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phenology status timers #468

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merged 32 commits into from
May 6, 2019
Merged

phenology status timers #468

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e2ca93d
Refactoring the phenology timing code
rgknox Jan 14, 2019
5bfa1bd
More refactors to phenology timing
rgknox Jan 15, 2019
6146799
Small syntax updates to phen refactor, added history tracking of site…
rgknox Jan 15, 2019
c1c3a53
Adding history flags that can specify something other than zero for n…
rgknox Jan 17, 2019
1d319ce
Small bugfix on the nonfates history flag
rgknox Jan 17, 2019
b08ba2a
added spval to flushval for STATUS flags
rgknox Jan 18, 2019
85f78ce
Added diagnostics for site level phenology statistics
rgknox Jan 24, 2019
219967d
Merge branch 'rgknox-fix-10day-phen' of github.com:rgknox/fates into …
rgknox Jan 24, 2019
30cdb72
Added special flags to fates phenology diagnostics, re-added the flus…
rgknox Jan 24, 2019
4a2980a
Preventing flickering from pre-mature leaf-on in cold-deciduous, remo…
rgknox Jan 25, 2019
51ef6e6
Zeroing gdd counter when cold leaves drop to prevent reflushing
rgknox Jan 26, 2019
42ed191
Minor syntax updates to cold deciduous formulation, fixed Botta et al…
rgknox Jan 26, 2019
7c00439
Removed the set_nonfates stuff
rgknox Jan 27, 2019
f96eb77
Fixed type that removed dim_kinds_index
rgknox Jan 27, 2019
1f841db
Removed status condition to dayssinced counters in drought phenology
rgknox Jan 30, 2019
1842b2d
allowances for first year drought phenology timing
rgknox Jan 30, 2019
c65a6f6
typo in leaf drop date
rgknox Jan 30, 2019
fe00e5b
Add a reset of days since leaf on when leaves flush, so that leaf-off…
rgknox Jan 31, 2019
f7880a2
Merge resolution between phenology fixes and master, conflicts mostly…
rgknox Feb 11, 2019
6d48d68
Small fixes to resolution between the phenology fixes and leaf age ch…
rgknox Feb 11, 2019
b7212e3
Fixing a call for drought stress as logical instead of integer flag
rgknox Feb 11, 2019
61ea412
Add logic to cold phenology in first year started with normal timing.
rgknox Feb 13, 2019
3b14955
Changed drought phenology soil layer to match desired depth. Added a …
rgknox Feb 15, 2019
4678e92
Fixed bug that was saving the doy to the phenology leaf-off date inst…
rgknox Feb 15, 2019
4d0821b
Tweaking phenology logic
rgknox Feb 15, 2019
9f034f2
Reverted the waiting time to trigger a forced flush for time-imposed …
rgknox Feb 21, 2019
3c1f3e6
Conflict resolutions for phenology refactor. Most related to saving a…
rgknox Apr 11, 2019
b96f529
Updates to PR #468 (phenology status timers)
glemieux Apr 15, 2019
e1d278f
Merge pull request #1 from glemieux/rgknox-fix-10day-phen
rgknox Apr 16, 2019
40334e5
Syntax improvements to site level phenology flags. Added named const…
rgknox Apr 30, 2019
5420fb6
Updated some history long-name syntax for phen status, added an expli…
rgknox Apr 30, 2019
4b7293d
Resolved conflict in inventory init between phen refactor and allowin…
rgknox Apr 30, 2019
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452 changes: 274 additions & 178 deletions biogeochem/EDPhysiologyMod.F90
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130 changes: 68 additions & 62 deletions main/EDInitMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ module EDInitMod
use FatesConstantsMod , only : r8 => fates_r8
use FatesConstantsMod , only : ifalse
use FatesConstantsMod , only : itrue
use FatesConstantsMod , only : fates_unset_int
use FatesConstantsMod , only : primaryforest
use FatesGlobals , only : endrun => fates_endrun
use EDTypesMod , only : nclmax
Expand All @@ -17,14 +18,21 @@ module EDInitMod
use EDPatchDynamicsMod , only : create_patch
use EDTypesMod , only : ed_site_type, ed_patch_type, ed_cohort_type
use EDTypesMod , only : ncwd
use EDTypesMod , only : nuMWaterMem
use EDTypesMod , only : numWaterMem
use EDTypesMod , only : num_vegtemp_mem
use EDTypesMod , only : maxpft
use EDTypesMod , only : AREA
use EDTypesMod , only : init_spread_near_bare_ground
use EDTypesMod , only : init_spread_inventory
use EDTypesMod , only : first_leaf_aclass
use EDTypesMod , only : leaves_on
use EDTypesMod , only : leaves_off
use EDTypesMod , only : phen_cstat_nevercold
use EDTypesMod , only : phen_cstat_iscold
use EDTypesMod , only : phen_dstat_timeoff
use EDTypesMod , only : phen_dstat_moistoff
use EDTypesMod , only : phen_cstat_notcold
use EDTypesMod , only : phen_dstat_moiston
use FatesInterfaceMod , only : bc_in_type
use FatesInterfaceMod , only : hlm_use_planthydro
use FatesInterfaceMod , only : hlm_use_inventory_init
Expand Down Expand Up @@ -110,17 +118,18 @@ subroutine zero_site( site_in )
site_in%total_burn_flux_to_atm = 0._r8

