Solar Atmospheric Modelling (SAM) (completed)

About the project

Solar Atmospheric Modelling (SAM) is a project funded by the Research Council of Norway for 2014-2017 and is a continuation of earlier projects with the same name funded for 2006-2013.


Solar magnetism lies at the root of most solar and heliospheric physics. The intricate structure of the solar field, the activity cycle and the influence of the field on the heliosphere represent major quests of (astro-) physics which bear directly on the human environment. The Sun’s magnetic field is generated by enigmatic dynamo processes in the solar interior, is organized into the highly complex patterns of solar activity observed in the solar photosphere, dominates the structure of the outer solar atmosphere (chromosphere, transition region, corona), regulates the solar wind, and affects the whole extended heliosphere into the Earth’s upper atmosphere.

A wealth of observational data is now available through the highly successful SOHO (SOlar and Heliospheric Observatory) satellite, the Swedish 1-m Solar Telescope (SST), the Japanese Hinode satellite (named Solar-B before launch in 2006) and the Solar Dynamics Observatory (SDO). More data will arrive through the projects under development such as Solar Orbiter, the Interface Region Imaging Spectrograph (IRIS), the Advanced Technology Solar Telescope (ATST) and the European Solar Telescope (EST). The overwhelming complexity of these new high resolution observations underscores the need for a commensurate effort into theoretical modelling. The project “Solar Atmospheric Modelling” aims at being such an effort.

State of the art and objectives

The long term goal is to achieve a coherent picture of the physics of the outer solar atmosphere. Our contribution towards this goal in this project is to explore advanced numerical modelling of the solar atmosphere and combine these models with observations from leading observing facilities.

The central science objective of SAM is to understand the flow of energy and mass through the Sun’s chromosphere and transition region in which the magnetic field, density, and temperature exhibit dramatic gradients — a critical interface through which all non-thermal energy that drives space weather is transported. This objective is captured in four crucial questions that are further expanded in the following sections:


The project relies on a combination of large scale, realistic, radiation-magnetohydrodynamic simulations and cutting edge observations. We first describe the developed tools for the simulations in relation to the state of the art with a special focus on the novel and unconventional aspects. We also describe the development work proposed during the project period.

Existing codes

Radiation magnetohydrodynamics. To model the full system from the convection zone to the corona we have developed a 3D radiation magnetohydrodynamic code (Hansteen, 2004, Hansteen, Carlsson & Gudiksen, 2007) using a sixth-order finite difference compact scheme building on a Fortran-90 code originally written by Nordlund & Galsgaard. The radiation is treated with multi-group opacities (Nordlund, 1982). Conduction is treated implicitly using a multi-grid approach. Novel aspects of the code are the extension of the multi- group opacity method to include scattering (Skartlien, 2000) and the treatment of the radiative exchange in strong lines in the middle and upper chromosphere. We have there used the detailed 1D radiation- hydrodynamic simulations of Carlsson & Stein (1992, 1995, 1997, 2002) to develop recipes that contain the essentials of the physics while keeping the computational expenses at tractable levels.
The original shared-memory code (Oslo Stagger Code, OSC) has been completely rewritten using domain decomposition and MPI for parallelization (Gudiksen et al 2011) with proven scalability to at least 4000 cores. The new code, named Bifrost, is the current state of the art in self-consistent chromospheric modelling.
Spectral synthesis. It is impossible to directly measure physical parameters such as temperatures or magnetic field strengths on the Sun. This information has to be decoded from the observed images, spectra and polarization signal using inversions. Such inversion of observations often gives only rough estimates of the physical parameters and suffers, especially in the case of chromospheric diagnostics, from degeneracy: different configurations may produce the same observed spectrum. On the other hand, radiation hydrodynamic simulations deliver quantities as the temperature and magnetic field strength as output but cannot be compared directly with observations. Instead, images and spectra are synthesized from such simulations and then compared to observations. Such spectral synthesis is done with dedicated radiative transfer codes that compute the emergent spectrum in great detail, as opposed to the approximate radiative transfer within the radiation magnetohydrodynamic simulations that only aims to compute frequency-integrated radiative losses and gains.
There are currently two generally available radiative transfer codes that are capable of performing such 3D radiative transfer; RH developed by Uitenbroek (2001), and our own MULTI3D (Botnen & Carlsson 1999; Leenaarts & Carlsson 2009). The former code has more detailed physics but lacks efficient parallelization and consequently cannot handle the large computational domains delivered by radiation magnetohydrodynamic codes. The latter code is MPIparallelized using domain-decomposition and has successfully run on up to 256 processors with excellent scaling. This code can handle large 3D input atmospheres and has been used to study the formation of the mid-chromospheric Ca II 854.2 nm infrared line and the low-chromospheric Na I D1 line at 589.6 nm (Leenaarts et al. 2009, 2010).

