Fixes for GNU compilation issues (from @XiaqiongZhou-NOAA)

driver/fvGFS/atmosphere.F90

@@ -944,14 +944,14 @@ subroutine atmosphere_hgt (hgt, position, relative, flip)
    !--- if needed, flip the indexing during this step
    if (flip) then
      if (.not. relative) then
-       z(:,:,1) = Atm(mygrid)%phis(:,:)/grav
+       z(1:iec-isc+1,1:jec-jsc+1,1) = Atm(mygrid)%phis(isc:iec,jsc:jec)/grav
      endif
      do k = 2,npz+1
        z(:,:,k) = z(:,:,k-1) - dz(:,:,npz+2-k)
      enddo
    else
      if (.not. relative) then
-       z(:,:,npz+1) = Atm(mygrid)%phis(:,:)/grav
+       z(1:iec-isc+1,1:jec-jsc+1,npz+1) = Atm(mygrid)%phis(isc:iec,jsc:jec)/grav
      endif
      do k = npz,1,-1
        z(:,:,k) = z(:,:,k+1) - dz(:,:,k)

model/boundary.F90

@@ -2365,7 +2365,7 @@ subroutine update_coarse_grid_mpp(var_coarse, var_nest, nest_domain, dx, dy, are
       position = CENTER
    end if
 
-   !Note that *_c does not have values on the parent_proc. 
+   !Note that *_c does not have values on the parent_proc.
    !Must use isu, etc. to get bounds of update region on parent.
    call mpp_get_F2C_index(nest_domain, is_c, ie_c, js_c, je_c, is_f, ie_f, js_f, je_f, nest_level=nest_level, position=position)
    if (child_proc) then
@@ -2536,7 +2536,7 @@ subroutine fill_var_coarse(var_coarse, coarse_dat_recv, isd_p, ied_p, jsd_p, jed
       select case (nestupdate) 
       case (1,2,6,7,8) ! 1 = Conserving update on all variables; 2 = conserving update for cell-centered values; 6 = conserving remap-update
 
-!$OMP parallel do default(none) shared(npz,jsu,jeu,isu,ieu,coarse_dat_recv,parent_grid,var_coarse) 
+!$OMP parallel do default(none) shared(npz,jsu,jeu,isu,ieu,coarse_dat_recv,parent_grid,var_coarse)
          do k=1,npz
          do j=jsu,jeu
          do i=isu,ieu
@@ -2559,7 +2559,7 @@ subroutine fill_var_coarse(var_coarse, coarse_dat_recv, isd_p, ied_p, jsd_p, jed
       select case (nestupdate) 
       case (1,6,7,8)
 
-!$OMP parallel do default(none) shared(npz,jsu,jeu,isu,ieu,coarse_dat_recv,parent_grid,var_coarse) 
+!$OMP parallel do default(none) shared(npz,jsu,jeu,isu,ieu,coarse_dat_recv,parent_grid,var_coarse)
          do k=1,npz
          do j=jsu,jeu+1
          do i=isu,ieu
@@ -2579,7 +2579,7 @@ subroutine fill_var_coarse(var_coarse, coarse_dat_recv, isd_p, ied_p, jsd_p, jed
       select case (nestupdate) 
       case (1,6,7,8)   !averaging update; in-line average for face-averaged values instead of areal average
 
-!$OMP parallel do default(none) shared(npz,jsu,jeu,isu,ieu,coarse_dat_recv,parent_grid,var_coarse) 
+!$OMP parallel do default(none) shared(npz,jsu,jeu,isu,ieu,coarse_dat_recv,parent_grid,var_coarse)
          do k=1,npz
          do j=jsu,jeu
          do i=isu,ieu+1

