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Use HLM-provided land-use time series data to drive FATES harvest #663

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merged 42 commits into from
Jul 29, 2020
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Use HLM-provided land-use time series data to drive FATES harvest #663

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e9faf6a
Merge pull request #1 from NGEET/master
aldivi Feb 9, 2020
12e9e1c
Merge pull request #2 from NGEET/master
aldivi Feb 20, 2020
14e34f4
Initial setup for receiving harvest from hlm
May 7, 2020
f0dc220
Initial code for land use harvest passed to fates
May 12, 2020
22adbed
Made sure that LoggingMortality_frac had arguments
May 12, 2020
d292629
Fixed num_lu_harvest_cats variable bug
May 12, 2020
40a3c0a
HLM harvest data passed to FATES
May 13, 2020
8ffedd9
merged master (post-circulur-dep-fix) and resovled conflicts
ckoven May 19, 2020
30af2ac
bugfixes to get it to compile and run
ckoven May 21, 2020
c1e8b35
added disturbance rate diagnostics to site type and history vars
ckoven Jun 2, 2020
597f404
added site-level diagnostic and history variable for tracking primary…
ckoven Jun 2, 2020
0b6ab98
changed patch insertion logic to put newly-disturbed primary patch af…
ckoven Jun 2, 2020
6320c5c
added logic to normalize logging rates by primary and secondary fraction
ckoven Jun 5, 2020
4517c20
adding non-woody PFT area to secondary patches at same rate
ckoven Jun 5, 2020
42e3c2e
added logic to disturb a fraction of bare-ground patch area, if any e…
ckoven Jun 5, 2020
7847c61
added calculation of total_canopy_area prior to bare-ground harvest-a…
ckoven Jun 8, 2020
29dabcc
added diagnostic history variable of primary forest rates from BCs
ckoven Jun 8, 2020
6b574f9
fixed error on logging-related disturbance of bare-ground area
ckoven Jun 9, 2020
3afe8ed
adding patch area conservation error term to history output
ckoven Jun 9, 2020
2bf49b8
Revert "adding patch area conservation error term to history output"
ckoven Jun 9, 2020
a9bb15e
Revert "added diagnostic history variable of primary forest rates fro…
ckoven Jun 9, 2020
3d32b1a
added site-level diagnostic variable for carbon flux of harvested wood
ckoven Jun 10, 2020
0cd417e
Updated fates logging calc to account for all secondary land creation
Jun 12, 2020
1749dc4
bugfixes on prior
ckoven Jun 17, 2020
4f9a485
added dbhmax logic to logging code
ckoven Jun 17, 2020
a317ef5
bugfix and changed value of use_this_pft when not on restart to 1.
ckoven Jun 18, 2020
c2332b9
added PFTcanopycrownarea variable
ckoven May 6, 2020
b78f410
adding more diagnostics to dump_patch
ckoven Jun 22, 2020
2905a9b
adding more logic in fuse_patches to handle case where only tiny amou…
ckoven Jun 22, 2020
5e6fa21
bugfix on history-outputting of site-level diagnostic variables
ckoven Jun 23, 2020
cbc4ca0
fixing conservation of patch%age_since_anthro_disturbance during patc…
ckoven Jun 25, 2020
bb04f89
Apply suggestions from code review
ckoven Jul 1, 2020
dafd55f
Apply suggestions from code review
ckoven Jul 1, 2020
7afdb04
made a bunch of minor changes based on code review
ckoven Jul 1, 2020
3807a36
moved harvest unit specification to bc_in structure
ckoven Jul 2, 2020
d08dfd4
clarifying some variable names and documentation in spawn_patches
ckoven Jul 2, 2020
8d9f189
replacing valeu of cpatch%age_since_anthro_disturbance for primary pa…
ckoven Jul 6, 2020
568648f
changes to land degradation logic to fix bugs
ckoven Jul 22, 2020
abd57ec
bugfixes upon bugfixes
ckoven Jul 22, 2020
8872a91
adding runtime check on logging parameter values
ckoven Jul 22, 2020
4f087cf
Merge branch 'ngeet-master' into fates_harvest_offmaster-deconflict
glemieux Jul 23, 2020
ffaa76e
Merge pull request #10 from glemieux/fates_harvest_offmaster-deconflict
ckoven Jul 24, 2020
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192 changes: 171 additions & 21 deletions biogeochem/EDLoggingMortalityMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ module EDLoggingMortalityMod
use EDParamsMod , only : logging_export_frac
use EDParamsMod , only : logging_event_code
use EDParamsMod , only : logging_dbhmin
use EDParamsMod , only : logging_dbhmax
use EDParamsMod , only : logging_collateral_frac
use EDParamsMod , only : logging_direct_frac
use EDParamsMod , only : logging_mechanical_frac
Expand All @@ -44,6 +45,8 @@ module EDLoggingMortalityMod
use FatesInterfaceTypesMod , only : hlm_model_day
use FatesInterfaceTypesMod , only : hlm_day_of_year
use FatesInterfaceTypesMod , only : hlm_days_per_year
use FatesInterfaceTypesMod , only : hlm_use_lu_harvest
use FatesInterfaceTypesMod , only : hlm_num_lu_harvest_cats
use FatesInterfaceTypesMod , only : hlm_use_logging
use FatesInterfaceTypesMod , only : hlm_use_planthydro
use FatesConstantsMod , only : itrue,ifalse
Expand All @@ -55,6 +58,9 @@ module EDLoggingMortalityMod
use PRTGenericMod , only : sapw_organ, struct_organ, leaf_organ
use PRTGenericMod , only : fnrt_organ, store_organ, repro_organ
use FatesAllometryMod , only : set_root_fraction
use FatesConstantsMod , only : primaryforest, secondaryforest, secondary_age_threshold
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An idea for down the road, in the US Forest Service most harvesting/logging is done with a specific age class outcome as an object. The classes are: even-age (one age class, total range of ages present <20% of the rotation age), two-aged (two age classes), and uneven-aged (three or more distinct age classes), all of which have their own harvest practices associated with them. This may be useful designation in the future as more logging/harvest features are added.

