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minor updates #12

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c574f02
minor updates to phenology timers and comments
rgknox Oct 13, 2025
cc31024
reverting changes to history interface for 10 average refactor
rgknox Oct 13, 2025
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70 changes: 34 additions & 36 deletions biogeochem/EDPhysiologyMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -920,7 +920,6 @@ subroutine phenology( currentSite, bc_in )
!
! !LOCAL VARIABLES:

integer :: model_day_int ! integer model day 1 - inf
integer :: ncolddays ! no days underneath the threshold for leaf drop
integer :: i_tmem ! Loop counter for veg temp mem days
integer :: ipft ! plant functional type index
Expand Down Expand Up @@ -970,14 +969,13 @@ subroutine phenology( currentSite, bc_in )
logical :: last_flush_long_ago ! Has it been a very long time since last flushing?


! This is the elapsed number of days since the very beginning of the simulation time
model_day_int = currentSite%phen_model_date


!Parameters: defaults from Botta et al. 2000 GCB,6 709-725
!Parameters, default from from SDGVM model of senesence

! Retrieve average canopy temperature of the current day
! Retrieve average canopy temperature for the previous
! 24 hours. The indices of vegtemp_memory represent
! the previous 10 days, index 1 is the most recent day

temp_in_C = currentSite%vegtemp_memory(1)


Expand Down Expand Up @@ -1032,19 +1030,19 @@ subroutine phenology( currentSite, bc_in )

!this logic is to prevent GDD accumulating after the leaves have fallen and before the
! beginnning of the accumulation period, to prevend erroneous autumn leaf flushing.
if(model_day_int> ndays_per_year)then !only do this after the first year to prevent odd behaviour
if(currentSite%phen_model_date> ndays_per_year)then !only do this after the first year to prevent odd behaviour

if(currentSite%lat .gt. 0.0_r8)then !Northern Hemisphere
! In the north, don't accumulate when we are past the leaf fall date.
! Accumulation starts on day 1 of year in NH.
! The 180 is to prevent going into an 'always off' state after initialization
if( model_day_int .gt. currentSite%cleafoffdate.and.hlm_day_of_year.gt.180)then !
if( currentSite%phen_model_date .gt. currentSite%cleafoffdate.and.hlm_day_of_year.gt.180)then !
currentSite%grow_deg_days = 0._r8
endif
else !Southern Hemisphere
! In the South, don't accumulate after the leaf off date, and before the start of
! the accumulation phase (day 181).
if(model_day_int .gt. currentSite%cleafoffdate.and.hlm_day_of_year.lt.gddstart) then!
if(currentSite%phen_model_date .gt. currentSite%cleafoffdate.and.hlm_day_of_year.lt.gddstart) then!
currentSite%grow_deg_days = 0._r8
endif
endif
Expand All @@ -1054,16 +1052,16 @@ subroutine phenology( currentSite, bc_in )
! and off. If this is the beginning of the simulation, that day might
! not had occured yet, so set it to last year to get things rolling

if (model_day_int < currentSite%cleafoffdate) then
currentSite%cndaysleafoff = model_day_int - (currentSite%cleafoffdate - ndays_per_year)
if (currentSite%phen_model_date < currentSite%cleafoffdate) then
currentSite%cndaysleafoff = currentSite%phen_model_date - (currentSite%cleafoffdate - ndays_per_year)
else
currentSite%cndaysleafoff = model_day_int - currentSite%cleafoffdate
currentSite%cndaysleafoff = currentSite%phen_model_date - currentSite%cleafoffdate
end if

if (model_day_int < currentSite%cleafondate) then
currentSite%cndaysleafon = model_day_int - (currentSite%cleafondate - ndays_per_year)
if (currentSite%phen_model_date < currentSite%cleafondate) then
currentSite%cndaysleafon = currentSite%phen_model_date - (currentSite%cleafondate - ndays_per_year)
else
currentSite%cndaysleafon = model_day_int - currentSite%cleafondate
currentSite%cndaysleafon = currentSite%phen_model_date - currentSite%cleafondate
end if


Expand All @@ -1081,7 +1079,7 @@ subroutine phenology( currentSite, bc_in )
(currentSite%cndaysleafoff > ED_val_phen_mindayson) .and. &
(currentSite%nchilldays >= 1)) then
currentSite%cstatus = phen_cstat_notcold ! Set to not-cold status (leaves can come on)
currentSite%cleafondate = model_day_int
currentSite%cleafondate = currentSite%phen_model_date
currentSite%cndaysleafon = 0
currentSite%grow_deg_days = 0._r8 ! zero GDD for the rest of the year until counting season begins.
if ( debug ) write(fates_log(),*) 'leaves on'
Expand All @@ -1099,7 +1097,7 @@ subroutine phenology( currentSite, bc_in )


if ( (currentSite%cstatus == phen_cstat_notcold) .and. &
(model_day_int > num_vegtemp_mem) .and. &
(currentSite%phen_model_date > num_vegtemp_mem) .and. &
(ncolddays > ED_val_phen_ncolddayslim) .and. &
(currentSite%cndaysleafon > ED_val_phen_mindayson) )then

