Merge branch 'development' into tj2016

.gitignore

@@ -25,6 +25,7 @@ test/include/*.o
 test/unit/tmp
 test/system/*.log
 test/system/cime-tests.o*
+test_driver_*.sh
 
 # Ignore editor temporaries and backups
 *.swp

src/control/cam_comp.F90

@@ -252,7 +252,17 @@ subroutine cam_timestep_init()
       !-----------------------------------------------------------------------
 
       use phys_comp, only: phys_timestep_init
+      use stepon,    only: stepon_timestep_init
 
+      !----------------------------------------------------------
+      ! First phase of dynamics (at least couple from dynamics to physics)
+      ! Return time-step for physics from dynamics.
+      !----------------------------------------------------------
+      call t_barrierf('sync_stepon_timestep_init', mpicom)
+      call t_startf('stepon_timestep_init')
+      call stepon_timestep_init(dtime_phys, cam_runtime_opts, phys_state, phys_tend,   &
+           dyn_in, dyn_out)
+      call t_stopf('stepon_timestep_init')
       !
       !----------------------------------------------------------
       ! PHYS_TIMESTEP_INIT Call the Physics package
@@ -274,22 +284,11 @@ subroutine cam_run1(cam_in, cam_out)
       !-----------------------------------------------------------------------
 
       use phys_comp, only: phys_run1
-      use stepon,    only: stepon_run1
 !      use ionosphere_interface, only: ionosphere_run1
 
       type(cam_in_t),  pointer, intent(inout) :: cam_in  ! Input from surface to CAM
       type(cam_out_t), pointer, intent(inout) :: cam_out ! Output from CAM to surface
 
-      !----------------------------------------------------------
-      ! First phase of dynamics (at least couple from dynamics to physics)
-      ! Return time-step for physics from dynamics.
-      !----------------------------------------------------------
-      call t_barrierf('sync_stepon_run1', mpicom)
-      call t_startf('stepon_run1')
-      call stepon_run1(dtime_phys, cam_runtime_opts, phys_state, phys_tend,   &
-           dyn_in, dyn_out)
-      call t_stopf('stepon_run1')
-
       !----------------------------------------------------------
       ! first phase of ionosphere -- write to IC file if needed
       !----------------------------------------------------------

src/data/write_init_files.py

@@ -1014,12 +1014,12 @@ def write_phys_read_subroutine(outfile, host_dict, host_vars, host_imports,
     outfile.write("end if", 8)
     outfile.write("field_data_ptr(:,:,constituent_idx) = constituent_default_value", 8)
     outfile.write("if (masterproc) then", 8)
-    outfile.write("write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value", 9)
+    outfile.write("write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ', constituent_default_value", 9)
     outfile.write("end if", 8)
     outfile.write("else", 7)
     outfile.write("field_data_ptr(:,:,constituent_idx) = 0._kind_phys", 8)
     outfile.write("if (masterproc) then", 8)
-    outfile.write("write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'", 9)
+    outfile.write("write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'", 9)
     outfile.write("end if", 8)
     outfile.write("end if", 7)
     outfile.write("end if", 6)

src/dynamics/mpas/stepon.F90

@@ -10,7 +10,7 @@ module stepon
     private
     ! Provide APIs required by CAM Control.
     public :: stepon_init
-    public :: stepon_run1
+    public :: stepon_timestep_init
     public :: stepon_run2
     public :: stepon_run3
     public :: stepon_final
@@ -23,15 +23,15 @@ subroutine stepon_init(cam_runtime_opts, dyn_in, dyn_out)
     type(dyn_export_t),    intent(in) :: dyn_out
 end subroutine stepon_init
 