use FatesConstantsMod , only : fates_tiny
use FatesConstantsMod, only : fates_check_param_set

implicit none
private
Expand All @@ -80,6 +86,9 @@ module EDLoggingMortalityMod
public :: logging_litter_fluxes
public :: logging_time
public :: IsItLoggingTime
public :: get_harvest_rate_area
integer, parameter, public :: hlm_harvest_area_fraction = 1
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integer, parameter, public :: hlm_harvest_carbon = 2
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contains

Expand All @@ -104,10 +113,17 @@ subroutine IsItLoggingTime(is_master,currentSite)
logging_time = .false.
icode = int(logging_event_code)

! this is true for either hlm harvest or fates logging
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How is it true for both those cases? Is it set elsewhere?

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To clarify, hlm_use_logging is set to true if hlm harvest is active or if fates logging is active (based on namelist inputs). This is so that just one variable is used to determine whether today is a logging/harvest day or not.
The relationship between hlm harvest and logging is this:
Hlm harvest uses hlm input timeseries of harvest prescription to drive the fates logging module, so if hlm harvest is on, then fates logging is automatically turned on.
The fates logging module can still be used on its own by setting its namelist option to true (use_fates_logging), and not setting the hlm do_harvest namelist option (leaving as false).

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Ah yes. I think I understood this more as I went through the code...

if(hlm_use_logging.eq.ifalse) return

! all of these are valid for hlm harvest
! so adjust annual harvest inputs accordingly in LoggingMortality_frac
! note that the specific event will allow only one hlm harvest, regardless of input
! code 3, every day, may not work properly because of the exclusive mortality selection
! even less fequent low harvest rates may be excluded - may need to give harvest priority

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@rosiealice rosiealice Jul 1, 2020 •
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Are they valid in the sense that logging happens in addition to the harvesting? This maybe needs elaborating.

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This means that they can each be set as an input value, and they should run.
The issue is that if the harvest is distributed in time it may be superseded by another disturbance on any given day because the largest disturbance wins the day (which would reduce the total annual harvest simulated).

if(icode .eq. 1) then
! Logging is turned off
! Logging is turned off - not sure why we need another switch
logging_time = .false.

else if(icode .eq. 2) then
Expand Down Expand Up @@ -168,41 +184,88 @@ end subroutine IsItLoggingTime
! ======================================================================================

subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
lmort_collateral,lmort_infra, l_degrad )
lmort_collateral,lmort_infra, l_degrad, &
hlm_harvest, hlm_harvest_catnames, &
use_history, secondary_age, &
frac_site_primary)

! Arguments
integer, intent(in) :: pft_i ! pft index
real(r8), intent(in) :: dbh ! diameter at breast height (cm)
integer, intent(in) :: canopy_layer ! canopy layer of this cohort
real(r8), intent(in) :: hlm_harvest(:) ! annual harvest rate per hlm category
character(len=64), intent(in) :: hlm_harvest_catnames(:) ! names of hlm harvest categories
integer, intent(in) :: use_history ! patch level anthro_disturbance_label
real(r8), intent(in) :: secondary_age ! patch level age_since_anthro_disturbance
real(r8), intent(out) :: lmort_direct ! direct (harvestable) mortality fraction
real(r8), intent(out) :: lmort_collateral ! collateral damage mortality fraction
real(r8), intent(out) :: lmort_infra ! infrastructure mortality fraction
real(r8), intent(out) :: l_degrad ! fraction of trees that are not killed
! but suffer from forest degradation (i.e. they
! are moved to newly-anthro-disturbed secondary
! forest patch)
real(r8), intent(in) :: frac_site_primary