! PHENOLOGY
site_in%is_cold = .false. ! Is cold deciduous leaf-off triggered?
site_in%is_drought = .false. ! Is drought deciduous leaf-off triggered?
site_in%ED_GDD_site = nan ! growing degree days
site_in%ncd = nan ! no chilling days
site_in%last_n_days(:) = 999 ! record of last 10 days temperature for senescence model.
site_in%leafondate = 999 ! doy of leaf on
site_in%leafoffdate = 999 ! doy of leaf off
site_in%dleafondate = 999 ! doy of leaf on drought
site_in%dleafoffdate = 999 ! doy of leaf on drought
site_in%water_memory(:) = nan

site_in%cstatus = fates_unset_int ! are leaves in this pixel on or off?
site_in%dstatus = fates_unset_int
site_in%grow_deg_days = nan ! growing degree days
site_in%nchilldays = fates_unset_int
site_in%ncolddays = fates_unset_int
site_in%cleafondate = fates_unset_int ! doy of leaf on
site_in%cleafoffdate = fates_unset_int ! doy of leaf off
site_in%dleafondate = fates_unset_int ! doy of leaf on drought
site_in%dleafoffdate = fates_unset_int ! doy of leaf on drought
site_in%water_memory(:) = nan
site_in%vegtemp_memory(:) = nan ! record of last 10 days temperature for senescence model.

! SEED
site_in%seed_bank(:) = 0._r8
Expand Down Expand Up @@ -185,66 +194,61 @@ subroutine set_site_properties( nsites, sites)
!
! !LOCAL VARIABLES:
integer :: s
real(r8) :: leafon
real(r8) :: leafoff
logical :: stat
real(r8) :: NCD
integer :: cstat ! cold status phenology flag
real(r8) :: GDD
logical :: dstat
integer :: dstat ! drought status phenology flag
real(r8) :: acc_NI
real(r8) :: watermem
integer :: dleafoff
integer :: dleafon
real(r8) :: watermem
integer :: cleafon ! DOY for cold-decid leaf-on, initial guess
integer :: cleafoff ! DOY for cold-decid leaf-off, initial guess
integer :: dleafoff ! DOY for drought-decid leaf-off, initial guess
integer :: dleafon ! DOY for drought-decid leaf-on, initial guess
!----------------------------------------------------------------------

if ( hlm_is_restart == ifalse ) then
!initial guess numbers for site condition.
NCD = 0.0_r8
GDD = 30.0_r8
leafon = 100.0_r8
leafoff = 300.0_r8
stat = .false.
acc_NI = 0.0_r8
dstat = .false.
dleafoff = 300
dleafon = 100
watermem = 0.5_r8

else ! assignements for restarts
! If this is not a restart, we need to start with some reasonable
! starting points. If this is a restart, we leave the values
! as unset ints and reals, and let the restart values be read in
! after this routine

if ( hlm_is_restart == ifalse ) then

NCD = 1.0_r8 ! NCD should be 1 on restart
GDD = 0.0_r8
leafon = 0.0_r8
leafoff = 0.0_r8
stat = .false.
GDD = 30.0_r8
cleafon = 100
cleafoff = 300
cstat = phen_cstat_notcold ! Leaves are on
acc_NI = 0.0_r8
dstat = .false.
dstat = phen_dstat_moiston ! Leaves are on
dleafoff = 300
dleafon = 100
watermem = 0.5_r8

endif

do s = 1,nsites
sites(s)%ncd = NCD
sites(s)%leafondate = leafon
sites(s)%leafoffdate = leafoff
sites(s)%dleafoffdate = dleafoff
sites(s)%dleafondate = dleafon
sites(s)%ED_GDD_site = GDD

if ( hlm_is_restart == ifalse ) then
do s = 1,nsites
sites(s)%nchilldays = 0
sites(s)%ncolddays = 0 ! recalculated in phenology
! immediately, so yes this
! is memory-less, but needed
! for first value in history file

sites(s)%cleafondate = cleafon
sites(s)%cleafoffdate = cleafoff
sites(s)%dleafoffdate = dleafoff
sites(s)%dleafondate = dleafon
sites(s)%grow_deg_days = GDD

