To me, there appears to be an implied relationship between is_Dirichlet, dirichlet_activation_vector, and dirichlet_activation_vectors. It seems dirichlet_activation_vectors is an $n_\text{voxels}\times n_\text{substrates}$ array and the others are (supposed to be) the result of any along the two dimensions.

If this is correct, then current implementations in BioFVM_microenvironment.cpp do not maintain this consistency. It can lead to unexpected behaviors in which a command such as update_dirichlet_node targeting a single substrate actually affects other substrates as well.