Carbon monoxide in the solar atmosphere I. Numerical method and   two-dimensional models
  The radiation hydrodynamic code CO5BOLD has been supplemented with the time-dependent treatment of chemical reaction networks. Advection of particle densities due to the hydrodynamic flow field is also included. The radiative transfer is treated frequency-independently, i.e. grey, so far. The upgraded code has been applied to two-dimensional simulations of carbon monoxide (CO) in the non-magnetic solar photosphere and low chromosphere. For this purpose a reaction network has been constructed, taking into account the reactions which are most important for the formation and dissociation of CO under the physical conditions of the solar atmosphere. The network has been strongly reduced to 27 reactions, involving the chemical species H, H2, C, O, CO, CH, OH, and a representative metal. The resulting CO number density is highest in the cool regions of the reversed granulation pattern at mid-photospheric heights and decreases strongly above. There, the CO abundance stays close to a value of 8.3 on the usual logarithmic abundance scale with [H]=12 but is reduced in hot shock waves which are a ubiquitous phenomenon of the model atmosphere. For comparison, the corresponding equilibrium densities have been calculated, based on the reaction network but also under assumption of instantaneous chemical equilibrium by applying the Rybicki & Hummer (RH) code by Uitenbroek (2001). Owing to the short chemical timescales, the assumption holds for a large fraction of the atmosphere, in particular the photosphere. In contrast, the CO number density deviates strongly from the corresponding equilibrium value in the vicinity of chromospheric shock waves. Simulations with altered reaction network clearly show that the formation channel via hydroxide (OH) is the most important one under the conditions of the solar atmosphere. 
S. Wedemeyer-Boehm, I. Kamp, J. Bruls, B. Freytag