sites(s)%water_memory(1:numWaterMem) = watermem
end if

sites(s)%is_cold = stat
sites(s)%is_drought = dstat

sites(s)%acc_NI = acc_NI
sites(s)%frac_burnt = 0.0_r8
sites(s)%old_stock = 0.0_r8

end do
sites(s)%vegtemp_memory(1:num_vegtemp_mem) = 0._r8

sites(s)%cstatus = cstat
sites(s)%dstatus = dstat

sites(s)%acc_NI = acc_NI
sites(s)%frac_burnt = 0.0_r8
sites(s)%old_stock = 0.0_r8

end do

end if

return
end subroutine set_site_properties
Expand Down Expand Up @@ -439,13 +443,15 @@ subroutine init_cohorts( site_in, patch_in, bc_in)
temp_cohort%laimemory = 0._r8
cstatus = leaves_on

if( EDPftvarcon_inst%season_decid(pft) == itrue .and. site_in%is_cold ) then
if( EDPftvarcon_inst%season_decid(pft) == itrue .and. &
any(site_in%cstatus == [phen_cstat_nevercold,phen_cstat_iscold])) then
temp_cohort%laimemory = b_leaf
b_leaf = 0._r8
cstatus = leaves_off
endif

if ( EDPftvarcon_inst%stress_decid(pft) == itrue .and. site_in%is_drought ) then

if ( EDPftvarcon_inst%stress_decid(pft) == itrue .and. &
any(site_in%dstatus == [phen_dstat_timeoff,phen_dstat_moistoff])) then
temp_cohort%laimemory = b_leaf
b_leaf = 0._r8
cstatus = leaves_off
Expand Down
15 changes: 11 additions & 4 deletions main/EDMainMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,8 @@ module EDMainMod
use EDtypesMod , only : ed_patch_type
use EDtypesMod , only : ed_cohort_type
use EDTypesMod , only : AREA
use EDTypesMod , only : phen_dstat_moiston
use EDTypesMod , only : phen_dstat_timeon
use FatesConstantsMod , only : itrue,ifalse
use FatesConstantsMod , only : primaryforest, secondaryforest
use FatesPlantHydraulicsMod , only : do_growthrecruiteffects
Expand Down Expand Up @@ -270,6 +272,7 @@ subroutine ed_integrate_state_variables(currentSite, bc_in )
real(r8) :: cohort_biomass_store ! remembers the biomass in the cohort for balance checking
real(r8) :: dbh_old ! dbh of plant before daily PRT [cm]
real(r8) :: hite_old ! height of plant before daily PRT [m]
logical :: is_drought ! logical for if the plant (site) is in a drought state
real(r8) :: leaf_c
real(r8) :: delta_dbh ! correction for dbh
real(r8) :: delta_hite ! correction for hite
Expand Down Expand Up @@ -361,9 +364,13 @@ subroutine ed_integrate_state_variables(currentSite, bc_in )


! Conduct Maintenance Turnover (parteh)

call currentCohort%prt%CheckMassConservation(ft,3)
call PRTMaintTurnover(currentCohort%prt,ft,currentSite%is_drought)
if(any(currentSite%dstatus == [phen_dstat_moiston,phen_dstat_timeon])) then
is_drought = .false.
else
is_drought = .true.
end if
call PRTMaintTurnover(currentCohort%prt,ft,is_drought)
call currentCohort%prt%CheckMassConservation(ft,4)

leaf_c = currentCohort%prt%GetState(leaf_organ, all_carbon_elements)
Expand Down Expand Up @@ -750,8 +757,8 @@ subroutine bypass_dynamics(currentSite)
currentCohort%frmort = 0.0_r8

currentCohort%dndt = 0.0_r8
currentCohort%dhdt = 0.0_r8
currentCohort%ddbhdt = 0.0_r8
currentCohort%dhdt = 0.0_r8
currentCohort%ddbhdt = 0.0_r8

currentCohort => currentCohort%taller
enddo
Expand Down
46 changes: 36 additions & 10 deletions main/EDTypesMod.F90
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Expand Up @@ -76,6 +76,7 @@ module EDTypesMod

integer, parameter :: leaves_on = 2 ! Flag specifying that a deciduous plant has leaves
! and should be allocating to them as well

integer, parameter :: leaves_off = 1 ! Flag specifying that a deciduous plant has dropped
! its leaves and should not be trying to allocate
! towards any growth.
Expand Down Expand Up @@ -107,14 +108,28 @@ module EDTypesMod
integer, parameter :: numWaterMem = 10 ! watermemory saved as site level var

