Merge pull request #368 from mvertens/feature/escomp_merge_of_cdeps1.0.83_noresm_v3

bugfix for reading in multi-level unstructured data plus additional cleanup

### Description of changes
This PR fixes a CDEPS bug that was found using stream input ne16pg3 with 58 vertical levels using NorESM. CDEPS aborted trying to read this in.

### Specific notes
This PR also does the following:
- new error checking for most allocations
- cleanup of stdout formatting
- replacement of` character(*) with character(len=*)`
- introduction  `logunit `and `mainproc` in shr_strdata_type and both `logunit` and `mainproc` in shr_stream_streamType. This is needed since the inline interface was not always writing all log output consistently.
- new expanded API for setting stream pointers with optional arguments in `dshr_strdata_mod.F90` for
shr_strdata_get_stream_pointer_1d and shr_strdata_get_stream_pointer_2d
  
```
 subroutine shr_strdata_get_stream_pointer_1d(sdat, strm_fld, strm_ptr, rc, requirePointer, errmsg) 
    type(shr_strdata_type)     , intent(in)    :: sdat
    character(len=*)           , intent(in)    :: strm_fld
    real(r8)                   , pointer       :: strm_ptr(:)
    integer                    , intent(out)   :: rc
    logical,          optional , intent(in)    :: requirePointer
    character(len=*), optional , intent(in)    :: errmsg
```
and
```
 subroutine shr_strdata_get_stream_pointer_2d(sdat, strm_fld, strm_ptr, rc, requirePointer, errmsg) 
    type(shr_strdata_type)     , intent(in)    :: sdat
    character(len=*)           , intent(in)    :: strm_fld
    real(r8)                   , pointer       :: strm_ptr(:,:)
    integer                    , intent(out)   :: rc
    logical,          optional , intent(in)    :: requirePointer
    character(len=*), optional , intent(in)    :: errmsg
```
If requirePointer is not provided - then if the pointer is not found, the subroutine returns without an error. If requirePointer is an argument and is true, than normally an errmsg is provided that describes why the pointer is required. Also - now if the pointer is required and is found - then the pointer is initialized to NaN.
The new setting of NaNs in the stream and state pointers resulted in the following additional changes that needed to be brought in:
- refactored dlnd code to remove presence of present nans in stream pointers
- fixed problem in drof that came up due to presence of presence of nans
- fixed problem in datm/cplhist that cam up due to presence of nans

Contributors other than yourself, if any: None

CDEPS Issues Fixed:

Are there dependencies on other component PRs: None

Are changes expected to change answers (bfb, different to roundoff, more substantial): bfb

Any User Interface Changes (namelist or namelist defaults changes): None

Author: billsacks

cime_config/stream_cdeps.py

@@ -716,11 +716,11 @@ def _sub_paths(
                             date_string = (year_format + "-{:02d}-{:02d}").format(
                                 adjusted_year, adjusted_month, adjusted_day
                             )
-                            new_file = line.replace(match.group(0), date_string)
-                            if os.path.exists(new_file):
-                                new_lines.append(new_file)
+                            new_line = line.replace(match.group(0), date_string)
+                            if os.path.exists(new_line):
+                                new_lines.append(new_line)
                             else:
-                                print(f"   WARNING:not adding missing file {new_file}")
+                                print(f"   WARNING:not adding missing file {new_line}")
                 elif match.group("month"):
                     for month in range(1, 13):
                         date_string = (year_format + "-{:02d}").format(year, month)

datm/datm_datamode_cplhist_mod.F90

@@ -24,8 +24,6 @@ module datm_datamode_cplhist_mod
   real(r8), pointer :: Sa_tbot(:)           => null()
   real(r8), pointer :: Sa_ptem(:)           => null()
   real(r8), pointer :: Sa_shum(:)           => null()
-  ! TODO: water isotope support
-  !  real(r8), pointer :: Sa_shum_wiso(:,:)    => null() ! water isotopes
   real(r8), pointer :: Sa_dens(:)           => null()
   real(r8), pointer :: Sa_pbot(:)           => null()
   real(r8), pointer :: Sa_pslv(:)           => null()
@@ -38,7 +36,6 @@ module datm_datamode_cplhist_mod
   real(r8), pointer :: Faxa_swndf(:)        => null()
   real(r8), pointer :: Faxa_swvdr(:)        => null()
   real(r8), pointer :: Faxa_swvdf(:)        => null()
-  real(r8), pointer :: Faxa_swnet(:)        => null()
   real(r8), pointer :: Faxa_ndep(:,:)       => null()
 
