Bifrost

Bifrost is a massively parallel code developed for tridimensional numerical experiments of stellar atmospheres (Gudiksen et al. 2011). In order to explicitly solve the standard partial differential equations of magnetohydrodynamics (MHD), its core uses a staggered mesh in cartesian coordinates (x,y,z). The positioning of the variables in the mesh is as follows: the scalar variables, e.g., the density ρ, are defined in the center of the numerical cells; the components of the basic vector fields, namely, the magnetic field B_i and linear momentum p_i, are located at the center of the cell faces; and the cross product or curl of those vectors, like (vxB)_i or J_i, are defined on the cell edges.

The numerical scheme is a classic method of lines (MOL). It is based on a sixth order operator for the spatial derivatives. Since Bifrost uses a staggered mesh, it is not possible to avoid the use of interpolations to re-collocate the variables in space during the computations. Those interpolations are of fifth order. The time derivatives can follow a predictor-corrector scheme of third order described by Hyman (1979) or a third order Runge Kuttta method. In both cases, the timestep is controlled by the Courant-Friedrichs-Lewy (CFL) criterion (Courant et al. 1928).

In spite of using high-order methods, the numerical codes are diffusive by their own nature due to the discretization of the equations. To ensure stability, Bifrost employs a diffusive operator that consists of two main terms: a small global diffusive term and the so called hyperdiffusion term inspired by Nordlund & Galsgaard (1995). The latter is a location-specific diffusion that acts in small regions of large gradients or jumps in the variables, like in current sheets or shocks.

The advantage of using the Bifrost code is that it includes different modules that provide relevant physics for the solar atmosphere.

Bifrost literature

In the following, we list the papers that describe the main modules of Bifrost:

Installation

Getting Bifrost

Bifrost is located on github. The repository is private, meaning you should be logged in with your github username to see it at:

Bifrost repository

To get started with the new repository, you'll need to have git (pre-installed in most machines) and configure it to use your name and email address you registered with github, by doing something like:

git config --global user.name "Your name"  
git config --global user.email username@example.com

You can clone the repository through HTTPS like this:

git clone https://username@github.com/ITA-Solar/Bifrost.git

replacing "username" with your github username.

Terminal configuration

It can be useful to create (or modify) your .login (in csh/tcsh) or .zlogin (in zsh) file in your home directory to add a Bifrost system variable.

In case of working with zsh:

export BIFROST="/folder/Bifrost"
In case of tcsh:
setenv BIFROST "/folder/Bifrost"
where folder is the location where you have cloned the Bifrost repository.

To use the IDL routines of Bifrost, modify your .zlogin file to add the following system variables. In case of working with tcsh: 

export BIFROST_IDL=$BIFROST"/IDL"
where BIFROST is a system variable for your Bifrost repository (see Bifrost section). Then, modifiy your IDL_PATH to the the Bifrost IDL folder:

export IDL_PATH="/Applications/exelis/idl85/bin"":+"$BIFROST_IDL

It is also necessary to define a system variable called OSC_CSTAGGER, which depends on your operative system.

  • If you use a Linux system: 
    export OSC_CSTAGGER=$BIFROST_IDL"/cstagger/linux"
  • In case of a intelmac: 
    export OSC_CSTAGGER=$BIFROST_IDL"/cstagger/intelmac"

The next step is to go to your stagger folder, typing in your terminal

cd $OSC_CSTAGGER

and then

make

That would create the following six files:

  • cstagger.pro
  • cstagger.c
  • cstagger.o
  • init_stagger.o
  • inverse.o
  • cstagger.so

which are necessary for stagger operations.

After all this steps, create a IDL startup file. This file is going to be executed automatically each time IDL is started. For example, you can create it in your IDLWorkspace and then add a similar line in your .login file (in case of using tcsh) with the location:

export IDL_STARTUP="/Users/yourname/IDLWorkspace85/startup.pro"
Edit the startup.pro file to add the following line

.r $OSC_CSTAGGER/cstagger
whici will compile the Stagger routines each time you execute IDL. With all the information above, you should be able to use the IDL routines of Bifrost without any problem.

I also have the following useful lines in startup.pro

br_select_idlparam, idlparam
d=obj_new('br_data', idlparam)
br_getsnapind, idlparam, snaps
PRINT, '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
PRINT, ' Project : ', idlparam, '  ', strtrim(string(min(snaps)),2), '-',strtrim(string(max(snaps)),2)
PRINT, '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
PRINT, '

so everytime I run IDL within a folder containing a numerical experiment carried out with Bifrost, I get the object to load Bifrost variables (d), the name of the simulation (idlparam) and all the snapshots I have in that folder (snaps). Then I print on the screen some of that information.