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We apply the Gillespie algorithm [ 32] to compute the time of the next reaction, choose the reaction channel from the list of all possible reactions and update the number of molecules according to the reaction stoichiometry.
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The basic function of the reaction module is to take component concentrations from the model cells of the transport simulator, run geochemical reactions, and return updated component concentrations to the transport simulator.
These reactions and their updated constraints are given in Table 1.
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Given the reaction and diffusion probabilities, each step of the calculation involves generating the numbers of particles diffusing across each possible boundary, the number of reactions taking place, and updating the number of particles of each type in each element accordingly (Fig. S1A).
Since both directions of a reversible reaction are considered independently, reversibilities can optionally easily be preserved by choosing only forward reactions in line 1, and updating the reversed reaction accordingly after line 6.
Mass transport, chemical reactions, solid updates and migration are included in the model which are solved by the combination of lattice Boltzmann and finite volume methods.
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