model/fv_control.F90

@@ -143,7 +143,7 @@ module fv_control_mod
    use fv_mp_mod,           only: mp_start, domain_decomp, mp_assign_gid, global_nest_domain
    use fv_mp_mod,           only: broadcast_domains, mp_barrier, is_master, setup_master, grids_master_procs, tile_fine
    use fv_mp_mod,           only: MAX_NNEST, MAX_NTILE
-   !use test_cases_mod,      only: test_case, bubble_do, alpha, nsolitons, soliton_Umax, soliton_size
+   use test_cases_mod,      only: read_namelist_test_case_nml
    use fv_timing_mod,       only: timing_on, timing_off, timing_init, timing_prt
    use mpp_domains_mod,     only: domain2D
    use mpp_domains_mod,     only: mpp_define_nest_domains, nest_domain_type, mpp_get_global_domain
@@ -200,7 +200,7 @@ subroutine fv_control_init(Atm, dt_atmos, this_grid, grids_on_this_pe, p_split)
      integer, dimension(MAX_NNEST) :: grid_pes = 0
      integer, dimension(MAX_NNEST) :: grid_coarse = -1
      integer, dimension(MAX_NNEST) :: nest_refine = 3 
-     integer, dimension(MAX_NNEST) :: nest_ioffsets, nest_joffsets
+     integer, dimension(MAX_NNEST) :: nest_ioffsets = -999, nest_joffsets = -999
      integer, dimension(MAX_NNEST) :: all_npx = 0
      integer, dimension(MAX_NNEST) :: all_npy = 0
      integer, dimension(MAX_NNEST) :: all_npz = 0
@@ -537,7 +537,7 @@ subroutine fv_control_init(Atm, dt_atmos, this_grid, grids_on_this_pe, p_split)
 #endif
      call read_namelist_fv_grid_nml
      call read_namelist_fv_core_nml(Atm(this_grid)) ! do options processing here too?
-     !TODO test_case_nml moved to test_cases
+     call read_namelist_test_case_nml(Atm(this_grid)%nml_filename)
      call mpp_get_current_pelist(Atm(this_grid)%pelist, commID=commID) ! for commID
      call mp_start(commID,halo_update_type)
 
@@ -679,7 +679,7 @@ subroutine fv_control_init(Atm, dt_atmos, this_grid, grids_on_this_pe, p_split)
 
      endif
 
-     allocate(Atm(this_grid)%neststruct%child_grids(ngrids)) 
+     allocate(Atm(this_grid)%neststruct%child_grids(ngrids))
      do n=1,ngrids
         Atm(this_grid)%neststruct%child_grids(n) = (grid_coarse(n) == this_grid)
         allocate(Atm(n)%neststruct%do_remap_bc(ngrids))
@@ -1218,7 +1218,6 @@ subroutine setup_update_regions
        upoff = Atm(this_grid)%neststruct%upoff
 
        do n=2,ngrids
-          write(*,'(I, A, 4I)') mpp_pe(), 'SETUP_UPDATE_REGIONS 0: ', mpp_pe(), tile_coarse(n), Atm(this_grid)%global_tile
           if (tile_coarse(n) == Atm(this_grid)%global_tile) then
 
              isu = nest_ioffsets(n)

model/fv_nesting.F90

@@ -1870,7 +1870,7 @@ end subroutine set_BCs_t0
 
  subroutine d2c_setup(u, v, &
       ua, va, &
-	  uc, vc, dord4, &
+      uc, vc, dord4, &
       isd,ied,jsd,jed, is,ie,js,je, npx,npy, &
       grid_type, bounded_domain, &
       se_corner, sw_corner, ne_corner, nw_corner, &

model/tp_core.F90

@@ -159,7 +159,7 @@ subroutine fv_tp_2d(q, crx, cry, npx, npy, hord, fx, fy, xfx, yfx,  &
    ord_ou = hord
 
    if (.not. gridstruct%bounded_domain) &
-	call copy_corners(q, npx, npy, 2, gridstruct%bounded_domain, bd, &
+        call copy_corners(q, npx, npy, 2, gridstruct%bounded_domain, bd, &
                           gridstruct%sw_corner, gridstruct%se_corner, gridstruct%nw_corner, gridstruct%ne_corner)
 
    call yppm(fy2, q, cry, ord_in, isd,ied,isd,ied, js,je,jsd,jed, npx,npy, gridstruct%dya, gridstruct%bounded_domain, gridstruct%grid_type, lim_fac)
@@ -178,7 +178,7 @@ subroutine fv_tp_2d(q, crx, cry, npx, npy, hord, fx, fy, xfx, yfx,  &
    call xppm(fx, q_i, crx(is,js), ord_ou, is,ie,isd,ied, js,je,jsd,jed, npx,npy, gridstruct%dxa, gridstruct%bounded_domain, gridstruct%grid_type, lim_fac)
 
   if (.not. gridstruct%bounded_domain) &
-	call copy_corners(q, npx, npy, 1, gridstruct%bounded_domain, bd, &
+       call copy_corners(q, npx, npy, 1, gridstruct%bounded_domain, bd, &
                                gridstruct%sw_corner, gridstruct%se_corner, gridstruct%nw_corner, gridstruct%ne_corner)
 
