Merge clm4_5_8_r176, commit '997ff5a1', into andre-ed-clm-16x.

ChangeLog

@@ -1,4 +1,112 @@
 ===============================================================
+Tag name:  clm4_5_8_r176
+Originator(s):  sacks (Bill Sacks)
+Date: Wed Apr 13 09:32:56 MDT 2016
+One-line Summary: Calculate active flags and filters earlier in initialization
+
+Purpose of changes
+------------------
+
+Main purpose is to compute the active flags and filters (via reweight_wrapup)
+earlier in initialization. These are now computed initially before the restart
+file is read, and tehn updated as soon as possible in the midst of the restart
+file read. This is useful in case any of the clm_instMod restart routines want
+to use the active flags or filters, directly or indirectly (e.g., via a call to
+subgridAveMod) - e.g., for the sake of backwards compatibility. This is
+something that's needed in an upcoming tag.
+
+Also: change some CN product history fields, so that they are more consistent -
+so totals just give totals for wood:
+
+- Renamed TOTPROD to TOT_WOODPROD
+
+- Removed PRODUCT_CLOSS and similar fields, added TOT_WOODPRODC_LOSS and similar
+  fields: now just include losses from wood product pools
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions): none
+
+Changes to CLM's user interface (e.g., new/renamed XML or namelist variables):
+- renamed CN product history fields: see above
+
+Changes made to namelist defaults (e.g., changed parameter values): none
+
+Changes to the datasets (e.g., parameter, surface or initial files): none
+
+Substantial timing or memory changes: none
+
+
+Code reviews and testing
+------------------------
+
+Code reviewed by: self
+
+CLM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    yellowstone - not run
+
+  unit-tests (components/clm/src):
+
+    yellowstone - pass
+
+  tools-tests (components/clm/test/tools):
+
+    yellowstone - not run
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     yellowstone - not run
+
+  regular tests (aux_clm40, aux_clm45):
+
+    yellowstone_intel - ok
+    yellowstone_pgi - ok
+    yellowstone_gnu (clm45 only) - ok
+    hobart_nag - ok
+
+    ok means tests pass or xfail, plus expected failures in CLM5 ERP tests with
+    threading, just in the NPP_BURNEDOFF field, due to bug 2292 (leading to
+    differences both in the baseline comparison and in the comparison of the
+    restart to the baseline)
+
+CLM tag used for the baseline comparisons: clm4_5_8_r175
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+Detailed list of changes
+------------------------
+
+List any svn externals directories updated (cime, rtm, cism, etc.): none
+
+List all files eliminated: none
+
+List all files added and what they do: none
+
+List all existing files that have been modified, and describe the changes:
+
+========= Compute active flags and filters earlier in initialization
+M       components/clm/src/main/clm_initializeMod.F90
+M       components/clm/src/main/restFileMod.F90
+
+========= Change CN product history fields (see above for details)
+M       components/clm/src/biogeochem/CNProductsMod.F90
+
+========= Unrelated change: fix argument intent
+M       components/clm/src/biogeochem/CNPhenologyMod.F90
+
+===============================================================
+===============================================================
 Tag name:  clm4_5_8_r175
 Originator(s):  sacks (Bill Sacks)
 Date: Sat Apr  9 15:48:47 MDT 2016

