Merge pull request #1 from glemieux/SP_next_api-add_tests

Adding in test suite definition and pre-merge

Externals_CLM.cfg

@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.34.0_api.9.0.0
+tag = sci.1.35.0_api.10.0.0
 required = True
 
 [PTCLM]

bld/namelist_files/namelist_defaults_clm4_5.xml

@@ -378,7 +378,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.8.1.0_12pft_c200103.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.10.0.0_12pft_c200420.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->

cime_config/testdefs/testlist_clm.xml

@@ -1853,7 +1853,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_Ld3" grid="f09_g16" compset="I2000Clm45Fates" testmods="clm/FatesColdDef">
+  <test name="ERP_Ld3" grid="f09_g16" compset="I2000Clm50Fates" testmods="clm/FatesColdDef">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
@@ -1968,6 +1968,16 @@
     <options>
       <option name="wallclock">00:40:00</option>
     </options>
+  </test>
+    <test name="ERS_Ld30" grid="f45_f45_mg37" compset="I2000Clm50FatesCruGs" testmods="clm/FatesReducedComplexFixedBiogeo">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="fates"/>
+      <machine name="izumi" compiler="nag" category="fates"/>
+      <machine name="lawrencium-lr3" compiler="intel" category="fates"/>      
+    </machines>
+    <options>
+      <option name="wallclock">00:40:00</option>
+    </options>
   </test>
   <test name="ERS_Ld60" grid="f45_f45_mg37" compset="I2000Clm50FatesCruGs" testmods="clm/FatesPPhys">
     <machines>
@@ -2001,6 +2011,7 @@
   <test name="SMS_Lm13" grid="1x1_brazil" compset="I2000Clm50FatesCruGs" testmods="clm/FatesColdDef">
     <machines>
       <machine name="cheyenne" compiler="intel" category="fates"/>
+      <machine name="cheyenne" compiler="gnu" category="fates"/>
       <machine name="lawrencium-lr3" compiler="intel" category="fates"/>
     </machines>
     <options>

cime_config/testdefs/testmods_dirs/clm/FatesHydro/user_nl_clm

@@ -1,5 +1,9 @@
 hist_empty_htapes = .true.
 use_fates_planthydro= .true.
-hist_fincl1       = 'FATES_ERRH2O_SCPF','FATES_TRAN_SCPF','FATES_ROOTUPTAKE_SCPF','FATES_ROOTUPTAKE01_SCPF',
-'FATES_SAPFLOW_COL_SCPF','FATES_ITERH1_COL_SCPF','FATES_ATH_COL_SCPF','FATES_TTH_COL_SCPF',
-'FATES_STH_COL_SCPF','FATES_LTH_COL_SCPF','FATES_AWP_COL_SCPF','FATES_BTRAN_COL_SCPF'
+hist_fincl1       = 'FATES_ERRH2O_SCPF','FATES_TRAN_SCPF',
+'FATES_SAPFLOW_SCPF','FATES_ITERH1_SCPF','FATES_ATH_SCPF','FATES_TTH_SCPF',
+'FATES_STH_SCPF','FATES_LTH_SCPF','FATES_AWP_SCPF','FATES_BTRAN_SCPF',
+'FATES_ROOTWGT_SOILVWC_SI','FATES_ROOTWGT_SOILVWCSAT_SI',
+'FATES_ROOTWGT_SOILMATPOT_SI','FATES_SOILMATPOT_SL','FATES_SOILVWC_SL','FATES_SOILVWCSAT_SL',
+'FATES_ROOTUPTAKE_SI','FATES_ROOTUPTAKE_SL','FATES_ROOTUPTAKE0_SCPF','FATES_ROOTUPTAKE10_SCPF',
+'FATES_ROOTUPTAKE50_SCPF','FATES_ROOTUPTAKE100_SCPF'

cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexFixedBiogeo/include_user_mods

@@ -0,0 +1 @@
+../FatesColdDef

cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexFixedBiogeo/user_nl_clm

@@ -0,0 +1 @@
+use_fates_fixed_biogeog=.true.

