fix GNU out-of-bounds error in a diagnostic in GFDL driver (NOAA-EMC#35)

* updates for double-periodic initialization

* fix GNU compiler out-of-bounds issue in GFDL/atmosphere.F90

driver/GFDL/atmosphere.F90

@@ -434,7 +434,7 @@ subroutine atmosphere_dynamics ( Time, surf_diff )
 !miz
    if ( id_tdt_dyn>0 .or. query_cmip_diag_id(ID_tnta) ) ttend(:, :, :) = Atm(mygrid)%pt(isc:iec, jsc:jec, :)
    if ( any((/ id_qdt_dyn, id_qldt_dyn, id_qidt_dyn, id_qadt_dyn /) > 0) .or. &
-        query_cmip_diag_id(ID_tnhusa) ) qtend(:, :, :, :) = Atm(mygrid)%q (isc:iec, jsc:jec, :, :)
+        query_cmip_diag_id(ID_tnhusa) ) qtend(:, :, :, 1:4) = Atm(mygrid)%q (isc:iec, jsc:jec, :, 1:4)
 !miz
    do itrac = 1, num_tracers
      if (id_tracerdt_dyn (itrac) >0 ) &

model/fv_control.F90

@@ -53,7 +53,7 @@ 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
@@ -432,7 +432,7 @@ 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)
 

tools/test_cases.F90

@@ -154,7 +154,7 @@ 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
       public :: case9_forcing1, case9_forcing2, case51_forcing
       public :: init_double_periodic