   call xppm(fx2, q, crx, ord_in, is,ie,isd,ied, jsd,jed,jsd,jed, npx,npy, gridstruct%dxa, gridstruct%bounded_domain, gridstruct%grid_type, lim_fac)

tools/external_ic.F90

@@ -810,15 +810,15 @@ subroutine get_nggps_ic (Atm, fv_domain, dt_atmos )
                    Atm%gridstruct%dxc, Atm%gridstruct%dyc, Atm%gridstruct%sin_sg, &
                    Atm%flagstruct%n_zs_filter, cnst_0p20*Atm%gridstruct%da_min, &
                    .false., oro_g, Atm%gridstruct%bounded_domain, &
-	           Atm%domain, Atm%bd)
+                    Atm%domain, Atm%bd)
             if ( is_master() ) write(*,*) 'Warning !!! del-2 terrain filter has been applied ', &
                    Atm%flagstruct%n_zs_filter, ' times'
           else if( Atm%flagstruct%nord_zs_filter == 4 ) then
             call del4_cubed_sphere(Atm%npx, Atm%npy, Atm%phis, Atm%gridstruct%area_64, &
                    Atm%gridstruct%dx, Atm%gridstruct%dy,   &
                    Atm%gridstruct%dxc, Atm%gridstruct%dyc, Atm%gridstruct%sin_sg, &
                    Atm%flagstruct%n_zs_filter, .false., oro_g, &
-	           Atm%gridstruct%bounded_domain, &
+                   Atm%gridstruct%bounded_domain, &
                    Atm%domain, Atm%bd)
             if ( is_master() ) write(*,*) 'Warning !!! del-4 terrain filter has been applied ', &
                    Atm%flagstruct%n_zs_filter, ' times'

tools/fv_diagnostics.F90

@@ -2036,7 +2036,7 @@ subroutine fv_diag(Atm, zvir, Time, print_freq)
 
 
 
-       if( idiag%id_slp>0 .or. idiag%id_tm>0 .or. idiag%id_any_hght>0 .or. idiag%id_hght3d .or. idiag%id_c15>0 .or. idiag%id_ctz ) then
+       if( idiag%id_slp>0 .or. idiag%id_tm>0 .or. idiag%id_any_hght>0 .or. idiag%id_hght3d>0 .or. idiag%id_c15>0 .or. idiag%id_ctz>0 ) then
 
           allocate ( wz(isc:iec,jsc:jec,npz+1) )
           call get_height_field(isc, iec, jsc, jec, ngc, npz, Atm(n)%flagstruct%hydrostatic, Atm(n)%delz,  &

tools/fv_restart.F90

@@ -541,7 +541,7 @@ subroutine fv_restart(fv_domain, Atm, dt_atmos, seconds, days, cold_start, grid_
 
 
     do n = ntileMe,1,-1
-       if (new_nest_topo(n)) then
+       if (new_nest_topo(n) > 0 ) then
           call twoway_topo_update(Atm(n), n==this_grid)
        endif
     end do
@@ -566,7 +566,7 @@ subroutine fv_restart(fv_domain, Atm, dt_atmos, seconds, days, cold_start, grid_
        ntdiag = size(Atm(n)%qdiag,4)
 
 
-       if (.not. ideal_test_case(n)) then
+       if ( ideal_test_case(n) == 0 ) then
 #ifdef SW_DYNAMICS
           Atm(n)%pt(:,:,:)=1.
 #else

tools/test_cases.F90

@@ -230,7 +230,7 @@ module test_cases_mod
      integer, parameter :: interpOrder = 1
 
       public :: pz0, zz0
-      public :: test_case, bubble_do, alpha, tracer_test, wind_field, nsolitons, soliton_Umax, soliton_size
+      public :: read_namelist_test_case_nml, alpha
       public :: init_case
 #ifdef NCDF_OUTPUT
       public :: output, output_ncdf
@@ -6360,26 +6360,26 @@ subroutine init_double_periodic(u,v,w,pt,delp,q,phis, ps,pe,peln,pk,pkz,  uc,vc,
            call hydro_eq(npz, is, ie, js, je, ps, phis, dry_mass,      &
                          delp, ak, bk, pt, delz, area, ng, .false., hydrostatic, hybrid_z, domain)
 
