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removed slascaler and various fates parameter changes #287

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Oct 10, 2017
Merged

removed slascaler and various fates parameter changes #287

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d75b48c
Removal of slascalar from leaf biomass allometry.
rgknox Oct 3, 2017
e4be102
Added and modified new parameter file variables.
rgknox Oct 5, 2017
87c0fd7
Changed some parameter names to add clarity, allom_dbh_maxheight dbh_…
rgknox Oct 6, 2017
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20 changes: 8 additions & 12 deletions biogeochem/EDGrowthFunctionsMod.F90
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Expand Up @@ -83,10 +83,10 @@ real(r8) function Hite( cohort_in )
! if the hite is larger than the maximum allowable height (set by dbhmax) then
! set the height to the maximum value.
! this could do with at least re-factoring and probably re-thinking. RF
if(cohort_in%dbh <= EDPftvarcon_inst%max_dbh(cohort_in%pft)) then
if(cohort_in%dbh <= EDPftvarcon_inst%allom_dbh_maxheight(cohort_in%pft)) then
h = (10.0_r8**(log10(cohort_in%dbh) * m + c))
else
h = (10.0_r8**(log10(EDPftvarcon_inst%max_dbh(cohort_in%pft))*m + c))
h = (10.0_r8**(log10(EDPftvarcon_inst%allom_dbh_maxheight(cohort_in%pft))*m + c))
endif
Hite = h

Expand All @@ -107,26 +107,22 @@ real(r8) function Bleaf( cohort_in )
real(r8) :: dbh2bl_a
real(r8) :: dbh2bl_b
real(r8) :: dbh2bl_c
real(r8) :: slascaler ! changes the target biomass according to the SLA

dbh2bl_a = EDPftvarcon_inst%allom_d2bl1(cohort_in%pft)
dbh2bl_b = EDPftvarcon_inst%allom_d2bl2(cohort_in%pft)
dbh2bl_c = EDPftvarcon_inst%allom_d2bl3(cohort_in%pft)
slascaler = EDPftvarcon_inst%allom_d2bl_slascaler(cohort_in%pft)/EDPftvarcon_inst%slatop(cohort_in%pft)

if(cohort_in%dbh < 0._r8.or.cohort_in%pft == 0.or.cohort_in%dbh > 1000.0_r8)then
write(fates_log(),*) 'problems in bleaf',cohort_in%dbh,cohort_in%pft
endif

if(cohort_in%dbh <= EDPftvarcon_inst%max_dbh(cohort_in%pft))then
if(cohort_in%dbh <= EDPftvarcon_inst%allom_dbh_maxheight(cohort_in%pft))then
bleaf = dbh2bl_a * (cohort_in%dbh**dbh2bl_b) * EDPftvarcon_inst%wood_density(cohort_in%pft)**dbh2bl_c
else
bleaf = dbh2bl_a * (EDPftvarcon_inst%max_dbh(cohort_in%pft)**dbh2bl_b) * &
bleaf = dbh2bl_a * (EDPftvarcon_inst%allom_dbh_maxheight(cohort_in%pft)**dbh2bl_b) * &
EDPftvarcon_inst%wood_density(cohort_in%pft)**dbh2bl_c
endif

bleaf = bleaf * slascaler

!write(fates_log(),*) 'bleaf',bleaf, slascaler,cohort_in%pft

!Adjust for canopies that have become so deep that their bottom layer is not producing any carbon...
Expand Down Expand Up @@ -240,14 +236,14 @@ real(r8) function c_area( cohort_in )

if (DEBUG_growth) then
write(fates_log(),*) 'z_area 1',cohort_in%dbh,cohort_in%pft
write(fates_log(),*) 'z_area 2',EDPftvarcon_inst%max_dbh
write(fates_log(),*) 'z_area 2',EDPftvarcon_inst%allom_dbh_maxheight
write(fates_log(),*) 'z_area 3',EDPftvarcon_inst%woody
write(fates_log(),*) 'z_area 4',cohort_in%n
write(fates_log(),*) 'z_area 5',cohort_in%siteptr%spread
write(fates_log(),*) 'z_area 6',cohort_in%canopy_layer
end if

dbh = min(cohort_in%dbh,EDPftvarcon_inst%max_dbh(cohort_in%pft))
dbh = min(cohort_in%dbh,EDPftvarcon_inst%allom_dbh_maxheight(cohort_in%pft))

