Three-dimensional non-LTE radiative transfer computation of the Ca 8542 infrared line from a radiation-MHD simulation

Interpretation of imagery of the solar chromosphere in the widely used \CaIIIR infrared line is hampered by its complex, three-dimensional and non-LTE formation. Forward modelling is required to aid understanding. We use a 3D non-LTE radiative transfer code to compute synthetic \CaIIIR images from a radiation-MHD simulation of the solar atmosphere spanning from the convection zone to the corona. We compare the simulation with observations obtained with the CRISP filter at the Swedish 1--m Solar Telescope. We find that the simulation reproduces dark patches in the blue line wing caused by Doppler shifts, brightenings in the line core caused by upward-propagating shocks and thin dark elongated structures in the line core that form the interface between upward and downward gas motion in the chromosphere. The synthetic line core is narrower than the observed one, indicating that the sun exhibits both more vigorous large-scale dynamics as well as small scale motions that are not resolved within the simulation, presumably owing to a lack of spatial resolution.Comment: accepted as ApJ lette

Parallel Mapper

The construction of Mapper has emerged in the last decade as a powerful and effective topological data analysis tool that approximates and generalizes other topological summaries, such as the Reeb graph, the contour tree, split, and joint trees. In this paper, we study the parallel analysis of the construction of Mapper. We give a provably correct parallel algorithm to execute Mapper on multiple processors and discuss the performance results that compare our approach to a reference sequential Mapper implementation. We report the performance experiments that demonstrate the efficiency of our method

Fast algorithms and efficient GPU implementations for the Radon transform and the back-projection operator represented as convolution operators

The Radon transform and its adjoint, the back-projection operator, can both be expressed as convolutions in log-polar coordinates. Hence, fast algorithms for the application of the operators can be constructed by using FFT, if data is resampled at log-polar coordinates. Radon data is typically measured on an equally spaced grid in polar coordinates, and reconstructions are represented (as images) in Cartesian coordinates. Therefore, in addition to FFT, several steps of interpolation have to be conducted in order to apply the Radon transform and the back-projection operator by means of convolutions. Both the interpolation and the FFT operations can be efficiently implemented on Graphical Processor Units (GPUs). For the interpolation, it is possible to make use of the fact that linear interpolation is hard-wired on GPUs, meaning that it has the same computational cost as direct memory access. Cubic order interpolation schemes can be constructed by combining linear interpolation steps which provides important computation speedup. We provide details about how the Radon transform and the back-projection can be implemented efficiently as convolution operators on GPUs. For large data sizes, speedups of about 10 times are obtained in relation to the computational times of other software packages based on GPU implementations of the Radon transform and the back-projection operator. Moreover, speedups of more than a 1000 times are obtained against the CPU-implementations provided in the MATLAB image processing toolbox

Non-equilibrium hydrogen ionization in 2D simulations of the solar atmosphere

The ionization of hydrogen in the solar chromosphere and transition region does not obey LTE or instantaneous statistical equilibrium because the timescale is long compared with important hydrodynamical timescales, especially of magneto-acoustic shocks. We implement an algorithm to compute non-equilibrium hydrogen ionization and its coupling into the MHD equations within an existing radiation MHD code, and perform a two-dimensional simulation of the solar atmosphere from the convection zone to the corona. Analysis of the simulation results and comparison to a companion simulation assuming LTE shows that: a) Non-equilibrium computation delivers much smaller variations of the chromospheric hydrogen ionization than for LTE. The ionization is smaller within shocks but subsequently remains high in the cool intershock phases. As a result, the chromospheric temperature variations are much larger than for LTE because in non-equilibrium, hydrogen ionization is a less effective internal energy buffer. The actual shock temperatures are therefore higher and the intershock temperatures lower. b) The chromospheric populations of the hydrogen n = 2 level, which governs the opacity of Halpha, are coupled to the ion populations. They are set by the high temperature in shocks and subsequently remain high in the cool intershock phases. c) The temperature structure and the hydrogen level populations differ much between the chromosphere above photospheric magnetic elements and above quiet internetwork. d) The hydrogen n = 2 population and column density are persistently high in dynamic fibrils, suggesting that these obtain their visibility from being optically thick in Halpha also at low temperature.Comment: 10 pages, 4 figure

Four-dimensional tomographic reconstruction by time domain decomposition

Since the beginnings of tomography, the requirement that the sample does not change during the acquisition of one tomographic rotation is unchanged. We derived and successfully implemented a tomographic reconstruction method which relaxes this decades-old requirement of static samples. In the presented method, dynamic tomographic data sets are decomposed in the temporal domain using basis functions and deploying an L1 regularization technique where the penalty factor is taken for spatial and temporal derivatives. We implemented the iterative algorithm for solving the regularization problem on modern GPU systems to demonstrate its practical use

Fast hyperbolic Radon transform represented as convolutions in log-polar coordinates

