16 research outputs found
Mancha3D code: Multi-purpose Advanced Non-ideal MHD Code for High resolution simulations in Astrophysics
The Mancha3D code is a versatile tool for numerical simulations of
magnetohydrodynamic processes in solar/stellar atmospheres. The code includes
non-ideal physics derived from plasma partial ionization, a realistic equation
of state and radiative transfer, which allows performing high quality realistic
simulations of magneto-convection, as well as idealized simulations of
particular processes, such as wave propagation, instabilities or energetic
events. The paper summarizes the equations and methods used in the Mancha3D
code. It also describes its numerical stability and parallel performance and
efficiency. The code is based on a finite difference discretization and
memory-saving Runge-Kutta (RK) scheme. It handles non-ideal effects through
super-time stepping and Hall diffusion schemes, and takes into account thermal
conduction by solving an additional hyperbolic equation for the heat flux. The
code is easily configurable to perform different kinds of simulations. Several
examples of the code usage are given. It is demonstrated that splitting
variables into equilibrium and perturbation parts is essential for simulations
of wave propagation in a static background. A perfectly matched layer (PML)
boundary condition built into the code greatly facilitates a non-reflective
open boundary implementation. Spatial filtering is an important numerical
remedy to eliminate grid-size perturbations enhancing the code stability.
Parallel performance analysis reveals that the code is strongly memory bound,
which is a natural consequence of the numerical techniques used, such as split
variables and PML boundary conditions. Both strong and weak scalings show
adequate performance up till several thousands of CPUs
Two-fluid implementation in
Context. The chromosphere is a partially ionized layer of the solar atmosphere, which acts as the transition between the photosphere where the gas is almost neutral and the fully ionized corona. As the collisional coupling between neutral and charged particles decreases in the upper part of the chromosphere, the hydrodynamical timescales may become comparable to the collisional timescale, thus calling for the application of a two-fluid model.
Aims. In this paper, we describe the implementation and validation of a two-fluid model that simultaneously evolves charges and neutrals, coupled by collisions.
Methods. The two-fluid equations are implemented in the fully open-source MPI-AMRVA
Effects of ambipolar diffusion on waves in the solar chromosphere
Context. The chromosphere is a partially ionized layer of the solar atmosphere that mediates the transition between the photosphere where the gas motion is determined by the gas pressure and the corona dominated by the magnetic field.
Aims. We study the effect of partial ionization for 2D wave propagation in a gravitationally stratified, magnetized atmosphere characterized by properties that are similar to those of the solar chromosphere.
Methods. We adopted an oblique uniform magnetic field in the plane of propagation with a strength that is suitable for a quiet sun region. The theoretical model we used is a single fluid magnetohydrodynamic approximation, where ion-neutral interaction is modeled by the ambipolar diffusion term. Magnetic energy can be converted into internal energy through the dissipation of the electric current produced by the drift between ions and neutrals. We used numerical simulations in which we continuously drove fast waves at the bottom of the atmosphere. The collisional coupling between ions and neutrals decreases with the decrease in the density and the ambipolar effect thus becomes important.
Results. Fast waves excited at the base of the atmosphere reach the equipartition layer and are reflected or transmitted as slow waves. While the waves propagate through the atmosphere and the density drops, the waves steepen into shocks.
