Import ed_v0.1.0 changes into a branch from r120.

Created patch file between clm4_5_1_r097 and ed_v010_21_clm4_5_1_r097 tags with the command: svn diff \ https://svn-ccsm-models.cgd.ucar.edu/clm2/trunk_tags/clm4_5_1_r097/ \ https://svn-ccsm-models.cgd.ucar.edu/clm2/branch_tags/ed_v0.1.0_tags/ed_v010_21_clm4_5_1_r097 > \ ed_v0.1.0-21_r097.patch Manually edit patch file to remove property changes. Manually edit patch file to change 'models/lnd' to 'components' in patch file paths. There are some failed hunks in SVN_EXTERNAL_DIRECTORIES that failed to apply and were ignored. It looks like most of these are irrelevent because of cime changes, but one may need to be revisited: https://svn-ccsm-models.cgd.ucar.edu/scripts/branch_tags/refKovenMuszala_tags/rkm_01_scripts4_141023 Testing: Branch has not been compiled or tested.
NGEET · Dec 15, 2015 · 308312f · 308312f
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diff --git a/.ChangeLogED b/.ChangeLogED
diff --git a/ChangeLog b/ChangeLog
@@ -4266,27 +4266,12 @@ Changes answers relative to baseline: YES (but only because of bug 1998)
 ===============================================================
 Tag name:  clm4_5_1_r089
 Originator(s):  erik (Erik)
-Date: Mon Oct 13 13:46:43 MDT 2014
+Date: Fri Oct 10 13:52:12 MDT 2014
 One-line Summary: Bring new urban building temperature to trunk as a clm5.0 feature 
                   as well as human-stress index calculations
 
 Purpose of changes:
 
-New prognostic internal building air temperature methodology for CLM5.0. Retain the older simpler method
-for CLM4.5. The namelist toggle to switch between them is: building_temp_method. By default for clm4_5 physics
-the older method is used and for clm5_0 the newer one is used. Also add in a package of human-stress index
-calculations. Again this is by default on for clm5_0 and off for clm4_5. 
-
-The new building air temperature methodology, solves the system of equations for internal: air, roof, floor, 
-and wall (shade and sunlit) Temperatures. It uses the LAPACK subroutine DGESV to solve the system. It also
-figures out the energy flux needed to either cool the building air temperature to a maximum allowed temperature
-or to heat it to the minimum allowed temperature.
-
-Add in the new load balancing tool and the PyReshaper tool (changes multi-variable 
-monthly history files into single-variable time-series files).
-
-Remove the now unneeded clm4_5 interpinic as well as the mkmapgrids FORTRAN program.
-
 Requirements for tag: Bring in new clm5_0 building temperature as option, Fix scripts bugs, bug 2053/2032
 
 Test level of tag: regular
@@ -4320,13 +4305,12 @@ Describe any changes made to the namelist: new namelists and namelist items
 List any changes to the defaults for the boundary datasets: None
 
 Describe any substantial timing or memory changes:
-   clm5_0 memory use is greater than clm4_5 due to human_stress_indices calculations
-   and output on history (I've seen it make up to a 20% difference)
+   clm5_0 memory use is about 20% greater than clm4_5 due to human_stress_indices calculations
+   and output on history
 
 Code reviewed by: self, oleson, sacks, mvertens, andre
 
 List any svn externals directories updated (csm_share, mct, etc.): scripts, Machines, rtm, cism, csm_share
-   Update to cesm1_3_alpha13c externals.
    Also add in load_balancing_tool and pyReshaper
 
     scripts             to scripts4_141009
@@ -4339,7 +4323,7 @@ List any svn externals directories updated (csm_share, mct, etc.): scripts, Mach
 
 List all files eliminated:
 
---------- Remove clm4_5 interpinic, online interpinic supersedes it
+--------- Remove clm4_5 interpinic, online interpinic superseeds it
 D       models/lnd/clm/tools/clm4_5/interpinic
 D       models/lnd/clm/tools/clm4_5/interpinic/*
 D       models/lnd/clm/tools/clm4_5/interpinic/src/*
@@ -4492,9 +4476,7 @@ CLM testing:
 
