PPE mods from /glade/work/linnia/PPEn14trans brought to ctsm5.2.015

Bringing the diffs between branch_tags/PPE16... and branch_tags/PPE15...
to b4b-dev manually

src/biogeochem/CNFUNMod.F90

@@ -53,7 +53,6 @@ module CNFUNMod
   public:: CNFUN                 ! Run FUN
 
   type, private :: params_type
-     real(r8) :: ndays_on        ! number of days to complete leaf onset
      real(r8) :: ndays_off       ! number of days to complete leaf offset
   end type params_type   
 
@@ -64,7 +63,6 @@ module CNFUNMod
   !
   ! !PRIVATE DATA MEMBERS:
   real(r8) :: dt              ! decomp timestep (seconds)
-  real(r8) :: ndays_on        ! number of days to complete onset
   real(r8) :: ndays_off       ! number of days to complete offset
 
   integer, private, parameter :: COST_METHOD = 2 !new way of doing the N uptake
@@ -104,11 +102,6 @@ subroutine readParams ( ncid )
 
   ! read in parameters
 
-    tString='ndays_on'
-    call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
-    if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
-    params_inst%ndays_on=tempr
-
     tString='ndays_off'
     call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv)
     if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
@@ -172,7 +165,6 @@ subroutine CNFUNInit (bounds,cnveg_state_inst,cnveg_carbonstate_inst,cnveg_nitro
   timestep_fun = real(secspday * fun_period)
   nstep_fun    = int(secspday * dayspyr / dt) 
 
-  ndays_on     = params_inst%ndays_on
   ndays_off    = params_inst%ndays_off
 
   !--------------------------------------------------------------------

src/biogeochem/CNPhenologyMod.F90

@@ -94,7 +94,6 @@ module CNPhenologyMod
      real(r8) :: crit_dayl_lat_slope   ! Slope of time for critical day length with latitude (sec/deg) 
                                        ! (Birch et. all 2021 it was 720 see line below)
                                        ! 15hr-11hr/(65N-45N)=linear slope = 720 min/latitude (Birch et. al 2021)
-     real(r8) :: ndays_on              ! number of days to complete leaf onset
      real(r8) :: ndays_off             ! number of days to complete leaf offset
      real(r8) :: fstor2tran            ! fraction of storage to move to transfer for each onset
      real(r8) :: crit_onset_fdd        ! critical number of freezing days to set gdd counter
@@ -113,7 +112,6 @@ module CNPhenologyMod
   real(r8) :: dt                            ! time step delta t (seconds)
   real(r8) :: fracday                       ! dtime as a fraction of day
   real(r8) :: crit_dayl                     ! critical daylength for offset (seconds)
-  real(r8) :: ndays_on                      ! number of days to complete onset
   real(r8) :: ndays_off                     ! number of days to complete offset
   real(r8) :: fstor2tran                    ! fraction of storage to move to transfer on each onset
   real(r8) :: crit_onset_fdd                ! critical number of freezing days
@@ -310,7 +308,6 @@ subroutine readParams ( ncid )
     call readNcdioScalar(ncid, 'crit_dayl', subname, params_inst%crit_dayl)
     call readNcdioScalar(ncid, 'crit_dayl_at_high_lat', subname, params_inst%crit_dayl_at_high_lat)
     call readNcdioScalar(ncid, 'crit_dayl_lat_slope', subname, params_inst%crit_dayl_lat_slope)
-    call readNcdioScalar(ncid, 'ndays_on', subname, params_inst%ndays_on)
     call readNcdioScalar(ncid, 'ndays_off', subname, params_inst%ndays_off)
     call readNcdioScalar(ncid, 'fstor2tran', subname, params_inst%fstor2tran)
     call readNcdioScalar(ncid, 'crit_onset_fdd', subname, params_inst%crit_onset_fdd)
@@ -471,7 +468,6 @@ subroutine CNPhenologyInit(bounds)
     crit_dayl=params_inst%crit_dayl
 
     ! Set constants for CNSeasonDecidPhenology and CNStressDecidPhenology
-    ndays_on=params_inst%ndays_on
     ndays_off=params_inst%ndays_off
 
