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

Breakdown of adiabatic invariance in spherical tokamaks

Thermal ions in spherical tokamaks have two adiabatic invariants: the magnetic moment and the longitudinal invariant. For hot ions, variations in magnetic-field strength over a gyro period can become sufficiently large to cause breakdown of the adiabatic invariance. The magnetic moment is more sensitive to perturbations than the longitudinal invariant and there exists an intermediate regime, super-adiabaticity, where the longitudinal invariant remains adiabatic, but the magnetic moment does not. The motion of super-adiabatic ions remains integrable and confinement is thus preserved. However, above a threshold energy, the longitudinal invariant becomes non-adiabatic too, and confinement is lost as the motion becomes chaotic. We predict beam ions in present-day spherical tokamaks to be super-adiabatic but fusion alphas in proposed burning-plasma spherical tokamaks to be non-adiabatic.Comment: 6 pages, 8 figure

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

Chromospheric polarimetry through multi-line observations of the 850 nm spectral region

Future solar missions and ground-based telescopes aim to understand the magnetism of the solar chromosphere. We performed a supporting study in Quintero Noda et al. (2016) focused on the infrared Ca II 8542 A line and we concluded that is one of the best candidates because it is sensitive to a large range of atmospheric heights, from the photosphere to the middle chromosphere. However, we believe that it is worth to try improving the results produced by this line observing additional spectral lines. In that regard, we examined the neighbour solar spectrum looking for spectral lines that could increase the sensitivity to the atmospheric parameters. Interestingly, we discovered several photospheric lines that greatly improve the photospheric sensitivity to the magnetic field vector. Moreover, they are located close to a second chromospheric line that also belongs to the Ca II infrared triplet, i.e. the Ca II 8498 A line, and enhances the sensitivity to the atmospheric parameters at chromospheric layers. We conclude that the lines in the vicinity of the Ca II 8542 A line not only increase its sensitivity to the atmospheric parameters at all layers, but also they constitute an excellent spectral window for chromospheric polarimetry.Comment: 11 pages, 8 figures, 1 tabl

Study of the polarization produced by the Zeeman effect in the solar Mg I b lines

The next generation of solar observatories aim to understand the magnetism of the solar chromosphere. Therefore, it is crucial to understand the polarimetric signatures of chromospheric spectral lines. For this purpose, we here examine the suitability of the three Fraunhofer Mg I b1, b2, and b4 lines at 5183.6, 5172.7, and 5167.3 A, respectively. We start by describing a simplified atomic model of only 6 levels and 3 line transitions for computing the atomic populations of the 3p-4s (multiplet number 2) levels involved in the Mg I b line transitions assuming non-local thermodynamic conditions and considering only the Zeeman effect using the field-free approximation. We test this simplified atom against more complex ones finding that, although there are differences in the computed profiles, they are small compared with the advantages provided by the simple atom in terms of speed and robustness. After comparing the three Mg I lines, we conclude that the most capable one is the b2 line as b1 forms at similar heights and always show weaker polarization signals while b4 is severely blended with photospheric lines. We also compare Mg I b2 with the K I D1 and Ca II 8542 A lines finding that the former is sensitive to the atmospheric parameters at heights that are in between those covered by the latter two lines. This makes Mg I b2 an excellent candidate for future multi-line observations that aim to seamlessly infer the thermal and magnetic properties of different features in the lower solar atmosphere.Comment: 14 pages, 11 figures, and 5 table

Chromospheric polarimetry through multi-line observations of the 850 nm spectral region II: A magnetic flux tube scenario

In this publication we continue the work started in Quintero Noda et al. (2017) examining this time a numerical simulation of a magnetic flux tube concentration. Our goal is to study if the physical phenomena that take place in it, in particular, the magnetic pumping, leaves a specific imprint on the examined spectral lines. We find that the profiles from the interior of the flux tube are periodically dopplershifted following an oscillation pattern that is also reflected in the amplitude of the circular polarization signals. In addition, we analyse the properties of the Stokes profiles at the edges of the flux tube discovering the presence of linear polarization signals for the Ca II lines, although they are weak with an amplitude around 0.5% of the continuum intensity. Finally, we compute the response functions to perturbations in the longitudinal field and we estimate the field strength using the weak field approximation. Our results indicate that the height of formation of the spectral lines changes during the magnetic pumping process which makes the interpretation of the inferred magnetic field strength and its evolution more difficult. These results complement those from previous works demonstrating the capabilities and limitations of the 850 nm spectrum for chromospheric Zeeman polarimetry in a very dynamic and complex atmosphere.Comment: 12 pages, 12 figures, 0 tables, MNRAS main journal publicatio

Solar polarimetry through the K I lines at 770 nm

We characterize the K I D1 & D2 lines in order to determine whether they could complement the 850 nm window, containing the Ca II infrared triplet lines and several Zeeman sensitive photospheric lines, that was studied previously. We investigate the effect of partial redistribution on the intensity profiles, their sensitivity to changes in different atmospheric parameters, and the spatial distribution of Zeeman polarization signals employing a realistic magnetohydrodynamic simulation. The results show that these lines form in the upper photosphere at around 500 km and that they are sensitive to the line of sight velocity and magnetic field strength at heights where neither the photospheric lines nor the Ca II infrared lines are. However, at the same time, we found that their sensitivity to the temperature essentially comes from the photosphere. Then, we conclude that the K I lines provide a complement to the lines in the 850 nm window for the determination of atmospheric parameters in the upper photosphere, especially for the line of sight velocity and the magnetic field.Comment: 10 pages, 9 figures, main journal publicatio

Chromospheric polarimetry through multi-line observations of the 850 nm spectral region III: Chromospheric jets driven by twisted magnetic fields

We investigate the diagnostic potential of the spectral lines at 850 nm for understanding the magnetism of the lower atmosphere. For that purpose, we use a newly developed 3D simulation of a chromospheric jet to check the sensitivity of the spectral lines to this phenomenon as well as our ability to infer the atmospheric information through spectropolarimetric inversions of noisy synthetic data. We start comparing the benefits of inverting the entire spectrum at 850 nm versus only the Ca II 8542 A spectral line. We found a better match of the input atmosphere for the former case, mainly at lower heights. However, the results at higher layers were not accurate. After several tests, we determined that we need to weight more the chromospheric lines than the photospheric ones in the computation of the goodness of the fit. The new inversion configuration allows us to obtain better fits and consequently more accurate physical parameters. Therefore, to extract the most from multi-line inversions, a proper set of weights needs to be estimated. Besides that, we conclude again that the lines at 850 nm, or a similar arrangement with Ca II 8542 A plus Zeeman sensitive photospheric lines, poses the best observing configuration for examining the thermal and magnetic properties of the lower solar atmosphere.Comment: 14 pages, 11 figure

Linear response strength functions with iterative Arnoldi diagonalization

We report on an implementation of a new method to calculate RPA strength functions with iterative non-hermitian Arnoldi diagonalization method, which does not explicitly calculate and store the RPA matrix. We discuss the treatment of spurious modes, numerical stability, and how the method scales as the used model space is enlarged. We perform the particle-hole RPA benchmark calculations for double magic nucleus 132Sn and compare the resulting electromagnetic strength functions against those obtained within the standard RPA.Comment: 9 RevTeX pages, 11 figures, submitted to Physical Review