 CLM tag used for the baseline comparisons:  clm4_5_1_r088
 
-Changes answers relative to baseline: No for CLM40 and CLM45
-       But, answers DO change for CLM50
-       (except scripts tag update changes history files for IG and irrigation compsets/tests)
+Changes answers relative to baseline: No (except scripts tag update changes history files for IG compsets)
 
 
 ===============================================================

diff --git a/components/clm/doc/ChangeLog b/components/clm/doc/ChangeLog
@@ -4266,27 +4266,12 @@ Changes answers relative to baseline: YES (but only because of bug 1998)
 ===============================================================
 Tag name:  clm4_5_1_r089
 Originator(s):  erik (Erik)
-Date: Mon Oct 13 13:46:43 MDT 2014
+Date: Fri Oct 10 13:52:12 MDT 2014
 One-line Summary: Bring new urban building temperature to trunk as a clm5.0 feature 
                   as well as human-stress index calculations
 
 Purpose of changes:
 
-New prognostic internal building air temperature methodology for CLM5.0. Retain the older simpler method
-for CLM4.5. The namelist toggle to switch between them is: building_temp_method. By default for clm4_5 physics
-the older method is used and for clm5_0 the newer one is used. Also add in a package of human-stress index
-calculations. Again this is by default on for clm5_0 and off for clm4_5. 
-
-The new building air temperature methodology, solves the system of equations for internal: air, roof, floor, 
-and wall (shade and sunlit) Temperatures. It uses the LAPACK subroutine DGESV to solve the system. It also
-figures out the energy flux needed to either cool the building air temperature to a maximum allowed temperature
-or to heat it to the minimum allowed temperature.
-
-Add in the new load balancing tool and the PyReshaper tool (changes multi-variable 
-monthly history files into single-variable time-series files).
-
-Remove the now unneeded clm4_5 interpinic as well as the mkmapgrids FORTRAN program.
-
 Requirements for tag: Bring in new clm5_0 building temperature as option, Fix scripts bugs, bug 2053/2032
 
 Test level of tag: regular
@@ -4320,13 +4305,12 @@ Describe any changes made to the namelist: new namelists and namelist items
 List any changes to the defaults for the boundary datasets: None
 
 Describe any substantial timing or memory changes:
-   clm5_0 memory use is greater than clm4_5 due to human_stress_indices calculations
-   and output on history (I've seen it make up to a 20% difference)
+   clm5_0 memory use is about 20% greater than clm4_5 due to human_stress_indices calculations
+   and output on history
 
 Code reviewed by: self, oleson, sacks, mvertens, andre
 
 List any svn externals directories updated (csm_share, mct, etc.): scripts, Machines, rtm, cism, csm_share
-   Update to cesm1_3_alpha13c externals.
    Also add in load_balancing_tool and pyReshaper
 
     scripts             to scripts4_141009
@@ -4339,7 +4323,7 @@ List any svn externals directories updated (csm_share, mct, etc.): scripts, Mach
 
 List all files eliminated:
 
---------- Remove clm4_5 interpinic, online interpinic supersedes it
+--------- Remove clm4_5 interpinic, online interpinic superseeds it
 D       models/lnd/clm/tools/clm4_5/interpinic
 D       models/lnd/clm/tools/clm4_5/interpinic/*
 D       models/lnd/clm/tools/clm4_5/interpinic/src/*
@@ -4492,9 +4476,7 @@ CLM testing:
 
 CLM tag used for the baseline comparisons:  clm4_5_1_r088
 
-Changes answers relative to baseline: No for CLM40 and CLM45
-       But, answers DO change for CLM50
-       (except scripts tag update changes history files for IG and irrigation compsets/tests)
+Changes answers relative to baseline: No (except scripts tag update changes history files for IG compsets)
 
