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MIMICS with plus option & moisture function, compiles
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@elisacw
elisacw committed Jan 10, 2025
1 parent 7f236f3 commit 09a9e5c
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4 changes: 2 additions & 2 deletions src/biogeochem/CNDriverMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -347,8 +347,8 @@ subroutine CNDriverNoLeaching(bounds,
else if (decomp_method == mimics_decomp .or. decomp_method == mimicsplus_decomp) then
call decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
num_bgc_vegp, filter_bgc_vegp, clm_fates, &
soilstate_inst, temperature_inst, cnveg_carbonflux_inst, ch4_inst, &
soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, &
soilstate_inst, temperature_inst, cnveg_carbonflux_inst, waterstatebulk_inst, ch4_inst, &
soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_state_inst, &
cnveg_state_inst%idop_patch)
end if
call t_stopf('DecompRate')
Expand Down
75 changes: 67 additions & 8 deletions src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ module SoilBiogeochemDecompCascadeMIMICSMod
use GridcellType , only : grc
use SoilBiogeochemStateType , only : get_spinup_latitude_term
use CLMFatesInterfaceMod , only : hlm_fates_interface_type
use WaterStateBulkType , only : waterstatebulk_type

!
implicit none
Expand Down Expand Up @@ -127,7 +128,24 @@ module SoilBiogeochemDecompCascadeMIMICSMod
real(r8) :: mimics_cn_mod_num ! adjusts microbial CN based on fmet
real(r8) :: mimics_t_soi_ref ! reference soil temperature (degC)
real(r8) :: mimics_initial_Cstocks_depth ! Soil depth for initial C stocks for a cold-start (m)
real(r8) :: mimics_fi
real(r8), allocatable :: mimics_initial_Cstocks(:) ! Initial C stocks for a cold-start (gC/m3)

real(r8) :: mimicsplus_k_myc_som
real(r8) :: mimicsplus_k_mo
real(r8) :: mimicsplus_vmax_myc
real(r8) :: mimicsplus_k_m_emyc
real(r8) :: mimicsplus_mge_ecm
real(r8) :: mimicsplus_mge_am
real(r8) :: mimicsplus_fphys_ecm
real(r8) :: mimicsplus_fchem_ecm
real(r8) :: mimicsplus_tau_ecm
real(r8) :: mimicsplus_fphys_am
real(r8) :: mimicsplus_fchem_am
real(r8) :: mimicsplus_tau_am
real(r8) :: mimicsplus_cn_myc


! The next few vectors are dimensioned by the number of decomposition
! transitions that make use of the corresponding parameters, currently
! six. The transitions are represented in this order:
Expand All @@ -154,6 +172,8 @@ module SoilBiogeochemDecompCascadeMIMICSMod
real(r8), allocatable :: mimics_desorp(:)
real(r8), allocatable :: mimics_tau_r(:)
real(r8), allocatable :: mimics_tau_k(:)


end type params_type
!
type(params_type), private :: params_inst
Expand Down Expand Up @@ -344,7 +364,7 @@ subroutine readParams ( ncid )
tString= trim(param_pref) // '_fi'
call ncd_io(trim(tString), tempr, 'read', ncid, readvar=readv)
if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
params_inst%mimicsplus_fi = tempr
params_inst%mimics_fi = tempr

! Parameters specific for mimicsplus / mimics parameters that have updated values in mimicsplus
!ECW currently the normal mimics parameters are in use (even if they are edited in mimicsplus)
Expand Down Expand Up @@ -471,8 +491,8 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat
is_metabolic => decomp_cascade_con%is_metabolic , & ! Output: [logical (:) ] TRUE => pool is metabolic material
is_cellulose => decomp_cascade_con%is_cellulose , & ! Output: [logical (:) ] TRUE => pool is cellulose
is_lignin => decomp_cascade_con%is_lignin , & ! Output: [logical (:) ] TRUE => pool is lignin
spinup_factor => decomp_cascade_con%spinup_factor & ! Output: [real(r8) (:) ] factor for AD spinup associated with each pool

