Diagnostic 3D instantaneous cloud fractions added (#154)

* Diagnostic 3D instantaneous cloud fractions added.
* Bug fix for reflectivity in restart files.
* Update to GFS_restart.F90 to include if block to test for reflectivity flag.

.gitmodules

@@ -8,5 +8,5 @@
 	branch = master
 [submodule "ccpp/physics"]
 	path = ccpp/physics
-	url = https://github.com/NCAR/ccpp-physics
-	branch = master
+	url =  https://github.com/NCAR/ccpp-physics.git 
+	branch = master 

gfsphysics/GFS_layer/GFS_diagnostics.F90

@@ -1937,6 +1937,17 @@ subroutine GFS_externaldiag_populate (ExtDiag, Model, Statein, Stateout, Sfcprop
       ExtDiag(idx)%data(nb)%var3 => IntDiag(nb)%refl_10cm(:,:)
     enddo
 
+    idx = idx + 1
+    ExtDiag(idx)%axes = 3
+    ExtDiag(idx)%name = 'cldfra'
+    ExtDiag(idx)%desc = 'Instantaneous 3D Cloud Fraction'
+    ExtDiag(idx)%unit = 'frac'
+    ExtDiag(idx)%mod_name = 'gfs_phys'
+    allocate (ExtDiag(idx)%data(nblks))
+    do nb = 1,nblks
+      ExtDiag(idx)%data(nb)%var3 => IntDiag(nb)%cldfra(:,:)
+    enddo
+
     idx = idx + 1
     ExtDiag(idx)%axes = 3
     ExtDiag(idx)%name = 'cnvw'

gfsphysics/GFS_layer/GFS_restart.F90

@@ -263,9 +263,12 @@ subroutine GFS_restart_populate (Restart, Model, Statein, Stateout, Sfcprop, &
       enddo
     endif
 #ifdef CCPP
+    if (Model%lrefres) then
+       num = Model%ntot3d+1
+    else
+       num = Model%ntot3d
+    endif
     !--- RAP/HRRR-specific variables, 3D
-    num = Model%ntot3d
-
     ! GF
     if (Model%imfdeepcnv == Model%imfdeepcnv_gf) then
       num = num + 1

gfsphysics/GFS_layer/GFS_typedefs.F90

@@ -1551,7 +1551,9 @@ module GFS_typedefs
 #ifdef CCPP
     real (kind=kind_phys), pointer :: TRAIN  (:,:)   => null()  !< accumulated stratiform T tendency (K s-1)
 #endif
-
+#ifdef CCPP
+    real (kind=kind_phys), pointer :: cldfra  (:,:)   => null()  !< instantaneous 3D cloud fraction
+#endif
     !--- MP quantities for 3D diagnositics 
     real (kind=kind_phys), pointer :: refl_10cm(:,:) => null()  !< instantaneous refl_10cm 
 !
@@ -5613,6 +5615,10 @@ subroutine diag_create (Diag, IM, Model)
     end if
 #endif
 
+#ifdef CCPP
+    allocate (Diag%cldfra     (IM,Model%levs))
+#endif
+
     allocate (Diag%ca_deep  (IM))
     allocate (Diag%ca_turb  (IM))
     allocate (Diag%ca_shal  (IM))
@@ -5930,6 +5936,10 @@ subroutine diag_phys_zero (Diag, Model, linit, iauwindow_center)
        Diag%TRAIN      = zero
     end if
 #endif
+#ifdef CCPP
+    Diag%cldfra      = zero
+#endif
+
     Diag%totprcpb   = zero
     Diag%cnvprcpb   = zero
     Diag%toticeb    = zero

gfsphysics/GFS_layer/GFS_typedefs.meta

@@ -6030,6 +6030,13 @@
   dimensions = (horizontal_dimension,vertical_dimension)
   type = real
   kind = kind_phys
+[cldfra]
+  standard_name = instantaneous_3d_cloud_fraction
+  long_name = instantaneous 3D cloud fraction for all MPs
+  units = frac
+  dimensions = (horizontal_dimension,vertical_dimension)
+  type = real
+  kind = kind_phys
 [ndust]
   standard_name = number_of_dust_bins_for_diagnostics
   long_name = number of dust bins for diagnostics