Expand All @@ -1109,7 +1107,7 @@ subroutine phenology( currentSite, bc_in )
! clear this value, it will cause
! leaves to flush later in the year
currentSite%cstatus = phen_cstat_iscold ! alter status of site to 'leaves off'
currentSite%cleafoffdate = model_day_int ! record leaf off date
currentSite%cleafoffdate = currentSite%phen_model_date ! record leaf off date
currentSite%cndaysleafoff = 0

if ( debug ) write(fates_log(),*) 'leaves off'
Expand All @@ -1129,7 +1127,7 @@ subroutine phenology( currentSite, bc_in )
currentSite%cstatus = phen_cstat_nevercold ! alter status of site to imply that this
! site is never really cold enough
! for cold deciduous
currentSite%cleafoffdate = model_day_int ! record leaf off date
currentSite%cleafoffdate = currentSite%phen_model_date ! record leaf off date
currentSite%cndaysleafoff = 0

if ( debug ) write(fates_log(),*) 'leaves off'
Expand Down Expand Up @@ -1165,15 +1163,15 @@ subroutine phenology( currentSite, bc_in )
! Calculate days since last flushing and shedding event, but make a provision
! for the first year of simulation, we have to assume leaf drop / leaf flush
! dates to start, so if that is in the future, set it to last year
if (model_day_int < currentSite%dleafoffdate(ipft)) then
currentSite%dndaysleafoff(ipft) = model_day_int - (currentSite%dleafoffdate(ipft)-ndays_per_year)
if (currentSite%phen_model_date < currentSite%dleafoffdate(ipft)) then
currentSite%dndaysleafoff(ipft) = currentSite%phen_model_date - (currentSite%dleafoffdate(ipft)-ndays_per_year)
else
currentSite%dndaysleafoff(ipft) = model_day_int - currentSite%dleafoffdate(ipft)
currentSite%dndaysleafoff(ipft) = currentSite%phen_model_date - currentSite%dleafoffdate(ipft)
end if
if (model_day_int < currentSite%dleafondate(ipft)) then
currentSite%dndaysleafon(ipft) = model_day_int - (currentSite%dleafondate(ipft)-ndays_per_year)
if (currentSite%phen_model_date < currentSite%dleafondate(ipft)) then
currentSite%dndaysleafon(ipft) = currentSite%phen_model_date - (currentSite%dleafondate(ipft)-ndays_per_year)
else
currentSite%dndaysleafon(ipft) = model_day_int - currentSite%dleafondate(ipft)
currentSite%dndaysleafon(ipft) = currentSite%phen_model_date - currentSite%dleafondate(ipft)
end if


Expand Down Expand Up @@ -1254,7 +1252,7 @@ subroutine phenology( currentSite, bc_in )
! up to one change occurs at any given time. Also, prevent changes until the
! soil moisture memory is populated (the outer if check).
!---~---
past_spinup_ifelse: if (model_day_int > numWaterMem) then
past_spinup_ifelse: if (currentSite%phen_model_date > numWaterMem) then
drought_smoist_ifelse: if ( prolonged_off_period .and. &
( .not. smoist_below_threshold ) ) then
! LEAF ON: DROUGHT DECIDUOUS WETNESS
Expand All @@ -1265,7 +1263,7 @@ subroutine phenology( currentSite, bc_in )
! b) Has there also been at least a nominaly short amount of "leaf-off"?
! c) Is the soil moisture sufficiently high?
currentSite%dstatus(ipft) = phen_dstat_moiston ! set status to leaf-on
currentSite%dleafondate(ipft) = model_day_int ! save the model day we start flushing
currentSite%dleafondate(ipft) = currentSite%phen_model_date ! save the model day we start flushing
currentSite%dndaysleafon(ipft) = 0
currentSite%elong_factor(ipft) = 1.

Expand All @@ -1279,7 +1277,7 @@ subroutine phenology( currentSite, bc_in )
! last year's bud-burst. If this is imposed, then we set the new
! status to indicate bud-burst was forced by timing
currentSite%dstatus(ipft) = phen_dstat_timeon ! force budburst!
currentSite%dleafondate(ipft) = model_day_int ! record leaf on date
currentSite%dleafondate(ipft) = currentSite%phen_model_date ! record leaf on date
currentSite%dndaysleafon(ipft) = 0
currentSite%elong_factor(ipft) = 1.