spinup_factor => decomp_cascade_con%spinup_factor & ! Output: [real(r8) (:) ] factor for AD spinup associated with each pool
)

allocate(desorp(bounds%begc:bounds%endc,1:nlevdecomp))
Expand Down Expand Up @@ -843,21 +863,22 @@ end subroutine init_decompcascade_mimics
!-----------------------------------------------------------------------
subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
num_soilp, filter_soilp, clm_fates, &
soilstate_inst, temperature_inst, cnveg_carbonflux_inst, &
soilstate_inst, temperature_inst, cnveg_carbonflux_inst, waterstatebulk_inst, &
ch4_inst, soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, &
idop)
soilbiogeochem_state_inst, idop)
!
! !DESCRIPTION:
! Calculate rates and decomposition pathways for the MIMICS
! decomposition cascade model
!
! !USES:
use clm_time_manager , only : get_average_days_per_year, get_step_size
use clm_varcon , only : secspday, secsphr, tfrz
use clm_varcon , only : secspday, secsphr, tfrz, spval
use clm_varcon , only : g_to_mg, cm3_to_m3
use subgridAveMod , only : p2c
use PatchType , only : patch
use pftconMod , only : pftname
use clm_varpar , only : nlevdecomp_full
use TillageMod , only : get_do_tillage
use TillageMod , only : get_apply_tillage_multipliers
!
Expand All @@ -873,13 +894,19 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
type(ch4_type) , intent(in) :: ch4_inst
type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst
type(soilbiogeochem_carbonstate_type), intent(in) :: soilbiogeochem_carbonstate_inst
type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst
type(hlm_fates_interface_type) , intent(inout) :: clm_fates
type(waterstatebulk_type) , intent(in) :: waterstatebulk_inst
integer, optional , intent(in) :: idop(:) ! patch day of planting
!
! !LOCAL VARIABLES:
real(r8), parameter :: eps = 1.e-6_r8
real(r8), parameter :: min_modifier = 0.1 ! minimum value in microbial turnover
real(r8):: frw(bounds%begc:bounds%endc) ! rooting fraction weight
real(r8), allocatable:: fr(:,:) ! column-level rooting fraction by soil depth
real(r8), allocatable:: norm_froot_prof(:,:) ! normalized fine root profile
real(r8):: min_froot !minimum root fraction in column
real(r8):: max_froot !maximum root fraction in column
real(r8):: psi ! temporary soilpsi for water scalar
real(r8):: k_frag ! fragmentation rate constant CWD (1/sec)
real(r8):: fmet
Expand Down Expand Up @@ -961,11 +988,13 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
minpsi => CNParamsShareInst%minpsi , & ! Input: [real(r8) ] minimum soil suction (mm)
maxpsi => CNParamsShareInst%maxpsi , & ! Input: [real(r8) ] maximum soil suction (mm)
soilpsi => soilstate_inst%soilpsi_col , & ! Input: [real(r8) (:,:) ] soil water potential in each soil layer (MPa)
watsat => soilstate_inst%watsat_col , & ! Input: [real(r8) (:,:) ] volumetric soil water at saturation (porosity)
t_soisno => temperature_inst%t_soisno_col , & ! Input: [real(r8) (:,:) ] soil temperature (Kelvin) (-nlevsno+1:nlevgrnd)
o2stress_sat => ch4_inst%o2stress_sat_col , & ! Input: [real(r8) (:,:) ] Ratio of oxygen available to that demanded by roots, aerobes, & methanotrophs (nlevsoi)
o2stress_unsat => ch4_inst%o2stress_unsat_col , & ! Input: [real(r8) (:,:) ] Ratio of oxygen available to that demanded by roots, aerobes, & methanotrophs (nlevsoi)
finundated => ch4_inst%finundated_col , & ! Input: [real(r8) (:) ] fractional inundated area
decomp_cpools_vr => soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col , & ! Input: [real(r8) (:,:,:) ] (gC/m3) vertically-resolved decomposing (litter, cwd, soil) C pools
froot_prof => soilbiogeochem_state_inst%froot_prof_patch , & ! Input: [real(r8) (:,:) ] (1/m) profile of fine roots
pathfrac_decomp_cascade => soilbiogeochem_carbonflux_inst%pathfrac_decomp_cascade_col , & ! Output: [real(r8) (:,:,:) ] what fraction of C leaving a given pool passes through a given transition (frac)
rf_decomp_cascade => soilbiogeochem_carbonflux_inst%rf_decomp_cascade_col , & ! Input: [real(r8) (:,:,:) ] respired fraction in decomposition step (frac)
w_scalar => soilbiogeochem_carbonflux_inst%w_scalar_col , & ! Output: [real(r8) (:,:) ] soil water scalar for decomp
Expand All @@ -974,7 +1003,10 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
ligninNratioAvg => soilbiogeochem_carbonflux_inst%litr_lig_c_to_n_col, & ! Input: [real(r8) (:) ] C:N ratio of litter lignin
decomp_k => soilbiogeochem_carbonflux_inst%decomp_k_col , & ! Output: [real(r8) (:,:,:) ] rate for decomposition (1./sec)
Ksoil => soilbiogeochem_carbonflux_inst%Ksoil , & ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec)
spinup_factor => decomp_cascade_con%spinup_factor & ! Input: [real(r8) (:) ] factor for AD spinup associated with each pool
spinup_factor => decomp_cascade_con%spinup_factor , & ! Input: [real(r8) (:) ] factor for AD spinup associated with each pool
h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) (new)
h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) (new)