! ----------------------------------------------------------------------------------
! The function c_area is called during the process of canopy position demotion
Expand Down Expand Up @@ -360,7 +356,7 @@ real(r8) function dDbhdBd( cohort_in )
dBD_dDBH = dbh2bd_c*dbh2bd_a*(cohort_in%hite**dbh2bd_b)*(cohort_in%dbh**(dbh2bd_c-1.0_r8))* &
(EDPftvarcon_inst%wood_density(cohort_in%pft)**dbh2bd_d)

if(cohort_in%dbh < EDPftvarcon_inst%max_dbh(cohort_in%pft))then
if(cohort_in%dbh < EDPftvarcon_inst%allom_dbh_maxheight(cohort_in%pft))then
dH_dDBH = (10.0_r8**c)*m*(cohort_in%dbh**(m-1.0_r8))

dBD_dDBH = dBD_dDBH + dbh2bd_b*dbh2bd_a*(cohort_in%hite**(dbh2bd_b - 1.0_r8))* &
Expand Down Expand Up @@ -396,7 +392,7 @@ real(r8) function dDbhdBl( cohort_in )
dblddbh = dbh2bl_b*dbh2bl_a*(cohort_in%dbh**dbh2bl_b)*(EDPftvarcon_inst%wood_density(cohort_in%pft)**dbh2bl_c)
dblddbh = dblddbh*cohort_in%canopy_trim

if( cohort_in%dbh<EDPftvarcon_inst%max_dbh(cohort_in%pft) ) then
if( cohort_in%dbh<EDPftvarcon_inst%allom_dbh_maxheight(cohort_in%pft) ) then
dDbhdBl = 1.0_r8/dblddbh
else
dDbhdBl = 1.0d15 ! At maximum size, the leaf biomass is saturated, dbl=0
Expand Down
2 changes: 1 addition & 1 deletion biogeochem/EDPhysiologyMod.F90
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Expand Up @@ -970,7 +970,7 @@ subroutine Growth_Derivatives( currentSite, currentCohort, bc_in)
!only if carbon balance is +ve
if ((currentCohort%balive >= target_balive).AND.(currentCohort%carbon_balance > 0._r8))then
! fraction of carbon going into active vs structural carbon
if (currentCohort%dbh <= EDPftvarcon_inst%max_dbh(currentCohort%pft))then ! cap on leaf biomass
if (currentCohort%dbh <= EDPftvarcon_inst%allom_dbh_maxheight(currentCohort%pft))then ! cap on leaf biomass
dbldbd = dDbhdBd(currentCohort)/dDbhdBl(currentCohort)
dbrdbd = EDPftvarcon_inst%allom_l2fr(currentCohort%pft) * dbldbd
dhdbd_fn = dhdbd(currentCohort)
Expand Down
10 changes: 10 additions & 0 deletions main/EDParamsMod.F90
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Expand Up @@ -88,6 +88,10 @@ module EDParamsMod

real(r8),protected :: logging_collateral_frac ! Ratio of collateral mortality to direct logging mortality
character(len=param_string_length),parameter :: logging_name_collateral_frac = "fates_logging_collateral_frac"

real(r8),protected :: logging_coll_under_frac ! Fraction of understory plants that die when logging disturbance
! is generated
character(len=param_string_length),parameter :: logging_name_coll_under_frac = "fates_logging_coll_under_frac"

real(r8),protected :: logging_direct_frac ! Fraction of stems logged per event
character(len=param_string_length),parameter :: logging_name_direct_frac = "fates_logging_direct_frac"
Expand Down Expand Up @@ -251,6 +255,9 @@ subroutine FatesRegisterParams(fates_params)
call fates_params%RegisterParameter(name=logging_name_collateral_frac, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names)

call fates_params%RegisterParameter(name=logging_name_coll_under_frac, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names)

call fates_params%RegisterParameter(name=logging_name_direct_frac, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names)

Expand Down Expand Up @@ -356,6 +363,9 @@ subroutine FatesReceiveParams(fates_params)

call fates_params%RetreiveParameter(name=logging_name_collateral_frac, &
data=logging_collateral_frac)

call fates_params%RetreiveParameter(name=logging_name_coll_under_frac, &
data=logging_coll_under_frac)

call fates_params%RetreiveParameter(name=logging_name_direct_frac, &
data=logging_direct_frac)
Expand Down
44 changes: 28 additions & 16 deletions main/EDPftvarcon.F90
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Expand Up @@ -26,10 +26,11 @@ module EDPftvarcon
!ED specific variables.
type, public :: EDPftvarcon_type
real(r8), allocatable :: pft_used (:) ! Switch to turn on and off PFTs
real(r8), allocatable :: max_dbh (:) ! maximum dbh at which height growth ceases...

