[production/RRFS.v1] saSAS sigmab initialization changes to reduce la…

…rge initial reflectivity in RRFS and inline post bug fix for RUC LSM (#869)

* add namelist parameter sigmab_coldstart
* fix for inline post when using RUC LSM
* pass landsfcmdl to iSF_SURFACE_PHYSICS in post_fv3
* update ccpp/physics
* another bug fix for LSM soil output with inline post
* update ccpp/physics and revert .gitmodules

ccpp/data/GFS_typedefs.F90

@@ -1231,6 +1231,7 @@ module GFS_typedefs
     real(kind=kind_phys) :: betascu         !< Tuning parameter for prog. closure shallow clouds
     real(kind=kind_phys) :: betamcu         !< Tuning parameter for prog. closure midlevel clouds 
     real(kind=kind_phys) :: betadcu         !< Tuning parameter for prog. closure deep clouds 
+    logical              :: sigmab_coldstart !< flag to cold start sigmab
 
     !--- MYNN parameters/switches
     logical              :: do_mynnedmf
@@ -4036,6 +4037,7 @@ subroutine control_initialize (Model, nlunit, fn_nml, me, master, &
     real(kind=kind_phys) :: betascu           = 8.0 !< Tuning parameter for prog. closure shallow clouds
     real(kind=kind_phys) :: betamcu           = 1.0 !< Tuning parameter for prog. closure midlevel clouds
     real(kind=kind_phys) :: betadcu           = 2.0 !< Tuning parameter for prog. closure deep clouds
+    logical              :: sigmab_coldstart  = .false. !< flag to cold start sigmab
     ! *DH
     logical              :: do_myjsfc         = .false.               !< flag for MYJ surface layer scheme
     logical              :: do_myjpbl         = .false.               !< flag for MYJ PBL scheme
@@ -4367,6 +4369,7 @@ subroutine control_initialize (Model, nlunit, fn_nml, me, master, &
                                do_myjsfc, do_myjpbl,                                        &
                                hwrf_samfdeep, hwrf_samfshal,progsigma,betascu,betamcu,      &
                                betadcu,h2o_phys, pdfcld, shcnvcw, redrag, hybedmf, satmedmf,&
+                               sigmab_coldstart,                                            &
                                shinhong, do_ysu, dspheat, lheatstrg, lseaspray, cnvcld,     &
                                random_clds, shal_cnv, imfshalcnv, imfdeepcnv, isatmedmf,    &
                                conv_cf_opt, do_deep, jcap,                                  &
@@ -5176,6 +5179,7 @@ subroutine control_initialize (Model, nlunit, fn_nml, me, master, &
     Model%betascu = betascu
     Model%betamcu = betamcu
     Model%betadcu = betadcu
+    Model%sigmab_coldstart = sigmab_coldstart 
 
     if (oz_phys .and. oz_phys_2015) then
        write(*,*) 'Logic error: can only use one ozone physics option (oz_phys or oz_phys_2015), not both. Exiting.'
@@ -7202,6 +7206,7 @@ subroutine control_print(Model)
       print *, 'betascu            : ', Model%betascu
       print *, 'betamcu            : ', Model%betamcu
       print *, 'betadcu            : ', Model%betadcu
+      print *, 'sigmab_coldstart   : ', Model%sigmab_coldstart
       print *, ' '
       print *, 'cellular automata'
       print *, ' nca               : ', Model%nca

ccpp/data/GFS_typedefs.meta

@@ -5566,6 +5566,12 @@
   dimensions = ()
   type = real
   kind = kind_phys
+[sigmab_coldstart]
+  standard_name = flag_to_cold_start_for_sigmab_init
+  long_name = flag to cold start for sigmab initialization
+  units = flag
+  dimensions = ()
+  type = logical
 [isatmedmf]
   standard_name = choice_of_scale_aware_TKE_moist_EDMF_PBL
   long_name = choice of scale-aware TKE moist EDMF PBL scheme

io/fv3atm_history_io.F90

@@ -186,7 +186,7 @@ subroutine history_type_register(hist, Diag, Time, Atm_block, Model, xlon, xlat,
     hist%fhzero = nint(Model%fhzero)
     !   hist%ncld   = Model%ncld
     hist%ncld   = Model%imp_physics
-    hist%nsoil  = Model%lsoil
+    hist%nsoil  = Model%lsoil_lsm
     hist%dtp    = Model%dtp
     hist%imp_physics  = Model%imp_physics
     hist%landsfcmdl  = Model%lsm

io/module_write_internal_state.F90

@@ -98,6 +98,7 @@ module write_internal_state
       integer                  :: ncld !< Number of hydrometeors.
       integer                  :: nsoil !< Number of soil layers.
       integer                  :: imp_physics !< Choice of microphysics scheme.
+      integer                  :: landsfcmdl !< Choice of land surface model
       integer                  :: dtp !< Physics timestep.
       real,dimension(:),allocatable :: ak !< a parameter for sigma pressure level calculations.
       real,dimension(:),allocatable :: bk !< b parameter for sigma pressure level calculations.

io/post_fv3.F90

@@ -430,6 +430,7 @@ subroutine post_getattr_fv3(wrt_int_state,grid_id)
             if (trim(attName) == 'nsoil')  wrt_int_state%nsoil=varival
             if (trim(attName) == 'fhzero') wrt_int_state%fhzero=varival
             if (trim(attName) == 'imp_physics') wrt_int_state%imp_physics=varival
+            if (trim(attName) == 'landsfcmdl') wrt_int_state%landsfcmdl=varival
           endif
         else if (typekind==ESMF_TYPEKIND_R4) then
           if(n==1) then
@@ -624,7 +625,7 @@ subroutine set_postvars_fv3(wrt_int_state,grid_id,mype,mpicomp)
 !
       imp_physics = wrt_int_state%imp_physics       !set GFS mp physics to 99 for Zhao scheme
       dtp         = wrt_int_state%dtp
-      iSF_SURFACE_PHYSICS = 2
+      iSF_SURFACE_PHYSICS = wrt_int_state%landsfcmdl 
       spval = 9.99e20
 !
 ! nems gfs has zhour defined