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

Modeling of Covalent Bonding in Solids by Inversion of Cohesive Energy Curves

We provide a systematic test of empirical theories of covalent bonding in solids using an exact procedure to invert ab initio cohesive energy curves. By considering multiple structures of the same material, it is possible for the first time to test competing angular functions, expose inconsistencies in the basic assumption of a cluster expansion, and extract general features of covalent bonding. We test our methods on silicon, and provide the direct evidence that the Tersoff-type bond order formalism correctly describes coordination dependence. For bond-bending forces, we obtain skewed angular functions that favor small angles, unlike existing models. As a proof-of-principle demonstration, we derive a Si interatomic potential which exhibits comparable accuracy to existing models.Comment: 4 pages revtex (twocolumn, psfig), 3 figures. Title and some wording (but no content) changed since original submission on 24 April 199

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

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

Approximations for radiative cooling and heating in the solar chromosphere

Context. The radiative energy balance in the solar chromosphere is dominated by strong spectral lines that are formed out of LTE. It is computationally prohibitive to solve the full equations of radiative transfer and statistical equilibrium in 3D time dependent MHD simulations. Aims. To find simple recipes to compute the radiative energy balance in the dominant lines under solar chromospheric conditions. Methods. We use detailed calculations in time-dependent and 2D MHD snapshots to derive empirical formulae for the radiative cooling and heating. Results. The radiative cooling in neutral hydrogen lines and the Lyman continuum, the H and K and intrared triplet lines of singly ionized calcium and the h and k lines of singly ionized magnesium can be written as a product of an optically thin emission (dependent on temperature), an escape probability (dependent on column mass) and an ionization fraction (dependent on temperature). In the cool pockets of the chromosphere the same transitions contribute to the heating of the gas and similar formulae can be derived for these processes. We finally derive a simple recipe for the radiative heating of the chromosphere from incoming coronal radiation. We compare our recipes with the detailed results and comment on the accuracy and applicability of the recipes.Comment: accepted for publication in Astronomy & Astrophysic

Vortices, shocks, and heating in the solar photosphere: effect of a magnetic field

Aims: We study the differences between non-magnetic and magnetic regions in the flow and thermal structure of the upper solar photosphere. Methods: Radiative MHD simulations representing a quiet region and a plage region, respectively, which extend into the layers around the temperature minimum, are analyzed. Results: The flow structure in the upper photospheric layers of the two simulations is considerably different: the non-magnetic simulation is dominated by a pattern of moving shock fronts while the magnetic simulation shows vertically extended vortices associated with magnetic flux concentrations. Both kinds of structures induce substantial local heating. The resulting average temperature profiles are characterized by a steep rise above the temperature minimum due to shock heating in the non-magnetic case and by a flat photospheric temperature gradient mainly caused by Ohmic dissipation in the magnetic run. Conclusions: Shocks in the quiet Sun and vortices in the strongly magnetized regions represent the dominant flow structures in the layers around the temperature minimum. They are closely connected with dissipation processes providing localized heating.Comment: Accepted for publicaton in 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 formation of IRIS diagnostics I. A quintessential model atom of Mg II and general formation properties of the Mg II h&k lines

NASA's Interface Region Imaging Spectrograph (IRIS) space mission will study how the solar atmosphere is energized. IRIS contains an imaging spectrograph that covers the Mg II h&k lines as well as a slit-jaw imager centered at Mg II k. Understanding the observations will require forward modeling of Mg II h&k line formation from 3D radiation-MHD models. This paper is the first in a series where we undertake this forward modeling. We discuss the atomic physics pertinent to h&k line formation, present a quintessential model atom that can be used in radiative transfer computations and discuss the effect of partial redistribution (PRD) and 3D radiative transfer on the emergent line profiles. We conclude that Mg II h&k can be modeled accurately with a 4-level plus continuum Mg II model atom. Ideally radiative transfer computations should be done in 3D including PRD effects. In practice this is currently not possible. A reasonable compromise is to use 1D PRD computations to model the line profile up to and including the central emission peaks, and use 3D transfer assuming complete redistribution to model the central depression.Comment: 13 pages, 13 figures, accepted for Ap