The hyperbolic Radon transform is a commonly used tool in seismic processing, for instance in seismic velocity analysis, data interpolation and for multiple removal. A direct implementation by summation of traces with different moveouts is computationally expensive for large data sets. In this paper we present a new method for fast computation of the hyperbolic Radon transforms. It is based on using a log-polar sampling with which the main computational parts reduce to computing convolutions. This allows for fast implementations by means of FFT. In addition to the FFT operations, interpolation procedures are required for switching between coordinates in the time-offset; Radon; and log-polar domains. Graphical Processor Units (GPUs) are suitable to use as a computational platform for this purpose, due to the hardware supported interpolation routines as well as optimized routines for FFT. Performance tests show large speed-ups of the proposed algorithm. Hence, it is suitable to use in iterative methods, and we provide examples for data interpolation and multiple removal using this approach.Comment: 21 pages, 10 figures, 2 table

Ellerman bombs and UV bursts: transient events in chromospheric current sheets

Ellerman bombs (EBs) and UV bursts are both brightenings related to flux emergence regions and specifically to magnetic flux of opposite polarity that meet in the photosphere. These two reconnection-related phenomena, nominally formed far apart, occasionally occur in the same location and at the same time, thus challenging our understanding of reconnection and heating of the lower solar atmosphere. We consider the formation of an active region, including long fibrils and hot and dense coronal plasma. The emergence of a untwisted magnetic flux sheet, injected $2.5$~Mm below the photosphere, is studied as it pierces the photosphere and interacts with the preexisting ambient field. Specifically, we aim to study whether EBs and UV bursts are generated as a result of such flux emergence and examine their physical relationship. The Bifrost radiative magnetohydrodynamics code was used to model flux emerging into a model atmosphere that contained a fairly strong ambient field, constraining the emerging field to a limited volume wherein multiple reconnection events occur as the field breaks through the photosphere and expands into the outer atmosphere. Synthetic spectra of the different reconnection events were computed using the $1.5$D RH code and the fully 3D MULTI3D code. The formation of UV bursts and EBs at intensities and with line profiles that are highly reminiscent of observed spectra are understood to be a result of the reconnection of emerging flux with itself in a long-lasting current sheet that extends over several scale heights through the chromosphere. Synthetic diagnostics suggest that there are no compelling reasons to assume that UV bursts occur in the photosphere. Instead, EBs and UV bursts are occasionally formed at opposite ends of a long current sheet that resides in an extended bubble of cool gas.Comment: 10 pages, 8 figures, accepted by A&

Twisted flux tube emergence from the convection zone to the corona

3D numerical simulations of a horizontal magnetic flux tube emergence with different twist are carried out in a computational domain spanning the upper layers of the convection zone to the lower corona. We use the Oslo Staggered Code to solve the full MHD equations with non-grey and non-LTE radiative transfer and thermal conduction along the magnetic field lines. The emergence of the magnetic flux tube input at the bottom boundary into a weakly magnetized atmosphere is presented. The photospheric and chromospheric response is described with magnetograms, synthetic images and velocity field distributions. The emergence of a magnetic flux tube into such an atmosphere results in varied atmospheric responses. In the photosphere the granular size increases when the flux tube approaches from below. In the convective overshoot region some 200km above the photosphere adiabatic expansion produces cooling, darker regions with the structure of granulation cells. We also find collapsed granulation in the boundaries of the rising flux tube. Once the flux tube has crossed the photosphere, bright points related with concentrated magnetic field, vorticity, high vertical velocities and heating by compressed material are found at heights up to 500km above the photosphere. At greater heights in the magnetized chromosphere, the rising flux tube produces a cool, magnetized bubble that tends to expel the usual chromospheric oscillations. In addition the rising flux tube dramatically increases the chromospheric scale height, pushing the transition region and corona aside such that the chromosphere extends up to 6Mm above the photosphere. The emergence of magnetic flux tubes through the photosphere to the lower corona is a relatively slow process, taking of order 1 hour.Comment: 53 pages,79 figures, Submitted to Ap

The stellar atmosphere simulation code Bifrost

Context: Numerical simulations of stellar convection and photospheres have been developed to the point where detailed shapes of observed spectral lines can be explained. Stellar atmospheres are very complex, and very different physical regimes are present in the convection zone, photosphere, chromosphere, transition region and corona. To understand the details of the atmosphere it is necessary to simulate the whole atmosphere since the different layers interact strongly. These physical regimes are very diverse and it takes a highly efficient massively parallel numerical code to solve the associated equations. Aims: The design, implementation and validation of the massively parallel numerical code Bifrost for simulating stellar atmospheres from the convection zone to the corona. Methods: The code is subjected to a number of validation tests, among them the Sod shock tube test, the Orzag-Tang colliding shock test, boundary condition tests and tests of how the code treats magnetic field advection, chromospheric radiation, radiative transfer in an isothermal scattering atmosphere, hydrogen ionization and thermal conduction. Results: Bifrost completes the tests with good results and shows near linear efficiency scaling to thousands of computing cores