     ! set transfer parameters
@@ -882,6 +878,8 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp       , &
          woody                               =>    pftcon%woody                                                , & ! Input:  binary flag for woody lifeform (1=woody, 0=not woody)
          season_decid                        =>    pftcon%season_decid                                         , & ! Input:  binary flag for seasonal-deciduous leaf habit (0 or 1)
          season_decid_temperate              =>    pftcon%season_decid_temperate                               , & ! Input:  binary flag for seasonal-deciduous temperate leaf habit (0 or 1)
+         crit_onset_gdd_sf                   =>    pftcon%crit_onset_gdd_sf                                    , & ! Input:  scale factor for crit_onset_gdd (unitless)
+         ndays_on                            =>    pftcon%ndays_on                                             , & ! Input:  number of days to complete leaf onset (days
 
          t_soisno                            =>    temperature_inst%t_soisno_col                               , & ! Input:  [real(r8)  (:,:) ]  soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd)
          soila10                             =>    temperature_inst%soila10_col                                , & ! Input:  [real(r8) (:)   ] 
@@ -1016,7 +1014,8 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp       , &
             lgsf(p) = 0._r8
 
             ! onset gdd sum from Biome-BGC, v4.1.2
-            crit_onset_gdd = exp(4.8_r8 + 0.13_r8*(annavg_t2m(p) - SHR_CONST_TKFRZ))
+            crit_onset_gdd = crit_onset_gdd_sf(ivt(p)) * exp(4.8_r8 + 0.13_r8*(annavg_t2m(p) &
+                             - SHR_CONST_TKFRZ))
 
             ! set flag for solstice period (winter->summer = 1, summer->winter = 0)
             if (dayl(g) >= prev_dayl(g)) then
@@ -1109,7 +1108,8 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp       , &
                   onset_gddflag(p) = 0.0_r8
                   onset_gdd(p) = 0.0_r8
                   do_onset = .false.
-                  onset_counter(p) = ndays_on * secspday
+                  onset_counter(p) = ndays_on(ivt(p)) * secspday
+
 
                   ! move all the storage pools into transfer pools,
                   ! where they will be transfered to displayed growth over the onset period.
@@ -1399,7 +1399,10 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
          stress_decid                        =>    pftcon%stress_decid                                         , & ! Input:  binary flag for stress-deciduous leaf habit (0 or 1)
          leafcn                              =>    pftcon%leafcn                                               , & ! Input:  leaf C:N (gC/gN)
          frootcn                             =>    pftcon%frootcn                                              , & ! Input:  fine root C:N (gC/gN) 
-
+
+         crit_onset_gdd_sf                   =>    pftcon%crit_onset_gdd_sf                                    , & ! Input:  scale factor for crit_onset_gdd (unitless)
+         ndays_on                            =>    pftcon%ndays_on                                             , & ! Input:  number of days to complete leaf onset (days)
+
          soilpsi                             =>    soilstate_inst%soilpsi_col                                  , & ! Input:  [real(r8)  (:,:) ]  soil water potential in each soil layer (MPa)   
 
          t_soisno                            =>    temperature_inst%t_soisno_col                               , & ! Input:  [real(r8)  (:,:) ]  soil temperature (Kelvin)  (-nlevsno+1:nlevgrnd)
@@ -1532,8 +1535,8 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
             psi = soilpsi(c, phenology_soil_layer)
 
             ! onset gdd sum from Biome-BGC, v4.1.2
-            crit_onset_gdd = exp(4.8_r8 + 0.13_r8*(annavg_t2m(p) - SHR_CONST_TKFRZ))
-
+            crit_onset_gdd = crit_onset_gdd_sf(ivt(p)) * exp(4.8_r8 + 0.13_r8*(annavg_t2m(p) &
+                             - SHR_CONST_TKFRZ))
 
             ! update offset_counter and test for the end of the offset period
             if (offset_flag(p) == 1._r8) then
@@ -1673,7 +1676,7 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , &
                   onset_fdd(p) = 0._r8
                   onset_gdd(p) = 0._r8
                   onset_swi(p) = 0._r8
-                  onset_counter(p) = ndays_on * secspday
+                  onset_counter(p) = ndays_on(ivt(p)) * secspday
 
