2020.02 candidate into NOAA-GFDL/dev/gfdl (#19)

* Add LICENSE.md

* Renamed driver directories and removed the null version of the nh extensions for the public release

* Update license header for FV3

* Added a README.md file

* Replace GPL header with LGPL header

* fixed license header in every file and added it to those without it

* commit of new version of dycore from Weather and Climate Dynamics Group at GFDL

* updated README.md with current release information

* updated message for gfdl version of FV3

* fixed merge issues with fv_diagnostics.F90

* remove trailing spaces from sources

* remove extra file

* changes necessary for updated FMS diag_manager

* Master test (#17)

* commit of new version of dycore from Weather and Climate Dynamics Group at GFDL

* updated versions of GFDL-specific files from dev/gfdl

* updated README.md with current release information

* cleaned up a few lines in fv_dynamics

* new file RELEASE.md with release notes documenting differences between this and the last release

* updated RELEASE.md message

* hand merge of diagnostic updates

* remove trailing spaces from sources

* updates to merge some GFDL specific updates into this public release

* Master test (#18)

* commit of new version of dycore from Weather and Climate Dynamics Group at GFDL

* updated versions of GFDL-specific files from dev/gfdl

* updated README.md with current release information

* cleaned up a few lines in fv_dynamics

* new file RELEASE.md with release notes documenting differences between this and the last release

* updated RELEASE.md message

* hand merge of diagnostic updates

* remove trailing spaces from sources

* updates to merge some GFDL specific updates into this public release

* updated README.md

* updated GFDL_tools/fv_cmip_diag to be consistent with dev/gfdl branch

* remove tab characters from source files

* fixed comment in the README

Co-authored-by: Seth Underwood <[email protected]>

GFDL_tools/fv_climate_nudge.F90

@@ -135,11 +135,11 @@ subroutine fv_climate_nudge_init ( Time, axes, flag )
 #else
    if (file_exist('input.nml') ) then
      unit = open_namelist_file()
-     ierr=1  
+     ierr=1
      do while (ierr /= 0)
-       read (unit, nml=fv_climate_nudge_nml, iostat=io, end=10) 
+       read (unit, nml=fv_climate_nudge_nml, iostat=io, end=10)
        ierr = check_nml_error (io, 'fv_climate_nudge_nml')
-     enddo   
+     enddo
 10   call close_file (unit)
    endif
 #endif
@@ -341,7 +341,7 @@ subroutine fv_climate_nudge (Time, dt, is, ie, js, je, npz, pfull, &
 
  ! vertically dependent factor
    call get_factor (npz,pfull, factor)
- ! first time allocate state 
+ ! first time allocate state
    if (do_state_alloc) then
       call var_state_init ( is, ie, js, je, npz, State(1) )
       call var_state_init ( is, ie, js, je, npz, State(2) )
@@ -634,7 +634,7 @@ subroutine get_factor (nlev,pfull,factor)
          factor(k,2) = 0.
       enddo
    endif
-   
+
 ! Specific humidity
    if (skip_top_q > 0) then
       do k = 1, skip_top_q
@@ -824,7 +824,7 @@ subroutine remap_coef( isd, ied, jsd, jed, lon_in, lat_in, &
 !
   integer, intent(out), dimension(is:ie,js:je  ):: id1, id2, jdc
   real,    intent(out), dimension(is:ie,js:je,4):: s2c
- 
+
 !===============================================================================================
 
 ! local:
@@ -833,7 +833,7 @@ subroutine remap_coef( isd, ied, jsd, jed, lon_in, lat_in, &
   real:: a1, b1
   integer i, j, i1, i2, jc, i0, j0
 
- !pk0(1) = ak_in(1)**KAPPA 
+ !pk0(1) = ak_in(1)**KAPPA
  !pn_top = log(ak_in(1))
 
   do i=isd,ied-1
@@ -1007,7 +1007,7 @@ subroutine remap_ps( is, ie, js, je, km, &
        gz(km+1) = gz_dat(i,j)
        pk0(km+1) = ph_dat(i,j,km+1)**KAPPA
        do k=km,1,-1
-           gz(k) = gz(k+1) + RDGAS*tp_dat(i,j,k)*(pn_dat(i,j,k+1)-pn_dat(i,j,k)) 
+           gz(k) = gz(k+1) + RDGAS*tp_dat(i,j,k)*(pn_dat(i,j,k+1)-pn_dat(i,j,k))
            pk0(k) = ph_dat(i,j,k)**KAPPA
        enddo
        if ( phis(i,j) .gt. gz_dat(i,j) ) then