   character(*), parameter :: nullstr = 'null'
@@ -87,7 +84,6 @@ subroutine datm_datamode_cplhist_advertise(exportState, fldsexport, flds_scalar_
     call dshr_fldList_add(fldsExport, 'Faxa_swvdr' )
     call dshr_fldList_add(fldsExport, 'Faxa_swndf' )
     call dshr_fldList_add(fldsExport, 'Faxa_swvdf' )
-    call dshr_fldList_add(fldsExport, 'Faxa_swnet' )
     call dshr_fldList_add(fldsExport, 'Faxa_lwdn'  )
     call dshr_fldList_add(fldsExport, 'Faxa_swdn'  )
     if (flds_co2) then
@@ -172,8 +168,6 @@ subroutine datm_datamode_cplhist_init_pointers(importState, exportState, sdat, r
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
     call dshr_state_getfldptr(exportState, 'Faxa_swndf' , fldptr1=Faxa_swndf , rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
-    call dshr_state_getfldptr(exportState, 'Faxa_swnet' , fldptr1=Faxa_swnet , rc=rc)
-    if (ChkErr(rc,__LINE__,u_FILE_u)) return
     call dshr_state_getfldptr(exportState, 'Faxa_lwdn'  , fldptr1=Faxa_lwdn  , rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 

dlnd/dlnd_datamode_glc_forcing_mod.F90

@@ -5,10 +5,10 @@ module dlnd_datamode_glc_forcing_mod
    use NUOPC            , only : NUOPC_CompAttributeGet, NUOPC_Advertise
    use shr_kind_mod     , only : r8=>shr_kind_r8, i8=>shr_kind_i8, cl=>shr_kind_cl, cs=>shr_kind_cs
    use shr_log_mod      , only : shr_log_error
+   use shr_const_mod    , only : SHR_CONST_SPVAL
    use dshr_methods_mod , only : dshr_state_getfldptr, chkerr
-   use dshr_strdata_mod , only : shr_strdata_type
+   use dshr_strdata_mod , only : shr_strdata_type, shr_strdata_get_stream_pointer
    use dshr_fldlist_mod , only : fldlist_type, dshr_fldlist_add
-   use dshr_dfield_mod  , only : dfield_type, dshr_dfield_add
    use glc_elevclass_mod, only : glc_elevclass_as_string, glc_elevclass_init
 
    implicit none
@@ -18,8 +18,19 @@ module dlnd_datamode_glc_forcing_mod
    public :: dlnd_datamode_glc_forcing_init_pointers
    public :: dlnd_datamode_glc_forcing_advance
 
-   ! module pointer arrays
-   real(r8), pointer :: lfrac(:)
+   ! export state pointer
+   real(r8), pointer :: lfrac(:)            => null()
+   real(r8), pointer :: Sl_tsrf_elev(:,:)   => null()
+   real(r8), pointer :: Sl_topo_elev(:,:)   => null()
+   real(r8), pointer :: Flgl_qice_elev(:,:) => null()
+
+   ! stream pointers (1d)
+   type, public :: stream_pointer_type
+      real(r8), pointer :: strm_ptr(:) => null()
+   end type stream_pointer_type
+   type(stream_pointer_type), allocatable :: strm_Sl_tsrf_elev(:)
+   type(stream_pointer_type), allocatable :: strm_Sl_topo_elev(:)
+   type(stream_pointer_type), allocatable :: strm_Flgl_qice_elev(:)
 
    integer :: glc_nec
 
@@ -31,7 +42,8 @@ module dlnd_datamode_glc_forcing_mod
 contains
 !===============================================================================
 
-   subroutine dlnd_datamode_glc_forcing_advertise(gcomp, exportState, fldsExport, flds_scalar_name, logunit, mainproc, rc)
+   subroutine dlnd_datamode_glc_forcing_advertise(gcomp, exportState, fldsExport, flds_scalar_name, &
+        logunit, mainproc, rc)
 
       ! determine export state to advertise to mediator
 
@@ -87,24 +99,20 @@ subroutine dlnd_datamode_glc_forcing_advertise(gcomp, exportState, fldsExport, f
    end subroutine dlnd_datamode_glc_forcing_advertise
 
    !===============================================================================
-   subroutine dlnd_datamode_glc_forcing_init_pointers(exportState, sdat, dfields, model_frac, datamode, logunit, mainproc, rc)
+   subroutine dlnd_datamode_glc_forcing_init_pointers(exportState, sdat, model_frac, datamode, rc)
 
       ! input/output variables
       type(ESMF_State)      , intent(inout) :: exportState
       type(shr_strdata_type), intent(in)    :: sdat
-      type(dfield_type)     , pointer       :: dfields
       real(r8)              , intent(in)    :: model_frac(:)
       character(len=*)      , intent(in)    :: datamode
-      integer               , intent(in)    :: logunit
-      logical               , intent(in)    :: mainproc
       integer               , intent(out)   :: rc
 