Conclusions. The main effect of ambipolar diffusion is damping of the waves. We find that for the parameters chosen in this work, the ambipolar diffusion affects the fast wave before it is reflected, with damping being more pronounced for waves which are launched in a direction perpendicular to the magnetic field. Slow waves are less affected by ambipolar effects. The damping increases for shorter periods and greater magnetic field strengths. Small scales produced by the nonlinear effects and the superposition of different types of waves created at the equipartition height are efficiently damped by ambipolar diffusion
Two-fluid reconnection jets in a gravitationally stratified atmosphere
The density decreases exponentially with height in the solar gravitationally
stratified atmosphere, therefore the collisional coupling between the ionized
plasma and the neutrals also decreases. Here, we investigate the role of
collisions between ions and neutrals on the reconnection process occurring at
various heights in the atmosphere. We perform simulations of magnetic
reconnection induced by a localized resistivity in a gravitationally stratified
atmosphere, where we vary the height of the initial reconnection X-point. We
compare a magnetohydrodynamic (MHD) model and two two-fluid configurations: one
where the collisional coupling is calculated from local plasma parameters and
another where the coupling is decreased, so that collisional effects are
enhanced. Simulations in a stratified atmosphere show similar structures in MHD
and two-fluid simulations with strong coupling. However, when collisional
effects are increased to attain representative parameter regimes, we find a
nonlinear runaway instability, which separates the plasma-neutral densities
across the current sheet (CS). With increased collisional effects, the initial
decoupling in velocity heats the neutrals and this sets up a nonlinear feedback
where neutrals migrate outside the CS, replacing charged particles which
accumulate towards the center of the CS. The reconnection rate has a maximum
value around 0.1, similar for both reconnection heights, and is consistent with
the use of a localized enhanced resistivity used in all three models. The
initial stages of plasmoid formation, observed near the end of our simulations,
is influenced by the outflow from the primary reconnection point, rather than
by collisions. We synthesize optically thin emission for both MHD and two-fluid
models, which can show a very different evolution when the charged particle
density is used instead of the total density
Two-fluid implementation in MPI-AMRVAC, with applications in the solar chromosphere
The chromosphere is a partially ionized layer of the solar atmosphere, the
transition between the photosphere where the gas is almost neutral and the
fully ionized corona. As the collisional coupling between neutral and charged
particles decreases in the upper part of the chromosphere, the hydrodynamical
timescales may become comparable to the collisional timescale, and a two-fluid
model is needed. In this paper we describe the implementation and validation of
a two-fluid model which simultaneously evolves charges and neutrals, coupled by
collisions. The two-fluid equations are implemented in the fully open-source
MPI-AMRVAC code. In the photosphere and the lower part of the solar atmosphere,
where collisions between charged and neutral particles are very frequent, an
explicit time-marching would be too restrictive, since for stability the
timestep needs to be proportional to the inverse of the collision frequency.
This is overcome by evaluating the collisional terms implicitly using an
explicit-implicit (IMEX) scheme. The cases presented cover very different
collisional regimes and our results are fully consistent with related
literature findings. If collisional time and length scales are smaller than the
hydrodynamical scales usually considered in the solar chromosphere, density
structures seen in the neutral and charged fluids are similar, with the effect
of elastic collisions between charges and neutrals being similar to
diffusivity. Otherwise, density structures are different and the decoupling in
velocity between the two species increases. The use of IMEX schemes efficiently
avoids the small timestep constraints of fully explicit implementations in
strongly collisional regimes. Adaptive Mesh Refinement (AMR) greatly decreases
the computational cost, compared to uniform grid runs at the same effective
resolution.Comment: accepted for publication in A&
Three-dimensional MHD wave propagation near a coronal null point: a new wave mode decomposition approach
We present a new MHD wave decomposition method that overcomes the limitations
of existing wave identification methods. Our method allows to investigate the
energy fluxes in different MHD modes at different locations of the solar
atmosphere as waves generated by vortex flows travel through the solar
atmosphere and pass near the magnetic null. We simulate wave dynamics through a
coronal null configuration and apply a rotational wave driver at our bottom
photospheric boundary. To identify the wave energy fluxes associated with
different MHD wave modes, we employ a wave-decomposition method that is able to
uniquely distinguish different MHD modes. Our proposed method utilizes the
geometry of an individual magnetic field-line in 3D space to separate out
velocity perturbations associated with the three fundamental MHD waves. Our
method for wave identification is consistent with previous flux-surface-based
methods and gives expected results in terms of wave energy fluxes at various
locations of the null configuration. We show that ubiquitous vortex flows
excite MHD waves that contribute significantly to the Poynting flux in the
solar corona. Alfv\'en wave energy flux accumulates on the fan surface and fast
wave energy flux accumulates near the null point. There is a strong current
density buildup at the spine and fan surface.The proposed method has advantages
over previously utilized wave decomposition methods, since it may be employed
in realistic simulations or magnetic extrapolations, as well as in real solar
observations, whenever the 3D fieldline shape is known. The enhancement in
energy flux associated with magneto-acoustic waves near nulls may have
important implications in the formation of jets and impulsive plasma flows.Comment: Accepted for publication in A&