! BIOLOGY/BIOGEOCHEMISTRY
integer , parameter :: SENES = 10 ! Window of time over which we track temp for cold sensecence (days)
integer , parameter :: num_vegtemp_mem = 10 ! Window of time over which we track temp for cold sensecence (days)
real(r8), parameter :: dinc_ed = 1.0_r8 ! size of VAI bins (LAI+SAI) [CHANGE THIS NAME WITH NEXT INTERFACE
! UPDATE]
integer , parameter :: N_DIST_TYPES = 3 ! Disturbance Modes 1) tree-fall, 2) fire, 3) logging
integer , parameter :: dtype_ifall = 1 ! index for naturally occuring tree-fall generated event
integer , parameter :: dtype_ifire = 2 ! index for fire generated disturbance event
integer , parameter :: dtype_ilog = 3 ! index for logging generated disturbance event


! Phenology status flag definitions (cold type is cstat, dry type is dstat)

integer, parameter :: phen_cstat_nevercold = 0 ! This (location/plant) has not experienced a cold period over a large number
! of days, leaves are dropped and flagged as non-cold region
integer, parameter :: phen_cstat_iscold = 1 ! This (location/plant) is in a cold-state where leaves should have fallen
integer, parameter :: phen_cstat_notcold = 2 ! This site is in a warm-state where leaves are allowed to flush

integer, parameter :: phen_dstat_timeoff = 0 ! Leaves off due to time exceedance (drought phenology)
integer, parameter :: phen_dstat_moistoff = 1 ! Leaves off due to moisture avail (drought phenology)
integer, parameter :: phen_dstat_moiston = 2 ! Leaves on due to moisture avail (drought phenology)
integer, parameter :: phen_dstat_timeon = 3 ! Leaves on due to time exceedance (drought phenology)


! SPITFIRE
integer, parameter :: NCWD = 4 ! number of coarse woody debris pools (twig,s branch,l branch, trunk)
integer , parameter :: NFSC = NCWD+2 ! number fuel size classes (4 cwd size classes, leaf litter, and grass)
Expand Down Expand Up @@ -611,15 +626,26 @@ module EDTypesMod


! PHENOLOGY
real(r8) :: ED_GDD_site ! ED Phenology growing degree days.
logical :: is_cold ! is this site/column in a cold-status where its cohorts drop leaves?
logical :: is_drought ! is this site/column in a drought-status where its cohorts drop leaves?
real(r8) :: ncd ! no chilling days:-
real(r8) :: last_n_days(senes) ! record of last 10 days temperature for senescence model. deg C
integer :: leafondate ! doy of leaf on:-
integer :: leafoffdate ! doy of leaf off:-
integer :: dleafondate ! doy of leaf on drought:-
integer :: dleafoffdate ! doy of leaf on drought:-
real(r8) :: grow_deg_days ! Phenology growing degree days

integer :: cstatus ! are leaves in this pixel on or off for cold decid
! 0 = this site has not experienced a cold period over at least
! 400 days, leaves are dropped and flagged as non-cold region
! 1 = this site is in a cold-state where leaves should have fallen
! 2 = this site is in a warm-state where leaves are allowed to flush
integer :: dstatus ! are leaves in this pixel on or off for drought decid
! 0 = leaves off due to time exceedance
! 1 = leaves off due to moisture avail
! 2 = leaves on due to moisture avail
! 3 = leaves on due to time exceedance
integer :: nchilldays ! num chilling days: (for botta gdd trheshold calculation)
integer :: ncolddays ! num cold days: (must exceed threshold to drop leaves)
real(r8) :: vegtemp_memory(num_vegtemp_mem) ! record of last 10 days temperature for senescence model. deg C
integer :: cleafondate ! model date (day integer) of leaf on (cold):-
integer :: cleafoffdate ! model date (day integer) of leaf off (cold):-
integer :: dleafondate ! model date (day integer) of leaf on drought:-
integer :: dleafoffdate ! model date (day integer) of leaf off drought:-

real(r8) :: water_memory(numWaterMem) ! last 10 days of soil moisture memory...

!SEED BANK
Expand Down
8 changes: 5 additions & 3 deletions main/FatesConstantsMod.F90
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Expand Up @@ -15,10 +15,12 @@ module FatesConstantsMod
integer, parameter :: fates_short_string_length = 32
integer, parameter :: fates_long_string_length = 199

! Unset and various other 'special' values
! Used to initialize and test unset integers
integer, parameter :: fates_unset_int = -9999
real(fates_r8), parameter :: fates_unset_r8 = -9999._fates_r8


! Used to initialize and test unset r8s
real(fates_r8), parameter :: fates_unset_r8 = -1.e36_fates_r8

! Integer equivalent of true (in case some compilers dont auto convert)
integer, parameter :: itrue = 1

Expand Down
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