Candidate branch main->dev/gfdl

Note that most of these commits are from previously squashed pull
requests, and this PR is restoring them.

- 6360dbb Merge branch 'main' into main_to_dev
- bac8031 Merge pull request mom-ocean#1566 from jiandewang/EMC-FMS-mixed-mode-20220411
- e532d86 Merge pull request mom-ocean#88 from marshallward/missing_attrib_with_class_bugfix
- d380f1d An alternate fix to class(*) issues with FMS 2022-01
- 8ecf333 Merge pull request mom-ocean#87 from jiandewang/feature/update-to-main-20220317
- ba37f94 Merge remote-tracking branch 'FSU/main' into feature/update-to-main-20220317 this is corresponding to MOM6 main 20220317 commit (hash # 399a7db)
- 44313d9 Merge pull request mom-ocean#85 from jiandewang/feature/update-to-main-20220217
- 966707f Merge remote-tracking branch 'GFDL/main' into feature/update-to-main-20220217 this is corresponding to MOM6 main branch 20220217 commit (hash # 6f6d4d6), which originally based on GFDL-candidate-20220129
- 32c0e1e Merge pull request mom-ocean#81 from jiandewang/feature/update-to-main-20211220
- 9642b1d delete external/OCEAN_stochastic_phyiscs directory as Phil re-coded in external/stochastic_physics directory
- e7c9ada solve minor conflict in mom_cap.F90 mom_ocean_model_nuopc.F90 and MOM_energetic_PBL.F90, add two new files: src/parameterizations/stochastic/MOM_stochastics.F90 and config_src/external/stochastic_physics/stochastic_physics.F90
- 90d5961 Merge pull request mom-ocean#78 from jiandewang/feature/update-to-GFDL-20211019
- fd02017 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20211019
- 36f17eb Merge pull request mom-ocean#72 from pjpegion/ocn_stoch_july2021
- a9a957e return a more accurate error message in MOM_stochasics
- 56bb41e Merge branch 'ocn_stoch_july2021' of https://github.com/pjpegion/MOM6 into ocn_stoch_july2021
- ca2ae1c update to dev/emc
- 14ca4a1 Merge pull request mom-ocean#76 from jiandewang/feature/update-to-GFDL-20210914
- 29016c2 Merge remote-tracking branch 'GFDL/main' into feature/update-to-GFDL-20210914 merge GFDL main 20210914 commit (hash # c09e199)
- a8577df Merge branch 'NOAA-EMC:dev/emc' into ocn_stoch_july2021
- f8a8e4c update to gfdl 20210806 (mom-ocean#74)
- 16e6af0 update to dev/emc
- 237a510 add comments
- 1b4273d revert logic wrt increments
- 5b2040e add logic to remove incrments from restart if outside IAU window
- c5f2b72 add write_stoch_restart_ocn to MOM_stochastics
- bdf2dc7 doxygen cleanup
- 8bc4acc move stochastics to external directory
- a3fa3a1 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch_july2021
- e4bc007 stochastic physics re-write
- 202cbd4 update to dev/emc
- 61717ee Merge remote-tracking branch 'origin/dev/emc' into ocn_stoch
- 565e0bb remove debug statements
- a4c0411 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch
- 689a73f remove PE_here from mom_ocean_model_nuopc.F90
- 8afe969 clean up of mom_ocean_model_nuopc.F90
- 25ed4fc revert MOM_domains.F90
- b8d9888 place stochastic array in fluxes container and make SPPT specific arrays allocatable
- d984a7e remove stochastics container
- eb88219 clean up of code for MOM6 coding standards
- 6e3ea1b correct coupled_driver/ocean_model_MOM.F90 and other cleanup
- 0b99c1f make stochastics optional
- 85023f8 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch
- 80f9f44 clean up MOM_domains
- 5443f8e remove blank link in MOM_diagnostics
- 1727d9a re-write of stochastic code to remove CPP directives
- 600ebf9 Merge remote-tracking branch 'upstream/dev/emc' into ocn_stoch
- 6bb9d0b fix non stochastic ePBL calculation
- 1d7ffa3 clean up code
- 040e1f1 Merge pull request mom-ocean#13 from NOAA-EMC/dev/emc
- 2cba995 Merge branch 'dev/emc' into ocn_stoch
- 1dc0f4f Merge remote-tracking branch 'upstream/dev/emc' into dev/emc
- 4bd9b9e clean up debug statements
- 25ed5ef additions for stochy restarts
- a2a374b add stochy_restart writing to mom_cap
- 0c15f4c Update MOM_diabatic_driver.F90
- 167a62e Merge pull request mom-ocean#12 from pjpegion/dev/emc
- bd477a9 Update MOM_diabatic_driver.F90
- 7212400 Update MOM_diabatic_driver.F90
- 7de295c cleanup of code and enhancement of ePBL perts
- cd06356 Merge pull request #11 from NOAA-EMC/dev/emc
- 9896d61 Merge pull request #9 from pjpegion/dev/emc_merge
- 0a62737 Merge branch 'ocn_stoch' into dev/emc_merge
- 3cad1ba Merge pull request #8 from NOAA-EMC/dev/emc
- c2aa2a8 updates from dev/emc
- 182ef34 additions for stochastic physics and ePBL perts
- 671c714 Merge pull request #1 from NOAA-EMC/dev/emc

