pysimone  1.0

The Stable Isotope MOdel for Nutrient cyclEs (SIMONE) is a tool that allows the calculation of the isotopic composition of a set of nutrient pools based on the mechanisms of fractionation and mixing. Mixing is calculated based on a mass balance according to Coplen (2011).

\[ AF_{res} = \frac{m_{orig} AF_{orig}+m_{added} AF_{added}}{m_{orig}+m_{added}} \]

In this mixing equation, the atom fraction (AF; please note the AF is used here instead of F in the model code as this may be confused with the residual fraction $f$) of the rare isotope (in our cases often ${}^{15}N$) in the resulting pool is calculated based on the original mass and AF ( $m_{orig}$, $AF_{orig}$) of the pool and the mass and AF of the pool compound that has been added ( $m_{added}$, $AF_{added}$). Isotopic fractionation during chemical transformation is calculated using the Rayleigh distillation equation (Mariotti et al. 1981).

\[ R_{s} = R_{s,0} f^{\alpha - 1} \]

This equation describes the isotope ratio of the transformation substrate $R_s$ based on the isotope ratio prior to the transformation reaction $R_{s,0}$, the residual fraction of substrate $f$, and the fractionation factor $\alpha$. The residual fraction is the share of substrate that has not been transformed to product during the reaction. Please note that isotopic fractionation is calculated based on isotope ratios and not on $\delta$-values as the latter is not accurate. However, published isotpic compositions are usually reported in $\delta$-notation, so that these notations have to be converted. To this end, the isotpe ratio of the reference material is required, with SIMONE using the value of 0.0036765 (Coplen, 2011). SIMONE reauires two input files, namely config.json and model.json. The file model.json contains information on the underlying model, i.e., it contains the names of the nutrient pools, the processes that link the pools and the processchain. The process chain is basically a list of processes that are called consecutively within one time step of the model. Please note that some processes may be called, for instance, daily while other sets of processes are repeated hourly. Please also note that in the code, source and target are used for both mixing and fractionation, though for fractionation, the terms substrate and product are more frequently used.