GFDL_tools/fv_cmip_diag.F90

@@ -170,7 +170,7 @@ subroutine fv_cmip_diag_init ( Atm, axes, Time )
 
     ID_va = register_cmip_diag_field_3d (mod_name, 'va', Time, &
                        'Northward Wind', 'm s-1', standard_name='northward_wind')
-    
+
     ID_hus = register_cmip_diag_field_3d (mod_name, 'hus', Time, &
                        'Specific Humidity', '1.0', standard_name='specific_humidity')
 
@@ -187,7 +187,7 @@ subroutine fv_cmip_diag_init ( Atm, axes, Time )
                        'Geopotential Height', 'm', standard_name='geopotential_height', axis='half')
 
 !-----------------------------------------------------------------------
-! register products of 3D variables (on model levels and pressure levels) 
+! register products of 3D variables (on model levels and pressure levels)
 
     ID_u2 = register_cmip_diag_field_3d (mod_name, 'u2', Time, &
                       'Square of Eastward Wind', 'm2 s-2', standard_name='square_of_eastward_wind')
@@ -362,7 +362,7 @@ subroutine fv_cmip_diag_init ( Atm, axes, Time )
                   'Relative Vorticity at 200 hPa', 's-1', standard_name='atmosphere_relative_vorticity')
     if (id_rv200 > 0 .and. id_plevels(id_p200) > 0) &
         call diag_field_add_attribute (id_rv200, 'coordinates', 'p200')
-    
+
     id_rv500 = register_cmip_diag_field_2d (mod_name, 'rv500', Time, &
                   'Relative Vorticity at 500 hPa', 's-1', standard_name='atmosphere_relative_vorticity')
     if (id_rv500 > 0 .and. id_plevels(id_p500) > 0) &
@@ -374,13 +374,13 @@ subroutine fv_cmip_diag_init ( Atm, axes, Time )
         call diag_field_add_attribute (id_rv850, 'coordinates', 'p850')
 
   !---- mean relative vorticity 600, 700, 850 hPa ----
- 
+
     id_vortmean = register_cmip_diag_field_2d (mod_name, 'vortmean', Time, &
                  'Mean Relative Vorticity over 600-850 hPa', 's-1',  &
                         standard_name='atmosphere_relative_vorticity')
     if (id_vortmean > 0 .and. id_pl700 > 0) &
         call diag_field_add_attribute (id_vortmean, 'coordinates', 'pl700')
-    
+
   !---- omega at 500 hPa ----
 
     id_wap500 = register_cmip_diag_field_2d (mod_name, 'wap500', Time, &
@@ -432,7 +432,7 @@ subroutine fv_cmip_diag ( Atm, zvir, Time )
 real, dimension(Atm(1)%bd%isc:Atm(1)%bd%iec, &
                 Atm(1)%bd%jsc:Atm(1)%bd%jec) :: pfull, dat2, &
                                                 rv850, rv700, rv600
-                
+
 real, dimension(Atm(1)%bd%isc:Atm(1)%bd%iec, &
                 Atm(1)%bd%jsc:Atm(1)%bd%jec,1) :: dat3
 