config_src/infra/FMS1/MOM_diag_manager_infra.F90

@@ -236,9 +236,15 @@ integer function register_static_field_infra(module_name, field_name, axes, long
   integer,            optional, intent(in) :: area      !< Diagnostic ID of the field containing the area attribute
   integer,            optional, intent(in) :: volume    !< Diagnostic ID of the field containing the volume attribute
 
-  register_static_field_infra = register_static_field_fms(module_name, field_name, axes, long_name, units,&
-       & missing_value, range, mask_variant, standard_name, dynamic=.false.,do_not_log=do_not_log, &
+  if(present(missing_value) .or. present(range)) then
+    register_static_field_infra = register_static_field_fms(module_name, field_name, axes, long_name, units,&
+       & missing_value, range, mask_variant=mask_variant, standard_name=standard_name, dynamic=.false.,&
+       do_not_log=do_not_log, interp_method=interp_method,tile_count=tile_count, area=area, volume=volume)
+  else
+    register_static_field_infra = register_static_field_fms(module_name, field_name, axes, long_name, units,&
+       &  mask_variant=mask_variant, standard_name=standard_name, dynamic=.false.,do_not_log=do_not_log, &
        interp_method=interp_method,tile_count=tile_count, area=area, volume=volume)
+  endif
 end function register_static_field_infra
 
 !> Returns true if the argument data are successfully passed to a diagnostic manager
@@ -267,7 +273,20 @@ logical function send_data_infra_1d(diag_field_id, field, is_in, ie_in, time, ma
   character(len=*),      optional, intent(out) :: err_msg !< A log indicating the status of the post upon
                                                        !! returning to the calling routine
 
-  send_data_infra_1d = send_data_fms(diag_field_id, field, time, is_in, mask, rmask, ie_in, weight, err_msg)
+  if(present(rmask) .or. present(weight)) then
+   if(present(rmask) .and. present(weight)) then
+  send_data_infra_1d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, mask=mask, rmask=rmask, ie_in=ie_in,&
+                                     weight=weight, err_msg=err_msg)
+   elseif(present(rmask)) then
+  send_data_infra_1d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, mask=mask, rmask=rmask, ie_in=ie_in,&
+                                     err_msg=err_msg)
+   elseif(present(weight)) then
+  send_data_infra_1d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, ie_in=ie_in, weight=weight,&
+                                     err_msg=err_msg)
+   endif
+  else
+  send_data_infra_1d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, ie_in=ie_in, err_msg=err_msg)
+  endif
 
 end function send_data_infra_1d
 
@@ -289,9 +308,21 @@ logical function send_data_infra_2d(diag_field_id, field, is_in, ie_in, js_in, j
   character(len=*),        optional, intent(out) :: err_msg !< A log indicating the status of the post upon
                                                          !! returning to the calling routine
 
-  send_data_infra_2d = send_data_fms(diag_field_id, field, time, is_in, js_in, mask, &
-                                rmask, ie_in, je_in, weight, err_msg)
-
+  if(present(rmask) .or. present(weight)) then
+   if(present(rmask) .and. present(weight)) then
+    send_data_infra_2d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, js_in=js_in, mask=mask, &
+                                rmask=rmask, ie_in=ie_in, je_in=je_in, weight=weight, err_msg=err_msg)
+   elseif(present(rmask)) then
+    send_data_infra_2d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, js_in=js_in, mask=mask, &
+                                rmask=rmask, ie_in=ie_in, je_in=je_in, err_msg=err_msg)
+   elseif(present(weight)) then
+    send_data_infra_2d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, js_in=js_in, mask=mask, &
+                                ie_in=ie_in, je_in=je_in, weight=weight, err_msg=err_msg)
+   endif
+  else
+    send_data_infra_2d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, js_in=js_in, mask=mask, &
+                                ie_in=ie_in, je_in=je_in, err_msg=err_msg)
+  endif
 end function send_data_infra_2d
 
