Sm jan102020 (NOAA-EMC#44)

* github version of latest branch

* some fixes to physics driver

* adding import field of z0 surface roughness length and
cplwav2atm flag for coupling wave to atm

* removing 271.2 near line 1884

* minor update of atmos_model.F90

* updating GFS_typedef for includeing ras in ccpp, plus minor mod in physics driver

* after merging with Jessica's wave update in fv3

* coupling with ww3

* after merging with fv3atm develop branch and updating for ras

* FV3 updates for RAS MG3 SHOC so that IPD and CCPP reproduce in REPRO mode

* updating mg driver, physics driver and typedef

* updating gcm_shoc.f90 to turn on commented code in assumed pdf

* constraing imported ice fraction in atmos_model.F90

* after merging with NOAA-EMC/fv3atm/develop

* minor fix to atmos_model.F90 and IPD physics driver

* updating .gitmodules

* adding two couplrd suites

* a bug fix in atmos_model.F90, added a logical frac_grid_off to enable reading fractional grid orography file and run as no fractional grid, and minor bug fix in physics driver related to the fractional grid - FV3GFS_io.F90 is modified to use lake fraction if it exists to distinguish lake from ocean

* adding con_csol to GFS_typedefs.F90 and GFS_typedefs.meta for CCPP

* Update long names of hydrometeors to match the ccpp-physics change

* reverting white space changes in .gitmodules

* adding ignore_lake flag to GFS_typedefs.F90 andFV3GFS_io.F90 to preserve the option used in current s2s benchmarks

* settng the momentum, sensible and latent heat fluxes over land exported to the mediator set to large values and over 100% sea ice set to values imported from icemodel. The mask identifying the ocean points to the mediator is correted based on ocean fraction.  Updates also include name changes for the ice fields as changed by Denise Worthen.  Also added an ignore_lake option to the namelist

* changing variable puny to epsln in atmos_model.F90 on Denise's recommendation

* added a new namelist parameter, min_lake_height, with default value of 250m, changeable by user to give more generality

* update gcycle

* point atmos_cubed_sphere to NOAA-EMC repo and ccpp/physics to SMoorthi-EMC SM_Jan102020 branch

* reverting definition of do_cnvgwd in GFS_typedefs.F90

* removed 3 lines from gcycle.F90, which I previously forgot to delete

* fixing a bug in gcycle update

* removing updating tsfco in gcycle when nsstr is on

* updating .gitmodules to point to NCAR/ccpp-physics master branch

Co-authored-by: Jessica.Meixner <Jessica.Meixner@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
Co-authored-by: Jun.Wang <Jun.Wang@noaa.gov>

atmos_model.F90

@@ -223,7 +223,8 @@ module atmos_model_mod
 #endif
 
   real(kind=IPD_kind_phys), parameter :: zero = 0.0_IPD_kind_phys, &
-                                         one  = 1.0_IPD_kind_phys
+                                         one  = 1.0_IPD_kind_phys, &
+                                         epsln = 1.0e-10_IPD_kind_phys
 
 contains
 
@@ -1596,6 +1597,7 @@ subroutine assign_importdata(rc)
     real(kind=ESMF_KIND_R4),  dimension(:,:), pointer  :: datar42d
     real(kind=ESMF_KIND_R8),  dimension(:,:), pointer  :: datar82d
     real(kind=IPD_kind_phys), dimension(:,:), pointer  :: datar8
+    real(kind=IPD_kind_phys)                           :: tem
     logical found, isFieldCreated, lcpl_fice
 !
 !------------------------------------------------------------------------------
@@ -1663,6 +1665,29 @@ subroutine assign_importdata(rc)
 !          endif
 !        endif
 
