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conflict resolutions #7

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merged 37 commits into from
Jan 14, 2019
Merged

conflict resolutions #7

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44544db
Merge remote-tracking branch 'ngeet_repo/master'
jkshuman Sep 25, 2018
3c8e46e
changed diagnostic calculation of fmort to correct for changing N. a…
ckoven Aug 20, 2018
7ec0472
stratified site-level fire mort by canopy, incldued carbon flux term,…
ckoven Aug 20, 2018
eff4c3f
Typo update in support of fire mortality diagnostics
jkshuman Oct 3, 2018
040a2c4
Correct typo for diffuse surface albedo
jkshuman Oct 3, 2018
8577d46
Conflict Resolutions with PARTEH
rgknox Oct 24, 2018
6f0efd1
Merge pull request #1 from rgknox/fire_mortality
jkshuman Oct 25, 2018
90310d7
Merge remote-tracking branch 'ngeet_repo/master'
jkshuman Dec 20, 2018
96a28d6
Remove Lasslop et al 2014 wind effect
jkshuman Dec 20, 2018
3fe14e5
Remove SF_val_wind_max from SFParams
jkshuman Dec 20, 2018
34f580c
remove wind_max from SFMainMod
Dec 20, 2018
9f5b6a4
Expanded reporting of carbon conservation failure. Updated cohort and…
rgknox Dec 24, 2018
e64f26a
Add some numerical protections to zero area patch spawning
rgknox Dec 27, 2018
b8df885
Fix to net assimilation tracker used for trimming
rgknox Dec 27, 2018
979cb6b
Merge pull request #455 from jkshuman/remove_Lasslop_wind
rgknox Jan 2, 2019
b935cce
Merge branch 'master' into rgknox-spawnpatch-cfix
rgknox Jan 3, 2019
0990f54
Moved a cal to zero distrubance rates to outside of a conditional.
rgknox Jan 3, 2019
b879547
Removed unused global call to SiteCarbonStock and removed commented o…
rgknox Jan 4, 2019
a6ac612
Removed commented out code
rgknox Jan 4, 2019
6f4d4e3
Merge pull request #458 from rgknox/rgknox-spawnpatch-cfix
rgknox Jan 7, 2019
120e49c
Merge pull request #459 from rgknox/rgknox-lmr-fix
rgknox Jan 7, 2019
2b5330b
Conflict resolutions, and fixing some diagnostics that sum over nclmax
rgknox Jan 7, 2019
1828428
Minor fixes related to new fire mortality diagnostics
rgknox Jan 8, 2019
898ac97
Merge pull request #2 from rgknox/fire_mortality
jkshuman Jan 8, 2019
90b603e
Remove SF_alpha_FMC, add SF_drying_ratio
Jan 8, 2019
b47e931
Remove extra space
Jan 8, 2019
0641a3e
Fix typo
Jan 8, 2019
f686da8
Updated termination diagnostic arrays to fill over canopy layer
rgknox Jan 8, 2019
b349a79
Merge pull request #3 from rgknox/fire_mortality
jkshuman Jan 8, 2019
5f7a452
Correct dimensions for drying_ratio
Jan 9, 2019
5c77081
Add missing comma to SFParamsMod
Jan 9, 2019
c079597
Half-way through adding new restarts for site level diagnostics
rgknox Jan 10, 2019
82be6b0
First pass through adding site diagnostics fmort/nindivs etc, to rest…
rgknox Jan 11, 2019
3df34c2
Fixed various problems with first implementation of site level diagno…
rgknox Jan 11, 2019
be04146
Merge pull request #4 from rgknox/fire_mortality
jkshuman Jan 11, 2019
fb4086b
Merge pull request #431 from jkshuman/fire_mortality
rgknox Jan 12, 2019
4f0310d
Trival conflict resolutions with master
rgknox Jan 14, 2019
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31 changes: 17 additions & 14 deletions biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ module EDCohortDynamicsMod
use EDTypesMod , only : min_npm2, min_nppatch
use EDTypesMod , only : min_n_safemath
use EDTypesMod , only : nlevleaf
use EDTypesMod , only : ican_upper
use FatesInterfaceMod , only : hlm_use_planthydro
use FatesInterfaceMod , only : hlm_parteh_mode
use FatesPlantHydraulicsMod, only : FuseCohortHydraulics
Expand Down Expand Up @@ -633,21 +634,25 @@ subroutine terminate_cohorts( currentSite, currentPatch, level )
endif ! if (.not.currentCohort%isnew .and. level == 2) then