real(r8), allocatable :: freezetol (:) ! minimum temperature tolerance (NOT CURRENTY USED)
real(r8), allocatable :: wood_density (:) ! wood density g cm^-3 ...
real(r8), allocatable :: hgt_min (:) ! sapling height m
real(r8), allocatable :: dbh_repro_threshold(:) ! diameter at which mature plants shift allocation
real(r8), allocatable :: dleaf (:) ! leaf characteristic dimension length (m)
real(r8), allocatable :: z0mr (:) ! ratio of roughness length of vegetation to height (-)
real(r8), allocatable :: displar (:) ! ratio of displacement height to canopy top height (-)
Expand All @@ -45,6 +46,7 @@ module EDPftvarcon
real(r8), allocatable :: root_long (:) ! root longevity (yrs)
real(r8), allocatable :: clone_alloc (:) ! fraction of carbon balance allocated to clonal reproduction.
real(r8), allocatable :: seed_alloc (:) ! fraction of carbon balance allocated to seeds.
real(r8), allocatable :: c2b (:) ! Carbon to biomass multiplier [kg/kgC]
real(r8), allocatable :: woody(:)
real(r8), allocatable :: stress_decid(:)
real(r8), allocatable :: season_decid(:)
Expand Down Expand Up @@ -98,7 +100,9 @@ module EDPftvarcon
! Equation 16 Thonicke et al 2010

! Allometry Parameters
! --------------------------------------------------------------------------------------------
! --------------------------------------------------------------------------------------------
real(r8), allocatable :: allom_dbh_maxheight(:) ! dbh at which height growth ceases

real(r8), allocatable :: allom_hmode(:) ! height allometry function type
real(r8), allocatable :: allom_lmode(:) ! maximum leaf allometry function type
real(r8), allocatable :: allom_fmode(:) ! maximum root allometry function type
Expand All @@ -117,7 +121,6 @@ module EDPftvarcon
real(r8), allocatable :: allom_d2bl2(:) ! Parameter 2 for d2bl allometry (slope)
real(r8), allocatable :: allom_d2bl3(:) ! Parameter 3 for d2bl allometry (optional)
real(r8), allocatable :: allom_sai_scaler(:) !
real(r8), allocatable :: allom_d2bl_slascaler(:) !
real(r8), allocatable :: allom_blca_expnt_diff(:) ! Any difference in the exponent between the leaf
! biomass and crown area scaling
real(r8), allocatable :: allom_d2ca_coefficient_max(:) ! upper (savanna) value for crown area to dbh coefficient
Expand Down Expand Up @@ -252,7 +255,7 @@ subroutine Register_PFT(this, fates_params)
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_max_dbh'
name = 'fates_dbh_repro_threshold'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

Expand Down Expand Up @@ -312,6 +315,10 @@ subroutine Register_PFT(this, fates_params)
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_c2b'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_woody'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)
Expand Down Expand Up @@ -428,6 +435,10 @@ subroutine Register_PFT(this, fates_params)
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_allom_dbh_maxheight'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_allom_hmode'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)
Expand Down Expand Up @@ -500,10 +511,6 @@ subroutine Register_PFT(this, fates_params)
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_allom_d2bl_slascaler'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)

name = 'fates_allom_sai_scaler'
call fates_params%RegisterParameter(name=name, dimension_shape=dimension_shape_1d, &
dimension_names=dim_names, lower_bounds=dim_lower_bound)
Expand Down Expand Up @@ -648,9 +655,9 @@ subroutine Receive_PFT(this, fates_params)
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%pft_used)

name = 'fates_max_dbh'
name = 'fates_dbh_repro_threshold'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%max_dbh)
data=this%dbh_repro_threshold)

name = 'fates_freezetol'
call fates_params%RetreiveParameterAllocate(name=name, &
Expand Down Expand Up @@ -708,6 +715,10 @@ subroutine Receive_PFT(this, fates_params)
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%seed_alloc)

name = 'fates_c2b'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%c2b)

name = 'fates_woody'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%woody)
Expand Down Expand Up @@ -820,6 +831,10 @@ subroutine Receive_PFT(this, fates_params)
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%fire_alpha_SH)

