Merge pull request #169 from DeniseWorthen/feature/dstmapbilnPR

Retrieval of dstStatusField and optionally writing to file; add mapbilnr_nstod mapping
### Description of changes
Adds ability to write dstStatusField from RegridStore. Adds bilinear mapping with NSTOD extrapolation.
### Specific notes
A flag is added (dststatus_print, default false) in med_map_mod.F90 to write the dstStatusField from the RegridStore operation. Since ESMF_FieldWrite does not order the written field correctly, a field containing the index order is also retrieved and written. This can be used off-line to re-order the data in the dststatus file. 
A bilinear mapping type with NSTOD extrapolation is added. This is currently unused but will be implemented in the ufs-model system for mapping the ATM states (bottom T,P,Q,U,V) using bilinear instead of conservative mapping.
A small change is added to abort if coupling_mode is not supported. 

Trailing white space cleanup, primarily in fd_nems.yaml

CMEPS Issues Fixed (include github issue #):
NOAA-EMC#38

Are changes expected to change answers?
 - [X] bit for bit
 - [ ] different at roundoff level
 - [ ] more substantial 

Any User Interface Changes (namelist or namelist defaults changes)?
 - [ ] Yes
 - [X] No

Testing performed if application target is CESM:(either UFS-S2S or CESM testing is required):
- [ ] (recommended) CIME_DRIVER=nuopc scripts_regression_tests.py
   - machines:
   - details (e.g. failed tests):
- [ ] (recommended) CESM testlist_drv.xml
   - machines and compilers:
   - details (e.g. failed tests):
- [ ] (optional) CESM prealpha test
   - machines and compilers
   - details (e.g. failed tests):
- [ ] (other) please described in detail
   - machines and compilers
   - details (e.g. failed tests):

Testing performed if application target is UFS-coupled:
- [X] (recommended) UFS-coupled testing
   - description: ufs-weather-model (3e46f5b) switched to this branch for CMEPS with shr_mod_pio.F90 from CMakeLists.txt in CMEPS-interface
   - details (e.g. failed tests): All ufs-coupled and ufs-datm tests pass current baselines
 CESM - verified that SMS_Vnuopc_Ld1.f09_g17.B1850.cheyenne_intel was bfb with these changes

mediator/esmFlds.F90

@@ -34,6 +34,8 @@ module esmflds
   integer, public :: num_icesheets = 1
   logical, public :: ocn2glc_coupling  ! obtained from attribute
 
+  logical, public :: dststatus_print = .false.
+
   !-----------------------------------------------
   ! Set mappers
   !-----------------------------------------------
@@ -54,7 +56,8 @@ module esmflds
   integer , public, parameter :: map_glc2ocn_liq   = 13 ! custom smoothing map to map liq from glc->ocn (cesm only)
   integer , public, parameter :: map_glc2ocn_ice   = 14 ! custom smoothing map to map ice from glc->ocn (cesm only)
   integer , public, parameter :: mapfillv_bilnr    = 15 ! fill value followed by bilinear
-  integer , public, parameter :: nmappers          = 15
+  integer , public, parameter :: mapbilnr_nstod    = 16 ! bilinear with nstod extrapolation
+  integer , public, parameter :: nmappers          = 16
 
   character(len=*) , public, parameter :: mapnames(nmappers) = &
        (/'bilnr      ',&
@@ -71,7 +74,8 @@ module esmflds
          'rof2ocn_liq',&
          'glc2ocn_ice',&
          'glc2ocn_liq',&
-         'fillv_bilnr'/)
+         'fillv_bilnr',&
+         'bilnr_nstod'/)
 
   !-----------------------------------------------
   ! Set coupling mode

mediator/esmFldsExchange_hafs_mod.F90

@@ -187,7 +187,7 @@ subroutine esmFldsExchange_hafs_advt(gcomp, phase, rc)
     call addfld(fldListTo(compatm)%flds, 'So_ofrac')
 
     !----------------------------------------------------------
-    ! to atm: surface temperatures from ocn 
+    ! to atm: surface temperatures from ocn
     !----------------------------------------------------------
     call addfld(fldListFr(compocn)%flds, 'So_t')
     call addfld(fldListTo(compatm)%flds, 'So_t')

