Allow lai streams with FATES

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.67.1_api.27.0.0
+tag = sci.1.67.2_api.27.0.0
 required = True
 
 [externals_description]

bld/CLMBuildNamelist.pm

@@ -3890,8 +3890,10 @@ sub setup_logic_lai_streams {
   if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams'))  ) {
     $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true.");
   }
-  if ( $nl_flags->{'bgc_mode'} eq "sp" ) {
-
+  if ( ($nl_flags->{'bgc_mode'} eq "sp" || $nl_flags->{'bgc_mode'} eq "fates") ) {
+     if ( $nl_flags->{'bgc_mode'} eq "fates" && ! &value_is_true($nl->get_value('use_fates_sp')) && &value_is_true($nl->get_value('use_lai_streams'))) { 
+          $log->fatal_error("Must have use_fates_sp turned on to run FATES with LAI streams.");
+      }
      if ( &value_is_true($nl->get_value('use_lai_streams')) ) {
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams');
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo',
@@ -3917,15 +3919,19 @@ sub setup_logic_lai_streams {
        }
      }
   } else {
-     # If bgc is CN/CNDV then make sure none of the LAI settings are set
-     if ( defined($nl->get_value('stream_year_first_lai')) ||
-          defined($nl->get_value('stream_year_last_lai'))  ||
-          defined($nl->get_value('model_year_align_lai'))  ||
-          defined($nl->get_value('lai_tintalgo'        ))  ||
+     # If bgc is BGC/BGCDV then make sure none of the LAI settings are set
+     if ( &value_is_true($nl->get_value('use_lai_streams'))) {
+        $log->fatal_error("When bgc is NOT SP use_lai_streams cannot be .true.\n" .
+                          "(eg. don't use this option with BGC or BGCDV).");
+     }
+     if ( defined($nl->get_value('stream_year_first_lai'))  ||
+          defined($nl->get_value('stream_year_last_lai'))   ||
+          defined($nl->get_value('model_year_align_lai'))   ||
+          defined($nl->get_value('lai_tintalgo'        ))   ||
           defined($nl->get_value('stream_fldfilename_lai'))   ) {
         $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" .
                           "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" .
-                          "stream_fldfilename_lai (eg. don't use this option with BGC,CN,CNDV nor BGDCV).");
+                          "stream_fldfilename_lai (eg. don't use this option with BGC or BGCDV).");
      }
   }
 }

cime_config/config_compsets.xml

@@ -205,6 +205,10 @@
     <alias>I2000Clm45BgcCropQianRs</alias>
     <lname>2000_DATM%QIA_CLM45%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV</lname>
   </compset>
+  <compset>
+    <alias>I2000Clm50FatesQian</alias>
+    <lname>2000_DATM%QIA_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+  </compset>
 
   <compset>
     <alias>I2000Clm50BgcCruRs</alias>

cime_config/testdefs/testlist_clm.xml

@@ -2324,17 +2324,16 @@
       <option name="comment"  >Run a test with MEGAN on and FATES-SP</option>
     </options>
   </test>
-<!--    Don't active this test until #1722 is fixed
-  <test name="SMS_Ld3" grid="f09_f09_mg17" compset="I2000Clm51FatesCruRsGs" testmods="clm/FatesColdSatPhen_prescribed">
+
+  <test name="SMS_Ld3" grid="f09_g17" compset="I2000Clm51FatesSpCruRsGs" testmods="clm/FatesColdSatPhen_prescribed">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
-      <option name="comment">Test with prescribed LAI and soil-moisture with FatesSP mode, has to be at f09 and 2000</option>
+      <option name="comment">Test with prescribed LAI and soil moisture with FatesSP mode</option>
     </options>
   </test>
--->
   <test name="SMS_Lm1" grid="f45_f45_mg37" compset="I2000Clm51FatesSpCruRsGs" testmods="clm/FatesColdBasic">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>

cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/include_user_mods

@@ -1,2 +1 @@
 ../FatesColdSatPhen
-../prescribed

cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm

@@ -0,0 +1,3 @@
+use_lai_streams = .true.
+lai_tintalgo = 'lower'      ! set time interpolation to use lower value, so can compare more directly to input dataset
+