Expand All @@ -1289,7 +1287,7 @@ subroutine phenology( currentSite, bc_in )
! flush again as soon as they exceed a minimum off time
! This typically occurs in a perennially wet system.
currentSite%dstatus(ipft) = phen_dstat_timeon ! force budburst!
currentSite%dleafondate(ipft) = model_day_int ! record leaf on date
currentSite%dleafondate(ipft) = currentSite%phen_model_date ! record leaf on date
currentSite%dndaysleafon(ipft) = 0
currentSite%elong_factor(ipft) = 1.

Expand All @@ -1298,15 +1296,15 @@ subroutine phenology( currentSite, bc_in )
! Are the leaves rouhgly at the end of their lives? If so, shed leaves
! even if it is not dry.
currentSite%dstatus(ipft) = phen_dstat_timeoff !alter status of site to 'leaves off'
currentSite%dleafoffdate(ipft) = model_day_int !record leaf on date
currentSite%dleafoffdate(ipft) = currentSite%phen_model_date !record leaf on date
currentSite%dndaysleafoff(ipft) = 0
currentSite%elong_factor(ipft) = 0.

elseif ( exceed_min_on_period .and. smoist_below_threshold ) then
! LEAF OFF: DROUGHT DECIDUOUS DRYNESS - if the soil gets too dry,
! and the leaves have already been on a while...
currentSite%dstatus(ipft) = phen_dstat_moistoff ! alter status of site to 'leaves off'
currentSite%dleafoffdate(ipft) = model_day_int ! record leaf on date
currentSite%dleafoffdate(ipft) = currentSite%phen_model_date ! record leaf on date
currentSite%dndaysleafoff(ipft) = 0
currentSite%elong_factor(ipft) = 0.
end if drought_smoist_ifelse
Expand Down Expand Up @@ -1360,22 +1358,22 @@ subroutine phenology( currentSite, bc_in )


! Make sure elongation factor is bounded and check for special cases.
drought_gradual_ifelse: if ( model_day_int <= numWaterMem ) then
drought_gradual_ifelse: if ( currentSite%phen_model_date <= numWaterMem ) then
! Too early in the simulation, keep the same elongation factor as the day before.
currentSite%elong_factor(ipft) = elongf_prev

elseif ( prolonged_on_period ) then
! Leaves have been on for too long and exceeded leaf lifespan. Force abscission
currentSite%elong_factor(ipft) = 0.0_r8 ! Force full budburst
currentSite%dstatus(ipft) = phen_dstat_timeoff ! Flag that this has been forced
currentSite%dleafoffdate(ipft) = model_day_int ! Record leaf off date
currentSite%dleafoffdate(ipft) = currentSite%phen_model_date ! Record leaf off date
currentSite%dndaysleafoff(ipft) = 0 ! Reset clock

elseif ( last_flush_long_ago ) then
! Plant has not flushed at all for a very long time. Force flushing
currentSite%elong_factor(ipft) = elongf_min ! Force minimum budburst
currentSite%dstatus(ipft) = phen_dstat_timeon ! Flag that this has been forced
currentSite%dleafondate(ipft) = model_day_int ! Record leaf on date
currentSite%dleafondate(ipft) = currentSite%phen_model_date ! Record leaf on date
currentSite%dndaysleafon(ipft) = 0 ! Reset clock

elseif ( recent_flush .and. elongf_1st < elongf_prev ) then
Expand All @@ -1395,7 +1393,7 @@ subroutine phenology( currentSite, bc_in )
if (elongf_prev >= elongf_min ) then
! This is the first day moisture fell below minimum. Flag change of status.
currentSite%dstatus(ipft) = phen_dstat_moistoff ! Flag that this has not been forced
currentSite%dleafoffdate(ipft) = model_day_int ! Record leaf off date
currentSite%dleafoffdate(ipft) = currentSite%phen_model_date ! Record leaf off date
currentSite%dndaysleafoff(ipft) = 0 ! Reset clock
end if

Expand All @@ -1407,7 +1405,7 @@ subroutine phenology( currentSite, bc_in )
if (elongf_prev < elongf_min ) then
! This is the first day moisture allows leaves to exist. Flag change of status.
currentSite%dstatus(ipft) = phen_dstat_moiston ! Flag that this has not been forced
currentSite%dleafondate(ipft) = model_day_int ! Record leaf on date
currentSite%dleafondate(ipft) = currentSite%phen_model_date ! Record leaf on date
currentSite%dndaysleafon(ipft) = 0 ! Reset clock
elseif (elongf_1st < elongf_prev) then
currentSite%dstatus(ipft) = phen_dstat_pshed ! Flag partial shedding,
Expand Down
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