mediator/fd_nems.yaml

@@ -575,7 +575,7 @@
        description:   atmosphere export - latent heat flux conversion
      - alias: Faox_evap
        standard_name : mean_evap_rate
-       description: mediator calculation - atm/ocn specific humidity flux 
+       description: mediator calculation - atm/ocn specific humidity flux
      #
      #-----------------------------------
      # section: atmosphere fields that need to be defined but are not used
@@ -694,8 +694,8 @@
      #-----------------------------------
      #
      - standard_name: sea_surface_height_above_sea_level
-       canonical_units: m 
-       description: ww3 import 
+       canonical_units: m
+       description: ww3 import
      #
      - standard_name: sea_surface_salinity
        alias: s_surf
@@ -705,22 +705,22 @@
      - standard_name: surface_eastward_sea_water_velocity
        alias: ocn_current_zonal
        canonical_units: m s-1
-       description: ww3 import 
+       description: ww3 import
      #
      - standard_name: surface_northward_sea_water_velocity
        alias: ocn_current_merid
        canonical_units: m s-1
-       description: ww3 import 
+       description: ww3 import
      #
      - standard_name: eastward_wind_at_10m_height
        alias: inst_zonal_wind_height10m
        canonical_units: m s-1
-       description: ww3 import 
+       description: ww3 import
      #
      - standard_name: northward_wind_at_10m_height
        alias: inst_merid_wind_height10m
        canonical_units: m s-1
-       description: ww3 import 
+       description: ww3 import
      #
      - standard_name: sea_ice_concentration
        alias: ice_fraction
@@ -732,77 +732,77 @@
      #
      - standard_name: wave_induced_charnock_parameter
        canonical_units: 1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: wave_z0_roughness_length
        canonical_units: 1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: northward_stokes_drift_current
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: eastward_stokes_drift_current
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: eastward_partitioned_stokes_drift_1
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: eastward_partitioned_stokes_drift_2
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: eastward_partitioned_stokes_drift_3
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: northward_partitioned_stokes_drift_1
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: northward_partitioned_stokes_drift_2
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: northward_partitioned_stokes_drift_3
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: eastward_wave_bottom_current
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: northward_wave_bottom_current
        canonical_units: m s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: wave_bottom_current_radian_frequency
        canonical_units: rad s-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: eastward_wave_radiation_stress_gradient
        canonical_units: Pa
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: northward_wave_radiation_stress_gradient
        canonical_units: Pa
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: eastward_wave_radiation_stress
        canonical_units: N m-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: eastward_northward_wave_radiation_stress
        canonical_units: N m-1
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: wave_bottom_current_period
        canonical_units: s
-       description: ww3 export 
+       description: ww3 export
      #
      - standard_name: northward_wave_radiation_stress
        canonical_units: Pa
-       description: ww3 export 
+       description: ww3 export
      #

mediator/med.F90

@@ -557,7 +557,8 @@ subroutine InitializeP0(gcomp, importState, exportState, clock, rc)
     use ESMF  , only : ESMF_LogWrite, ESMF_LOGMSG_INFO, ESMF_METHOD_INITIALIZE
     use NUOPC , only : NUOPC_CompFilterPhaseMap, NUOPC_CompAttributeGet
     use med_internalstate_mod, only : mastertask, logunit
-
+    use esmFlds, only : dststatus_print
+
     type(ESMF_GridComp)   :: gcomp
     type(ESMF_State)      :: importState, exportState
     type(ESMF_Clock)      :: clock
@@ -626,6 +627,13 @@ subroutine InitializeP0(gcomp, importState, exportState, clock, rc)
     write(msgString,'(A,i6)') trim(subname)//': Mediator dbug_flag is ',dbug_flag
     call ESMF_LogWrite(trim(msgString), ESMF_LOGMSG_INFO)
 
+    ! Obtain dststatus_print setting if present
+    call NUOPC_CompAttributeGet(gcomp, name='dststatus_print', value=cvalue, isPresent=isPresent, isSet=isSet, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    if (isPresent .and. isSet) dststatus_print=(trim(cvalue)=="true")
+    write(msgString,*) trim(subname)//': Mediator dststatus_print is ',dststatus_print
+    call ESMF_LogWrite(trim(msgString), ESMF_LOGMSG_INFO)
+
     ! Switch to IPDv03 by filtering all other phaseMap entries
     call NUOPC_CompFilterPhaseMap(gcomp, ESMF_METHOD_INITIALIZE, acceptStringList=(/"IPDv03p"/), rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -644,6 +652,7 @@ subroutine InitializeIPDv03p1(gcomp, importState, exportState, clock, rc)
 
     use ESMF  , only : ESMF_GridComp, ESMF_State, ESMF_Clock, ESMF_SUCCESS, ESMF_LogFoundAllocError
     use ESMF  , only : ESMF_LogMsg_Info, ESMF_LogWrite
+    use ESMF  , only : ESMF_END_ABORT, ESMF_Finalize
     use NUOPC , only : NUOPC_AddNamespace, NUOPC_Advertise, NUOPC_AddNestedState
     use NUOPC , only : NUOPC_CompAttributeGet, NUOPC_CompAttributeSet, NUOPC_CompAttributeAdd
 
