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overflow respiration bug fixes #3491 #4014

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e8fb92b
overflow respiration bug fixes #3491
wwieder Sep 23, 2025
fcface4
Remove commented out sections with c_overflow_vr
slevis-lmwg May 11, 2026
7b2c365
Merge tag 'ctsm5.4.038' into mimics_5.2.028_working
slevis-lmwg May 11, 2026
ef8f5d5
Add c_overflow and c_overflow_vr to history
slevis-lmwg May 11, 2026
12eb3e5
Correct units in a comment, as per code review
slevis-lmwg May 12, 2026
aed226f
Finish adding and rename the c_overflow vars going to history
slevis-lmwg May 12, 2026
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83 changes: 78 additions & 5 deletions src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,9 @@ module SoilBiogeochemCarbonFluxType

! decomposition fluxes
real(r8), pointer :: decomp_cpools_sourcesink_col (:,:,:) ! change in decomposing c pools. Used to update concentrations concurrently with vertical transport (gC/m3/timestep)
real(r8), pointer :: c_overflow_vr (:,:,:) ! vertically-resolved C rejected by microbes that cannot process it (gC/m3/s)
real(r8), pointer :: c_overflow_hr_vr (:,:,:) ! vertically-resolved C rejected by microbes that cannot process it (gC/m3/s) (included in the heterotrophic respiration)
real(r8), pointer :: c_overflow_hr (:,:) ! vertically-integrated C rejected by microbes that cannot process it (gC/m2/s) (included in the heterotrophic respiration)
real(r8), pointer :: c_overflow_hr_sum (:) ! vertically-integrated and summed over all transitions, C rejected by microbes that cannot process it (gC/m2/s) (included in the heterotrophic respiration)
real(r8), pointer :: decomp_cascade_hr_vr_col (:,:,:) ! vertically-resolved het. resp. from decomposing C pools (gC/m3/s)
real(r8), pointer :: decomp_cascade_hr_col (:,:) ! vertically-integrated (diagnostic) het. resp. from decomposing C pools (gC/m2/s)
real(r8), pointer :: decomp_cascade_ctransfer_vr_col (:,:,:) ! vertically-resolved C transferred along deomposition cascade (gC/m3/s)
Expand Down Expand Up @@ -139,8 +141,14 @@ subroutine InitAllocate(this, bounds)
allocate(this%decomp_cpools_sourcesink_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools))
this%decomp_cpools_sourcesink_col(:,:,:)= nan

allocate(this%c_overflow_vr(begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions))
this%c_overflow_vr(:,:,:) = nan
allocate(this%c_overflow_hr_vr(begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions))
this%c_overflow_hr_vr(:,:,:) = nan

allocate(this%c_overflow_hr(begc:endc,1:ndecomp_cascade_transitions))
this%c_overflow_hr(:,:) = nan

allocate(this%c_overflow_hr_sum(begc:endc))
this%c_overflow_hr_sum(:) = nan

allocate(this%decomp_cascade_hr_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_cascade_transitions))
this%decomp_cascade_hr_vr_col(:,:,:)= spval
Expand Down Expand Up @@ -264,6 +272,11 @@ subroutine InitHistory(this, bounds, carbon_type)
ptr_col=this%hr_col)

if (decomp_method == mimics_decomp) then
this%c_overflow_hr_sum(begc:endc) = spval
call hist_addfld1d (fname='COVERFLOW_HR_SUM', units='gC/m^2/s', &
avgflag='A', long_name='C overflow (already included in the heterotrophic respiration)', &
ptr_col=this%c_overflow_hr_sum)

this%michr_col(begc:endc) = spval
call hist_addfld1d (fname='MICC_HR', units='gC/m^2/s', &
avgflag='A', long_name='microbial C heterotrophic respiration: donor-pool based, so expect zero with MIMICS', &
Expand Down Expand Up @@ -307,6 +320,8 @@ subroutine InitHistory(this, bounds, carbon_type)
ptr_col=data2dptr, default='inactive')
end do

this%c_overflow_hr(begc:endc,:) = spval
this%c_overflow_hr_vr(begc:endc,:,:) = spval
this%decomp_cascade_hr_col(begc:endc,:) = spval
this%decomp_cascade_hr_vr_col(begc:endc,:,:) = spval
this%decomp_cascade_ctransfer_col(begc:endc,:) = spval
Expand All @@ -316,6 +331,29 @@ subroutine InitHistory(this, bounds, carbon_type)
do l = 1, ndecomp_cascade_transitions