-! Called by `cam_run1` in `src/control/cam_comp.F90`.
-subroutine stepon_run1(dtime_phys, cam_runtime_opts, phys_state, phys_tend, dyn_in, dyn_out)
+! Called by `cam_timestep_init` in `src/control/cam_comp.F90`.
+subroutine stepon_timestep_init(dtime_phys, cam_runtime_opts, phys_state, phys_tend, dyn_in, dyn_out)
     real(r8),              intent(out)   :: dtime_phys
     type(runtime_options), intent(in)    :: cam_runtime_opts
     type(physics_state),   intent(inout) :: phys_state
     type(physics_tend),    intent(inout) :: phys_tend
     type(dyn_import_t),    intent(inout) :: dyn_in
     type(dyn_export_t),    intent(inout) :: dyn_out
-end subroutine stepon_run1
+end subroutine stepon_timestep_init
 
 ! Called by `cam_run2` in `src/control/cam_comp.F90`.
 subroutine stepon_run2(cam_runtime_opts, phys_state, phys_tend, dyn_in, dyn_out)

src/dynamics/none/stepon.F90

@@ -9,7 +9,7 @@ module stepon
    private
 
    public :: stepon_init
-   public :: stepon_run1
+   public :: stepon_timestep_init
    public :: stepon_run2
    public :: stepon_run3
    public :: stepon_final
@@ -30,8 +30,8 @@ end subroutine stepon_init
 
    !===========================================================================
 
-   subroutine stepon_run1(dtime_out, cam_runtime_opts, phys_state, phys_tend, &
-        dyn_in, dyn_out)
+   subroutine stepon_timestep_init(dtime_out, cam_runtime_opts, phys_state,   &
+        phys_tend, dyn_in, dyn_out)
 
       use runtime_obj,    only: runtime_options
       use time_manager,   only: get_step_size
@@ -51,10 +51,10 @@ subroutine stepon_run1(dtime_out, cam_runtime_opts, phys_state, phys_tend, &
 
       !Ensure that the time-step is a positive value:
       if (iam < npes) then
-         if (dtime_out <= 0)  call endrun('stepon_run1: bad dtime')
+         if (dtime_out <= 0)  call endrun('stepon_timestep_init: bad dtime')
       end if
 
-   end subroutine stepon_run1
+   end subroutine stepon_timestep_init
 
    !===========================================================================
 

src/dynamics/se/namelist_definition_se_dycore.xml

@@ -215,6 +215,7 @@
     </desc>
     <values>
       <value>0</value>
+      <value csne="3">3</value>
       <value csne="5">5</value>
       <value csne="16">16</value>
       <value csne="30">30</value>

src/dynamics/se/stepon.F90

@@ -16,7 +16,7 @@ module stepon
 save
 
 public stepon_init
-public stepon_run1
+public stepon_timestep_init
 public stepon_run2
 public stepon_run3
 public stepon_final
@@ -36,7 +36,8 @@ end subroutine stepon_init
 
 !=========================================================================================
 
-subroutine stepon_run1(dtime_out, cam_runtime_opts, phys_state, phys_tend, dyn_in, dyn_out)
+subroutine stepon_timestep_init(dtime_out, cam_runtime_opts, phys_state,      &
+     phys_tend, dyn_in, dyn_out)
 
    use time_manager,   only: get_step_size
    use cam_abortutils, only: endrun
@@ -59,8 +60,8 @@ subroutine stepon_run1(dtime_out, cam_runtime_opts, phys_state, phys_tend, dyn_i
 
    !Ensure that the model and dynamics time-steps are positive values:
    if (iam < par%nprocs) then
-      if (tstep <= 0)      call endrun('stepon_run1: bad tstep')
-      if (dtime_out <= 0)  call endrun('stepon_run1: bad dtime')
+      if (tstep <= 0)      call endrun('stepon_timestep_init: bad tstep')
+      if (dtime_out <= 0)  call endrun('stepon_timestep_init: bad dtime')
 
       ! write diagnostic fields on gll grid and initial file
       call diag_dynvar_ic(dyn_out%elem, dyn_out%fvm)
@@ -73,7 +74,7 @@ subroutine stepon_run1(dtime_out, cam_runtime_opts, phys_state, phys_tend, dyn_i
    call d_p_coupling(cam_runtime_opts, phys_state, phys_tend, dyn_out)
    call t_stopf('d_p_coupling')
 