components/clm/doc/ChangeLog

@@ -1,4 +1,112 @@
 ===============================================================
+Tag name:  clm4_5_8_r176
+Originator(s):  sacks (Bill Sacks)
+Date: Wed Apr 13 09:32:56 MDT 2016
+One-line Summary: Calculate active flags and filters earlier in initialization
+
+Purpose of changes
+------------------
+
+Main purpose is to compute the active flags and filters (via reweight_wrapup)
+earlier in initialization. These are now computed initially before the restart
+file is read, and tehn updated as soon as possible in the midst of the restart
+file read. This is useful in case any of the clm_instMod restart routines want
+to use the active flags or filters, directly or indirectly (e.g., via a call to
+subgridAveMod) - e.g., for the sake of backwards compatibility. This is
+something that's needed in an upcoming tag.
+
+Also: change some CN product history fields, so that they are more consistent -
+so totals just give totals for wood:
+
+- Renamed TOTPROD to TOT_WOODPROD
+
+- Removed PRODUCT_CLOSS and similar fields, added TOT_WOODPRODC_LOSS and similar
+  fields: now just include losses from wood product pools
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions): none
+
+Changes to CLM's user interface (e.g., new/renamed XML or namelist variables):
+- renamed CN product history fields: see above
+
+Changes made to namelist defaults (e.g., changed parameter values): none
+
+Changes to the datasets (e.g., parameter, surface or initial files): none
+
+Substantial timing or memory changes: none
+
+
+Code reviews and testing
+------------------------
+
+Code reviewed by: self
+
+CLM testing:
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    yellowstone - not run
+
+  unit-tests (components/clm/src):
+
+    yellowstone - pass
+
+  tools-tests (components/clm/test/tools):
+
+    yellowstone - not run
+
+  PTCLM testing (components/clm/tools/shared/PTCLM/test):
+
+     yellowstone - not run
+
+  regular tests (aux_clm40, aux_clm45):
+
+    yellowstone_intel - ok
+    yellowstone_pgi - ok
+    yellowstone_gnu (clm45 only) - ok
+    hobart_nag - ok
+
+    ok means tests pass or xfail, plus expected failures in CLM5 ERP tests with
+    threading, just in the NPP_BURNEDOFF field, due to bug 2292 (leading to
+    differences both in the baseline comparison and in the comparison of the
+    restart to the baseline)
+
+CLM tag used for the baseline comparisons: clm4_5_8_r175
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: NO
+
+Detailed list of changes
+------------------------
+
+List any svn externals directories updated (cime, rtm, cism, etc.): none
+
+List all files eliminated: none
+
+List all files added and what they do: none
+
+List all existing files that have been modified, and describe the changes:
+
+========= Compute active flags and filters earlier in initialization
+M       components/clm/src/main/clm_initializeMod.F90
+M       components/clm/src/main/restFileMod.F90
+
+========= Change CN product history fields (see above for details)
+M       components/clm/src/biogeochem/CNProductsMod.F90
+
+========= Unrelated change: fix argument intent
+M       components/clm/src/biogeochem/CNPhenologyMod.F90
+
+===============================================================
+===============================================================
 Tag name:  clm4_5_8_r175
 Originator(s):  sacks (Bill Sacks)
 Date: Sat Apr  9 15:48:47 MDT 2016

components/clm/doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+   clm4_5_8_r176    sacks 04/13/2016 Calculate active flags and filters earlier in initialization
    clm4_5_8_r175    sacks 04/09/2016 For glc_mec, change downscaling and where SMB is computed
    clm4_5_8_r174     erik 03/25/2016 Bring Rosie's respiration changes to the trunk
    clm4_5_8_r173    sacks 03/17/2016 Major refactor of CN Products

components/clm/doc/UsersGuide/clm_ug.xml

@@ -162,7 +162,7 @@ The purpose of this guide is to instruct both the novice and experienced user, a
 </para>
 </abstract>
 
-<releaseinfo>$URL: https://svn-ccsm-models.cgd.ucar.edu/clm2/trunk_tags/clm4_5_8_r175/components/clm/doc/UsersGuide/clm_ug.xml $</releaseinfo>
+<releaseinfo>$URL: https://svn-ccsm-models.cgd.ucar.edu/clm2/trunk_tags/clm4_5_8_r176/components/clm/doc/UsersGuide/clm_ug.xml $</releaseinfo>
 