! output the vertically integrated fluxes only as default
!-- C overflow (ONLY c12 FOR NOW)
if (decomp_method == mimics_decomp) then
data1dptr => this%c_overflow_hr(:,l)
! check to see if there are multiple pathways that include respiration, and if so, note that in the history file
ii = 0
do jj = 1, ndecomp_cascade_transitions
if ( decomp_cascade_con%cascade_donor_pool(jj) == decomp_cascade_con%cascade_donor_pool(l) ) ii = ii+1
end do
if ( ii == 1 ) then
fieldname = &
trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_COVERFLOW'
else
fieldname = &
trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_COVERFLOW_'//&
trim(decomp_cascade_con%decomp_pool_name_short(decomp_cascade_con%cascade_receiver_pool(l)))
endif
longname = 'C overflow (already included in HR) from '//&
trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))
call hist_addfld1d (fname=fieldname, units='gC/m^2/s', &
avgflag='A', long_name=longname, &
ptr_col=data1dptr)
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Here and below: I decided to make them default active while we're testing. Can return them to inactive before merging if we prefer.

end if

!-- HR fluxes
data1dptr => this%decomp_cascade_hr_col(:,l)
! check to see if there are multiple pathways that include respiration, and if so, note that in the history file
Expand Down Expand Up @@ -352,6 +390,31 @@ subroutine InitHistory(this, bounds, carbon_type)

! output the vertically resolved fluxes
if ( nlevdecomp_full > 1 ) then
!-- C overflow (ONLY c12 FOR NOW)
if (decomp_method == mimics_decomp) then
data2dptr => this%c_overflow_hr_vr(:,:,l)
! check to see if there are multiple pathways that include respiration, and if so, note that in the history file
ii = 0
do jj = 1, ndecomp_cascade_transitions
if ( decomp_cascade_con%cascade_donor_pool(jj) == decomp_cascade_con%cascade_donor_pool(l) ) ii = ii+1
end do
if ( ii == 1 ) then
fieldname = &
trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))&
//'_COVERFLOW'//trim(vr_suffix)
else
fieldname = &
trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_COVERFLOW_'//&
trim(decomp_cascade_con%decomp_pool_name_short(decomp_cascade_con%cascade_receiver_pool(l)))&
//trim(vr_suffix)
endif
longname = 'C overflow (already included in HR) from '//&
trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))
call hist_addfld_decomp (fname=fieldname, units='gC/m^3/s', type2d='levdcmp', &
avgflag='A', long_name=longname, &
ptr_col=data2dptr)
end if

!-- HR fluxes
data2dptr => this%decomp_cascade_hr_vr_col(:,:,l)
! check to see if there are multiple pathways that include respiration, and if so, note that in the history file
Expand Down Expand Up @@ -731,8 +794,10 @@ subroutine SetValues ( this, num_column, filter_column, value_column)
do j = 1, nlevdecomp_full
do fi = 1,num_column
i = filter_column(fi)
this%c_overflow_hr_sum(i) = value_column
this%c_overflow_hr(i,l) = value_column
this%c_overflow_hr_vr(i,j,l) = value_column
this%decomp_cascade_hr_col(i,l) = value_column
this%c_overflow_vr(i,j,l) = value_column
this%decomp_cascade_hr_vr_col(i,j,l) = value_column
this%decomp_cascade_ctransfer_col(i,l) = value_column
this%decomp_cascade_ctransfer_vr_col(i,j,l) = value_column
Expand Down Expand Up @@ -850,6 +915,10 @@ subroutine Summary(this, bounds, &
do j = 1,nlevdecomp
do fc = 1,num_bgc_soilc
c = filter_bgc_soilc(fc)
this%c_overflow_hr(c,k) = &
this%c_overflow_hr(c,k) + &
this%c_overflow_hr_vr(c,j,k) * dzsoi_decomp(j)

this%decomp_cascade_hr_col(c,k) = &
this%decomp_cascade_hr_col(c,k) + &
this%decomp_cascade_hr_vr_col(c,j,k) * dzsoi_decomp(j)
Expand Down Expand Up @@ -898,13 +967,14 @@ subroutine Summary(this, bounds, &
end do
end do