-end subroutine stepon_run1
+end subroutine stepon_timestep_init
 
 !=========================================================================================
 

src/physics/utils/physics_data.F90

@@ -56,21 +56,18 @@ integer function find_input_name_idx(stdname, use_init_variables, constituent_in
       integer                       :: idx
       ! to test read_from_file status
       logical                       :: is_read
+      logical                       :: is_constituent
 
       !Initialize function:
       find_input_name_idx = no_exist_idx
       constituent_index = no_exist_idx
+      is_constituent = .false.
 
       !First check if quantity is a constituent:
       call const_get_index(trim(stdname), find_input_name_idx, abort=.false., warning=.false.)
-      if (find_input_name_idx < 0) then
-         find_input_name_idx = no_exist_idx
-      else
+      if (find_input_name_idx >= 0) then
          constituent_index = find_input_name_idx
-         find_input_name_idx = const_idx
-         !Return from function here,
-         !as variable has already been found:
-         return
+         is_constituent = .true.
       end if
 
       !Loop through physics variable standard names:
@@ -87,7 +84,11 @@ integer function find_input_name_idx(stdname, use_init_variables, constituent_in
                end if
                if (is_read) then
                   !If reading initialized variables, set to idx:
-                  find_input_name_idx = idx
+                  if (is_constituent) then
+                     find_input_name_idx = const_idx
+                  else
+                     find_input_name_idx = idx
+                  end if
                else
                   !Otherwise, set to init_mark_idx:
                   find_input_name_idx = init_mark_idx
@@ -96,7 +97,11 @@ integer function find_input_name_idx(stdname, use_init_variables, constituent_in
                find_input_name_idx = prot_no_init_idx
             else
                !If not already initialized, then pass on the real array index:
-               find_input_name_idx = idx
+               if (is_constituent) then
+                  find_input_name_idx = const_idx
+               else
+                  find_input_name_idx = idx
+               end if
             end if
             !Exit physics variable name loop:
             exit

test/unit/sample_files/write_init_files/physics_inputs_4D.F90

@@ -168,12 +168,13 @@ subroutine physics_read_data(file, suite_names, timestep, read_initialized_varia
                         end if
                         field_data_ptr(:,:,constituent_idx) = constituent_default_value
                         if (masterproc) then
-                           write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value
+                           write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ',                       &
+                                constituent_default_value
                         end if
                      else
                         field_data_ptr(:,:,constituent_idx) = 0._kind_phys
                         if (masterproc) then
-                           write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'
+                           write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'
                         end if
                      end if
                   end if

test/unit/sample_files/write_init_files/physics_inputs_bvd.F90

@@ -168,12 +168,13 @@ subroutine physics_read_data(file, suite_names, timestep, read_initialized_varia
                         end if
                         field_data_ptr(:,:,constituent_idx) = constituent_default_value
                         if (masterproc) then
-                           write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value
+                           write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ',                       &
+                                constituent_default_value
                         end if
                      else
                         field_data_ptr(:,:,constituent_idx) = 0._kind_phys
                         if (masterproc) then
-                           write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'
+                           write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'
                         end if
                      end if
                   end if

test/unit/sample_files/write_init_files/physics_inputs_cnst.F90

@@ -168,12 +168,13 @@ subroutine physics_read_data(file, suite_names, timestep, read_initialized_varia
                         end if
                         field_data_ptr(:,:,constituent_idx) = constituent_default_value
                         if (masterproc) then
-                           write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value
+                           write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ',                       &
+                                constituent_default_value
                         end if
                      else
                         field_data_ptr(:,:,constituent_idx) = 0._kind_phys
                         if (masterproc) then
-                           write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'
+                           write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'
                         end if
                      end if
                   end if