)

if (get_do_tillage() .and. .not. present(idop)) then
Expand All @@ -992,6 +1024,9 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
! translate to per-second time constant
k_frag = 1._r8 / (secspday * days_per_year * CNParamsShareInst%tau_cwd)

allocate(norm_froot_prof(bounds%begc:bounds%endc, 1:nlevdecomp_full))
norm_froot_prof(bounds%begc:bounds%endc, 1:nlevdecomp_full)=0._r8

! calc ref rate
if ( spinup_state >= 1 ) then
do fc = 1,num_bgc_soilc
Expand Down Expand Up @@ -1062,6 +1097,30 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
end do
endif

! root fraction is used for calculating microbial tunrover rate, it functions as a sort of depth profile
! get root fraction from patch to column level
call p2c(bounds, nlevdecomp_full, &
froot_prof(bounds%begp:bounds%endp,1:nlevdecomp_full), &
norm_froot_prof(bounds%begc:bounds%endc,1:nlevdecomp_full), 'unity')
! normalize root fraction
do fc = 1,num_bgc_soilc
c = filter_bgc_soilc(fc)
min_froot = minval(norm_froot_prof(c,1:nlevdecomp))
max_froot = maxval(norm_froot_prof(c,1:nlevdecomp))
do j = 1,nlevdecomp
! all turnover will be happening in just 1 soil layer
if ( nlevdecomp .eq. 1 ) then
norm_froot_prof(c,j) = 1._r8
else
if (max_froot - min_froot == 0._r8 .or. min_froot == spval .or. max_froot == spval) then
norm_froot_prof(c,j) = min_modifier
else
norm_froot_prof(c,j) = (norm_froot_prof(c,j) - min_froot) / (max_froot - min_froot)
endif
endif
enddo
enddo

!--- time dependent coefficients-----!
if ( nlevdecomp .eq. 1 ) then

Expand Down Expand Up @@ -1468,7 +1527,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, &
end associate

end subroutine decomp_rates_mimics


!Moisture function, based on testbed code: https://github.com/wwieder/biogeochem_testbed/blob/957a5c634b9f2d0b4cdba0faa06b5a91216ace33/SOURCE_CODE/mimics_cycle.f90#L401-L419
real(r8) function r_moist(h2osoi_liq,watsat, h2osoi_ice, dz) !As in testbed (and CLM) version of MIMICS
Expand Down

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