 
 ===============================================================

diff --git a/components/clm/src/CMakeLists.txt b/components/clm/src/CMakeLists.txt
@@ -24,6 +24,7 @@ add_subdirectory(${CLM_ROOT}/src/biogeophys clm_biogeophys)
 add_subdirectory(${CLM_ROOT}/src/dyn_subgrid clm_dyn_subgrid)
 add_subdirectory(${CLM_ROOT}/src/main clm_main)
 add_subdirectory(${CLM_ROOT}/src/ED/main ed_main)
+add_subdirectory(${CLM_ROOT}/src/ED/biogeophys ed_biogeophys)
 
 # Add general unit test directories (stubbed out files, etc.)
 add_subdirectory(unit_test_stubs)

diff --git a/components/clm/src/ED/biogeochem/EDCohortDynamicsMod.F90 b/components/clm/src/ED/biogeochem/EDCohortDynamicsMod.F90
@@ -211,6 +211,7 @@ subroutine allocate_live_biomass(cc_p)
        currentcohort%balive -currentcohort%bl- currentcohort%br - currentcohort%bsw, currentcohort%status_coh,currentcohort%balive
        write(iulog,*) 'actual vs predicted balive',ideal_balive,currentcohort%balive ,ratio_balive,leaf_frac
        write(iulog,*) 'leaf,root,stem',currentcohort%bl,currentcohort%br,currentcohort%bsw
+       write(iulog,*) 'pft',ft,pftcon%evergreen(ft),pftcon%season_decid(ft),leaves_off_switch
     endif
     currentCohort%b   = currentCohort%bdead + currentCohort%balive
 

diff --git a/components/clm/src/ED/biogeochem/EDGrowthFunctionsMod.F90 b/components/clm/src/ED/biogeochem/EDGrowthFunctionsMod.F90
@@ -103,6 +103,7 @@ real(r8) function Bleaf( cohort_in )
     ! ============================================================================
 
     type(ed_cohort_type), intent(in) :: cohort_in       
+    real(r8) :: slascaler ! changes the target biomass according to the SLA
 
     if(cohort_in%dbh < 0._r8.or.cohort_in%pft == 0.or.cohort_in%dbh > 1000.0_r8)then
        write(iulog,*) 'problems in bleaf',cohort_in%dbh,cohort_in%pft
@@ -111,12 +112,17 @@ real(r8) function Bleaf( cohort_in )
     if(cohort_in%dbh <= EDecophyscon%max_dbh(cohort_in%pft))then
        bleaf = 0.0419_r8 * (cohort_in%dbh**1.56) * EDecophyscon%wood_density(cohort_in%pft)**0.55_r8
     else  
-       bleaf = 0.0419_r8 * (EDecophyscon%max_dbh(cohort_in%pft)**1.56) * EDecophyscon%wood_density(cohort_in%pft)**0.55_r8       
-    endif
-
+       bleaf = 0.0419_r8 * (EDecophyscon%max_dbh(cohort_in%pft)**1.56) * EDecophyscon%wood_density(cohort_in%pft)**0.55_r8      
+    endif  
+    slascaler = 0.03_r8/pftcon%slatop(cohort_in%pft)
+    bleaf = bleaf * slascaler
+
+    !write(*,*) 'bleaf',bleaf, slascaler,cohort_in%pft
+
     !Adjust for canopies that have become so deep that their bottom layer is not producing any carbon... 
     !nb this will change the allometry and the effects of this remain untested. RF. April 2014  
-    bleaf = bleaf*cohort_in%canopy_trim
+
+     bleaf = bleaf * cohort_in%canopy_trim
 