-	   ! *** Add Initial perturbation ***
-	   if (bubble_do) then
-	       r0 = 100.*sqrt(dx_const**2 + dy_const**2)
-	       icenter = npx/2
-	       jcenter = npy/2
-
-	       do j=js,je
-		  do i=is,ie
-		     dist = (i-icenter)*dx_const*(i-icenter)*dx_const   &
-			   +(j-jcenter)*dy_const*(j-jcenter)*dy_const
-		     dist = min(r0, sqrt(dist))
-		     do k=1,npz
-			prf = ak(k) + ps(i,j)*bk(k)
-			if ( prf > 100.E2 ) then
-			     pt(i,j,k) = pt(i,j,k) + 0.01*(1. - (dist/r0)) * prf/ps(i,j) 
-			endif
-		     enddo
-		  enddo
-	       enddo
-	   endif
+           ! *** Add Initial perturbation ***
+           if (bubble_do) then
+               r0 = 100.*sqrt(dx_const**2 + dy_const**2)
+               icenter = npx/2
+               jcenter = npy/2
+
+               do j=js,je
+                  do i=is,ie
+                     dist = (i-icenter)*dx_const*(i-icenter)*dx_const   &
+                           +(j-jcenter)*dy_const*(j-jcenter)*dy_const
+                     dist = min(r0, sqrt(dist))
+                     do k=1,npz
+                        prf = ak(k) + ps(i,j)*bk(k)
+                        if ( prf > 100.E2 ) then
+                             pt(i,j,k) = pt(i,j,k) + 0.01*(1. - (dist/r0)) * prf/ps(i,j) 
+                        endif
+                     enddo
+                  enddo
+               enddo
+           endif
           if ( hydrostatic ) then
           call p_var(npz, is, ie, js, je, ptop, ptop_min, delp, delz, pt, ps,   &
                      pe, peln, pk, pkz, kappa, q, ng, ncnst, area, dry_mass, .false., .false., &
@@ -6734,26 +6734,26 @@ subroutine init_double_periodic(u,v,w,pt,delp,q,phis, ps,pe,peln,pk,pkz,  uc,vc,
                    .true., hydrostatic, nwat, domain, flagstruct%adiabatic)
 
 ! *** Add Initial perturbation ***
-	if (bubble_do) then
-	    r0 = 10.e3
-	    zc = 1.4e3         ! center of bubble  from surface
-	    icenter = (npx-1)/2 + 1
-	    jcenter = (npy-1)/2 + 1
-	    do k=1, npz
-	       zm = 0.5*(ze1(k)+ze1(k+1))
-	       ptmp = ( (zm-zc)/zc ) **2
-	       if ( ptmp < 1. ) then
-		  do j=js,je
-		     do i=is,ie
-		       dist = ptmp+((i-icenter)*dx_const/r0)**2+((j-jcenter)*dy_const/r0)**2
-		       if ( dist < 1. ) then
-			    pt(i,j,k) = pt(i,j,k) + pturb*(1.-sqrt(dist))
-		       endif
-		     enddo
-		  enddo
-	       endif
-	    enddo
-	 endif
+        if (bubble_do) then
+            r0 = 10.e3
+            zc = 1.4e3         ! center of bubble  from surface
+            icenter = (npx-1)/2 + 1
+            jcenter = (npy-1)/2 + 1
+            do k=1, npz
+               zm = 0.5*(ze1(k)+ze1(k+1))
+               ptmp = ( (zm-zc)/zc ) **2
+               if ( ptmp < 1. ) then
+                  do j=js,je
+                     do i=is,ie
+                        dist = ptmp+((i-icenter)*dx_const/r0)**2+((j-jcenter)*dy_const/r0)**2
+                         if ( dist < 1. ) then
+                              pt(i,j,k) = pt(i,j,k) + pturb*(1.-sqrt(dist))
+                         endif
+                     enddo
+                   enddo
+               endif
+             enddo
+        endif
 
         case ( 101 )
 
@@ -6904,14 +6904,14 @@ subroutine read_namelist_test_case_nml(nml_filename)
         integer :: ierr, f_unit, unit, ios
 
 #include<file_version.h>
+        namelist /test_case_nml/test_case, bubble_do, alpha, nsolitons,soliton_Umax, soliton_size
 
         unit = stdlog()
 
         ! Make alpha = 0 the default:
         alpha = 0.
         bubble_do = .false.
         test_case = 11   ! (USGS terrain)
-        namelist /test_case_nml/test_case, bubble_do, alpha, nsolitons, soliton_Umax, soliton_size
 
 #ifdef INTERNAL_FILE_NML
         ! Read Test_Case namelist