! Parameters
real(r8), parameter :: adjustment = 1.0 ! adjustment for mortality rates

! Local variables
real(r8) :: harvest_rate ! the final harvest rate to apply to this cohort today

! todo: probably lower the dbhmin default value to 30 cm
! todo: change the default logging_event_code to 1 september (-244)
! todo: change the default logging_direct_frac to 1.0 for cmip inputs
! todo: check outputs against the LUH2 carbon data
! todo: eventually set up distinct harvest practices, each with a set of input paramaeters
! todo: implement harvested carbon inputs

if (logging_time) then
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! Pass logging rates to cohort level

if (hlm_use_lu_harvest == 0) then
! 0=use fates logging parameters directly when logging_time == .true.
! this means harvest the whole cohort area
harvest_rate = 1._r8

else if (hlm_use_lu_harvest == hlm_harvest_area_fraction) then
! 1=use area fraction from hlm
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! combine forest and non-forest fracs and then apply:
! primary and secondary area fractions to the logging rates, which are fates parameters

! Definitions of the underlying harvest land category variables
! these are hardcoded to match the LUH input data via landuse.timseries file (see dynHarvestMod)
! these are fraction of vegetated area harvested, split into five land category variables
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! HARVEST_VH1 = harvest from primary forest
! HARVEST_VH2 = harvest from primary non-forest
! HARVEST_SH1 = harvest from secondary mature forest
! HARVEST_SH2 = harvest from secondary young forest
! HARVEST_SH3 = harvest from secondary non-forest (assume this is young for biomass)

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call get_harvest_rate_area (use_history, hlm_harvest_catnames, hlm_harvest, &
frac_site_primary, secondary_age, harvest_rate)

else if (hlm_use_lu_harvest == hlm_harvest_carbon) then
! 2=use carbon from hlm
! not implemented yet
write(fates_log(),*) 'HLM harvest carbon data not implemented yet. Exiting.'
call endrun(msg=errMsg(sourcefile, __LINE__))
endif

! transfer of area to secondary land is based on overall area affected, not just logged crown area
! l_degrad accounts for the affected area between logged crowns
if(EDPftvarcon_inst%woody(pft_i) == 1)then ! only set logging rates for trees

! Pass logging rates to cohort level

if (dbh >= logging_dbhmin ) then
lmort_direct = logging_direct_frac * adjustment
l_degrad = 0._r8

if (dbh >= logging_dbhmin .and. .not. &
((logging_dbhmax < fates_check_param_set) .and. (dbh < logging_dbhmax )) ) then
lmort_direct = harvest_rate * logging_direct_frac
l_degrad = harvest_rate * (1._r8 - logging_direct_frac)
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else
lmort_direct = 0.0_r8
l_degrad = logging_direct_frac * adjustment
lmort_direct = 0.0_r8
l_degrad = harvest_rate
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Does this mean that if trees are not large enough to log, the cohort is still degraded/moved to secondary patch?

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Oh, never mind I see, background degradation rate regardless of logging.

end if

if (dbh >= logging_dbhmax_infra) then
lmort_infra = 0.0_r8
l_degrad = l_degrad + logging_mechanical_frac * adjustment
l_degrad = l_degrad + harvest_rate * logging_mechanical_frac
else
lmort_infra = logging_mechanical_frac * adjustment
lmort_infra = harvest_rate * logging_mechanical_frac
end if
!damage rates for size class < & > threshold_size need to be specified seperately

Expand All @@ -213,16 +276,16 @@ subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
! for collateral damage, even understory collateral damage.

if (canopy_layer .eq. 1) then
lmort_collateral = logging_collateral_frac * adjustment
lmort_collateral = harvest_rate * logging_collateral_frac
else
lmort_collateral = 0._r8
lmort_collateral = 0._r8
endif

else
else ! non-woody plants in the canopy still become moved to secondary patch at same rate
lmort_direct = 0.0_r8
lmort_collateral = 0.0_r8
lmort_infra = 0.0_r8
l_degrad = 0.0_r8
lmort_infra = harvest_rate * logging_mechanical_frac
l_degrad = harvest_rate
end if
else
lmort_direct = 0.0_r8
Expand All @@ -235,6 +298,93 @@ end subroutine LoggingMortality_frac

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

subroutine get_harvest_rate_area (use_history, hlm_harvest_catnames, hlm_harvest, &
frac_site_primary, secondary_age, harvest_rate)