@@ -462,9 +462,9 @@ subroutine fv_cmip_diag ( Atm, zvir, Time )
   compute_wa = .false.
   if (count(ID_hur%field_id(:)>0) > 0) compute_rh = .true.
   if (count(ID_wa%field_id(:)>0)  > 0) compute_wa = .true.
-    
+
   ! compute relative humidity at model levels (if needed)
-  if (compute_rh .or. compute_wa) then 
+  if (compute_rh .or. compute_wa) then
     do k=1,npz
       do j=jsc,jec
       do i=isc,iec
@@ -580,80 +580,80 @@ subroutine fv_cmip_diag ( Atm, zvir, Time )
   if (query_cmip_diag_id(ID_cls))  used = send_cmip_data_3d (ID_cls,  Atm(n)%q(isc:iec,jsc:jec,:,nqa)*100., Time)
   if (query_cmip_diag_id(ID_clws)) used = send_cmip_data_3d (ID_clws, Atm(n)%q(isc:iec,jsc:jec,:,nql), Time)
   if (query_cmip_diag_id(ID_clis)) used = send_cmip_data_3d (ID_clis, Atm(n)%q(isc:iec,jsc:jec,:,nqi), Time)
- 
+
 !----------------------------------------------------------------------
 ! process 2D fields on specific pressure levels
-! 
+!
   if (id_ua10 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 10.e2, Atm(n)%peln, &
-                               Atm(n)%ua(isc:iec,jsc:jec,:), dat2)          
+                               Atm(n)%ua(isc:iec,jsc:jec,:), dat2)
     used = send_data (id_ua10, dat2, Time)
   endif
 
   if (id_ua200 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 200.e2, Atm(n)%peln, &
-                               Atm(n)%ua(isc:iec,jsc:jec,:), dat2)          
+                               Atm(n)%ua(isc:iec,jsc:jec,:), dat2)
     used = send_data (id_ua200, dat2, Time)
   endif
 
   if (id_va200 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 200.e2, Atm(n)%peln, &
-                               Atm(n)%va(isc:iec,jsc:jec,:), dat2)          
+                               Atm(n)%va(isc:iec,jsc:jec,:), dat2)
     used = send_data (id_va200, dat2, Time)
   endif
 
   if (id_ua850 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 850.e2, Atm(n)%peln, &
-                               Atm(n)%ua(isc:iec,jsc:jec,:), dat2)          
+                               Atm(n)%ua(isc:iec,jsc:jec,:), dat2)
     used = send_data (id_ua850, dat2, Time)
   endif
 
   if (id_va850 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 850.e2, Atm(n)%peln, &
-                               Atm(n)%va(isc:iec,jsc:jec,:), dat2)          
+                               Atm(n)%va(isc:iec,jsc:jec,:), dat2)
     used = send_data (id_va850, dat2, Time)
   endif
 
   if (id_ta500 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 500.e2, Atm(n)%peln, &
-                               Atm(n)%pt(isc:iec,jsc:jec,:), dat2)          
+                               Atm(n)%pt(isc:iec,jsc:jec,:), dat2)
     used = send_data (id_ta500, dat2, Time)
   endif
 
   if (id_ta700 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 700.e2, Atm(n)%peln, &
-                               Atm(n)%pt(isc:iec,jsc:jec,:), dat2)          
+                               Atm(n)%pt(isc:iec,jsc:jec,:), dat2)
     used = send_data (id_ta700, dat2, Time)
   endif
 
   if (id_ta850 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 850.e2, Atm(n)%peln, &
-                               Atm(n)%pt(isc:iec,jsc:jec,:), dat2)          
+                               Atm(n)%pt(isc:iec,jsc:jec,:), dat2)
     used = send_data (id_ta850, dat2, Time)
     endif
 
   if (id_hus850 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 850.e2, Atm(n)%peln, &
-                               Atm(n)%q(isc:iec,jsc:jec,:,sphum), dat2)          
+                               Atm(n)%q(isc:iec,jsc:jec,:,sphum), dat2)
     used = send_data (id_hus850, dat2, Time)
   endif
 
   if (id_wap500 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 500.e2, Atm(n)%peln, &
-                               Atm(n)%omga(isc:iec,jsc:jec,:), dat2)          
+                               Atm(n)%omga(isc:iec,jsc:jec,:), dat2)
     used = send_data (id_wap500, dat2, Time)
   endif
 
   if (id_rv200 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 200.e2, Atm(n)%peln, rv, dat2)
     used = send_data (id_rv200, dat2, Time)
   endif
-  
+
   if (id_rv500 > 0) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 500.e2, Atm(n)%peln, rv, dat2)
     used = send_data (id_rv500, dat2, Time)
   endif
-  
+
   if (id_rv850 > 0 .or. id_vortmean > 0 ) then
     call interpolate_vertical (isc, iec, jsc, jec, npz, 850.e2, Atm(n)%peln, rv, rv850)
     if (id_rv850 > 0) used = send_data (id_rv850, rv850, Time)
@@ -663,27 +663,27 @@ subroutine fv_cmip_diag ( Atm, zvir, Time )
       used = send_data (id_vortmean, (rv600+rv700+rv850)/3., Time)
     endif
   endif
-  
+
   if (id_zg10 > 0) then
-    call get_height_given_pressure (isc, iec, jsc, jec, ngc, npz, wz, 1, (/id_zg10/), &
+    call get_height_given_pressure (isc, iec, jsc, jec, npz, wz, 1, (/id_zg10/), &
                                     (/log(10.e2)/), Atm(n)%peln, dat3)
     used = send_data (id_zg10, dat3(:,:,1), Time)
   endif
 