+
+! get sea-state dependent surface roughness (if cplwav2atm=true)
+!----------------------------
+          fldname = 'wave_z0_roughness_length'
+          if (trim(impfield_name) == trim(fldname)) then
+            findex = QueryFieldList(ImportFieldsList,fldname)
+            if (importFieldsValid(findex) .and. IPD_control%cplwav2atm) then
+!$omp parallel do default(shared) private(i,j,nb,ix)
+              do j=jsc,jec
+                do i=isc,iec
+                  nb = Atm_block%blkno(i,j)
+                  ix = Atm_block%ixp(i,j)
+                  if (IPD_Data(nb)%Sfcprop%oceanfrac(ix) > zero) then
+                    tem = 100.0 * max(zero, min(0.1, datar8(i,j)))
+                    IPD_Data(nb)%Coupling%zorlwav_cpl(ix) = tem
+                    IPD_Data(nb)%Sfcprop%zorlo(ix)        = tem
+
+                  endif
+                enddo
+              enddo
+            endif
+          endif
+
 ! get sea ice surface temperature
 !--------------------------------
           fldname = 'sea_ice_surface_temperature'
@@ -1674,7 +1699,9 @@ subroutine assign_importdata(rc)
                 do i=isc,iec
                   nb = Atm_block%blkno(i,j)
                   ix = Atm_block%ixp(i,j)
-                  IPD_Data(nb)%Coupling%tisfcin_cpl(ix) = datar8(i,j)
+                  if (IPD_Data(nb)%Sfcprop%oceanfrac(ix) > zero) then
+                    IPD_Data(nb)%Coupling%tisfcin_cpl(ix) = datar8(i,j)
+                  endif
                 enddo
               enddo
             endif
@@ -1718,19 +1745,16 @@ subroutine assign_importdata(rc)
                   nb = Atm_block%blkno(i,j)
                   ix = Atm_block%ixp(i,j)
                   IPD_Data(nb)%Coupling%ficein_cpl(ix)   = zero
+                  IPD_Data(nb)%Coupling%slimskin_cpl(ix) = IPD_Data(nb)%Sfcprop%slmsk(ix)
                   if (IPD_Data(nb)%Sfcprop%oceanfrac(ix) > zero) then
                     if (datar8(i,j) >= IPD_control%min_seaice*IPD_Data(nb)%Sfcprop%oceanfrac(ix)) then
                       IPD_Data(nb)%Coupling%ficein_cpl(ix) = max(zero, min(datar8(i,j),one))
-!                     if (IPD_Data(nb)%Sfcprop%oceanfrac(ix) == one) IPD_Data(nb)%Sfcprop%slmsk(ix) = 2. !slmsk=2 crashes in gcycle on partial land points
                       IPD_Data(nb)%Sfcprop%slmsk(ix)         = 2.                                        !slmsk=2 crashes in gcycle on partial land points
                       IPD_Data(nb)%Coupling%slimskin_cpl(ix) = 4.
-                    else
-                      if (IPD_Data(nb)%Sfcprop%oceanfrac(ix) == one) IPD_Data(nb)%Sfcprop%slmsk(ix) = zero
+                    elseif (abs(one-IPD_Data(nb)%Sfcprop%oceanfrac(ix)) < epsln) then
+                      IPD_Data(nb)%Sfcprop%slmsk(ix)         = zero
                       IPD_Data(nb)%Coupling%slimskin_cpl(ix) = zero
                     endif
-                  else
-                    IPD_Data(nb)%Sfcprop%slmsk(ix)         = one
-                    IPD_Data(nb)%Coupling%slimskin_cpl(ix) = one
                   endif
                 enddo
               enddo
@@ -1906,6 +1930,7 @@ subroutine assign_importdata(rc)
               IPD_Data(nb)%Sfcprop%hice(ix)  = IPD_Data(nb)%Coupling%hicein_cpl(ix)
               IPD_Data(nb)%Sfcprop%snowd(ix) = IPD_Data(nb)%Coupling%hsnoin_cpl(ix)
             else 
+              IPD_Data(nb)%Sfcprop%tisfc(ix) = IPD_Data(nb)%Coupling%tseain_cpl(ix)
               IPD_Data(nb)%Sfcprop%fice(ix)  = zero
               IPD_Data(nb)%Sfcprop%hice(ix)  = zero
               IPD_Data(nb)%Sfcprop%snowd(ix) = zero
@@ -1916,12 +1941,30 @@ subroutine assign_importdata(rc)
               IPD_Data(nb)%Coupling%dvsfcin_cpl(ix)  = -99999.0 !                 ,,
               IPD_Data(nb)%Coupling%dtsfcin_cpl(ix)  = -99999.0 !                 ,,
               IPD_Data(nb)%Coupling%ulwsfcin_cpl(ix) = -99999.0 !                 ,,
-              if (IPD_Data(nb)%Sfcprop%oceanfrac(ix) == one) IPD_Data(nb)%Sfcprop%slmsk(ix) = zero ! 100% open water
+              if (abs(one-IPD_Data(nb)%Sfcprop%oceanfrac(ix)) < epsln) &
+                          IPD_Data(nb)%Coupling%slimskin_cpl(ix) = zero ! 100% open water
             endif
           endif
         enddo
       enddo
     endif
+!
+!-------------------------------------------------------------------------------
+!   do j=jsc,jec
+!     do i=isc,iec
+!       nb = Atm_block%blkno(i,j)
+!       ix = Atm_block%ixp(i,j)
+!       if (abs(IPD_Data(nb)%Grid%xlon_d(ix)-2.89) < 0.1 .and. &
+!           abs(IPD_Data(nb)%Grid%xlat_d(ix)+58.99) < 0.1) then
+!         write(0,*)' in assign tisfc=',IPD_Data(nb)%Sfcprop%tisfc(ix),     &
+!          ' oceanfrac=',IPD_Data(nb)%Sfcprop%oceanfrac(ix),' i=',i,' j=',j,&
+!          ' tisfcin=',IPD_Data(nb)%Coupling%tisfcin_cpl(ix),               &
+!          ' fice=',IPD_Data(nb)%Sfcprop%fice(ix)
+!       endif
+!     enddo
+!   enddo
+!-------------------------------------------------------------------------------
+!
 
