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Updates and fixes to maintenance respiration #138

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merged 13 commits into from
Oct 31, 2016
Merged

Updates and fixes to maintenance respiration #138

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32dd172
Science fixes on sapwood and fine root respiration. First pass, no te…
rgknox Oct 7, 2016
58e27de
fixed typo where MR of bg sapwood was double multiplied by bg root fr…
rgknox Oct 8, 2016
4416814
Added several AR diagnostics. Also changed the units of dark-respira…
rgknox Oct 10, 2016
0ca158e
minor fix to update the pft index during the scpf output for photosyn…
rgknox Oct 12, 2016
a3e1966
Merge resolution. EDCLMLinkMod was removed in master. That file had …
rgknox Oct 12, 2016
4ecda62
minor fix, livecrootn was still in a print statement that I overlooke…
rgknox Oct 12, 2016
d0150fe
fixed hard-coded pft index in grperc found in photosynthesis
rgknox Oct 13, 2016
f34bcb8
Merge branch 'andre-fates-constants' into rgknox-ckoven-froot-mr
rgknox Oct 13, 2016
15824a2
added some more global constants and uses in photosynthesis. Also, fi…
rgknox Oct 14, 2016
fe9f7a1
intercellular co2 in photosynthesis was being represented as an array…
rgknox Oct 14, 2016
fb3e9ca
renamed some local variables related to nitrogen content.
rgknox Oct 18, 2016
44d762d
Added cohort type variables size_class and size_by_pft_class. These v…
rgknox Oct 18, 2016
8e2b86f
Various syntactical fixes including: making rgas more explicit in its…
rgknox Oct 27, 2016
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27 changes: 7 additions & 20 deletions components/clm/src/ED/biogeochem/EDCanopyStructureMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -658,6 +658,7 @@ subroutine canopy_summarization( nsites, sites, bc_in )

use FatesInterfaceMod , only : bc_in_type
use EDPatchDynamicsMod , only : set_patchno
use EDCohortDynamicsMod , only : size_and_type_class_index
use EDGrowthFunctionsMod , only : tree_lai, c_area
use EDEcophysConType , only : EDecophyscon
use EDtypesMod , only : area
Expand All @@ -675,7 +676,6 @@ subroutine canopy_summarization( nsites, sites, bc_in )
integer :: ft ! plant functional type
integer :: ifp
integer :: patchn ! identification number for each patch.
real(r8) :: coarse_wood_frac
real(r8) :: canopy_leaf_area ! total amount of leaf area in the vegetated area. m2.

!----------------------------------------------------------------------
Expand Down Expand Up @@ -710,26 +710,13 @@ subroutine canopy_summarization( nsites, sites, bc_in )
do while(associated(currentCohort))

ft = currentCohort%pft
currentCohort%livestemn = currentCohort%bsw / pftcon%leafcn(currentCohort%pft)

currentCohort%livecrootn = 0.0_r8

if (pftcon%woody(ft) == 1) then
coarse_wood_frac = 0.5_r8
else
coarse_wood_frac = 0.0_r8
end if

if ( DEBUG ) then
write(fates_log(),*) 'canopy_summarization 724 ',currentCohort%livecrootn
write(fates_log(),*) 'canopy_summarization 725 ',currentCohort%br
write(fates_log(),*) 'canopy_summarization 726 ',coarse_wood_frac
write(fates_log(),*) 'canopy_summarization 727 ',pftcon%leafcn(ft)
endif

currentCohort%livecrootn = currentCohort%br * coarse_wood_frac / pftcon%leafcn(ft)


if ( DEBUG ) write(fates_log(),*) 'canopy_summarization 732 ',currentCohort%livecrootn
! Update the cohort's index within the size bin classes
! Update the cohort's index within the SCPF classification system
call size_and_type_class_index(currentCohort%dbh,currentCohort%pft, &
currentCohort%size_class,currentCohort%size_by_pft_class)


currentCohort%b = currentCohort%balive+currentCohort%bdead+currentCohort%bstore
currentCohort%treelai = tree_lai(currentCohort)
Expand Down
45 changes: 31 additions & 14 deletions components/clm/src/ED/biogeochem/EDCohortDynamicsMod.F90
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Expand Up @@ -27,7 +27,7 @@ module EDCohortDynamicsMod
public :: sort_cohorts
public :: copy_cohort
public :: count_cohorts
! public :: countCohorts
public :: size_and_type_class_index
public :: allocate_live_biomass

logical, parameter :: DEBUG = .false. ! local debug flag
Expand Down Expand Up @@ -92,6 +92,9 @@ subroutine create_cohort(patchptr, pft, nn, hite, dbh, &
new_cohort%balive = balive
new_cohort%bstore = bstore

