COSIMA · anton-seaice · Dec 6, 2024 · Dec 6, 2024 · Dec 6, 2024 · Dec 6, 2024
diff --git a/.gitmodules b/.gitmodules
@@ -1,9 +1,9 @@
 [submodule "MOM6/MOM6"]
 	path = MOM6/MOM6
-	url = https://github.com/ACCESS-NRI/mom6
+	url = https://github.com/ACCESS-NRI/MOM6
 [submodule "CICE6/CICE6"]
 	path = CICE/CICE
-	url = https://github.com/ESCOMP/CICE
+	url = https://github.com/ACCESS-NRI/CICE
 [submodule "CMEPS/CMEPS"]
 	path = CMEPS/CMEPS
 	url = https://github.com/ESCOMP/CMEPS

diff --git a/CDEPS/CDEPS b/CDEPS/CDEPS
diff --git a/CDEPS/CMakeLists.txt b/CDEPS/CMakeLists.txt
@@ -14,9 +14,9 @@ target_sources(OM3_cdeps_common PRIVATE
   CDEPS/streams/dshr_stream_mod.F90
   CDEPS/streams/dshr_tinterp_mod.F90
 
+  CDEPS/dshr/dshr_mod.F90
   CDEPS/dshr/dshr_dfield_mod.F90
   CDEPS/dshr/dshr_fldlist_mod.F90
-  CDEPS/dshr/dshr_mod.F90
 )
 
 ## DATM
@@ -52,6 +52,8 @@ target_sources(OM3_cdeps_docn PRIVATE
   CDEPS/docn/docn_datamode_aquaplanet_mod.F90
   CDEPS/docn/docn_datamode_copyall_mod.F90
   CDEPS/docn/docn_datamode_cplhist_mod.F90
+  CDEPS/docn/docn_datamode_multilev_mod.F90
+  CDEPS/docn/docn_datamode_multilev_dom_mod.F90
   CDEPS/docn/docn_datamode_iaf_mod.F90
   CDEPS/docn/docn_datamode_som_mod.F90
   CDEPS/docn/docn_import_data_mod.F90

diff --git a/CDEPS/extra_sources/datm_datamode_jra55do_mod.F90 b/CDEPS/extra_sources/datm_datamode_jra55do_mod.F90
@@ -10,7 +10,6 @@ module datm_datamode_jra55do_mod
   use shr_const_mod    , only : shr_const_tkfrz, shr_const_pi, shr_const_rdair
   use dshr_strdata_mod , only : shr_strdata_get_stream_pointer, shr_strdata_type
   use dshr_methods_mod , only : dshr_state_getfldptr, dshr_fldbun_getfldptr, dshr_fldbun_regrid, chkerr
-  use dshr_mod         , only : dshr_restart_read, dshr_restart_write
   use dshr_strdata_mod , only : shr_strdata_type
   use dshr_fldlist_mod , only : fldlist_type, dshr_fldlist_add
 
@@ -20,8 +19,7 @@ module datm_datamode_jra55do_mod
   public  :: datm_datamode_jra55do_advertise
   public  :: datm_datamode_jra55do_init_pointers
   public  :: datm_datamode_jra55do_advance
-  public  :: datm_datamode_jra55do_restart_write
-  public  :: datm_datamode_jra55do_restart_read
+
 
   ! export state pointers
   real(r8), pointer :: Sa_z(:)       => null()
@@ -283,39 +281,4 @@ subroutine datm_datamode_jra55do_advance(exportstate, target_ymd, target_tod, mo
 