     rc=0
 !
@@ -2518,7 +2561,7 @@ subroutine setup_exportdata (rc)
             exportData(i,j,idx) = DYCORE_Data(nb)%coupling%t_bot(ix)
           else 
             exportData(i,j,idx) = zero
-          endif 
+          endif
         enddo
       enddo
     endif
@@ -2536,7 +2579,7 @@ subroutine setup_exportdata (rc)
             exportData(i,j,idx) = DYCORE_Data(nb)%coupling%tr_bot(ix,1)
           else 
             exportData(i,j,idx) = zero
-          endif 
+          endif
         enddo
       enddo
     endif
@@ -2587,7 +2630,7 @@ subroutine setup_exportdata (rc)
             exportData(i,j,idx) = DYCORE_Data(nb)%coupling%p_bot(ix)
           else 
             exportData(i,j,idx) = zero
-          endif 
+          endif
         enddo
       enddo
     endif
@@ -2603,8 +2646,8 @@ subroutine setup_exportdata (rc)
           if (associated(DYCORE_Data(nb)%coupling%z_bot)) then
             exportData(i,j,idx) = DYCORE_Data(nb)%coupling%z_bot(ix)
           else 
-            exportData(i,j,idx) = zero 
-          endif 
+            exportData(i,j,idx) = zero
+          endif
         enddo
       enddo
     endif
@@ -2623,14 +2666,14 @@ subroutine setup_exportdata (rc)
         enddo
       enddo
     endif
-    endif !cplflx 
+    endif !cplflx
 
 !---
 ! Fill the export Fields for ESMF/NUOPC style coupling
     call fillExportFields(exportData)
 
 !---
-    if (IPD_Control%cplflx) then 
+    if (IPD_Control%cplflx) then
 ! zero out accumulated fields
 !$omp parallel do default(shared) private(i,j,nb,ix)
       do j=jsc,jec
@@ -2663,20 +2706,20 @@ subroutine setup_exportdata (rc)
 
   end subroutine setup_exportdata
 
-  subroutine addLsmask2grid(fcstgrid, rc)
+  subroutine addLsmask2grid(fcstGrid, rc)
 
     use ESMF
 !
     implicit none
-    type(ESMF_Grid)      :: fcstgrid
+    type(ESMF_Grid)      :: fcstGrid
     integer, optional, intent(out) :: rc
 !
 !  local vars
     integer isc, iec, jsc, jec
     integer i, j, nb, ix
 !    integer CLbnd(2), CUbnd(2), CCount(2), TLbnd(2), TUbnd(2), TCount(2)
     type(ESMF_StaggerLoc) :: staggerloc
-    integer, allocatable :: lsmask(:,:)
+    integer, allocatable  :: lsmask(:,:)
     integer(kind=ESMF_KIND_I4), pointer  :: maskPtr(:,:)
 !
     isc = IPD_control%isc
@@ -2691,16 +2734,16 @@ subroutine addLsmask2grid(fcstgrid, rc)
         nb = Atm_block%blkno(i,j)
         ix = Atm_block%ixp(i,j)
 ! use land sea mask: land:1, ocean:0
-        lsmask(i,j) = floor(IPD_Data(nb)%SfcProp%landfrac(ix))
+        lsmask(i,j) = floor(one + epsln - IPD_Data(nb)%SfcProp%oceanfrac(ix))
       enddo
     enddo
 !
 ! Get mask
-    call ESMF_GridAddItem(fcstgrid, itemflag=ESMF_GRIDITEM_MASK,   &
+    call ESMF_GridAddItem(fcstGrid, itemflag=ESMF_GRIDITEM_MASK,   &
                           staggerloc=ESMF_STAGGERLOC_CENTER, rc=rc)
     if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return
 