   if (id_zg100 > 0) then
-    call get_height_given_pressure (isc, iec, jsc, jec, ngc, npz, wz, 1, (/id_zg100/), &
+    call get_height_given_pressure (isc, iec, jsc, jec, npz, wz, 1, (/id_zg100/), &
                                     (/log(100.e2)/), Atm(n)%peln, dat3)
     used = send_data (id_zg100, dat3(:,:,1), Time)
   endif
 
   if (id_zg500 > 0) then
-    call get_height_given_pressure (isc, iec, jsc, jec, ngc, npz, wz, 1, (/id_zg500/), &
+    call get_height_given_pressure (isc, iec, jsc, jec, npz, wz, 1, (/id_zg500/), &
                                     (/log(500.e2)/), Atm(n)%peln, dat3)
     used = send_data (id_zg500, dat3(:,:,1), Time)
   endif
 
   if (id_zg1000 > 0) then
-    call get_height_given_pressure (isc, iec, jsc, jec, ngc, npz, wz, 1, (/id_zg1000/), &
+    call get_height_given_pressure (isc, iec, jsc, jec, npz, wz, 1, (/id_zg1000/), &
                                     (/log(1000.e2)/), Atm(n)%peln, dat3)
     used = send_data (id_zg1000, dat3(:,:,1), Time)
   endif

GFDL_tools/read_climate_nudge_data.F90

@@ -61,7 +61,7 @@ module read_climate_nudge_data_mod
                         INDEX_U  = 8, INDEX_V  = 9
   character(len=8), dimension(NUM_REQ_FLDS) :: required_field_names = &
        (/ 'P0  ', 'hyai', 'hybi', 'PHI ', 'PS  ', 'T   ', 'Q   ', 'U   ', 'V   ' /)
- 
+
   integer, parameter :: MAXFILES = 53
   character(len=256) :: filenames(MAXFILES)
   character(len=256) :: filename_tails(MAXFILES)
@@ -85,7 +85,7 @@ module read_climate_nudge_data_mod
   integer, dimension(NUM_REQ_FLDS) :: field_index   ! varid for variables
   integer, dimension(NUM_REQ_AXES) :: axis_index    ! varid for dimensions
   type(axistype),  dimension(NUM_REQ_FLDS) :: axes
-  type(fieldtype), dimension(NUM_REQ_FLDS) :: fields  
+  type(fieldtype), dimension(NUM_REQ_FLDS) :: fields
 end type
 
   type(filedata_type), allocatable :: Files(:)
@@ -301,7 +301,7 @@ subroutine read_grid ( lon, lat, ak, bk )
       else
          ak = 0.
       endif
- 
+
       call mpp_read(Files(1)%ncid, Files(1)%fields(INDEX_BK), bk)
 
 
@@ -392,7 +392,7 @@ subroutine read_climate_nudge_data_2d (itime, field, dat, is, js)
          call error_mesg ('read_climate_nudge_data_mod', 'itime out of range', FATAL)
       endif
 