       ! local variables
-      integer                     :: n
-      character(len=2)            :: nec_str
-      character(CS), allocatable  :: strm_flds_topo(:)
-      character(CS), allocatable  :: strm_flds_tsrf(:)
-      character(CS), allocatable  :: strm_flds_qice(:)
+      integer          :: ng
+      character(len=2) :: nec_str
+      character(CS)    :: strm_fld
+      integer          :: istat
       character(len=*), parameter :: subname='(dlnd_datamode_glc_forcing_init_pointers): '
       !-------------------------------------------------------------------------------
 
@@ -114,87 +122,84 @@ subroutine dlnd_datamode_glc_forcing_init_pointers(exportState, sdat, dfields, m
       call dshr_state_getfldptr(exportState, fldname='Sl_lfrin', fldptr1=lfrac, rc=rc)
       if (chkerr(rc,__LINE__,u_FILE_u)) return
       lfrac(:) = model_frac(:)
+      call dshr_state_getfldptr(exportState, 'Sl_tsrf_elev', fldptr2=Sl_tsrf_elev, rc=rc)
+      if (chkerr(rc,__LINE__,u_FILE_u)) return
+      call dshr_state_getfldptr(exportState, 'Sl_topo_elev', fldptr2=Sl_topo_elev, rc=rc)
+      if (chkerr(rc,__LINE__,u_FILE_u)) return
+      call dshr_state_getfldptr(exportState, 'Flgl_qice_elev', fldptr2=Flgl_qice_elev, rc=rc)
+      if (chkerr(rc,__LINE__,u_FILE_u)) return
 
-      ! Create stream-> export state mapping
-      ! Note that strm_flds is the model name for the stream field
-      ! Note that state_fld is the model name for the export field
-
-      if (trim(datamode) == 'glc_forcing_mct') then
-         allocate(strm_flds_tsrf(0:glc_nec))
-         allocate(strm_flds_topo(0:glc_nec))
-         allocate(strm_flds_qice(0:glc_nec))
-         do n = 0,glc_nec
-            write(nec_str, '(i2.2)') n
-            strm_flds_tsrf(n) = 'Sl_tsrf_elev'   // trim(nec_str)
-            strm_flds_topo(n) = 'Sl_topo_elev'   // trim(nec_str)
-            strm_flds_qice(n) = 'Flgl_qice_elev' // trim(nec_str)
-         end do
+      ! Obtain pointers to stream fields
 
-      else if (trim(datamode) == 'glc_forcing' ) then
-         allocate(strm_flds_tsrf(1:glc_nec+1))
-         allocate(strm_flds_topo(1:glc_nec+1))
-         allocate(strm_flds_qice(1:glc_nec+1))
-         do n = 1,glc_nec+1
-            write(nec_str, '(i0)') n
-            strm_flds_tsrf(n) = 'Sl_tsrf_elev'   // trim(nec_str)
-            strm_flds_topo(n) = 'Sl_topo_elev'   // trim(nec_str)
-            strm_flds_qice(n) = 'Flgl_qice_elev' // trim(nec_str)
-         end do
-      else
-         call shr_log_error(subname//'ERROR illegal datamode = '//trim(datamode), rc=rc)
+      allocate(strm_Sl_tsrf_elev(glc_nec+1), &
+               strm_Sl_topo_elev(glc_nec+1), &
+               strm_Flgl_qice_elev(glc_nec+1), stat=istat)
+      if ( istat /= 0 ) then
+         call shr_log_error(subName//&
+              ': allocation error for strm_Sl_tsrf_elev, Strm_Sl_topo_elev and strm_Flgl_qice_elev',rc=rc)
          return
       end if
 