src/biogeophys/CanopyFluxesMod.F90

@@ -1277,7 +1277,7 @@ subroutine CanopyFluxes(bounds,  num_exposedvegp, filter_exposedvegp,
 
 
          call clm_fates%wrap_accumulatefluxes(nc,fn,filterp(1:fn))
-         call clm_fates%wrap_hydraulics_drive(bounds,nc,soilstate_inst, &
+         call clm_fates%wrap_hydraulics_drive(bounds,nc,fn,filterp(1:fn),soilstate_inst, &
                waterstate_inst,waterflux_inst,solarabs_inst,energyflux_inst)
 
       else

src/biogeophys/SoilStateType.F90

@@ -9,7 +9,7 @@ module SoilStateType
   use abortutils      , only : endrun
   use clm_varpar      , only : nlevsoi, nlevgrnd, nlevlak, nlayer, nlevsno
   use clm_varcon      , only : spval
-  use clm_varctl      , only : use_hydrstress, use_cn, use_lch4, use_dynroot
+  use clm_varctl      , only : use_hydrstress, use_cn, use_lch4, use_dynroot, use_fates
   use clm_varctl      , only : iulog, hist_wrtch4diag
   use LandunitType    , only : lun                
   use ColumnType      , only : col                
@@ -214,15 +214,15 @@ subroutine InitHistory(this, bounds)
          avgflag='A', long_name='soil matric potential (vegetated landunits only)', &
          ptr_col=this%smp_l_col, set_spec=spval, l2g_scale_type='veg')
 
-       this%root_conductance_patch(begp:endp,:) = spval
-       call hist_addfld2d (fname='KROOT', units='1/s', type2d='levsoi', &
-          avgflag='A', long_name='root conductance each soil layer', &
-          ptr_patch=this%root_conductance_patch, default='inactive')
-
-       this%soil_conductance_patch(begp:endp,:) = spval
-       call hist_addfld2d (fname='KSOIL', units='1/s', type2d='levsoi', &
-          avgflag='A', long_name='soil conductance in each soil layer', &
-          ptr_patch=this%soil_conductance_patch, default='inactive')
+    this%root_conductance_patch(begp:endp,:) = spval
+    call hist_addfld2d (fname='KROOT', units='1/s', type2d='levsoi', &
+         avgflag='A', long_name='root conductance each soil layer', &
+         ptr_patch=this%root_conductance_patch, default='inactive')
+    
+    this%soil_conductance_patch(begp:endp,:) = spval
+    call hist_addfld2d (fname='KSOIL', units='1/s', type2d='levsoi', &
+         avgflag='A', long_name='soil conductance in each soil layer', &
+         ptr_patch=this%soil_conductance_patch, default='inactive')
 
     if (use_cn) then
        this%bsw_col(begc:endc,:) = spval 
@@ -260,7 +260,7 @@ subroutine InitHistory(this, bounds)
 
     end if
 
-    if (use_cn) then
+    if (use_cn .or. use_fates) then
        this%soilpsi_col(begc:endc,:) = spval
        call hist_addfld2d (fname='SOILPSI', units='MPa', type2d='levgrnd', &
             avgflag='A', long_name='soil water potential in each soil layer', &

src/biogeophys/WaterStateType.F90

@@ -11,6 +11,7 @@ module WaterstateType
   use shr_log_mod    , only : errMsg => shr_log_errMsg
   use decompMod      , only : bounds_type
   use clm_varctl     , only : use_vancouver, use_mexicocity, use_cn, iulog, use_luna
+  use clm_varctl     , only : use_fates_planthydro
   use clm_varpar     , only : nlevgrnd, nlevurb, nlevsno   
   use clm_varcon     , only : spval
   use LandunitType   , only : lun                
@@ -766,7 +767,11 @@ subroutine InitCold(this, bounds, &
                   if (j > nbedrock) then
                      this%h2osoi_vol_col(c,j) = 0.0_r8
                   else
-                     this%h2osoi_vol_col(c,j) = 0.15_r8
+                     if(use_fates_planthydro) then
+                         this%h2osoi_vol_col(c,j) = 0.75_r8*watsat_col(c,j)
+                     else
+                         this%h2osoi_vol_col(c,j) = 0.15_r8
+                     end if
                   endif
                end do
             else if (lun%urbpoi(l)) then