if (terminate == 1) then

! preserve a record of the to-be-terminated cohort for mortality accounting
if (currentCohort%canopy_layer .eq. 1) then
levcan = 1
else
levcan = 2
endif
levcan = currentCohort%canopy_layer

currentSite%terminated_nindivs(currentCohort%size_class,currentCohort%pft,levcan) = &
currentSite%terminated_nindivs(currentCohort%size_class,currentCohort%pft,levcan) + currentCohort%n
!
currentSite%termination_carbonflux(levcan) = currentSite%termination_carbonflux(levcan) + &
currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)

if( hlm_use_planthydro == itrue ) then
if( hlm_use_planthydro == itrue ) &
call AccumulateMortalityWaterStorage(currentSite,currentCohort,currentCohort%n)

if(levcan==ican_upper) then
currentSite%term_nindivs_canopy(currentCohort%size_class,currentCohort%pft) = &
currentSite%term_nindivs_canopy(currentCohort%size_class,currentCohort%pft) + currentCohort%n

currentSite%term_carbonflux_canopy = currentSite%term_carbonflux_canopy + &
currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)
else
currentSite%term_nindivs_ustory(currentCohort%size_class,currentCohort%pft) = &
currentSite%term_nindivs_ustory(currentCohort%size_class,currentCohort%pft) + currentCohort%n

currentSite%term_carbonflux_ustory = currentSite%term_carbonflux_ustory + &
currentCohort%n * (struct_c+sapw_c+leaf_c+fnrt_c+store_c+repro_c)
end if

!put the litter from the terminated cohorts straight into the fragmenting pools
Expand Down Expand Up @@ -965,7 +970,6 @@ subroutine fuse_cohorts(currentSite, currentPatch, bc_in)
currentCohort%cmort = (currentCohort%n*currentCohort%cmort + nextc%n*nextc%cmort)/newn
currentCohort%hmort = (currentCohort%n*currentCohort%hmort + nextc%n*nextc%hmort)/newn
currentCohort%bmort = (currentCohort%n*currentCohort%bmort + nextc%n*nextc%bmort)/newn
currentCohort%fmort = (currentCohort%n*currentCohort%fmort + nextc%n*nextc%fmort)/newn
currentCohort%frmort = (currentCohort%n*currentCohort%frmort + nextc%n*nextc%frmort)/newn

! logging mortality, Yi Xu
Expand Down Expand Up @@ -1352,7 +1356,6 @@ subroutine copy_cohort( currentCohort,copyc )
! Mortality diagnostics
n%cmort = o%cmort
n%bmort = o%bmort
n%fmort = o%fmort
n%hmort = o%hmort
n%frmort = o%frmort

Expand Down
81 changes: 58 additions & 23 deletions biogeochem/EDPatchDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ module EDPatchDynamicsMod
use EDTypesMod , only : dtype_ifall
use EDTypesMod , only : dtype_ilog
use EDTypesMod , only : dtype_ifire
use EDTypesMod , only : ican_upper
use FatesInterfaceMod , only : hlm_use_planthydro
use FatesInterfaceMod , only : hlm_numSWb
use FatesInterfaceMod , only : bc_in_type
Expand Down Expand Up @@ -139,7 +140,6 @@ subroutine disturbance_rates( site_in, bc_in)
currentCohort%bmort = bmort
currentCohort%hmort = hmort
currentCohort%frmort = frmort
currentCohort%fmort = 0.0_r8 ! Fire mortality is initialized as zero, but may be changed