@@ -749,12 +758,16 @@ subroutine InitializeIPDv03p1(gcomp, importState, exportState, clock, rc)
     if (trim(coupling_mode) == 'cesm') then
        call esmFldsExchange_cesm(gcomp, phase='advertise', rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-    else if (trim(coupling_mode(1:4)) == 'nems') then
+    else if (trim(coupling_mode) == 'nems_orig' .or. trim(coupling_mode) == 'nems_frac' &
+       .or. trim(coupling_mode) == 'nems_orig_data') then
        call esmFldsExchange_nems(gcomp, phase='advertise', rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
     else if (trim(coupling_mode(1:4)) == 'hafs') then
        call esmFldsExchange_hafs(gcomp, phase='advertise', rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    else
+        call ESMF_LogWrite(trim(coupling_mode)//' is not a valid coupling_mode', ESMF_LOGMSG_INFO)
+        call ESMF_Finalize(endflag=ESMF_END_ABORT)
     end if
 
     !------------------

mediator/med_diag_mod.F90

@@ -22,7 +22,7 @@ module med_diag_mod
   use ESMF                  , only : ESMF_GridComp, ESMF_Clock, ESMF_Time
   use ESMF                  , only : ESMF_VM, ESMF_VMReduce, ESMF_REDUCE_SUM
   use ESMF                  , only : ESMF_GridCompGet, ESMF_ClockGet, ESMF_TimeGet
-  use ESMF                  , only : ESMF_Alarm, ESMF_ClockGetAlarm, ESMF_AlarmIsRinging, ESMF_AlarmRingerOff  
+  use ESMF                  , only : ESMF_Alarm, ESMF_ClockGetAlarm, ESMF_AlarmIsRinging, ESMF_AlarmRingerOff
   use ESMF                  , only : ESMF_FieldBundle, ESMF_Field, ESMF_FieldGet
   use shr_const_mod         , only : shr_const_rearth, shr_const_pi, shr_const_latice
   use shr_const_mod         , only : shr_const_ice_ref_sal, shr_const_ocn_ref_sal, shr_const_isspval
@@ -800,7 +800,7 @@ subroutine diag_atm_wiso_recv(FB, fldname, nf_16O, nf_18O, nf_HDO, areas, lats,
       integer                , intent(out)   :: rc
       ! local variables
       integer           :: n, ip
-      type(ESMF_Field)  :: lfield 
+      type(ESMF_Field)  :: lfield
       real(r8), pointer :: data(:,:) => null()
       ! ------------------------------------------------------------------
       rc = ESMF_SUCCESS
@@ -857,7 +857,7 @@ subroutine diag_atm_wiso_send(FB, fldname, nf_16O, nf_18O, nf_HDO, areas, lats,
       integer                , intent(out)   :: rc
       ! local variables
       integer           :: n, ip
-      type(ESMF_Field)  :: lfield 
+      type(ESMF_Field)  :: lfield
       real(r8), pointer :: data(:,:) => null()
       ! ------------------------------------------------------------------
       rc = ESMF_SUCCESS
@@ -1575,7 +1575,7 @@ subroutine diag_ice_recv(FB, fldname, nf, areas, lats, ifrac, budget, minus, sca
       integer                , intent(out)   :: rc
       ! local variables
       integer           :: n, ip
-      type(ESMF_Field)  :: lfield 
+      type(ESMF_Field)  :: lfield
       real(r8), pointer :: data(:) => null()
       ! ------------------------------------------------------------------
       rc = ESMF_SUCCESS
@@ -1621,7 +1621,7 @@ subroutine diag_ice_recv_wiso(FB, fldname, nf_16O, nf_18O, nf_HDO, areas, lats,
       integer                , intent(out)   :: rc
       ! local variables
       integer           :: n, ip
-      type(ESMF_Field)  :: lfield 
+      type(ESMF_Field)  :: lfield
       real(r8), pointer :: data(:,:) => null()
       ! ------------------------------------------------------------------
       rc = ESMF_SUCCESS
@@ -1754,7 +1754,7 @@ subroutine diag_ice_send(FB, fldname, nf, areas, lats, ifrac, budget, rc)
       integer                , intent(out)   :: rc
       ! local variables
       integer           :: n, ip
-      type(ESMF_Field)  :: lfield 
+      type(ESMF_Field)  :: lfield
       real(r8), pointer :: data(:) => null()
       ! ------------------------------------------------------------------
       rc = ESMF_SUCCESS
@@ -1788,7 +1788,7 @@ subroutine diag_ice_send_wiso(FB, fldname, nf_16O, nf_18O, nf_HDO, areas, lats,
 