 !> Returns true if the argument data are successfully passed to a diagnostic manager

config_src/infra/FMS2/MOM_diag_manager_infra.F90

@@ -236,9 +236,15 @@ integer function register_static_field_infra(module_name, field_name, axes, long
   integer,            optional, intent(in) :: area      !< Diagnostic ID of the field containing the area attribute
   integer,            optional, intent(in) :: volume    !< Diagnostic ID of the field containing the volume attribute
 
-  register_static_field_infra = register_static_field_fms(module_name, field_name, axes, long_name, units,&
-       & missing_value, range, mask_variant, standard_name, dynamic=.false.,do_not_log=do_not_log, &
+  if(present(missing_value) .or. present(range)) then
+    register_static_field_infra = register_static_field_fms(module_name, field_name, axes, long_name, units,&
+       & missing_value, range, mask_variant=mask_variant, standard_name=standard_name, dynamic=.false.,&
+       do_not_log=do_not_log, interp_method=interp_method,tile_count=tile_count, area=area, volume=volume)
+  else
+    register_static_field_infra = register_static_field_fms(module_name, field_name, axes, long_name, units,&
+       &  mask_variant=mask_variant, standard_name=standard_name, dynamic=.false.,do_not_log=do_not_log, &
        interp_method=interp_method,tile_count=tile_count, area=area, volume=volume)
+  endif
 end function register_static_field_infra
 
 !> Returns true if the argument data are successfully passed to a diagnostic manager
@@ -267,7 +273,20 @@ logical function send_data_infra_1d(diag_field_id, field, is_in, ie_in, time, ma
   character(len=*),      optional, intent(out) :: err_msg !< A log indicating the status of the post upon
                                                        !! returning to the calling routine
 
-  send_data_infra_1d = send_data_fms(diag_field_id, field, time, is_in, mask, rmask, ie_in, weight, err_msg)
+  if(present(rmask) .or. present(weight)) then
+   if(present(rmask) .and. present(weight)) then
+  send_data_infra_1d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, mask=mask, rmask=rmask, ie_in=ie_in,&
+                                     weight=weight, err_msg=err_msg)
+   elseif(present(rmask)) then
+  send_data_infra_1d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, mask=mask, rmask=rmask, ie_in=ie_in,&
+                                     err_msg=err_msg)
+   elseif(present(weight)) then
+  send_data_infra_1d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, ie_in=ie_in, weight=weight,&
+                                     err_msg=err_msg)
+   endif
+  else
+  send_data_infra_1d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, ie_in=ie_in, err_msg=err_msg)
+  endif
 
 end function send_data_infra_1d
 
@@ -289,9 +308,21 @@ logical function send_data_infra_2d(diag_field_id, field, is_in, ie_in, js_in, j
   character(len=*),        optional, intent(out) :: err_msg !< A log indicating the status of the post upon
                                                          !! returning to the calling routine
 
-  send_data_infra_2d = send_data_fms(diag_field_id, field, time, is_in, js_in, mask, &
-                                rmask, ie_in, je_in, weight, err_msg)
-
+  if(present(rmask) .or. present(weight)) then
+   if(present(rmask) .and. present(weight)) then
+    send_data_infra_2d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, js_in=js_in, mask=mask, &
+                                rmask=rmask, ie_in=ie_in, je_in=je_in, weight=weight, err_msg=err_msg)
+   elseif(present(rmask)) then
+    send_data_infra_2d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, js_in=js_in, mask=mask, &
+                                rmask=rmask, ie_in=ie_in, je_in=je_in, err_msg=err_msg)
+   elseif(present(weight)) then
+    send_data_infra_2d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, js_in=js_in, mask=mask, &
+                                ie_in=ie_in, je_in=je_in, weight=weight, err_msg=err_msg)
+   endif
+  else
+    send_data_infra_2d = send_data_fms(diag_field_id, field, time=time, is_in=is_in, js_in=js_in, mask=mask, &
+                                ie_in=ie_in, je_in=je_in, err_msg=err_msg)
+  endif
 end function send_data_infra_2d
 
 !> Returns true if the argument data are successfully passed to a diagnostic manager