test/unit/sample_files/write_init_files/physics_inputs_ddt.F90

@@ -168,12 +168,13 @@ subroutine physics_read_data(file, suite_names, timestep, read_initialized_varia
                         end if
                         field_data_ptr(:,:,constituent_idx) = constituent_default_value
                         if (masterproc) then
-                           write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value
+                           write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ',                       &
+                                constituent_default_value
                         end if
                      else
                         field_data_ptr(:,:,constituent_idx) = 0._kind_phys
                         if (masterproc) then
-                           write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'
+                           write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'
                         end if
                      end if
                   end if

test/unit/sample_files/write_init_files/physics_inputs_ddt2.F90

@@ -168,12 +168,13 @@ subroutine physics_read_data(file, suite_names, timestep, read_initialized_varia
                         end if
                         field_data_ptr(:,:,constituent_idx) = constituent_default_value
                         if (masterproc) then
-                           write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value
+                           write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ',                       &
+                                constituent_default_value
                         end if
                      else
                         field_data_ptr(:,:,constituent_idx) = 0._kind_phys
                         if (masterproc) then
-                           write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'
+                           write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'
                         end if
                      end if
                   end if

test/unit/sample_files/write_init_files/physics_inputs_ddt_array.F90

@@ -168,12 +168,13 @@ subroutine physics_read_data(file, suite_names, timestep, read_initialized_varia
                         end if
                         field_data_ptr(:,:,constituent_idx) = constituent_default_value
                         if (masterproc) then
-                           write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value
+                           write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ',                       &
+                                constituent_default_value
                         end if
                      else
                         field_data_ptr(:,:,constituent_idx) = 0._kind_phys
                         if (masterproc) then
-                           write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'
+                           write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'
                         end if
                      end if
                   end if

test/unit/sample_files/write_init_files/physics_inputs_host_var.F90

@@ -168,12 +168,13 @@ subroutine physics_read_data(file, suite_names, timestep, read_initialized_varia
                         end if
                         field_data_ptr(:,:,constituent_idx) = constituent_default_value
                         if (masterproc) then
-                           write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value
+                           write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ',                       &
+                                constituent_default_value
                         end if
                      else
                         field_data_ptr(:,:,constituent_idx) = 0._kind_phys
                         if (masterproc) then
-                           write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'
+                           write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'
                         end if
                      end if
                   end if

test/unit/sample_files/write_init_files/physics_inputs_mf.F90

@@ -169,12 +169,13 @@ subroutine physics_read_data(file, suite_names, timestep, read_initialized_varia
                         end if
                         field_data_ptr(:,:,constituent_idx) = constituent_default_value
                         if (masterproc) then
-                           write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value
+                           write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ',                       &
+                                constituent_default_value
                         end if
                      else
                         field_data_ptr(:,:,constituent_idx) = 0._kind_phys
                         if (masterproc) then
-                           write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'
+                           write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'
                         end if
                      end if
                   end if

test/unit/sample_files/write_init_files/physics_inputs_no_horiz.F90

@@ -168,12 +168,13 @@ subroutine physics_read_data(file, suite_names, timestep, read_initialized_varia
                         end if
                         field_data_ptr(:,:,constituent_idx) = constituent_default_value
                         if (masterproc) then
-                           write(iulog,*) 'Consitituent ', ccpp_required_data(req_idx), ' initialized to default value: ', constituent_default_value
+                           write(iulog,*) 'Consitituent ', trim(ccpp_required_data(req_idx)), ' initialized to default value: ',                       &
+                                constituent_default_value
                         end if
                      else
                         field_data_ptr(:,:,constituent_idx) = 0._kind_phys
                         if (masterproc) then
-                           write(iulog,*) 'Constituent ', ccpp_required_data(req_idx), ' default value not configured.  Setting to 0.'
+                           write(iulog,*) 'Constituent ', trim(ccpp_required_data(req_idx)), ' default value not configured.  Setting to 0.'
                         end if
                      end if
                   end if