! soil organic matter heterotrophic respiration
! soil organic matter heterotrophic respiration
associate(is_soil => decomp_cascade_con%is_soil) ! TRUE => pool is a soil pool
do k = 1, ndecomp_cascade_transitions
if ( is_soil(decomp_cascade_con%cascade_donor_pool(k)) ) then
do fc = 1,num_bgc_soilc
c = filter_bgc_soilc(fc)
this%somhr_col(c) = this%somhr_col(c) + this%decomp_cascade_hr_col(c,k)
this%c_overflow_hr_sum(c) = this%c_overflow_hr_sum(c) + this%c_overflow_hr(c,k)
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Rather than adding a unique new loop to sum the c_overflow_hr_sum variable, I introduced partial sums in the existing loops. This line here is in the "is_soil" loop, next is the litter loop, then cwd, and last the is_microbe loop.

@wwieder based on what you said this morning, we may need to have this in one or some of those and not all, but I went for full coverage since I do not know.

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@wwieder wwieder May 13, 2026

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I think that's fine. I'm curious to see what the history files from MIMICS tests look like, once you are able to run them on derecho.

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I think that's fine. I'm curious to see what the history files from MIMICS tests look like, once you are able to run them on derecho.

@wwieder in the next post I have posted four mimics tests that you could look at in this directory:
/glade/work/slevis/git_people/wwieder/mimics_5.2.028_working/tests_0513-205326de/

end do
end if
end do
Expand All @@ -917,6 +987,7 @@ subroutine Summary(this, bounds, &
do fc = 1,num_bgc_soilc
c = filter_bgc_soilc(fc)
this%lithr_col(c) = this%lithr_col(c) + this%decomp_cascade_hr_col(c,k)
this%c_overflow_hr_sum(c) = this%c_overflow_hr_sum(c) + this%c_overflow_hr(c,k)
end do
end if
end do
Expand All @@ -929,6 +1000,7 @@ subroutine Summary(this, bounds, &
do fc = 1,num_bgc_soilc
c = filter_bgc_soilc(fc)
this%cwdhr_col(c) = this%cwdhr_col(c) + this%decomp_cascade_hr_col(c,k)
this%c_overflow_hr_sum(c) = this%c_overflow_hr_sum(c) + this%c_overflow_hr(c,k)
end do
end if
end do
Expand All @@ -941,6 +1013,7 @@ subroutine Summary(this, bounds, &
do fc = 1,num_bgc_soilc
c = filter_bgc_soilc(fc)
this%michr_col(c) = this%michr_col(c) + this%decomp_cascade_hr_col(c,k)
this%c_overflow_hr_sum(c) = this%c_overflow_hr_sum(c) + this%c_overflow_hr(c,k)
end do
end if
end do
Expand Down
11 changes: 1 addition & 10 deletions src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -262,8 +262,6 @@ subroutine SoilBiogeochemCompetition (bounds, num_bgc_soilc, filter_bgc_soilc,nu
sminn_vr => soilbiogeochem_nitrogenstate_inst%sminn_vr_col , & ! Input: [real(r8) (:,:) ] (gN/m3) soil mineral N
smin_nh4_vr => soilbiogeochem_nitrogenstate_inst%smin_nh4_vr_col , & ! Input: [real(r8) (:,:) ] (gN/m3) soil mineral NH4
smin_no3_vr => soilbiogeochem_nitrogenstate_inst%smin_no3_vr_col , & ! Input: [real(r8) (:,:) ] (gN/m3) soil mineral NO3

c_overflow_vr => soilbiogeochem_carbonflux_inst%c_overflow_vr , & ! Output: [real(r8) (:,:,:)] (gC/m3/s) vertically-resolved C rejected by microbes that cannot process it
cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool , & ! Input: [integer (:) ] which pool is C added to for a given decomposition step