-      ! The following maps stream input fields to export fields that have an ungridded dimension
-      call dshr_dfield_add(dfields, sdat, state_fld='Sl_tsrf_elev', strm_flds=strm_flds_tsrf, state=exportState, &
-           logunit=logunit, mainproc=mainproc, rc=rc)
-      if (ChkErr(rc,__LINE__,u_FILE_u)) return
-      call dshr_dfield_add(dfields, sdat, state_fld='Sl_topo_elev', strm_flds=strm_flds_topo, state=exportState, &
-           logunit=logunit, mainproc=mainproc, rc=rc)
-      if (ChkErr(rc,__LINE__,u_FILE_u)) return
-      call dshr_dfield_add(dfields, sdat, state_fld='Flgl_qice_elev', strm_flds=strm_flds_qice, state=exportState, &
-           logunit=logunit, mainproc=mainproc, rc=rc)
-      if (ChkErr(rc,__LINE__,u_FILE_u)) return
+      do ng = 1,glc_nec+1
+         if (trim(datamode) == 'glc_forcing_mct') then
+            write(nec_str,'(i2.2)') ng-1
+         else
+            write(nec_str,'(i0)') ng
+         end if
+         strm_fld = 'Sl_tsrf_elev'//trim(nec_str)
+         call shr_strdata_get_stream_pointer( sdat, trim(strm_fld), strm_Sl_tsrf_elev(ng)%strm_ptr, requirePointer=.true., &
+              errmsg=trim(subname)//'ERROR: '//trim(strm_fld)//' must be associated for dlnd glc_forcing datamode', rc=rc)
+         if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-      deallocate(strm_flds_tsrf)
-      deallocate(strm_flds_topo)
-      deallocate(strm_flds_qice)
+         strm_fld = 'Sl_topo_elev'//trim(nec_str)
+         call shr_strdata_get_stream_pointer( sdat, trim(strm_fld), strm_Sl_topo_elev(ng)%strm_ptr, requirePointer=.true., &
+              errmsg=trim(subname)//'ERROR: '//trim(strm_fld)//' must be associated for dlnd glc_forcing datamode', rc=rc)
+         if (ChkErr(rc,__LINE__,u_FILE_u)) return
+
+         strm_fld = 'Flgl_qice_elev'//trim(nec_str)
+         call shr_strdata_get_stream_pointer( sdat, trim(strm_fld), strm_Flgl_qice_elev(ng)%strm_ptr, requirePointer=.true., &
+              errmsg=trim(subname)//'ERROR: '//trim(strm_fld)//' must be associated for dlnd glc_forcing datamode', rc=rc)
+         if (ChkErr(rc,__LINE__,u_FILE_u)) return
+      end do
 
    end subroutine dlnd_datamode_glc_forcing_init_pointers
 
    !===============================================================================
-   subroutine dlnd_datamode_glc_forcing_advance(exportState, rc)
-
-      ! input/output variables
-      type(ESMF_State)      , intent(inout) :: exportState
-      integer               , intent(out)   :: rc
+   subroutine dlnd_datamode_glc_forcing_advance()
 
       ! local variables
-      integer           :: n
-      real(r8), pointer :: fldptr2(:,:)
+      integer :: ni,ng
       character(len=*), parameter :: subname='(dlnd_datamode_glc_forcing_advance): '
       !-------------------------------------------------------------------------------
 
-      rc = ESMF_SUCCESS
-
       ! Set special value over masked points
-      call dshr_state_getfldptr(exportState, 'Sl_tsrf_elev', fldptr2=fldptr2, rc=rc)
-      if (chkerr(rc,__LINE__,u_FILE_u)) return
-      do n = 1,size(fldptr2,dim=2)
-         if (lfrac(n) == 0._r8) fldptr2(:,n) = 1.e30_r8
-      end do
+      ! Note that the inner dimension is the elevation class
+
+      elev_class_loop: do ng = 1,glc_nec+1
+         do ni = 1,size(Sl_tsrf_elev,dim=2)
+            if (lfrac(ni) == 0._r8) then
+               Sl_tsrf_elev(ng,ni) = SHR_CONST_SPVAL
+            else
+               Sl_tsrf_elev(ng,ni) = strm_Sl_tsrf_elev(ng)%strm_ptr(ni)
+            end if
+         end do
 
-      call dshr_state_getfldptr(exportState, 'Sl_topo_elev', fldptr2=fldptr2, rc=rc)
-      if (chkerr(rc,__LINE__,u_FILE_u)) return
-      do n = 1,size(fldptr2,dim=2)
-         if (lfrac(n) == 0._r8) fldptr2(:,n) = 1.e30_r8
-      end do
+         do ni = 1,size(Sl_topo_elev,dim=2)
+            if (lfrac(ni) == 0._r8) then
+               Sl_topo_elev(ng,ni) = SHR_CONST_SPVAL
+            else
+               Sl_topo_elev(ng,ni) = strm_Sl_topo_elev(ng)%strm_ptr(ni)
+            end if
+         end do
 
-      call dshr_state_getfldptr(exportState, 'Flgl_qice_elev', fldptr2=fldptr2, rc=rc)
-      if (chkerr(rc,__LINE__,u_FILE_u)) return
-      do n = 1,size(fldptr2,dim=2)
-         if (lfrac(n) == 0._r8) fldptr2(:,n) = 1.e30_r8
-      end do
+         do ni = 1,size(Flgl_qice_elev,dim=2)
+            if (lfrac(ni) == 0._r8) then
+               Flgl_qice_elev(ng,ni) = SHR_CONST_SPVAL
+            else
+               Flgl_qice_elev(ng,ni) = strm_Flgl_qice_elev(ng)%strm_ptr(ni)
+            end if
+         end do
+      end do elev_class_loop
 
    end subroutine dlnd_datamode_glc_forcing_advance