   end subroutine datm_datamode_jra55do_advance
 
-  !===============================================================================
-  subroutine datm_datamode_jra55do_restart_write(case_name, inst_suffix, ymd, tod, &
-       logunit, my_task, sdat)
-
-    ! input/output variables
-    character(len=*)            , intent(in)    :: case_name
-    character(len=*)            , intent(in)    :: inst_suffix
-    integer                     , intent(in)    :: ymd       ! model date
-    integer                     , intent(in)    :: tod       ! model sec into model date
-    integer                     , intent(in)    :: logunit
-    integer                     , intent(in)    :: my_task
-    type(shr_strdata_type)      , intent(inout) :: sdat
-    !-------------------------------------------------------------------------------
-
-    call dshr_restart_write(rpfile, case_name, 'datm', inst_suffix, ymd, tod, &
-         logunit, my_task, sdat)
-
-  end subroutine datm_datamode_jra55do_restart_write
-
-  !===============================================================================
-  subroutine datm_datamode_jra55do_restart_read(rest_filem, inst_suffix, logunit, my_task, mpicom, sdat)
-
-    ! input/output arguments
-    character(len=*)            , intent(inout) :: rest_filem
-    character(len=*)            , intent(in)    :: inst_suffix
-    integer                     , intent(in)    :: logunit
-    integer                     , intent(in)    :: my_task
-    integer                     , intent(in)    :: mpicom
-    type(shr_strdata_type)      , intent(inout) :: sdat
-    !-------------------------------------------------------------------------------
-
-    call dshr_restart_read(rest_filem, rpfile, inst_suffix, nullstr, logunit, my_task, mpicom, sdat)
-
-  end subroutine datm_datamode_jra55do_restart_read
-
 end module datm_datamode_jra55do_mod
diff --git a/CDEPS/patches/atm_comp_nuopc.F90.patch b/CDEPS/patches/atm_comp_nuopc.F90.patch
@@ -1,27 +1,27 @@
---- CDEPS/datm/atm_comp_nuopc.F90	2023-08-31 10:49:23.508874000 +1000
-+++ extra_sources/atm_comp_nuopc.F90	2023-08-31 10:48:55.428272000 +1000
-@@ -52,6 +52,12 @@
-   use datm_datamode_jra_mod     , only : datm_datamode_jra_restart_write
-   use datm_datamode_jra_mod     , only : datm_datamode_jra_restart_read
+diff --git a/datm/atm_comp_nuopc.F90 b/datm/atm_comp_nuopc.F90
+index b74e0d3..bb31c22 100644
+--- a/datm/atm_comp_nuopc.F90
++++ b/datm/atm_comp_nuopc.F90
+@@ -48,6 +48,10 @@ module cdeps_datm_comp
+   use datm_datamode_jra_mod     , only : datm_datamode_jra_init_pointers
+   use datm_datamode_jra_mod     , only : datm_datamode_jra_advance
 
 +  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_advertise
 +  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_init_pointers
 +  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_advance
-+  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_restart_write
-+  use datm_datamode_jra55do_mod , only : datm_datamode_jra55do_restart_read
 +
    use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_advertise
    use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_init_pointers
    use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_advance
-@@ -342,6 +348,7 @@
+@@ -357,6 +361,7 @@ contains
      if ( trim(datamode) == 'CORE2_NYF'    .or. &
           trim(datamode) == 'CORE2_IAF'    .or. &
           trim(datamode) == 'CORE_IAF_JRA' .or. &
-+         trim(datamode) == 'JRA55do'.or. &
++         trim(datamode) == 'JRA55do'      .or. &
           trim(datamode) == 'CLMNCEP'      .or. &
           trim(datamode) == 'CPLHIST'      .or. &
           trim(datamode) == 'GEFS'         .or. &
-@@ -361,6 +368,10 @@
+@@ -377,6 +382,10 @@ contains
         call datm_datamode_jra_advertise(exportState, fldsExport, flds_scalar_name, &
              flds_co2, flds_wiso, flds_presaero, flds_presndep, rc)
         if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -32,7 +32,7 @@
      case ('CLMNCEP')
         call datm_datamode_clmncep_advertise(exportState, fldsExport, flds_scalar_name, &
              flds_co2, flds_wiso, flds_presaero, flds_presndep, flds_preso3, rc)
-@@ -606,6 +617,9 @@
+@@ -627,6 +636,9 @@ contains
         case('CORE_IAF_JRA')
            call datm_datamode_jra_init_pointers(exportState, sdat, rc)
            if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -42,16 +42,16 @@
         case('CLMNCEP')
            call datm_datamode_clmncep_init_pointers(importState, exportState, sdat, rc)
            if (ChkErr(rc,__LINE__,u_FILE_u)) return
-@@ -630,6 +644,8 @@
-              call datm_datamode_core2_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-           case('CORE_IAF_JRA')
-              call datm_datamode_jra_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-+          case('JRA55do')
-+             call datm_datamode_jra55do_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-           case('CLMNCEP')
-              call datm_datamode_clmncep_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-           case('CPLHIST')
-@@ -677,6 +693,9 @@
+@@ -652,7 +664,7 @@ contains
+           call shr_get_rpointer_name(gcomp, 'atm', target_ymd, target_tod, rpfile, 'read', rc)
+           if (ChkErr(rc,__LINE__,u_FILE_u)) return
+           select case (trim(datamode))
+-          case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','SIMPLE')
++          case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','JRA55do','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','SIMPLE')
+              call dshr_restart_read(restfilm, rpfile, logunit, my_task, mpicom, sdat, rc)
+              if (ChkErr(rc,__LINE__,u_FILE_u)) return
+           case default
+@@ -694,6 +706,9 @@ contains
      case('CORE_IAF_JRA')
         call datm_datamode_jra_advance(exportstate, target_ymd, target_tod, sdat%model_calendar, rc)
         if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -61,13 +61,12 @@
      case('CLMNCEP')
         call datm_datamode_clmncep_advance(mainproc, logunit, mpicom,  rc)
         if (ChkErr(rc,__LINE__,u_FILE_u)) return
-@@ -705,6 +724,9 @@
-        case('CORE_IAF_JRA')
-           call datm_datamode_jra_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-                logunit, my_task, sdat)
-+       case('JRA55do')
-+          call datm_datamode_jra55do_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-+               logunit, my_task, sdat)
-        case('CLMNCEP')
-           call datm_datamode_clmncep_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-                logunit, my_task, sdat)
+@@ -722,7 +737,7 @@ contains
+        call shr_get_rpointer_name(gcomp, 'atm', target_ymd, target_tod, rpfile, 'write', rc)
+        if (ChkErr(rc,__LINE__,u_FILE_u)) return
+        select case (trim(datamode))
+-       case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','SIMPLE')
++       case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','JRA55do','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','SIMPLE')
+           call dshr_restart_write(rpfile, case_name, 'datm', inst_suffix, target_ymd, target_tod, logunit, &
+                my_task, sdat, rc)
+           if (ChkErr(rc,__LINE__,u_FILE_u)) return
diff --git a/CICE/CICE b/CICE/CICE
diff --git a/CICE/CMakeLists.txt b/CICE/CMakeLists.txt
@@ -26,6 +26,7 @@ target_sources(OM3_cice PRIVATE
   CICE/cicecore/shared/ice_arrays_column.F90
   CICE/cicecore/shared/ice_calendar.F90
   CICE/cicecore/shared/ice_constants.F90
+  CICE/cicecore/shared/ice_distribution.F90
   CICE/cicecore/shared/ice_domain_size.F90
   CICE/cicecore/shared/ice_fileunits.F90
   CICE/cicecore/shared/ice_init_column.F90
@@ -61,11 +62,13 @@ target_sources(OM3_cice PRIVATE
   CICE/cicecore/cicedyn/general/ice_flux_bgc.F90
   CICE/cicecore/cicedyn/general/ice_forcing.F90
   CICE/cicecore/cicedyn/general/ice_forcing_bgc.F90
+  CICE/cicecore/cicedyn/general/ice_init.F90
   CICE/cicecore/cicedyn/general/ice_state.F90
   CICE/cicecore/cicedyn/general/ice_step_mod.F90
 