src/utils/clmfates_interfaceMod.F90

@@ -104,7 +104,7 @@ module CLMFatesInterfaceMod
    use FatesInterfaceMod     , only : allocate_bcout
    use FatesInterfaceMod     , only : SetFatesTime
    use FatesInterfaceMod     , only : set_fates_ctrlparms
-   use FatesInterfaceMod     , only : InitPARTEHGlobals
+
 
    use FatesHistoryInterfaceMod, only : fates_history_interface_type
    use FatesRestartInterfaceMod, only : fates_restart_interface_type
@@ -118,6 +118,7 @@ module CLMFatesInterfaceMod
    use EDInitMod             , only : init_site_vars
    use EDInitMod             , only : init_patches
    use EDInitMod             , only : set_site_properties
+   use EDInitMod             , only : InitFatesGlobals
    use EDPftVarcon           , only : EDpftvarcon_inst
    use EDSurfaceRadiationMod , only : ED_SunShadeFracs, ED_Norman_Radiation
    use EDBtranMod            , only : btran_ed, &
@@ -503,7 +504,7 @@ subroutine init(this, bounds_proc )
          call this%init_soil_depths(nc)
 
          if (use_fates_planthydro) then
-            call InitHydrSites(this%fates(nc)%sites,this%fates(nc)%bc_in,numpft_fates)
+            call InitHydrSites(this%fates(nc)%sites,this%fates(nc)%bc_in)
          end if
 
          if( this%fates(nc)%nsites == 0 ) then
@@ -528,13 +529,10 @@ subroutine init(this, bounds_proc )
       end do
       !$OMP END PARALLEL DO
 
-      ! This will initialize all globals associated with the chosen
-      ! Plant Allocation and Reactive Transport hypothesis. This includes
-      ! mapping tables and global variables. These will be read-only
-      ! and only required once per machine instance (thus no requirements
-      ! to have it instanced on each thread
+      ! This will initialize all FATES globals,
+      ! particular PARTEH and HYDRO globals
 
-      call InitPARTEHGlobals()
+      call InitFatesGlobals(masterproc)
 
 
 
@@ -1186,8 +1184,24 @@ subroutine restart( this, bounds_proc, ncid, flag, waterstate_inst, &
                      nlevsoil = this%fates(nc)%bc_in(s)%nlevsoil
                      this%fates(nc)%bc_in(s)%hksat_sisl(1:nlevsoil) = &
                           soilstate_inst%hksat_col(c,1:nlevsoil)
+
+                     this%fates(nc)%bc_in(s)%watsat_sisl(1:nlevsoil) = &
+                          soilstate_inst%watsat_col(c,1:nlevsoil)
+
+                     this%fates(nc)%bc_in(s)%watres_sisl(1:nlevsoil) = &
+                          soilstate_inst%watres_col(c,1:nlevsoil)
+
+                     this%fates(nc)%bc_in(s)%sucsat_sisl(1:nlevsoil) = &
+                          soilstate_inst%sucsat_col(c,1:nlevsoil)
+
+                     this%fates(nc)%bc_in(s)%bsw_sisl(1:nlevsoil) = &
+                          soilstate_inst%bsw_col(c,1:nlevsoil)
+
+                     this%fates(nc)%bc_in(s)%h2o_liq_sisl(1:nlevsoil) = &
+                          waterstate_inst%h2osoi_liq_col(c,1:nlevsoil)
                   end do
 
+
                   call RestartHydrStates(this%fates(nc)%sites,  &
                                          this%fates(nc)%nsites, &
                                          this%fates(nc)%bc_in,  &
@@ -1920,13 +1934,15 @@ subroutine wrap_bgc_summary(this, nc, soilbiogeochem_carbonflux_inst,     &
          this%fates(nc)%bc_in(s)%tot_somc     = totsomc(c)
          this%fates(nc)%bc_in(s)%tot_litc     = totlitc(c)
       end do
-
+
+      dtime = get_step_size()
 