call size_and_type_class_index(new_cohort%dbh,new_cohort%pft, &
new_cohort%size_class,new_cohort%size_by_pft_class)

if ( DEBUG ) write(iulog,*) 'EDCohortDyn I ',bstore

if (new_cohort%dbh <= 0.0_r8 .or. new_cohort%n == 0._r8 .or. new_cohort%pft == 0 &
Expand Down Expand Up @@ -316,6 +319,8 @@ subroutine nan_cohort(cc_p)
currentCohort%canopy_layer = 999 ! canopy status of cohort (1 = canopy, 2 = understorey, etc.)
currentCohort%NV = 999 ! Number of leaf layers: -
currentCohort%status_coh = 999 ! growth status of plant (2 = leaves on , 1 = leaves off)
currentCohort%size_class = 999 ! size class index
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These magic numbers should be replaced with a parameter.

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ok, I grabbed your definition of fates_unset_int from the history PR, I will use that, we should expect a trivial merge conflict with either this or History refactors, which every gets pulled second.

I'm going to leave the nan initialization in that subroutine as is. I will be investigating that part of the code anyway while I'm applying the fix to #133.

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I'm not concerned about the conflict, it's easy enough to resolve. There are going to be a few conflicts with the hist mod anyway. At a minimum the set_hist_var calls need to be updated.

currentCohort%size_by_pft_class = 999 ! size by pft classification index

currentCohort%n = nan ! number of individuals in cohort per 'area' (10000m2 default)
currentCohort%dbh = nan ! 'diameter at breast height' in cm
Expand Down Expand Up @@ -361,7 +366,7 @@ subroutine nan_cohort(cc_p)


!RESPIRATION
currentCohort%rd = nan
currentCohort%rdark = nan
currentCohort%resp_m = nan ! Maintenance respiration. kGC/cohort/year
currentCohort%resp_g = nan ! Growth respiration. kGC/cohort/year
currentCohort%livestem_mr = nan ! Live stem maintenance respiration. kgC/indiv/s-1
Expand All @@ -381,11 +386,6 @@ subroutine nan_cohort(cc_p)
currentCohort%leaf_litter = nan ! leaf litter from phenology: KgC/m2
currentCohort%woody_turnover = nan ! amount of wood lost each day: kgC/indiv/year. Currently set to zero.

! NITROGEN POOLS
currentCohort%livestemn = nan ! live stem nitrogen : KgN/invid
currentCohort%livecrootn = nan ! live coarse root nitrogen: KgN/invid
currentCohort%frootn = nan ! fine root nitrogen : KgN/invid

! VARIABLES NEEDED FOR INTEGRATION
currentCohort%dndt = nan ! time derivative of cohort size
currentCohort%dhdt = nan ! time derivative of height
Expand Down Expand Up @@ -423,7 +423,7 @@ subroutine zero_cohort(cc_p)

currentCohort%NV = 0
currentCohort%status_coh = 0
currentCohort%rd = 0._r8
currentCohort%rdark = 0._r8
currentCohort%resp_m = 0._r8
currentCohort%resp_g = 0._r8
currentCohort%livestem_mr = 0._r8
Expand Down Expand Up @@ -1040,18 +1040,13 @@ subroutine copy_cohort( currentCohort,copyc )
n%npp_store = o%npp_store

!RESPIRATION
n%rd = o%rd
n%rdark = o%rdark
n%resp_m = o%resp_m
n%resp_g = o%resp_g
n%livestem_mr = o%livestem_mr
n%livecroot_mr = o%livecroot_mr
n%froot_mr = o%froot_mr

! NITROGEN POOLS
n%livestemn = o%livestemn
n%livecrootn = o%livecrootn
n%frootn = o%frootn

! ALLOCATION
n%md = o%md
n%leaf_md = o%leaf_md
Expand Down Expand Up @@ -1137,6 +1132,28 @@ function count_cohorts( currentPatch ) result ( backcount )

end function count_cohorts

! =====================================================================================

subroutine size_and_type_class_index(dbh,pft,size_class,size_by_pft_class)

use EDTypesMod, only: sclass_ed, &
nlevsclass_ed

! Arguments
real(r8),intent(in) :: dbh
integer,intent(in) :: pft
integer,intent(out) :: size_class
integer,intent(out) :: size_by_pft_class

size_class = count(dbh-sclass_ed.ge.0.0)
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Need an _r8.


size_by_pft_class = (pft-1)*nlevsclass_ed+size_class

return
end subroutine size_and_type_class_index



!-------------------------------------------------------------------------------------!
! function countCohorts( bounds, ed_allsites_inst ) result ( totNumCohorts )
!
Expand Down
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