pot_f_nit_vr => soilbiogeochem_nitrogenflux_inst%pot_f_nit_vr_col , & ! Input: [real(r8) (:,:) ] (gN/m3/s) potential soil nitrification flux
Expand Down Expand Up @@ -920,26 +918,19 @@ subroutine SoilBiogeochemCompetition (bounds, num_bgc_soilc, filter_bgc_soilc,nu
cascade_receiver_pool(k) == i_oli_mic) then
sum_ndemand_vr(c,j) = sum_no3_demand_scaled(c,j) + &
sum_nh4_demand_scaled(c,j)
! WW effectively turn this off now, since pmnf_decomp_cascade < 0 for mineralization
if (pmnf_decomp_cascade(c,j,k) > 0.0_r8 .and. &
sum_ndemand_vr(c,j) > 0.0_r8) then
amnf_immob_vr = (sminn_vr(c,j) / dt) * &
(pmnf_decomp_cascade(c,j,k) / &
sum_ndemand_vr(c,j))
n_deficit_vr = pmnf_decomp_cascade(c,j,k) - &
amnf_immob_vr
c_overflow_vr(c,j,k) = &
n_deficit_vr * p_decomp_cn_gain(c,j,cascade_receiver_pool(k))
else ! not pmnf and sum_ndemand > 0
c_overflow_vr(c,j,k) = 0.0_r8
end if
else ! not microbes receiving
c_overflow_vr(c,j,k) = 0.0_r8
end if
end do
end do
end do
else ! not mimics_decomp
c_overflow_vr(:,:,:) = 0.0_r8
end if

if(.not.local_use_fun)then
Expand Down
4 changes: 2 additions & 2 deletions src/soilbiogeochem/SoilBiogeochemDecompMod.F90
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Expand Up @@ -127,7 +127,7 @@ subroutine SoilBiogeochemDecomp (bounds, num_bgc_soilc, filter_bgc_soilc,
net_nmin => soilbiogeochem_nitrogenflux_inst%net_nmin_col , & ! Output: [real(r8) (:) ] net rate of N mineralization (gN/m2/s)

w_scalar => soilbiogeochem_carbonflux_inst%w_scalar_col , & ! Input: [real(r8) (:,:) ] fraction by which decomposition is limited by moisture availability
c_overflow_vr => soilbiogeochem_carbonflux_inst%c_overflow_vr , & ! Input: [real(r8) (:,:,:) ] vertically-resolved C rejected by microbes that cannot process it (gC/m3/s)
c_overflow_hr_vr => soilbiogeochem_carbonflux_inst%c_overflow_hr_vr , & ! Input: [real(r8) (:,:,:) ] vertically-resolved C rejected by microbes that cannot process it (gC/m3/s)
decomp_cascade_hr_vr => soilbiogeochem_carbonflux_inst%decomp_cascade_hr_vr_col , & ! Output: [real(r8) (:,:,:) ] vertically-resolved het. resp. from decomposing C pools (gC/m3/s)
decomp_cascade_ctransfer_vr => soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_vr_col , & ! Output: [real(r8) (:,:,:) ] vertically-resolved het. resp. from decomposing C pools (gC/m3/s)
phr_vr => soilbiogeochem_carbonflux_inst%phr_vr_col , & ! Input: [real(r8) (:,:) ] potential HR (gC/m3/s)
Expand Down Expand Up @@ -194,7 +194,7 @@ subroutine SoilBiogeochemDecomp (bounds, num_bgc_soilc, filter_bgc_soilc,
if (decomp_method == mimics_decomp) then
decomp_cascade_hr_vr(c,j,k) = min( &
p_decomp_cpool_loss(c,j,k), &
decomp_cascade_hr_vr(c,j,k) + c_overflow_vr(c,j,k))
decomp_cascade_hr_vr(c,j,k) + c_overflow_hr_vr(c,j,k))
decomp_cascade_ctransfer_vr(c,j,k) = max(0.0_r8, p_decomp_cpool_loss(c,j,k) - decomp_cascade_hr_vr(c,j,k))
end if
if (decomp_npools_vr(c,j,cascade_donor_pool(k)) > 0._r8 .and. cascade_receiver_pool(k) /= i_atm) then
Expand Down
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