                   ! call subroutine to move all the storage pools into transfer pools,
                   ! where they will be transfered to displayed growth over the onset period.

src/main/initVerticalMod.F90

@@ -47,6 +47,8 @@ module initVerticalMod
   type, private :: params_type
      real(r8) :: slopebeta      ! exponent for microtopography pdf sigma (unitless)
      real(r8) :: slopemax       ! max topographic slope for microtopography pdf sigma (unitless)
+     real(r8) :: zbedrock       ! parameter to substitute for zbedrock (m)
+     real(r8) :: zbedrock_sf    ! parameter to scale zbedrock (m)
   end type params_type
   type(params_type), private ::  params_inst
   !
@@ -79,6 +81,9 @@ subroutine readParams( ncid )
     ! Max topographic slope for microtopography pdf sigma (unitless) 
     call readNcdioScalar(ncid, 'slopemax', subname, params_inst%slopemax)
 
+    call readNcdioScalar(ncid, 'zbedrock', subname, params_inst%zbedrock)
+    call readNcdioScalar(ncid, 'zbedrock_sf', subname, params_inst%zbedrock_sf)
+
   end subroutine readParams
 
     !------------------------------------------------------------------------
@@ -447,6 +452,12 @@ subroutine initVertical(bounds, glc_behavior, thick_wall, thick_roof)
              call endrun( 'ERROR:: zbedrock not found on surface data set, and use_bedrock is true.'//errmsg(sourcefile, __LINE__) )
           end if
        end if
+       if (params_inst%zbedrock>=0._r8) then
+          zbedrock_in(:) = params_inst%zbedrock
+       end if
+       if (params_inst%zbedrock_sf/=1._r8) then
+          zbedrock_in(:) = params_inst%zbedrock_sf*zbedrock_in(:)
+       end if
 
     !  if use_bedrock = false, set zbedrock to lowest layer bottom interface
     else

src/main/pftconMod.F90

@@ -162,6 +162,8 @@ module pftconMod
      real(r8), allocatable :: taper  (:)          ! tapering ratio of height:radius_breast_height
      real(r8), allocatable :: rstem_per_dbh  (:)  ! stem resistance per dbh (s/m/m)
      real(r8), allocatable :: wood_density  (:)   ! wood density (kg/m3)
+     real(r8), allocatable :: crit_onset_gdd_sf(:)! scale factor for crit_onset_gdd
+     real(r8), allocatable :: ndays_on(:)         ! number of days to complete leaf onset
 
      !  crop
 
@@ -502,6 +504,8 @@ subroutine InitAllocate (this)
     allocate( this%taper         (0:mxpft) )
     allocate( this%rstem_per_dbh (0:mxpft) )
     allocate( this%wood_density  (0:mxpft) )
+    allocate( this%crit_onset_gdd_sf (0:mxpft) )
+    allocate( this%ndays_on      (0:mxpft) )
 
   end subroutine InitAllocate
 
@@ -843,6 +847,11 @@ subroutine InitRead(this)
 
     call ncd_io('season_decid_temperate', this%season_decid_temperate, 'read', ncid, readvar=readv, posNOTonfile=.true.)
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+    call ncd_io('crit_onset_gdd_sf', this%crit_onset_gdd_sf, 'read', ncid, readvar=readv, posNOTonfile=.true.)
+    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
+
+    call ncd_io('ndays_on', this%ndays_on, 'read', ncid, readvar=readv, posNOTonfile=.true.)
+    if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
 
     call ncd_io('pftpar20', this%pftpar20, 'read', ncid, readvar=readv, posNOTonfile=.true.)
     if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__))
@@ -1585,6 +1594,8 @@ subroutine Clean(this)
     deallocate( this%rstem_per_dbh)
     deallocate( this%wood_density)
     deallocate( this%taper)
+    deallocate( this%crit_onset_gdd_sf)
+    deallocate( this%ndays_on)
   end subroutine Clean
 
 end module pftconMod