Merge pull request #15 from HaibingShao/react_trans_GIA

React trans gia
proper initialization
correcting names of variables
setZero
_mat_S1_ast and _ma_S2_ast should be calculated seperately
correct names
fixing _mat_S1_orth
clean up
clean up
correct names
change the default from mobile and immobile(mineral) to mobile and immobile(kinetic[biomass])
choosing schemes (KIN_REACT_GIA and REACT_GIA); to be fixed later
add KINETIC to enum Comp_Mobility
avoid zero
passing dt. avoiding unnecessary calculations
initializing variables
initializing variables
get the right values
right water content for monod2d benchmark
changing the imput files