   # Infrastructure
   CICE/cicecore/cicedyn/infrastructure/ice_blocks.F90
+  CICE/cicecore/cicedyn/infrastructure/ice_domain.F90
   CICE/cicecore/cicedyn/infrastructure/ice_grid.F90
   CICE/cicecore/cicedyn/infrastructure/ice_memusage.F90
   CICE/cicecore/cicedyn/infrastructure/ice_memusage_gptl.c
@@ -152,10 +155,6 @@ elseif(OM3_CICE_IO MATCHES "Binary")
   )
 endif()
 
-add_patched_source(OM3_cice CICE/cicecore/cicedyn/infrastructure/ice_domain.F90)
-add_patched_source(OM3_cice CICE/cicecore/shared/ice_distribution.F90)
-add_patched_source(OM3_cice CICE/cicecore/cicedyn/general/ice_init.F90)
-
 ### Install and Export
 
 ## Library

diff --git a/CICE/patches/ice_distribution.F90.patch b/CICE/patches/ice_distribution.F90.patch
diff --git a/CICE/patches/ice_domain.F90.patch b/CICE/patches/ice_domain.F90.patch
diff --git a/CICE/patches/ice_init.F90.patch b/CICE/patches/ice_init.F90.patch
diff --git a/CMEPS/CMEPS b/CMEPS/CMEPS
diff --git a/CMEPS/CMakeLists.txt b/CMEPS/CMakeLists.txt
@@ -12,6 +12,7 @@ if(OpenMP_Fortran_FOUND)
 endif()
 target_sources(OM3_cmeps PRIVATE
   CMEPS/cesm/flux_atmocn/shr_flux_mod.F90
+  CMEPS/mediator/med_phases_history_mod.F90
   CMEPS/mediator/med_phases_restart_mod.F90
   CMEPS/mediator/med_map_mod.F90
   CMEPS/mediator/med_methods_mod.F90
@@ -31,7 +32,6 @@ target_sources(OM3_cmeps PRIVATE
   CMEPS/mediator/med_phases_prep_ocn_mod.F90
   CMEPS/mediator/esmFlds.F90
   CMEPS/mediator/med.F90
-  CMEPS/mediator/med_time_mod.F90
   CMEPS/mediator/med_phases_ocnalb_mod.F90
   CMEPS/mediator/med_phases_prep_wav_mod.F90
   CMEPS/mediator/med_utils_mod.F90
@@ -48,8 +48,6 @@ target_sources(OM3_cmeps PRIVATE
   CMEPS/mediator/med_phases_post_wav_mod.F90
 )
 