Code development

With OSC and Bifrost we have made the most realistic simulations of the convection zone to corona coupled system so far and have been able to address several fundamental problems. It is clear, however, that many important physical ingredients are still missing and one of the goals of SAM is to enable a concentrated effort with the development of new methods and laborintensive detailed analysis of simulations and observations in order to optimize the balance between approximations, realism and computing time. Particular code development projects are:

Non-equilibrium ionization of hydrogen. Ionization/recombination timescales for hydrogen are long compared with hydrodynamic timescales in the solar chromosphere. This has dramatic consequences for the electron densities and temperature structure (Carlsson and Stein, 2002; Leenaarts et al., 2007) and needs to be accounted for in the radiation magnetohydrodynamic simulations. The methods have been developed and implemented in OSC and Bifrost but there are stability and optimization issues that need to be solved before the formulation can be put into production.

Incident coronal radiation field. The strong coronal lines in the extreme ultraviolet illuminate the chromosphere from above. The radiation is absorbed in the continua of helium and hydrogen leading to a heating of the upper chromosphere (Carlsson & Stein 2002). The implementation is straightforward and will be finished the first year.

Non-LTE radiative exchange. The employed recipes rely on detailed 1D simulations. Since the coupling between radiation in strong spectral lines and the matter in non-equilibrium is very important for the chromospheric energy balance, it is crucial to continuously improve these recipes using detailed 3D non-LTE simulations from radiation magnetohydrodynamic snapshots. We will work on improving the recipes throughout the project period.

Ion-neutral interactions. The upper photosphere and chromosphere are only partially ionized and Bifrost does not take this into consideration when computing the electric field and the resistive terms in the equations. We plan to implement ion neutral effects in order to model the effects of the Hall and Cowling terms on the generalized Ohms law and resistive dissipation.  Preparation for this work has begun and seems to be a straightforward extension of the Bifrost code.

3D non-LTE diagnostics. The code MULTI3D is not directly applicable for the synthesis of the MgII h &k lines that will be observed with IRIS. Photon scattering in these lines is partially coherent. Accounting for partial redistribution (PRD) effects is computationally much more demanding (both in computing time and memory requirements) compared to the common assumption of complete redistribution (CRD). With Dr. Leenaarts we will implement PRD in MULTI3D. We also need to improve the robustness of MULTI3D - all 3D non-LTE codes have problems in treating realistic 3D simulations of the chromosphere because of very large gradients that appear in temperature and velocity. We will study these convergence issues in order to optimize the re-gridding normally performed between the radiation magnetohydrodynamic and 3D diagnostics steps.


The international collaboration is very central to the project. The active partners and their expertise for the project are:

  • Michigan State University, East Lansing, USA: Robert Stein was one of the pioneers in explaining the periodic variations in the solar spectrum as caused by standing waves and has together with Åke Nordlund made extensive contributions to our understanding of convection and (with Mats Carlsson) of the solar chromosphere.
  • Copenhagen University, Denmark: Åke Nordlund has developed 3D hydrodynamic codes for the study of solar convection and magnetohydrodynamic codes for the study of magnetic topology in the solar corona. His work has revolutionized our knowledge of solar/stellar convection.
  • Institute for Solar Physics, Sweden: Göran Scharmer has a background from radiative transfer theory but now concentrates his attention on observational solar physics. He is the director of the Swedish 1-m Solar Telescope on La Palma, widely acknowledged as the leading ground-based facility for high resolution solar observations.
  • Stanford-Lockheed Institute for Space Research, Palo Alto, USA: Alan Title is the leader of the group behind several of the most successful space based instruments in solar physics built during the last decades (SOHO/MDI, TRACE, Hinode/SOT, SDO/AIA, SDO/HMI, IRIS). Observations from these instruments are essential to achieving the scientific goals outlined in this proposal. Bart De Pontieu has played a crucial role for our work with data from these instruments and as science lead for the IRIS mission he will be a central person for our IRIS involvement.
  • Kyoto University: Kazunari Shibata is one of Japan’s foremost solar scientists with interests in solar MHD, solar flares and jets, magnetic reconnection, as well as non-solar fields such as AGNs and accretion disk MHD. Shibata has a numerical approach to his research and has supervised a large number of PhD students in numerical astrophysics. A PhD student from Oslo has been working with Shibata in Kyoto and a student from Kyoto is now in Oslo.

Their respective expertise will be very valuable to the SAM project. We plan on continuing the extensive collaboration through visits to the foreign groups by members of the SAM team, by inviting the foreign experts to Norway on shorter or longer visits and by continuing exchanging PhD students. We have recent joint publications with all the listed international collaborators.


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Tags: Japan, USA, Nordic
Published Feb. 28, 2011 11:28 AM - Last modified Nov. 1, 2021 12:44 PM