call LoggingMortality_frac(currentCohort%pft, currentCohort%dbh, &
lmort_direct,lmort_collateral,lmort_infra )
Expand Down Expand Up @@ -216,7 +216,6 @@ subroutine disturbance_rates( site_in, bc_in)
currentCohort => currentPatch%shortest
do while(associated(currentCohort))
if(currentCohort%canopy_layer == 1)then
currentCohort%fmort = 0.0_r8
currentCohort%cmort = currentCohort%cmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%hmort = currentCohort%hmort*(1.0_r8 - fates_mortality_disturbance_fraction)
currentCohort%bmort = currentCohort%bmort*(1.0_r8 - fates_mortality_disturbance_fraction)
Expand Down Expand Up @@ -267,7 +266,6 @@ subroutine disturbance_rates( site_in, bc_in)
currentCohort%lmort_direct = 0.0_r8
currentCohort%lmort_collateral = 0.0_r8
currentCohort%lmort_infra = 0.0_r8
currentCohort%fmort = 0.0_r8
end if
currentCohort => currentCohort%taller
enddo !currentCohort
Expand Down Expand Up @@ -323,12 +321,14 @@ subroutine spawn_patches( currentSite, bc_in)
real(r8) :: leaf_litter_local(maxpft) ! initial value of leaf litter. KgC/m2
real(r8) :: cwd_ag_local(ncwd) ! initial value of above ground coarse woody debris. KgC/m2
real(r8) :: cwd_bg_local(ncwd) ! initial value of below ground coarse woody debris. KgC/m2
integer :: levcan ! canopy level
real(r8) :: leaf_c ! leaf carbon [kg]
real(r8) :: fnrt_c ! fineroot carbon [kg]
real(r8) :: sapw_c ! sapwood carbon [kg]
real(r8) :: store_c ! storage carbon [kg]
real(r8) :: struct_c ! structure carbon [kg]
real(r8) :: total_c ! total carbon of plant [kg]
real(r8) :: fnrt_c ! fineroot carbon [kg]
real(r8) :: sapw_c ! sapwood carbon [kg]
real(r8) :: store_c ! storage carbon [kg]
real(r8) :: struct_c ! structure carbon [kg]
real(r8) :: total_c ! total carbon of plant [kg]

!---------------------------------------------------------------------

storesmallcohort => null() ! storage of the smallest cohort for insertion routine
Expand All @@ -351,12 +351,17 @@ subroutine spawn_patches( currentSite, bc_in)
call endrun(msg=errMsg(sourcefile, __LINE__))
end if

site_areadis = site_areadis + currentPatch%area * currentPatch%disturbance_rate
! Only create new patches that have non-negligible amount of land
if((currentPatch%area*currentPatch%disturbance_rate) > nearzero ) then
site_areadis = site_areadis + currentPatch%area * currentPatch%disturbance_rate
end if

currentPatch => currentPatch%older

enddo ! end loop over patches. sum area disturbed for all patches.

if (site_areadis > 0.0_r8) then
if (site_areadis > nearzero) then

cwd_ag_local = 0.0_r8
cwd_bg_local = 0.0_r8
leaf_litter_local = 0.0_r8
Expand All @@ -378,6 +383,8 @@ subroutine spawn_patches( currentSite, bc_in)
! This is the amount of patch area that is disturbed, and donated by the donor
patch_site_areadis = currentPatch%area * currentPatch%disturbance_rate

if (patch_site_areadis > nearzero) then

call average_patch_properties(currentPatch, new_patch, patch_site_areadis)

if (currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifall) .and. &
Expand Down Expand Up @@ -442,7 +449,6 @@ subroutine spawn_patches( currentSite, bc_in)
nc%cmort = nan ! The mortality diagnostics are set to nan because the cohort should dissappear
nc%hmort = nan
nc%bmort = nan
nc%fmort = nan
nc%frmort = nan
nc%lmort_direct = nan
nc%lmort_collateral = nan
Expand Down Expand Up @@ -485,7 +491,6 @@ subroutine spawn_patches( currentSite, bc_in)
! number density in EDCLMLink, and the number density of this new patch is donated
! so with the number density must come the effective mortality rates.

nc%fmort = 0.0_r8 ! Should had also been zero in the donor
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand All @@ -510,7 +515,6 @@ subroutine spawn_patches( currentSite, bc_in)
! Those remaining in the existing
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)

nc%fmort = 0.0_r8
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand All @@ -533,11 +537,40 @@ subroutine spawn_patches( currentSite, bc_in)
! loss of individuals from source patch due to area shrinking
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)

levcan = currentCohort%canopy_layer

if(levcan==ican_upper) then

! before changing number densities, track total rate of trees that died
! due to fire, as well as from each fire mortality term
currentSite%fmort_rate_canopy(currentCohort%size_class, currentCohort%pft) = &
currentSite%fmort_rate_canopy(currentCohort%size_class, currentCohort%pft) + &
nc%n * currentCohort%fire_mort / hlm_freq_day

currentSite%fmort_carbonflux_canopy = currentSite%fmort_carbonflux_canopy + &
(nc%n * currentCohort%fire_mort) * &
total_c * g_per_kg * days_per_sec * ha_per_m2

else
currentSite%fmort_rate_ustory(currentCohort%size_class, currentCohort%pft) = &
currentSite%fmort_rate_ustory(currentCohort%size_class, currentCohort%pft) + &
nc%n * currentCohort%fire_mort / hlm_freq_day