doc/ChangeLog

@@ -1,4 +1,68 @@
 ===============================================================
+Tag name: ctsm5.1.dev140
+Originator(s): afoster (Adrianna Foster)
+Date: Tue Sep 12 09:16:37 MDT 2023
+One-line Summary: add lai_streams capability for FATES
+
+Purpose and description of changes
+----------------------------------
+
+Removed checks in clm_driver and CLMBuildNamelist.pm so that now FATES can run when use_lai_streams=.true.
+
+I also had to modify the init in cpl/share_esmf/laiStreamMod to allocate the g_to_ig array in the lai_init method (rather than in the lai_advance method. This was required because SatellitePhenology is called in clim_initializedMod in FATES cases (here). This happens before lai_advance is ever called so at that point the g_to_ig array was not yet allocated. Moving the allocation/initialization to the lai_init method fixes this.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Bugs fixed or introduced
+------------------------
+
+CTSM issues fixed (include CTSM Issue #): #1722
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing: Added a test for lai_streams with FATES
+
+Testing summary:
+----------------
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    cheyenne ---- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: None
+
+Other details
+-------------
+
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates
+
+Pull Requests that document the changes (include PR ids): #2054
+(https://github.com/ESCOMP/ctsm/pull)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev139
 Originator(s): slevis (Samuel Levis)
 Date: Fri Aug 25 16:47:45 MDT 2023

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev140  afoster 09/12/2023 add lai_streams capability for FATES
     ctsm5.1.dev139   slevis 08/28/2023 Fix problems uncovered by nag -nan tests
     ctsm5.1.dev138   slevis 08/25/2023 Refactor max_patch_per_col and maxsoil_patches loops
     ctsm5.1.dev137   slevis 08/23/2023 Surface roughness modifications

src/cpl/share_esmf/laiStreamMod.F90

@@ -54,7 +54,7 @@ subroutine lai_init(bounds)
     type(bounds_type), intent(in) :: bounds          ! bounds
     !
     ! !LOCAL VARIABLES:
-    integer                 :: i,n                        ! index
+    integer                 :: i,n, ig, g                 ! index
     integer                 :: stream_year_first_lai      ! first year in Lai stream to use
     integer                 :: stream_year_last_lai       ! last year in Lai stream to use
     integer                 :: model_year_align_lai       ! align stream_year_first_lai with
@@ -151,6 +151,15 @@ subroutine lai_init(bounds)
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then
        call ESMF_Finalize(endflag=ESMF_END_ABORT)
     end if
+
+    if ( .not. allocated(g_to_ig) )then
+       allocate (g_to_ig(bounds%begg:bounds%endg) )
+       ig = 0
+       do g = bounds%begg,bounds%endg
+          ig = ig+1
+          g_to_ig(g) = ig
+       end do
+    end if
 
   end subroutine lai_init
 

src/main/clm_driver.F90

@@ -225,7 +225,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
     ! Specified phenology
     ! Done in SP mode, FATES-SP mode and also when dry-deposition is active
     ! ============================================================================
-
+    
     if (use_cn) then
        ! For dry-deposition need to call CLMSP so that mlaidiff is obtained
        ! NOTE: This is also true of FATES below
@@ -264,7 +264,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
        end if
 
     end if
-
+    
     ! ==================================================================================
     ! Determine decomp vertical profiles
     !
@@ -468,8 +468,8 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
 
     ! When LAI streams are being used
     ! NOTE: This call needs to happen outside loops over nclumps (as streams are not threadsafe)
-    if ((.not. use_cn) .and. (.not. use_fates) .and. (doalb) .and. use_lai_streams) then
-       call lai_advance( bounds_proc )
+    if (doalb .and. use_lai_streams) then
+       call lai_advance(bounds_proc)
     endif
 