       ! Update history variables that track these variables
       call this%fates_hist%update_history_cbal(nc, &
             this%fates(nc)%nsites,  &
             this%fates(nc)%sites,   &
-            this%fates(nc)%bc_in)
+            this%fates(nc)%bc_in,   &
+            dtime)
 
     end associate
  end subroutine wrap_bgc_summary
@@ -2237,7 +2253,16 @@ subroutine ComputeRootSoilFlux(this, bounds_clump, num_filterc, filterc, &
     do s = 1, this%fates(nc)%nsites
        c = this%f2hmap(nc)%fcolumn(s)
        nlevsoil = this%fates(nc)%bc_in(s)%nlevsoil
+
+       ! This is the water removed from the soil layers by roots (or added)
        waterflux_inst%qflx_rootsoi_col(c,1:nlevsoil) = this%fates(nc)%bc_out(s)%qflx_soil2root_sisl(1:nlevsoil)
+
+       ! This is the total amount of water transferred to surface runoff
+       ! (this is generated potentially from supersaturating soils
+       ! (currently this is unnecessary)
+       ! waterflux_inst%qflx_drain_vr_col(c,1:nlevsoil) = this%fates(nc)%bc_out(s)%qflx_ro_sisl(1:nlevsoil)
+
+
     end do
 
  end subroutine ComputeRootSoilFlux
@@ -2274,6 +2299,7 @@ end subroutine ComputeRootSoilFlux
  ! ======================================================================================
 
  subroutine wrap_hydraulics_drive(this, bounds_clump, nc, &
+                                 fn, filterp, &
                                  soilstate_inst, waterstate_inst, waterflux_inst, &
                                  solarabs_inst, energyflux_inst)
 
@@ -2282,6 +2308,8 @@ subroutine wrap_hydraulics_drive(this, bounds_clump, nc, &
    class(hlm_fates_interface_type), intent(inout) :: this
    type(bounds_type),intent(in)                   :: bounds_clump
    integer,intent(in)                             :: nc
+   integer, intent(in)                            :: fn
+   integer, intent(in)                            :: filterp(fn)
    type(soilstate_type)    , intent(inout)        :: soilstate_inst
    type(waterstate_type)   , intent(inout)        :: waterstate_inst
    type(waterflux_type)    , intent(inout)        :: waterflux_inst
@@ -2294,6 +2322,7 @@ subroutine wrap_hydraulics_drive(this, bounds_clump, nc, &
    integer :: j
    integer :: ifp
    integer :: p
+   integer :: f
    integer :: nlevsoil 
    real(r8) :: dtime
 
@@ -2331,10 +2360,21 @@ subroutine wrap_hydraulics_drive(this, bounds_clump, nc, &
          p = ifp+col%patchi(c)
          this%fates(nc)%bc_in(s)%swrad_net_pa(ifp) = solarabs_inst%fsa_patch(p)
          this%fates(nc)%bc_in(s)%lwrad_net_pa(ifp) = energyflux_inst%eflx_lwrad_net_patch(p)
-         this%fates(nc)%bc_in(s)%qflx_transp_pa(ifp) = waterflux_inst%qflx_tran_veg_patch(p)
       end do
    end do
 
+   ! The exposed vegetation filter "filterp" dictates which patches
+   ! had their transpiration updated during canopy_fluxes(). Patches
+   ! not in the filter had been zero'd during prep_canopyfluxes().
+
+   do f = 1,fn
+      p = filterp(f)
+      c = patch%column(p)
+      s = this%f2hmap(nc)%hsites(c)
+      ifp = p - col%patchi(c)
+      this%fates(nc)%bc_in(s)%qflx_transp_pa(ifp) = waterflux_inst%qflx_tran_veg_patch(p)
+   end do
+
    ! Call Fates Hydraulics
    ! ------------------------------------------------------------------------------------
 
@@ -2360,6 +2400,7 @@ subroutine wrap_hydraulics_drive(this, bounds_clump, nc, &
    call this%fates_hist%update_history_hydraulics(nc, &
          this%fates(nc)%nsites, &
          this%fates(nc)%sites, &
+         this%fates(nc)%bc_in, & 
          dtime)