 <date>&build_date;</date>
 

components/clm/src/biogeochem/CNPhenologyMod.F90

@@ -2372,7 +2372,7 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, &
     implicit none
     integer                       , intent(in)    :: num_soilp       ! number of soil patches in filter
     integer                       , intent(in)    :: filter_soilp(:) ! filter for soil patches
-    type(cnveg_state_type)        , intent(in)    :: cnveg_state_inst
+    type(cnveg_state_type)        , intent(inout) :: cnveg_state_inst
     type(cnveg_carbonstate_type)  , intent(in)    :: cnveg_carbonstate_inst
     type(cnveg_nitrogenstate_type), intent(in)    :: cnveg_nitrogenstate_inst
     type(cnveg_carbonflux_type)   , intent(inout) :: cnveg_carbonflux_inst

components/clm/src/biogeochem/CNProductsMod.F90

@@ -33,10 +33,10 @@ module CNProductsMod
      class(species_base_type), allocatable :: species    ! C, N, C13, C14, etc.
 
      ! States
-     real(r8), pointer :: cropprod1_col(:)  ! (g[C or N]/m2) grain product pool, 1-year lifespan
-     real(r8), pointer :: prod10_col(:)     ! (g[C or N]/m2) wood product pool, 10-year lifespan
-     real(r8), pointer :: prod100_col(:)    ! (g[C or N]/m2) wood product pool, 100-year lifespan
-     real(r8), pointer :: totprod_col(:)    ! (g[C or N]/m2) total WOOD product pool
+     real(r8), pointer :: cropprod1_col(:)    ! (g[C or N]/m2) grain product pool, 1-year lifespan
+     real(r8), pointer :: prod10_col(:)       ! (g[C or N]/m2) wood product pool, 10-year lifespan
+     real(r8), pointer :: prod100_col(:)      ! (g[C or N]/m2) wood product pool, 100-year lifespan
+     real(r8), pointer :: tot_woodprod_col(:) ! (g[C or N]/m2) total wood product pool
 
      ! Fluxes: gains
      real(r8), pointer :: dwt_prod10_gain_col(:)  ! (g[C or N]/m2/s) dynamic landcover addition to 10-year wood product pool
@@ -46,9 +46,10 @@ module CNProductsMod
      real(r8), pointer :: grain_to_cropprod1_col(:) ! (g[C or N]/m2/s) grain to 1-year crop product pool
 
      ! Fluxes: losses
-     real(r8), pointer :: cropprod1_loss_col(:) ! (g[C or N]/m2/s) decomposition loss from 1-yr grain product pool
-     real(r8), pointer :: prod10_loss_col(:)    ! (g[C or N]/m2/s) decomposition loss from 10-yr wood product pool
-     real(r8), pointer :: prod100_loss_col(:)   ! (g[C or N]/m2/s) decomposition loss from 100-yr wood product pool
+     real(r8), pointer :: cropprod1_loss_col(:)    ! (g[C or N]/m2/s) decomposition loss from 1-yr grain product pool
+     real(r8), pointer :: prod10_loss_col(:)       ! (g[C or N]/m2/s) decomposition loss from 10-yr wood product pool
+     real(r8), pointer :: prod100_loss_col(:)      ! (g[C or N]/m2/s) decomposition loss from 100-yr wood product pool
+     real(r8), pointer :: tot_woodprod_loss_col(:) ! (g[C or N]/m2/s) decompomposition loss from all wood product pools
 
    contains
 
@@ -113,7 +114,7 @@ subroutine InitAllocate(this, bounds)
     allocate(this%cropprod1_col(begc:endc)) ; this%cropprod1_col(:) = nan
     allocate(this%prod10_col(begc:endc)) ; this%prod10_col(:) = nan
     allocate(this%prod100_col(begc:endc)) ; this%prod100_col(:) = nan
-    allocate(this%totprod_col(begc:endc)) ; this%totprod_col(:) = nan
+    allocate(this%tot_woodprod_col(begc:endc)) ; this%tot_woodprod_col(:) = nan
 