name = 'fates_allom_dbh_maxheight'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%allom_dbh_maxheight)

name = 'fates_allom_hmode'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%allom_hmode)
Expand Down Expand Up @@ -896,10 +911,6 @@ subroutine Receive_PFT(this, fates_params)
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%allom_d2ca_coefficient_min)

name = 'fates_allom_d2bl_slascaler'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%allom_d2bl_slascaler)

name = 'fates_allom_sai_scaler'
call fates_params%RetreiveParameterAllocate(name=name, &
data=this%allom_sai_scaler)
Expand Down Expand Up @@ -1378,7 +1389,8 @@ subroutine FatesReportPFTParams(is_master)

write(fates_log(),*) '----------- FATES PFT Parameters -----------------'
write(fates_log(),fmt0) 'pft_used = ',EDPftvarcon_inst%pft_used
write(fates_log(),fmt0) 'max_dbh = ',EDPftvarcon_inst%max_dbh
write(fates_log(),fmt0) 'dbh max height = ',EDPftvarcon_inst%allom_dbh_maxheight
write(fates_log(),fmt0) 'dbh mature = ',EDPftvarcon_inst%dbh_repro_threshold
write(fates_log(),fmt0) 'freezetol = ',EDPftvarcon_inst%freezetol
write(fates_log(),fmt0) 'wood_density = ',EDPftvarcon_inst%wood_density
write(fates_log(),fmt0) 'hgt_min = ',EDPftvarcon_inst%hgt_min
Expand All @@ -1396,6 +1408,7 @@ subroutine FatesReportPFTParams(is_master)
write(fates_log(),fmt0) 'root_long = ',EDPftvarcon_inst%root_long
write(fates_log(),fmt0) 'clone_alloc = ',EDPftvarcon_inst%clone_alloc
write(fates_log(),fmt0) 'seed_alloc = ',EDPftvarcon_inst%seed_alloc
write(fates_log(),fmt0) 'C2B = ',EDPftvarcon_inst%c2b
write(fates_log(),fmt0) 'woody = ',EDPftvarcon_inst%woody
write(fates_log(),fmt0) 'stress_decid = ',EDPftvarcon_inst%stress_decid
write(fates_log(),fmt0) 'season_decid = ',EDPftvarcon_inst%season_decid
Expand Down Expand Up @@ -1457,7 +1470,6 @@ subroutine FatesReportPFTParams(is_master)
write(fates_log(),fmt0) 'allom_d2bl2 = ',EDPftvarcon_inst%allom_d2bl2
write(fates_log(),fmt0) 'allom_d2bl3 = ',EDPftvarcon_inst%allom_d2bl3
write(fates_log(),fmt0) 'allom_sai_scaler = ',EDPftvarcon_inst%allom_sai_scaler
write(fates_log(),fmt0) 'allom_d2bl_slascaler = ',EDPftvarcon_inst%allom_d2bl_slascaler
write(fates_log(),fmt0) 'allom_blca_expnt_diff = ',EDPftvarcon_inst%allom_blca_expnt_diff
write(fates_log(),fmt0) 'allom_d2ca_coefficient_max = ',EDPftvarcon_inst%allom_d2ca_coefficient_max
write(fates_log(),fmt0) 'allom_d2ca_coefficient_min = ',EDPftvarcon_inst%allom_d2ca_coefficient_min
Expand Down
8 changes: 2 additions & 6 deletions main/FatesHistoryInterfaceMod.F90
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Expand Up @@ -3192,16 +3192,12 @@ subroutine define_history_vars(this, initialize_variables)


!Logging
call this%set_history_var(vname='M7_SCPF', units = 'N/ha/event', &
long='logging mortalities by pft/size',use_default='inactive', &
call this%set_history_var(vname='M7_SCPF', units = 'N/ha/event', &
long='logging mortalities by pft/size',use_default='inactive', &
avgflag='A', vtype=site_size_pft_r8, hlms='CLM:ALM', flushval=0.0_r8, &
upfreq=1, ivar=ivar, initialize=initialize_variables, index = ih_m7_si_scpf )






call this%set_history_var(vname='MORTALITY_CANOPY_SCPF', units = 'N/ha/yr', &
long='total mortality of canopy plants by pft/size', use_default='inactive', &
avgflag='A', vtype=site_size_pft_r8, hlms='CLM:ALM', flushval=0.0_r8, &
Expand Down