currentSite%fmort_carbonflux_ustory = currentSite%fmort_carbonflux_ustory + &
(nc%n * currentCohort%fire_mort) * &
total_c * g_per_kg * days_per_sec * ha_per_m2
end if

currentSite%fmort_rate_cambial(currentCohort%size_class, currentCohort%pft) = &
currentSite%fmort_rate_cambial(currentCohort%size_class, currentCohort%pft) + &
nc%n * currentCohort%cambial_mort / hlm_freq_day
currentSite%fmort_rate_crown(currentCohort%size_class, currentCohort%pft) = &
currentSite%fmort_rate_crown(currentCohort%size_class, currentCohort%pft) + &
nc%n * currentCohort%crownfire_mort / hlm_freq_day

! loss of individual from fire in new patch.
nc%n = nc%n * (1.0_r8 - currentCohort%fire_mort)

nc%fmort = currentCohort%fire_mort/hlm_freq_day

nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand All @@ -546,7 +579,8 @@ subroutine spawn_patches( currentSite, bc_in)
nc%lmort_direct = currentCohort%lmort_direct
nc%lmort_collateral = currentCohort%lmort_collateral
nc%lmort_infra = currentCohort%lmort_infra



! Logging is the dominant disturbance
elseif (currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifall) .and. &
currentPatch%disturbance_rates(dtype_ilog) > currentPatch%disturbance_rates(dtype_ifire)) then ! Logging
Expand All @@ -567,7 +601,6 @@ subroutine spawn_patches( currentSite, bc_in)
nc%hmort = nan
nc%bmort = nan
nc%frmort = nan
nc%fmort = nan
nc%lmort_direct = nan
nc%lmort_collateral = nan
nc%lmort_infra = nan
Expand Down Expand Up @@ -609,7 +642,6 @@ subroutine spawn_patches( currentSite, bc_in)
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)


nc%fmort = 0.0_r8
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand All @@ -629,7 +661,6 @@ subroutine spawn_patches( currentSite, bc_in)
currentCohort%n = currentCohort%n * (1._r8 - patch_site_areadis/currentPatch%area)

! No grass impact mortality imposed on the newly created patch
nc%fmort = 0.0_r8
nc%cmort = currentCohort%cmort
nc%hmort = currentCohort%hmort
nc%bmort = currentCohort%bmort
Expand Down Expand Up @@ -682,10 +713,6 @@ subroutine spawn_patches( currentSite, bc_in)
enddo ! currentCohort
call sort_cohorts(currentPatch)

!zero disturbance accumulators
currentPatch%disturbance_rate = 0._r8
currentPatch%disturbance_rates = 0._r8

!update area of donor patch
currentPatch%area = currentPatch%area - patch_site_areadis

Expand All @@ -698,6 +725,12 @@ subroutine spawn_patches( currentSite, bc_in)
call terminate_cohorts(currentSite, currentPatch, 2)
call sort_cohorts(currentPatch)

end if ! if (patch_site_areadis > nearzero) then

!zero disturbance rate trackers
currentPatch%disturbance_rate = 0._r8
currentPatch%disturbance_rates = 0._r8

currentPatch => currentPatch%younger

enddo ! currentPatch patch loop.
Expand All @@ -723,9 +756,11 @@ subroutine spawn_patches( currentSite, bc_in)

endif !end new_patch area


call check_patch_area(currentSite)
call set_patchno(currentSite)

return
end subroutine spawn_patches

! ============================================================================
Expand Down
2 changes: 1 addition & 1 deletion biogeophys/FatesPlantRespPhotosynthMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -938,7 +938,7 @@ subroutine LeafLayerPhotosynthesis(f_sun_lsl, & ! in

if ( parsun_lsl <= 0._r8 ) then ! night time

anet_av_out = 0._r8
anet_av_out = -lmr
psn_out = 0._r8
rstoma_out = min(rsmax0, 1._r8/bbb * cf)

Expand Down
34 changes: 12 additions & 22 deletions fire/SFMainMod.F90
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Expand Up @@ -158,14 +158,15 @@ end subroutine fire_danger_index
subroutine charecteristics_of_fuel ( currentSite )
!*****************************************************************

use SFParamsMod, only : SF_val_alpha_FMC, SF_val_SAV, SF_val_FBD
use SFParamsMod, only : SF_val_drying_ratio, SF_val_SAV, SF_val_FBD

type(ed_site_type), intent(in), target :: currentSite

type(ed_patch_type), pointer :: currentPatch
type(ed_cohort_type), pointer :: currentCohort

real(r8) timeav_swc
real(r8) timeav_swc
real(r8) alpha_FMC(nfsc) ! Relative fuel moisture adjusted per drying ratio
real(r8) fuel_moisture(nfsc) ! Scaled moisture content of small litter fuels.
real(r8) MEF(nfsc) ! Moisture extinction factor of fuels integer n