       ! local variables
       integer           :: n, ip
-      type(ESMF_Field)  :: lfield 
+      type(ESMF_Field)  :: lfield
       real(r8), pointer :: data(:,:) => null()
       ! ------------------------------------------------------------------
       rc = ESMF_SUCCESS

mediator/med_fraction_mod.F90

@@ -295,7 +295,7 @@ subroutine med_fraction_init(gcomp, rc)
     end if
 
     !---------------------------------------
-    ! Set 'ofrac' in FBFrac(compocn) 
+    ! Set 'ofrac' in FBFrac(compocn)
     !---------------------------------------
 
     if (is_local%wrap%comp_present(compocn)) then
@@ -681,7 +681,7 @@ subroutine med_fraction_set(gcomp, rc)
        ! The model mask is normally assumed to be an selected ocean mask from a fully coupled run
        ! So in it is (1-land fraction) on the atm grid
 
-       ! set ifrac 
+       ! set ifrac
        if (associated(ifrac)) then
           ifrac(:) = Si_ifrac(:) * Si_imask(:)
        endif

mediator/med_io_mod.F90

@@ -181,7 +181,7 @@ subroutine med_io_init(gcomp, rc)
     call ESMF_VMGet(vm, mpiCommunicator=comm, localPet=localPet, petCount=petCount, rc=rc)
     if (chkerr(rc,__LINE__,u_FILE_u)) return
 
-    ! query component specific PIO attributes 
+    ! query component specific PIO attributes
     ! pio_netcdf_format
     call NUOPC_CompAttributeGet(gcomp, name='pio_netcdf_format', value=cvalue, isPresent=isPresent, isSet=isSet, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -212,9 +212,9 @@ subroutine med_io_init(gcomp, rc)
     if (isPresent .and. isSet) then
        cvalue = ESMF_UtilStringUpperCase(cvalue)
        if (trim(cvalue) .eq. 'NETCDF') then
-         pio_iotype = PIO_IOTYPE_NETCDF 
+         pio_iotype = PIO_IOTYPE_NETCDF
        else if (trim(cvalue) .eq. 'PNETCDF') then
-         pio_iotype = PIO_IOTYPE_PNETCDF 
+         pio_iotype = PIO_IOTYPE_PNETCDF
        else if (trim(cvalue) .eq. 'NETCDF4C') then
          pio_iotype = PIO_IOTYPE_NETCDF4C
        else if (trim(cvalue) .eq. 'NETCDF4P') then
@@ -276,7 +276,7 @@ subroutine med_io_init(gcomp, rc)
           write(logunit,*) ' parallel io requires at least two io pes - following parameters are updated:'
           write(logunit,*) trim(subname), ' : pio_stride = ', pio_stride
           write(logunit,*) trim(subname), ' : pio_numiotasks = ', pio_numiotasks
-       end if       
+       end if
     endif
 
     ! check/set/correct io pio parameters
@@ -294,7 +294,7 @@ subroutine med_io_init(gcomp, rc)
     end if
     if (pio_stride == 1) then
        pio_root = 0
-    endif    
+    endif
 
     if (pio_root + (pio_stride)*(pio_numiotasks-1) >= petCount .or. &
        pio_stride <= 0 .or. pio_numiotasks <= 0 .or. pio_root < 0 .or. pio_root > petCount-1) then
@@ -366,8 +366,8 @@ subroutine med_io_init(gcomp, rc)
     ! set PIO debug level
     call pio_setdebuglevel(pio_debug_level)
 
-    ! query shared PIO rearranger attributes 
-    ! pio_rearr_comm_type 
+    ! query shared PIO rearranger attributes
+    ! pio_rearr_comm_type
     call NUOPC_CompAttributeGet(gcomp, name='pio_rearr_comm_type', value=cvalue, isPresent=isPresent, isSet=isSet, rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
@@ -386,7 +386,7 @@ subroutine med_io_init(gcomp, rc)
        cvalue = 'P2P'
        pio_rearr_comm_type = PIO_REARR_COMM_P2P
     end if
-    if (localPet == 0) write(logunit,*) trim(subname), ' : pio_rearr_comm_type = ', trim(cvalue), pio_rearr_comm_type 
+    if (localPet == 0) write(logunit,*) trim(subname), ' : pio_rearr_comm_type = ', trim(cvalue), pio_rearr_comm_type
 
     ! pio_rearr_comm_fcd
     call NUOPC_CompAttributeGet(gcomp, name='pio_rearr_comm_fcd', value=cvalue, isPresent=isPresent, isSet=isSet, rc=rc)