-     ! check dimensions 
+     ! check dimensions
      if (present(js)) then
         if (size(dat,1) .ne. global_axis_size(INDEX_LON) .or. &
             size(dat,2) .ne. sub_domain_latitude_size) then
@@ -414,7 +414,7 @@ subroutine read_climate_nudge_data_2d (itime, field, dat, is, js)
      else
          call error_mesg ('read_climate_nudge_data_mod', 'incorrect field requested in read_climate_nudge_data_2d', FATAL)
      endif
-     
+
      ! file index and actual time index in file
      n = file_index(itime)
      atime = itime - Files(n)%time_offset
@@ -427,9 +427,9 @@ subroutine read_climate_nudge_data_2d (itime, field, dat, is, js)
      nread = 1
      nread(1) = size(dat,1)
      nread(2) = size(dat,2)
-     
+
      call mpp_read(Files(n)%ncid, Files(n)%fields(this_index), dat, start, nread)
-  
+
       ! geopotential height (convert to m2/s2 if necessary)
      if (field .eq. 'phis') then
         if (maxval(dat) > 1000.*GRAV) then
@@ -489,7 +489,7 @@ subroutine read_climate_nudge_data_3d (itime, field, dat, is, js)
      else
         call error_mesg ('read_climate_nudge_data_mod', 'incorrect field requested in read_climate_nudge_data_3d', FATAL)
      endif
-     
+
 
      ! file index and actual time index in file
      n = file_index(itime)

README.md

@@ -1,6 +1,6 @@
 # GFDL_atmos_cubed_sphere
 
-This is for the FV3 dynamical core used in the current GFDL models (AM4/CM4).
+The source contained herein reflects the 201912 release of the Finite Volume Cubed-Sphere Dynamical Core (FV3) for use in the current GFDL models (AM4/CM4/ESM4/SPEAR).
 
 # Where to find information
 
@@ -9,8 +9,7 @@ for more information.
 
 # Proper usage attribution
 
-Cite either Putman and Lin (2007) or Harris and Lin (2013) when describing a 
-model using the FV3 dynamical core.
+Cite Putman and Lin (2007) and Harris and Lin (2013) when describing a model using the FV3 dynamical core.
 
 # What files are what
 
@@ -21,15 +20,14 @@ The top level directory structure groups source code and input files as follow:
 | ```LICENSE.md```     | a copy of the Gnu lesser general public license, version 3. |
 | ```README.md```      | this file with basic pointers to more information |
 | ```model/```         | contains the source code for core of the FV3 dyanmical core |
-| ```model_nh_null/``` | contains the source stub code for satisfying references |
 | ```driver/```        | contains drivers used by different models/modeling systems |
 | ```tools/```         | contains source code of tools used within the core |
 | ```GFDL_tools/```    | contains source code of tools specific to GFDL models |
 
 # Dependencies
 
 The source code in this repository requires other NOAA-GFDL projects in
-order to compile.  As stated above, this branch is for use with the current 
+order to compile.  As stated above, this branch is for use with the current
 NOAA-GFDL/AM4 and NOAA-GFDL/CM4 projects and is included as a submodule within
 those projects.
 

RELEASE.md

@@ -0,0 +1,31 @@
+# RELEASE NOTES for FV3: Summary
+
+FV3-201912-public --- 10 January 2020
+Lucas Harris, GFDL <[email protected]>
+
+This version has been tested against the current GFDL AM4 phsyics
+and with release candidate 2020.02 of the FMS code at https://github.com/NOAA-GFDL/FMS
+
+Includes all of the features of the GFDL Release to EMC, as well as:
+
+- Updated 2017 GFDL Microphysics (from S-J Lin and L Zhou included in GFSv15)
+- Updates for GFSv15 ICs (from T Black/J Abeles, EMC)
+- Updates to support new nesting capabilities in FMS (from Z Liang)
+- Re-written grid nesting code for efficiency and parallelization
+- Re-organized fv_eta for improved vertical level selection
+- 2018 Stand-alone regional capabilities (from T Black/J Abeles, EMC)
+- Refactored model front-end (fv_control, fv_restart)
+- Support for point soundings
+- And other updates
+
+# Interface changes
+
+drivers: renamed 'fvGFS' directory to SHiELD
+
+atmosphere.F90: 'mytile' is renamed 'mygrid'
+
+The non-functional gfdl_cloud_microphys.F90 has been removed and replaced with the 2017 public release given to EMC. Also added a proper initialization routine, that includes the use of INTERNAL_FILE_NML and thereby requires the input_nml_file argument. If you do not define the compiler flag INTERNAL_FILE_NML then you can delete this argument.
+
+The namelist nggps_diag_nml has been eliminated. 'fdiag' is no longer handled by the dynamical core, and should be handled by the physics driver.
+
+For a complete technical description see the [forthcoming] GFDL Technical Memorandum.