Expand Down Expand Up @@ -235,13 +236,15 @@ subroutine charecteristics_of_fuel ( currentSite )
! Equation 6 in Thonicke et al. 2010. across leaves,twig, small branch, and large branch
! dead leaves and twigs included in 1hr pool per Thonicke (2010)
! Calculate fuel moisture for trunks to hold value for fuel consumption
fuel_moisture(dl_sf:tr_sf) = exp(-1.0_r8 * SF_val_alpha_FMC(dl_sf:tr_sf) * currentSite%acc_NI)
alpha_FMC(dl_sf:tr_sf) = SF_val_SAV(dl_sf:tr_sf)/SF_val_drying_ratio

fuel_moisture(dl_sf:tr_sf) = exp(-1.0_r8 * alpha_FMC(dl_sf:tr_sf) * currentSite%acc_NI)

if(write_SF == itrue)then
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'ff3 ',currentPatch%fuel_frac
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'fm ',fuel_moisture
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'csa ',currentSite%acc_NI
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'sfv ',SF_val_alpha_FMC
if ( hlm_masterproc == itrue ) write(fates_log(),*) 'sfv ',alpha_FMC
endif
! FIX(RF,032414): needs refactoring.
! average water content !is this the correct metric?
Expand Down Expand Up @@ -408,8 +411,8 @@ subroutine rate_of_spread ( currentSite )
use SFParamsMod, only : SF_val_miner_total, &
SF_val_part_dens, &
SF_val_miner_damp, &
SF_val_fuel_energy, &
SF_val_wind_max
SF_val_fuel_energy

use FatesInterfaceMod, only : hlm_current_day, hlm_current_month

type(ed_site_type), intent(in), target :: currentSite
Expand All @@ -426,7 +429,6 @@ subroutine rate_of_spread ( currentSite )
real(r8) beta_ratio ! ratio of beta/beta_op
real(r8) a_beta ! dummy variable for product of a* beta_ratio for react_v_opt equation
real(r8) a,b,c,e ! function of fuel sav
real(r8) wind_elev_fire !wind speed (m/min) at elevevation relevant for fire

logical,parameter :: debug_windspeed = .false. !for debugging

Expand Down Expand Up @@ -493,21 +495,9 @@ subroutine rate_of_spread ( currentSite )

! Equation A5 in Thonicke et al. 2010
! phi_wind (unitless)
! convert wind_elev_fire from m/min to ft/min for Rothermel ROS eqn
! wind max per Lasslop et al 2014 to linearly reduce ROS for high wind speeds
!OLD! phi_wind = c * ((3.281_r8*currentPatch%effect_wspeed)**b)*(beta_ratio**(-e))
if (currentPatch%effect_wspeed .le. SF_val_wind_max) then
wind_elev_fire = currentPatch%effect_wspeed
phi_wind = c * ((3.281_r8*wind_elev_fire)**b)*(beta_ratio**(-e))
if (debug_windspeed) write(fates_log(),*) 'SF wind LESS max ', currentPatch%effect_wspeed
if (debug_windspeed) write(fates_log(),*) 'month and day', hlm_current_month, hlm_current_day
else
!max condition 225 ft/min (FIREMIP Rabin table A10 JSBACH-Spitfire) convert to 68.577 m/min
wind_elev_fire = max(0.0_r8,(68.577_r8-0.5_r8*currentPatch%effect_wspeed))
phi_wind = c * ((3.281_r8*wind_elev_fire)**b)*(beta_ratio**(-e))
if (debug_windspeed) write(fates_log(),*) 'SF wind GREATER max ', currentPatch%effect_wspeed
if (debug_windspeed) write(fates_log(),*) 'month and day', hlm_current_month, hlm_current_day
endif
! convert current_wspeed (wind at elev relevant to fire) from m/min to ft/min for Rothermel ROS eqn
phi_wind = c * ((3.281_r8*currentPatch%effect_wspeed)**b)*(beta_ratio**(-e))


! ---propagating flux----
! Equation A2 in Thonicke et al.2010 and Eq. 42 Rothermal 1972
Expand Down
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