     ! When crop calendar streams are being used

src/main/clm_initializeMod.F90

@@ -691,7 +691,7 @@ subroutine initialize2(ni,nj)
     elseif ( use_fates_sp ) then
        call interpMonthlyVeg(bounds_proc, canopystate_inst)
     end if
-
+    
     ! Determine gridcell averaged properties to send to atm
     if (nsrest == nsrStartup) then
        call t_startf('init_map2gc')
@@ -727,7 +727,6 @@ subroutine initialize2(ni,nj)
           !$OMP PARALLEL DO PRIVATE (nc, bounds_clump)
           do nc = 1,nclumps
              call get_clump_bounds(nc, bounds_clump)
-
              ! FATES satellite phenology mode needs to include all active and inactive patch-level soil
              ! filters due to the translation between the hlm pfts and the fates pfts.
              ! E.g. in FATES, an active PFT vector of 1, 0, 0, 0, 1, 0, 1, 0 would be mapped into
@@ -740,11 +739,12 @@ subroutine initialize2(ni,nj)
           end do
           !$OMP END PARALLEL DO
        end if
+
        call clm_fates%init_coldstart(water_inst%waterstatebulk_inst, &
             water_inst%waterdiagnosticbulk_inst, canopystate_inst, &
             soilstate_inst, soilbiogeochem_carbonflux_inst)
     end if
-
+    
     ! topo_glc_mec was allocated in initialize1, but needed to be kept around through
     ! initialize2 because it is used to initialize other variables; now it can be deallocated
     deallocate(topo_glc_mec, fert_cft, irrig_method)

src/main/clm_varcon.F90

@@ -90,6 +90,7 @@ module clm_varcon
 
   integer, public, parameter  :: fun_period  = 1            ! A FUN parameter, and probably needs to be changed for testing
   real(r8),public, parameter  :: smallValue  = 1.e-12_r8    ! A small values used by FUN
+  real(r8),public, parameter  :: sum_to_1_tol = 1.e-13_r8   ! error tolerance 
 
   ! ------------------------------------------------------------------------
   ! Special value flags

src/main/controlMod.F90

@@ -491,6 +491,14 @@ subroutine control_init(dtime)
 
        end if
 
+       ! Check compatibility with use_lai_streams
+       if (use_lai_streams) then
+        if ((use_fates .and. .not. use_fates_sp) .or. use_cn) then 
+          call endrun(msg=' ERROR: cannot use LAI streams unless in SP mode (use_cn = .false. or use_fates_sp=.true.).'//&
+                  errMsg(sourcefile, __LINE__))
+        end if 
+       end if 
+
        ! If nfix_timeconst is equal to the junk default value, then it was not specified
        ! by the user namelist and we need to assign it the correct default value. If the
        ! user specified it in the namelist, we leave it alone.

src/main/surfrdUtilsMod.F90

@@ -7,6 +7,7 @@ module surfrdUtilsMod
   ! !USES:
 #include "shr_assert.h"
   use shr_kind_mod , only : r8 => shr_kind_r8
+  use clm_varcon   , only : sum_to_1_tol
   use clm_varctl   , only : iulog,use_fates
   use abortutils   , only : endrun
   use shr_log_mod  , only : errMsg => shr_log_errMsg
@@ -51,7 +52,6 @@ subroutine check_sums_equal_1(arr, lb, name, caller, ier, sumto)
     logical :: found
     integer :: nl
     integer :: nindx
-    real(r8), parameter :: eps = 1.e-13_r8
     real(r8), allocatable :: TotalSum(:)
     integer :: ub  ! upper bound of the first dimension of arr
     !-----------------------------------------------------------------------
@@ -64,7 +64,7 @@ subroutine check_sums_equal_1(arr, lb, name, caller, ier, sumto)
     found = .false.
 
     do nl = lb, ub
-       if (abs(sum(arr(nl,:)) - TotalSum(nl)) > eps) then
+       if (abs(sum(arr(nl,:)) - TotalSum(nl)) > sum_to_1_tol) then
           found = .true.
           nindx = nl
           exit

src/utils/clmfates_interfaceMod.F90

@@ -68,6 +68,7 @@ module CLMFatesInterfaceMod
    use clm_varcon        , only : spval
    use clm_varcon        , only : denice
    use clm_varcon        , only : ispval
+   use clm_varcon        , only : sum_to_1_tol
    use clm_varpar        , only : surfpft_lb,surfpft_ub
    use clm_varpar        , only : numrad
    use clm_varpar        , only : ivis
@@ -715,10 +716,10 @@ subroutine init(this, bounds_proc )
                this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m)
             end do
 
-            if(abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub))-1.0_r8).gt.1.0e-9)then
-               write(iulog,*) 'pft_area error in interfc ',s, sum(this%fates(nc)%bc_in(s)%pft_areafrac(:))-1.0_r8
+            if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) > sum_to_1_tol) then
+               write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s)%pft_areafrac(:)) - 1.0_r8
                call endrun(msg=errMsg(sourcefile, __LINE__))
-              endif
+              end if
           end do !site
 
         ! Initialize site-level static quantities dictated by the HLM