the energy conversion than compared to the multispacecraft methods. These sign ambiguities arise from the orientation of the magnetopause, choosing the interval to be analyzed, large normal current and time offset of the current density inferred from the two methods. By using the Finnish Meteorological Institute global MHD simulation GUMICS-4, we are able to determine which sign is likely to be correct, introducing an opportunity to correct the ambiguous energy conversion values. After correcting the few ambiguous cases, we find that the energy conversion estimated from single-spacecraft methods is generally lower by 70% compared to the multispacecraft methods.Peer reviewe

Tail reconnection in the global magnetospheric context : Vlasiator first results

The key dynamics of the magnetotail have been researched for decades and have been associated with either three-dimensional (3-D) plasma instabilities and/or magnetic reconnection. We apply a global hybrid-Vlasov code, Vlasiator, to simulate reconnection self-consistently in the ion kinetic scales in the noon-midnight meridional plane, including both dayside and nightside reconnection regions within the same simulation box. Our simulation represents a numerical experiment, which turns off the 3-D instabilities but models ion-scale reconnection physically accurately in 2-D. We demonstrate that many known tail dynamics are present in the simulation without a full description of 3-D instabilities or without the detailed description of the electrons. While multiple reconnection sites can coexist in the plasma sheet, one reconnection point can start a global reconfiguration process, in which magnetic field lines become detached and a plasmoid is released. As the simulation run features temporally steady solar wind input, this global reconfiguration is not associated with sudden changes in the solar wind. Further, we show that lobe density variations originating from dayside reconnection may play an important role in stabilising tail reconnection.Peer reviewe

Turbulence Heating ObserveR – satellite mission proposal

The Universe is permeated by hot, turbulent, magnetized plasmas. Turbulent plasma is a major constituent of active galactic nuclei, supernova remnants, the intergalactic and interstellar medium, the solar corona, the solar wind and the Earth’s magnetosphere, just to mention a few examples. Energy dissipation of turbulent fluctuations plays a key role in plasma heating and energization, yet we still do not understand the underlying physical mechanisms involved. THOR is a mission designed to answer the questions of how turbulent plasma is heated and particles accelerated, how the dissipated energy is partitioned and how dissipation operates in different regimes of turbulence. THOR is a single-spacecraft mission with an orbit tuned to maximize data return from regions in near-Earth space – magnetosheath, shock, foreshock and pristine solar wind – featuring different kinds of turbulence. Here we summarize the THOR proposal submitted on 15 January 2015 to the ‘Call for a Medium-size mission opportunity in ESAs Science Programme for a launch in 2025 (M4)’. THOR has been selected by European Space Agency (ESA) for the study phase

Natural history of progression of HPV infection to cervical lesion or clearance: analysis of the control arm of the large, randomised PATRICIA study

Background: The control arm of PATRICIA (PApillomaTRIal against Cancer In young Adults, NCT00122681) was used to investigate the risk of progression from cervical HPV infection to cervical intraepithelial neoplasia (CIN) or clearance of infection, and associated determinants. Methods and Findings: Women aged 15-25 years were enrolled. A 6-month persistent HPV infection (6MPI) was defined as detection of the same HPV type at two consecutive evaluations over 6 months and clearance as ≥2 type-specific HPV negative samples taken at two consecutive intervals of approximately 6 months following a positive sample. The primary endpoint was CIN grade 2 or greater (CIN2+) associated with the same HPV type as a 6MPI. Secondary endpoints were CIN1+/CIN3+ associated with the same HPV type as a 6MPI; CIN1+/CIN2+/CIN3+ associated with an infection of any duration; and clearance of infection. The analyses included 4825 women with 16,785 infections (3363 womenwith 6902 6MPIs). Risk of developing a CIN1+/CIN2+/CIN3+ associated with same HPV type as a 6MPI varied with HPV type and was significantly higher for oncogenic versus non-oncogenic types. Hazard ratios for development of CIN2+ were 10.44 (95% CI: 6.96-15.65), 9.65 (5.97-15.60), 5.68 (3.50-9.21), 5.38 (2.87-10.06) and 3.87 (2.38-6.30) for HPV-16, HPV-33, HPV-31, HPV-45 and HPV-18, respectively. HPV-16 or HPV-33 6MPIs had ~25-fold higher risk for progression to CIN3+. Previous or concomitant HPV infection or CIN1+ associated with a different HPV type increased risk. Of the different oncogenic HPV types, HPV-16 and HPV-31 infections were least likely to clear. Conclusions: Cervical infections with oncogenic HPV types increased the risk of CIN2+ and CIN3+. Previous or concomitant infection or CIN1+ also increased the risk. HPV-16 and HPV-33 have by far the highest risk of progression to CIN3+, and HPV-16 and HPV-31 have the lowest chance of clearance