-!    call ESMF_GridGetItemBounds(fcstgrid, itemflag=ESMF_GRIDITEM_MASK,   &
+!    call ESMF_GridGetItemBounds(fcstGrid, itemflag=ESMF_GRIDITEM_MASK,   &
 !         staggerloc=ESMF_STAGGERLOC_CENTER, computationalLBound=ClBnd,  &
 !         computationalUBound=CUbnd, computationalCount=Ccount,  &
 !         totalLBound=TLbnd, totalUBound=TUbnd, totalCount=Tcount, rc=rc)
@@ -2709,7 +2752,7 @@ subroutine addLsmask2grid(fcstgrid, rc)
 !     'TlBnd=',TlBnd,'TUbnd=',TUbnd,'Tcount=',Tcount
 !    if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) return
 
-    call ESMF_GridGetItem(fcstgrid, itemflag=ESMF_GRIDITEM_MASK,   &
+    call ESMF_GridGetItem(fcstGrid, itemflag=ESMF_GRIDITEM_MASK,   &
                           staggerloc=ESMF_STAGGERLOC_CENTER,farrayPtr=maskPtr, rc=rc)
 !    print *,'in set up grid, aft get maskptr, rc=',rc, 'size=',size(maskPtr,1),size(maskPtr,2), &
 !      'bound(maskPtr)=', LBOUND(maskPtr,1),LBOUND(maskPtr,2),UBOUND(maskPtr,1),UBOUND(maskPtr,2)

ccpp/config/ccpp_prebuild_config.py

@@ -219,6 +219,7 @@
     'FV3/ccpp/physics/physics/precpd.f'                          : [ 'slow_physics' ],
     'FV3/ccpp/physics/physics/radlw_main.f'                      : [ 'slow_physics' ],
     'FV3/ccpp/physics/physics/radsw_main.f'                      : [ 'slow_physics' ],
+    'FV3/ccpp/physics/physics/rascnv.F90'                        : [ 'slow_physics' ],
     'FV3/ccpp/physics/physics/rayleigh_damp.f'                   : [ 'slow_physics' ],
     'FV3/ccpp/physics/physics/rrtmg_lw_post.F90'                 : [ 'slow_physics' ],
     'FV3/ccpp/physics/physics/rrtmg_lw_pre.F90'                  : [ 'slow_physics' ],

ccpp/suites/suite_FV3_CPT_v0.xml

@@ -54,7 +54,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017.xml

@@ -49,7 +49,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_coupled.xml

@@ -48,7 +48,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>
@@ -58,7 +57,7 @@
       <scheme>GFS_GWD_generic_pre</scheme>
       <scheme>cires_ugwp</scheme>
       <scheme>cires_ugwp_post</scheme>
-       <scheme>GFS_GWD_generic_post</scheme>
+      <scheme>GFS_GWD_generic_post</scheme>
       <scheme>rayleigh_damp</scheme>
       <scheme>GFS_suite_stateout_update</scheme>
       <scheme>ozphys</scheme>

ccpp/suites/suite_FV3_GFS_2017_csawmg.xml

@@ -49,7 +49,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_csawmgshoc.xml

@@ -49,7 +49,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_gfdlmp.xml

@@ -54,7 +54,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_gfdlmp_noahmp.xml

@@ -54,7 +54,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_gfdlmp_regional.xml

@@ -49,7 +49,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_gfdlmp_regional_c768.xml

@@ -49,7 +49,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_h2ophys.xml

@@ -49,7 +49,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_myj.xml

@@ -54,7 +54,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_ntiedtke.xml

@@ -54,7 +54,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_ozphys_2015.xml

@@ -49,7 +49,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_sas.xml

@@ -54,7 +54,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_satmedmf.xml

@@ -49,7 +49,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_satmedmfq.xml

@@ -49,7 +49,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_shinhong.xml

@@ -54,7 +54,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>

ccpp/suites/suite_FV3_GFS_2017_stretched.xml

@@ -54,7 +54,6 @@
     <!-- End of surface iteration loop -->
     <subcycle loop="1">
       <scheme>GFS_surface_composites_post</scheme>
-      <scheme>dcyc2t3_post</scheme>
       <scheme>sfc_diag</scheme>
       <scheme>sfc_diag_post</scheme>
       <scheme>GFS_surface_generic_post</scheme>