     return
   end function Bleaf

diff --git a/components/clm/src/ED/biogeochem/EDPatchDynamicsMod.F90 b/components/clm/src/ED/biogeochem/EDPatchDynamicsMod.F90
@@ -1096,7 +1096,11 @@ subroutine fuse_2_patches(dp, rp)
     rp%frac_burnt           = (dp%frac_burnt*dp%area + rp%frac_burnt*rp%area)/(dp%area + rp%area)
     rp%burnt_frac_litter(:) = (dp%burnt_frac_litter(:)*dp%area + rp%burnt_frac_litter(:)*rp%area)/(dp%area + rp%area)
     rp%btran_ft(:)          = (dp%btran_ft(:)*dp%area + rp%btran_ft(:)*rp%area)/(dp%area + rp%area)
-
+    rp%dleaf_litter_dt(:)   = (dp%dleaf_litter_dt(:)*dp%area + rp%dleaf_litter_dt(:)*rp%area)/(dp%area+rp%area)
+    rp%leaf_litter_in(:)    = (dp%leaf_litter_in(:)*dp%area  + rp%leaf_litter_in(:)*rp%area)/(dp%area+rp%area)
+    rp%leaf_litter_out(:)   = (dp%leaf_litter_out(:)*dp%area + rp%leaf_litter_out(:)*rp%area)/(dp%area+rp%area)
+
+
     rp%area = rp%area + dp%area !THIS MUST COME AT THE END!
 
     !insert donor cohorts into recipient patch

diff --git a/components/clm/src/ED/biogeochem/EDPhenologyType.F90 b/components/clm/src/ED/biogeochem/EDPhenologyType.F90
@@ -37,6 +37,7 @@ module EDPhenologyType
      ! Public procedures
      procedure, public  :: accumulateAndExtract
      procedure, public  :: init
+     procedure, public  :: restart
      procedure, public  :: initAccVars
      procedure, public  :: initAccBuffer
      procedure, public  :: clean
@@ -51,6 +52,40 @@ module EDPhenologyType
 contains
 
   !------------------------------------------------------------------------------
+
+ !------------------------------------------------------------------------
+  subroutine Restart(this, bounds, ncid, flag)
+    ! 
+    ! !DESCRIPTION:
+    ! Read/Write module information to/from restart file.
+    !
+    ! !USES:
+    use shr_log_mod     , only : errMsg => shr_log_errMsg
+    use spmdMod         , only : masterproc
+    use abortutils      , only : endrun
+    use ncdio_pio       , only : file_desc_t, ncd_double
+    use restUtilMod
+    !
+    ! !ARGUMENTS:
+    class(ed_phenology_type) :: this
+    type(bounds_type), intent(in)    :: bounds 
+    type(file_desc_t), intent(inout) :: ncid   
+    character(len=*) , intent(in)    :: flag   
+
+    !
+    ! !LOCAL VARIABLES:
+    integer :: j,c       ! indices
+    logical :: readvar   ! determine if variable is on initial file
+    !-----------------------------------------------------------------------
+
+    call restartvar(ncid=ncid, flag=flag, varname='ED_GDD', xtype=ncd_double,   &
+         dim1name='pft', &
+         long_name='growing degree days for ED', units='ddays', &
+         interpinic_flag='interp', readvar=readvar, data=this%ED_GDD_patch)
+
+
+ end subroutine restart
+
   subroutine accumulateAndExtract( this, bounds,     &
        t_ref2m_patch,    &
        gridcell, latdeg, &
@@ -78,6 +113,7 @@ subroutine accumulateAndExtract( this, bounds,     &
     ! local variables
     !
     ! update_accum_field expects a pointer, can't make this an allocatable
+    !
     real(r8), pointer :: rbufslp(:)           ! temporary single level - pft level
     integer           :: g, p                 ! local index for gridcell and pft
     integer           :: ier                  ! error code
@@ -91,7 +127,7 @@ subroutine accumulateAndExtract( this, bounds,     &
 
     ! Accumulate and extract GDD0 for ED
     do p = bounds%begp,bounds%endp
-
+      
        g = gridcell(p)
 
        if (latdeg(g) >= 0._r8) then
@@ -120,11 +156,10 @@ subroutine accumulateAndExtract( this, bounds,     &
        if( latdeg(g) < 0._r8 .and. month < calParams%june ) then !do not accumulate in earlier half of year.
           rbufslp(p) = accumResetVal
        endif
-
     end do
 
     call update_accum_field  ( trim(this%accString), rbufslp, get_nstep() )
-    call extract_accum_field ( trim(this%accstring), this%ED_GDD_patch, get_nstep() )
+    call extract_accum_field ( trim(this%accString), this%ED_GDD_patch, get_nstep() )
 
     deallocate(rbufslp)