Mancha3D (Multiphysics Advanced Nonideal Code for Highresolution simulations of the solar Atmosphere)
Mancha3D is a versatile numerical code for modeling of the solar and stellar atmospheres. The code solves timedependent equations of the magnetohydrodynamics (MHD) on 3D Cartesian grid. Depending on the setup, \mancha can solve either full or linearized MHD equations. In addition to the set of MHD equations, there are various terms and modules available: nonideal terms (ambipolar diffusion, Hall's term and Biermann's battery), radiative transfer equation, realistic equation of state. The code is written in modern Fortran language and fully parallelized (spatial domain decomposition) using the MPI library.
The name Mancha goes back to the earliest version of the code that was designed to simulate propagation of waves in sunspots ("mancha solar'' means sunspot in Spanish). Written in all capitals, it is an acronym for Multifluid (purpose, physics, dimensional) Advanced Nonideal MHD Code for Highres simulations of the solar Atmosphere.
The earliest version of Mancha (2D prototype) was written by Elena Khomenko and Manolo Collados in 20042006 for the purpose of wave simulation in sunspots (Khomenko & Collados, 2006). The initial code was extended to 3D and paralellized by Tobias Felipe (Felipe et al., 2010, see also PhD thesis of T. Felipe). In the framework of the ERC supported SPIA project (20122016), Mancha parallelization and numerical performance was optimized (Angel de Vicente), variables changed from adimensional to having physical units and nonideal terms were implemented (Khomenko & Collados, 2012), 3D aspects were improved (Manuel Luna), radiative transfer and equation of state were added (Nikola Vitas), (see Vitas & Khomenko, 2015, Khomenko et al., 2017, Khomenko et al., 2018). Finally, a supertime stepping scheme is incorporated (P. GonzálezMorales et al., 2018, see also P. GonzálezMorales PhD thesis, 2020). Within the the PI2FA ERC project, some numerical treatments are improved, the code is cleaned and further optimized (Nikola Vitas, Mikhail Modestov), further setups are designed (David Martinez, Andrea Perdomo, Valeria Liakh) and the thermal conduction module is developed (Anamaria Navarro).
The main features of the code are:

Solves nonlinear nonideal MHD equations for perturbations in 3D;

Magnetostatic equilibrium is explicitly removed from the equations;

Ambipolar diffusion, Hall and Biermann battery effects from generalized Ohm’s law;

4th order in space and time; STS for Ambipolar diffusion; HDS for Hall effect

Stabilized by hyperdiffusive terms;

PML absorption layer boundary conditions;

Energy losses according LTE RT;

Realistic equation of state for solar chemical mixture;

MPI parallelized using domain decomposition, up to 80% efficiency for 4000 CPUs
ManchaTwoFluid
The twofluid code represents an extension of the existing Mancha3D code.
The code solves twofluid equations of conservation of mass, momentum and energy, together with the induction equation, for the case of the purely hydrogen plasma with collisional coupling between the charged and neutral fluid components, and with inclusion of physical viscosity and thermal conductivity. The implementation of a semiimplicit algorithm allows to overcome the numerical stability constraints due to the stiff collisional terms. Viscosity and thermal conduction are treated implicitly using the BiCGStab algorithm.
References
 Khomenko, E.; Collados, M. "Numerical Modeling of Magnetohydrodynamic Wave Propagation and Refraction in Sunspots", 2006, The Astrophysical Journal, Volume 653, Issue 1, pp. 739755, 2006ApJ...653..739K
 Felipe, T.; Khomenko, E.; Collados, M. "Magnetoacoustic Waves in Sunspots: First Results From a New Threedimensional Nonlinear Magnetohydrodynamic Code", 2010, The Astrophysical Journal, Volume 719, Issue 1, pp. 357377, 2010ApJ...719..357F
 Khomenko, E.; Collados, M. "Heating of the Magnetized Solar Chromosphere by Partial Ionization Effects", 2012, The Astrophysical Journal, Volume 747, Issue 2, article id. 87, 2012ApJ...747...87K
 Vitas, N.; Khomenko, E. "Equation of state for solar nearsurface convection", 2015, Annales Geophysicae, Volume 33, Issue 6, 2015, pp.703709, 2015AnGeo..33..703V
 GonzálezMorales, P. A.; Khomenko, E.; Downes, T. P.; de Vicente, A. "MHDSTS: a new explicit numerical scheme for simulations of partially ionised solar plasma", 2018, Astronomy & Astrophysics, Volume 615, id.A67, 2018A%26A...615A..67G
 Khomenko, E.; Vitas, N.; Collados, M.; de Vicente, A. "Threedimensional simulations of solar magnetoconvection including effects of partial ionization", 2018, Astronomy & Astrophysics, Volume 618, id.A87, 2018A%26A...618A..87K
 Popescu Braileanu, B.; Lukin, V. S.; Khomenko, E.; de Vicente, A. "Twofluid simulations of waves in the solar chromosphere I: numerical code verification", 2019, Astronomy & Astrophysics, in press, 2019arXiv190503559P