     allocate(this%dwt_prod10_gain_col(begc:endc)) ; this%dwt_prod10_gain_col(:) = nan
     allocate(this%dwt_prod100_gain_col(begc:endc)) ; this%dwt_prod100_gain_col(:) = nan
@@ -124,6 +125,7 @@ subroutine InitAllocate(this, bounds)
     allocate(this%cropprod1_loss_col(begc:endc)) ; this%cropprod1_loss_col(:) = nan
     allocate(this%prod10_loss_col(begc:endc)) ; this%prod10_loss_col(:) = nan
     allocate(this%prod100_loss_col(begc:endc)) ; this%prod100_loss_col(:) = nan
+    allocate(this%tot_woodprod_loss_col(begc:endc)) ; this%tot_woodprod_loss_col(:) = nan
     allocate(this%product_loss_col(begc:endc)) ; this%product_loss_col(:) = nan
 
   end subroutine InitAllocate
@@ -171,13 +173,13 @@ subroutine InitHistory(this, bounds)
          long_name = '100-yr wood product ' // this%species%get_species(), &
          ptr_col = this%prod100_col)
 
-    this%totprod_col(begc:endc) = spval
+    this%tot_woodprod_col(begc:endc) = spval
     call hist_addfld1d( &
-         fname = this%species%hist_fname('TOTPROD'), &
+         fname = this%species%hist_fname('TOT_WOODPROD'), &
          units = 'g' // this%species%get_species() // '/m^2', &
          avgflag = 'A', &
          long_name = 'total wood product ' // this%species%get_species(), &
-         ptr_col = this%totprod_col)
+         ptr_col = this%tot_woodprod_col)
 
     this%dwt_prod10_gain_col(begc:endc) = spval
     call hist_addfld1d( &
@@ -219,13 +221,13 @@ subroutine InitHistory(this, bounds)
          long_name = 'loss from 100-yr wood product pool', &
          ptr_col = this%prod100_loss_col)
 
-    this%product_loss_col(begc:endc) = spval
+    this%tot_woodprod_loss_col(begc:endc) = spval
     call hist_addfld1d( &
-         fname = this%species%hist_fname('PRODUCT_', suffix='LOSS'), &
+         fname = this%species%hist_fname('TOT_WOODPROD', suffix='_LOSS'), &
          units = 'g' // this%species%get_species() // '/m^2/s', &
          avgflag = 'A', &
          long_name = 'total loss from wood product pools', &
-         ptr_col = this%product_loss_col)
+         ptr_col = this%tot_woodprod_loss_col)
 
   end subroutine InitHistory
 
@@ -245,7 +247,7 @@ subroutine InitCold(this, bounds)
        this%cropprod1_col(c) = 0._r8
        this%prod10_col(c) = 0._r8
        this%prod100_col(c) = 0._r8
-       this%totprod_col(c) = 0._r8
+       this%tot_woodprod_col(c) = 0._r8
     end do
 
     ! TODO(wjs, 2016-03-11) I think the only reason this should be necessary is to set the
@@ -261,6 +263,7 @@ subroutine InitCold(this, bounds)
        this%cropprod1_loss_col(c) = 0._r8
        this%prod10_loss_col(c) = 0._r8
        this%prod100_loss_col(c) = 0._r8
+       this%tot_woodprod_loss_col(c) = 0._r8
        this%product_loss_col(c) = 0._r8
     end do
 
@@ -618,10 +621,15 @@ subroutine ComputeSummaryVars(this, bounds, num_soilc, filter_soilc)
        c = filter_soilc(fc)
 
        ! total wood products
-       this%totprod_col(c) = &
+       this%tot_woodprod_col(c) = &
             this%prod10_col(c) + &
             this%prod100_col(c)
 
+       ! total loss from wood products
+       this%tot_woodprod_loss_col(c) = &
+            this%prod10_loss_col(c) + &
+            this%prod100_loss_col(c)
+
        ! total loss from ALL products
        this%product_loss_col(c) = &
             this%cropprod1_loss_col(c) + &