-add_patched_source(OM3_cmeps CMEPS/mediator/med_phases_history_mod.F90)
-
 ## NUOPC cap share
 add_fortran_library(OM3_nuopc_cap_share mod/nuopc_cap_share STATIC)
 add_library(AccessOM3::nuopc_cap_share ALIAS OM3_nuopc_cap_share)
@@ -61,7 +59,6 @@ target_sources(OM3_nuopc_cap_share PRIVATE
   CMEPS/cesm/nuopc_cap_share/driver_pio_mod.F90
   CMEPS/cesm/nuopc_cap_share/esm_utils_mod.F90
   CMEPS/cesm/nuopc_cap_share/glc_elevclass_mod.F90
-  CMEPS/cesm/nuopc_cap_share/nuopc_shr_methods.F90
 )
 
 

diff --git a/CMEPS/patches/med_phases_history_mod.F90.patch b/CMEPS/patches/med_phases_history_mod.F90.patch
+4 −4		.github/workflows/extbuild.yml
+0 −4		.gitignore
+16 −0		.gitmodules
+1 −18		CMakeLists.txt
+43 −25		cime_config/buildlib
+21 −0		cime_config/stream_cdeps.py
+2 −1		cime_config/stream_definition_v2.0.xsd
+0 −150		cime_config/testdefs/testlist_cdeps.xml
+63 −79		datm/atm_comp_nuopc.F90
+12 −5		datm/cime_config/buildnml
+13 −2		datm/cime_config/config_component.xml
+40 −7		datm/cime_config/namelist_definition_datm.xml
+334 −9		datm/cime_config/stream_definition_datm.xml
+39 −34		datm/cime_config/testdefs/testlist_datm.xml
+0 −40		datm/datm_datamode_cfsr_mod.F90
+0 −38		datm/datm_datamode_clmncep_mod.F90
+12 −39		datm/datm_datamode_core2_mod.F90
+2 −41		datm/datm_datamode_cplhist_mod.F90
+2 −40		datm/datm_datamode_era5_mod.F90
+0 −39		datm/datm_datamode_gefs_mod.F90
+18 −39		datm/datm_datamode_jra_mod.F90
+0 −39		datm/datm_datamode_simple_mod.F90
+34 −0		dglc/CMakeLists.txt
+1 −0		dglc/cime_config/buildlib
+197 −0		dglc/cime_config/buildnml
+11 −0		dglc/cime_config/config_archive.xml
+92 −0		dglc/cime_config/config_component.xml
+140 −0		dglc/cime_config/namelist_definition_dglc.xml
+49 −0		dglc/cime_config/stream_definition_dglc.xml
+42 −0		dglc/cime_config/testdefs/testlist_dglc.xml
+13 −0		dglc/cime_config/user_nl_dglc
+33 −0		dglc/cime_config/user_nl_dglc_streams
+697 −0		dglc/dglc_datamode_noevolve_mod.F90
+842 −0		dglc/glc_comp_nuopc.F90
+6 −4		dice/cime_config/testdefs/testlist_dice.xml
+12 −9		dice/dice_datamode_ssmi_mod.F90
+13 −7		dice/ice_comp_nuopc.F90
+3 −2		dlnd/cime_config/testdefs/testlist_dlnd.xml
+20 −11		dlnd/lnd_comp_nuopc.F90
+4 −1		doc/source/datm.rst
+117 −0		doc/source/dglc.rst
+1 −0		doc/source/index.rst
+2 −1		doc/source/introduction.rst
+3 −1		doc/source/streams.rst
+2 −0		docn/CMakeLists.txt
+6 −2		docn/cime_config/config_component.xml
+5 −1		docn/cime_config/namelist_definition_docn.xml
+99 −1		docn/cime_config/stream_definition_docn.xml
+10 −7		docn/cime_config/testdefs/testlist_docn.xml
+0 −39		docn/docn_datamode_copyall_mod.F90
+0 −39		docn/docn_datamode_cplhist_mod.F90
+0 −44		docn/docn_datamode_iaf_mod.F90
+221 −0		docn/docn_datamode_multilev_dom_mod.F90
+186 −0		docn/docn_datamode_multilev_mod.F90
+15 −9		docn/docn_datamode_som_mod.F90
+77 −35		docn/ocn_comp_nuopc.F90
