take the new xikin if it is changed in optimization step
get xi local from previous time step
declare and initialize non-mineral concentration vector for biomass at log scale.
take the log of biomass concentration.
put the log concentraiton of biomass in vector of unknowns.
Retreive the concentration of biomass after solving the local problem.
Get the concentration of biomass in residual function of local problem.
define a new variable (cminbar) for clarity.
fixing a bug. We need to take the update mineral concentrations regardless of presence of absence of minerals.
getting the old value of xi local.
getting the old value of xi local.
getting the old time step values of xis.
getting the old value of xis.
fixing a bug in residual evaluations of 3.44 equations for mineral reactions.
re-arrange the active and inactive minerals after calculating vprime.
put stricter convergence tolerance for calcite example (1E-10) and reduce the time step size to 300s.
change epsilon to 1E-8.