Contributions to Loss Across the Magnetopause During an Electron Dropout Event

Dropout events are dramatic decreases in radiation belt electron populations that can occur in as little as 30 minutes. Loss to magnetopause due to a combination of magnetopause shadowing and outward radial transport plays a significant role in these events. We examine the dropout of relativistic electron populations during the October 2012 geomagnetic storm using simulated electron phase space density, evaluating the contribution of different processes to losses across the magnetopause. We compare loss contribution from outward transport calculated using a standard empirical radial diffusion model that assumes a dipolar geomagnetic field to an event-specific radial diffusion model evaluated with a non-dipolar geomagnetic field. We additionally evaluate the contribution of Shabansky type 1 particles, which bounce along magnetic field lines with local equatorial maxima, to the loss calculated during this event. We find that the empirical radial diffusion model with a dipolar background field underestimates the contribution of radial diffusion to this dropout event by up to 10% when compared to the event-specific, non-dipolar radial diffusion model. We additionally find that including Shabansky type 1 particles in the initial electron phase space density, that is, allowing some magnetic field lines distorted from the typical single-minima configuration in drift shell construction, increases the calculated loss by an average of 0.75%. This shows that the treatment of the geomagnetic field significantly impacts the calculation of electron losses to the magnetopause during dropout events, with the non-dipolar treatment of radial diffusion being essential to accurately quantify the loss of outer radiation belt populations.Peer reviewe

Evapotranspiration estimation considering anthropogenic heat based on remote sensing in urban area

Urbanization influences hydrologic cycle significantly on local, regional even global scale. With urbanization the water resources demand for dense population sharpened, thus it is a great challenge to ensure water supply for some metropolises such as Beijing. Urban area is traditionally considered as the area with lower evapotranspiration (ET) on account of the impervious surface and the lower wind speed. For most remote sensing models, the ET, defined as latent heat in energy budget, is estimated as the difference between net radiation and sensible heat. The sensible heat is generally higher in urban area due to the high surface temperature caused by heat island, therefore the latent heat (i.e. the ET) in urban area is lower than that in other region. We estimated water consumption from 2003 to 2012 in Beijing based on water balance method and found that the annual mean ET in urban area was about 654 mm. However, using Surface Energy Balance System (SEBS) model, the annual mean ET in urban area was only 348 mm. We attributed this inconsistence to the impact of anthropogenic heat and quantified this impact on the basis of the night-light maps. Therefore, a new model SEBS-Urban, coupling SEBS model and anthropogenic heat was developed to estimate the ET in urban area. The ET in urban area of Beijing estimated by SEBS-Urban showed a good agreement with the ET from water balance method. The findings from this study highlighted that anthropogenic heat should be included in the surface energy budget for a highly urbanized area

Ion Acceleration by Flux Transfer Events in the Terrestrial Magnetosheath

We report ion acceleration by flux transfer events in the terrestrial magnetosheath in a global two-dimensional hybrid-Vlasov polar plane simulation of Earth's solar wind interaction. In the model we find that propagating flux transfer events created in magnetic reconnection at the dayside magnetopause drive fast-mode bow waves in the magnetosheath, which accelerate ions in the shocked solar wind flow. The acceleration at the bow waves is caused by a shock drift-like acceleration process under stationary solar wind and interplanetary magnetic field upstream conditions. Thus, the energization is not externally driven but results from plasma dynamics within the magnetosheath. Energetic proton populations reach the energy of 30 keV, and their velocity distributions resemble time-energy dispersive ion injections observed by the Cluster spacecraft in the magnetosheath.Peer reviewe

Fast plasma sheet flows and X line motion in the Earth's magnetotail: results from a global hybrid-Vlasov simulation

Fast plasma flows produced as outflow jets from reconnection sites or X lines are a key feature of the dynamics in the Earth's magnetosphere. We have used a polar plane simulation of the hybrid-Vlasov model Vlasiator, driven by steady southward interplanetary magnetic field and fast solar wind, to study fast plasma sheet ion flows and related magnetic field structures in the Earth's magnetotail. In the simulation, lobe reconnection starts to produce fast flows after the increasing pressure in the lobes has caused the plasma sheet to thin sufficiently. The characteristics of the earthward and tailward fast flows and embedded magnetic field structures produced by multi-point tail reconnection are in general agreement with spacecraft measurements reported in the literature. The structuring of the flows is caused by internal processes: interactions between major X points determine the earthward or tailward direction of the flow, while interactions between minor X points, associated with leading edges of magnetic islands carried by the flow, induce local minima and maxima in the flow speed. Earthward moving flows are stopped and diverted duskward in an oscillatory (bouncing) manner at the transition region between tail-like and dipolar magnetic fields. Increasing and decreasing dynamic pressure of the flows causes the transition region to shift earthward and tailward, respectively. The leading edge of the train of earthward flow bursts is associated with an earthward propagating dipolarization front, while the leading edge of the train of tailward flow bursts is associated with a tailward propagating plasmoid. The impact of the dipolarization front with the dipole field causes magnetic field variations in the Pi2 range. Major X points can move either earthward or tailward, although tailward motion is more common. They are generally not advected by the ambient flow. Instead, their velocity is better described by local parameters, such that an X point moves in the direction of increasing reconnection electric field strength. Our results indicate that ion kinetics might be sufficient to describe the behavior of plasma sheet bulk ion flows produced by tail reconnection in global near-Earth simulations.</p