+4 −2		drof/cime_config/config_component.xml
+2 −1		drof/cime_config/namelist_definition_drof.xml
+32 −0		drof/cime_config/stream_definition_drof.xml
+3 −2		drof/cime_config/testdefs/testlist_drof.xml
+18 −11		drof/rof_comp_nuopc.F90
+16 −4		dshr/dshr_dfield_mod.F90
+1 −0		dshr/dshr_fldlist_mod.F90
+16 −23		dshr/dshr_mod.F90
+3 −2		dwav/cime_config/testdefs/testlist_dwav.xml
+17 −9		dwav/wav_comp_nuopc.F90
+1 −0		fox
+2 −1		share/CMakeLists.txt
+1 −0		share/genf90
+936 −0		share/nuopc_shr_methods.F90
+6 −3		streams/dshr_methods_mod.F90
+50 −18		streams/dshr_strdata_mod.F90
+8 −8		streams/dshr_stream_mod.F90
+16 −12		.github/workflows/extbuild.yml
+44 −57		.github/workflows/srt.yml
+1 −3		cesm/driver/ensemble_driver.F90
+39 −18		cesm/driver/esm.F90
+12 −306		cesm/driver/esm_time_mod.F90
+14 −3		cesm/flux_atmocn/shr_flux_mod.F90
+0 −859		cesm/nuopc_cap_share/nuopc_shr_methods.F90
+0 −2		cesm/nuopc_cap_share/seq_drydep_mod.F90
+222 −0		cesm/nuopc_cap_share/shr_dust_emis_mod.F90
+4 −2		cime_config/buildexe
+36 −12		cime_config/buildnml
+83 −71		cime_config/config_component.xml
+71 −24		cime_config/config_component_cesm.xml
+178 −252		cime_config/namelist_definition_drv.xml
+27 −0		cime_config/namelist_definition_drv_flds.xml
+3 −3		cime_config/runseq/driver_config.py
+4 −2		cime_config/runseq/runseq_TG.py
+22 −19		cime_config/runseq/runseq_general.py
+10 −0		cime_config/testdefs/testlist_drv.xml
+1 −0		cime_config/testdefs/testmods_dirs/drv/aoflux_ogrid/user_nl_cpl
+11 −16		doc/source/addendum/req_attributes_cesm.rst
+1 −1		mediator/CMakeLists.txt
+3 −4		mediator/Makefile
+556 −498		mediator/esmFldsExchange_cesm_mod.F90
+242 −121		mediator/esmFldsExchange_hafs_mod.F90
+48 −29		mediator/esmFldsExchange_ufs_mod.F90
+505 −398		mediator/fd_cesm.yaml
+73 −18		mediator/med.F90
+38 −15		mediator/med_diag_mod.F90
+121 −34		mediator/med_fraction_mod.F90
+99 −18		mediator/med_internalstate_mod.F90
+81 −43		mediator/med_io_mod.F90
+198 −68		mediator/med_map_mod.F90
+69 −2		mediator/med_methods_mod.F90
+50 −21		mediator/med_phases_aofluxes_mod.F90
+291 −0		mediator/med_phases_cdeps_mod.F90
+56 −50		mediator/med_phases_history_mod.F90
+2 −0		mediator/med_phases_post_atm_mod.F90
+12 −12		mediator/med_phases_post_glc_mod.F90
+1 −0		mediator/med_phases_post_ocn_mod.F90
+334 −17		mediator/med_phases_post_rof_mod.F90
+41 −28		mediator/med_phases_prep_atm_mod.F90
+73 −69		mediator/med_phases_prep_glc_mod.F90
+82 −23		mediator/med_phases_prep_ocn_mod.F90
+40 −12		mediator/med_phases_prep_rof_mod.F90
+30 −3		mediator/med_phases_prep_wav_mod.F90
+12 −7		mediator/med_phases_profile_mod.F90
+12 −11		mediator/med_phases_restart_mod.F90
+0 −302		mediator/med_time_mod.F90
+8 −8		ufs/ccpp/config/ccpp_prebuild_config.py
+12 −0		ufs/ccpp/data/MED_typedefs.F90
+28 −2		ufs/ccpp/data/MED_typedefs.meta
+4 −1		ufs/glc_elevclass_mod.F90
+350 −329		ufs/ufs_io_mod.F90