! -------------------------------------------------------------------------------------------
!
! DESCRIPTION:
! get the area-based harvest rates based on info passed to FATES from the bioundary conditions in.
! assumes logging_time == true

! Arguments
real(r8), intent(in) :: hlm_harvest(:) ! annual harvest rate per hlm category
character(len=64), intent(in) :: hlm_harvest_catnames(:) ! names of hlm harvest categories
integer, intent(in) :: use_history ! patch level anthro_disturbance_label
real(r8), intent(in) :: secondary_age ! patch level age_since_anthro_disturbance
real(r8), intent(in) :: frac_site_primary
real(r8), intent(out) :: harvest_rate

! Local Variables
integer :: h_index ! for looping over harvest categories
integer :: icode ! Integer equivalent of the event code (parameter file only allows reals)

! Parameters
real(r8), parameter :: months_per_year = 12.0
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! determine the annual hlm harvest rate for the current cohort based on patch info
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harvest_rate = 0._r8
do h_index = 1,hlm_num_lu_harvest_cats
if (use_history .eq. primaryforest) then
if(hlm_harvest_catnames(h_index) .eq. "HARVEST_VH1" .or. &
hlm_harvest_catnames(h_index) .eq. "HARVEST_VH2") then
harvest_rate = harvest_rate + hlm_harvest(h_index)
endif
else if (use_history .eq. secondaryforest .and. &
secondary_age >= secondary_age_threshold) then
if(hlm_harvest_catnames(h_index) .eq. "HARVEST_SH1") then
harvest_rate = harvest_rate + hlm_harvest(h_index)
endif
else if (use_history .eq. secondaryforest .and. &
secondary_age < secondary_age_threshold) then
if(hlm_harvest_catnames(h_index) .eq. "HARVEST_SH2" .or. &
hlm_harvest_catnames(h_index) .eq. "HARVEST_SH3") then
harvest_rate = harvest_rate + hlm_harvest(h_index)
endif
endif
end do

! normalize by site-level fractio primary or secondary forest fraction
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! since harvest_rate is specified in fraction of the gridcell
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! also need to put a cap so as not to harvest more primary or secondary area than there is in a gridcell
if (use_history .eq. primaryforest) then
if (frac_site_primary .gt. fates_tiny) then
harvest_rate = min((harvest_rate / frac_site_primary),frac_site_primary)
else
harvest_rate = 0._r8
endif
else
if ((1._r8-frac_site_primary) .gt. fates_tiny) then
harvest_rate = min((harvest_rate / (1._r8-frac_site_primary)),&
(1._r8-frac_site_primary))
else
harvest_rate = 0._r8
endif
endif

! calculate today's harvest rate
! whether to harvest today has already been determined by IsItLoggingTime
! for icode == 2, icode < 0, and icode > 10000 apply the annual rate one time (no calc)
! Bad logging event flag is caught in IsItLoggingTime, so don't check it here
icode = int(logging_event_code)
if(icode .eq. 1) then
! Logging is turned off - not sure why we need another switch
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harvest_rate = 0._r8
else if(icode .eq. 3) then
! Logging event every day - this may not work due to the mortality exclusivity
harvest_rate = harvest_rate / hlm_days_per_year
else if(icode .eq. 4) then
! logging event once a month
if(hlm_current_day.eq.1 ) then
harvest_rate = harvest_rate / months_per_year
end if
end if

end subroutine get_harvest_rate_area

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

subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site_areadis)

! -------------------------------------------------------------------------------------------
Expand Down
10 changes: 8 additions & 2 deletions biogeochem/EDMortalityFunctionsMod.F90
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Expand Up @@ -208,7 +208,7 @@ end subroutine mortality_rates

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

subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
subroutine Mortality_Derivative( currentSite, currentCohort, bc_in, frac_site_primary)

!
! !DESCRIPTION:
Expand All @@ -224,6 +224,7 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
type(ed_site_type), intent(inout), target :: currentSite
type(ed_cohort_type),intent(inout), target :: currentCohort
type(bc_in_type), intent(in) :: bc_in
real(r8), intent(in) :: frac_site_primary
!
! !LOCAL VARIABLES:
real(r8) :: cmort ! starvation mortality rate (fraction per year)
Expand All @@ -245,7 +246,12 @@ subroutine Mortality_Derivative( currentSite, currentCohort, bc_in)
currentCohort%lmort_direct, &
currentCohort%lmort_collateral, &
currentCohort%lmort_infra, &
currentCohort%l_degrad)
currentCohort%l_degrad, &
bc_in%hlm_harvest, &
bc_in%hlm_harvest_catnames, &
currentCohort%patchptr%anthro_disturbance_label, &
currentCohort%patchptr%age_since_anthro_disturbance, &
frac_site_primary)



Expand Down
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