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merge dev/emc into fork #1

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Nov 16, 2019
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52b018b
Add time0 and timenow in MCT
gustavo-marques Aug 15, 2019
bd57605
Add time0 and timenow in NUOPC
gustavo-marques Aug 15, 2019
4191689
Deletes unecessary if statement
gustavo-marques Aug 16, 2019
52225e3
Deletes blank line contains spaces
gustavo-marques Aug 16, 2019
b61053b
Replaces timenow with time_start and corrects comments.
gustavo-marques Aug 16, 2019
b595da4
Merge pull request #116 from gustavo-marques/fix_ocean_stats
alperaltuntas Aug 19, 2019
6e145df
Obsolete parameter ADD_KV_SLOW
gustavo-marques Aug 20, 2019
9f2f709
Removes visc%Kv_slow from restart files
gustavo-marques Aug 20, 2019
5ff5a93
Merge pull request #117 from gustavo-marques/remove_kv_slow
alperaltuntas Aug 21, 2019
93727f8
Fix first four loop indices suggested by Bob
gustavo-marques Aug 22, 2019
e778191
Deletes max_diss_rate_bt since it is never used
gustavo-marques Aug 23, 2019
3b7cb69
Fixes the remaining loop indices related to GME
gustavo-marques Aug 23, 2019
3257801
Removes unneeded calls to pass_var and add calls to pass_vector
gustavo-marques Aug 23, 2019
b339108
Groups terms for rotational invariance and deletes beta_h and beta_q …
gustavo-marques Aug 23, 2019
0aeec9d
Adds correct calculation of GME at q points
gustavo-marques Aug 26, 2019
fa773cd
Created new variables dvdx3/dudy3 for shearing strain on the Laplacian
gustavo-marques Aug 26, 2019
2ac12ce
Deleting comments
gustavo-marques Aug 26, 2019
d29a435
Adds consistency check between mesh and mom6 grid
gustavo-marques Aug 27, 2019
fb1133e
Replaces CICE to MOM in error messages
gustavo-marques Aug 27, 2019
d6277ca
Merge pull request #118 from gustavo-marques/consistency_check_nuopc
alperaltuntas Aug 28, 2019
7ad7296
remove labeled format specifiers
alperaltuntas Aug 28, 2019
cc9e33d
Adds new parameter, MEKE_EQUILIBRIUM_ALT
gustavo-marques Aug 28, 2019
d05235f
Final GME code fix
gustavo-marques Aug 28, 2019
18c6f1e
replace hard-coded mesh diff. limit with a param: eps_omesh
alperaltuntas Aug 28, 2019
66f808b
add units to EPS_OMESH
alperaltuntas Aug 28, 2019
c698b1a
call get_eps_omesh and remove hardcoded limit
alperaltuntas Aug 28, 2019
d9a00d7
call MOM_error if mesh is inconsistent
alperaltuntas Aug 28, 2019
e02b358
compare mod 360 of diff and eps
alperaltuntas Aug 29, 2019
7f7e8c0
Add EPS_OMESH value in error message
alperaltuntas Aug 29, 2019
d329136
Merge pull request #119 from NCAR/improve_consistency_check
gustavo-marques Aug 29, 2019
b810e26
Fixes line length exceeded
gustavo-marques Aug 29, 2019
38be24e
Merge pull request #120 from gustavo-marques/fix_gme
alperaltuntas Aug 29, 2019
cfe0e70
Merge branch 'dev/ncar' into merge-dev-master-candidate-2019-08-30
gustavo-marques Aug 30, 2019
15a03c5
Commented out variables left over from merge
gustavo-marques Sep 3, 2019
ab9bc8a
Adds OS%US as argument in add_shelf_forces
gustavo-marques Sep 3, 2019
25b409b
Adding back 2018_answers and cleanning the code
gustavo-marques Sep 3, 2019
fe44289
Fixes a bug when computing PE_release_h
gustavo-marques Sep 12, 2019
584177f
Deletes whitespace
gustavo-marques Sep 13, 2019
466903b
Deletes more whitespace
gustavo-marques Sep 13, 2019
69ee7bc
Merge pull request #121 from gustavo-marques/fix_MEKE_GM_src
alperaltuntas Sep 13, 2019
4d0e180
Merge branch 'dev/ncar' into merge-dev-master-candidate-2019-08-30
gustavo-marques Sep 16, 2019
1852356
Removes white space
gustavo-marques Sep 16, 2019
fda9848
Merge pull request #5 from NCAR/dev/ncar
alperaltuntas Sep 16, 2019
ba2f186
Removed diagnostics related to FrictWork_diss and FrictWork_Max
gustavo-marques Sep 17, 2019
992e826
Avoids posting Kv_slow when it is not initialized
gustavo-marques Sep 17, 2019
6eeeea5
Merge pull request #122 from gustavo-marques/merge-dev-master-candida…
alperaltuntas Sep 17, 2019
353cea1
remove unused modules
alperaltuntas Sep 17, 2019
c295ce1
add ncar version of Doxyfile
alperaltuntas Sep 17, 2019
46d4385
use Doxyfile_ncar_rtd if env var NCAR_FORK defined
alperaltuntas Sep 17, 2019
3513c68
Merge pull request #123 from alperaltuntas/create_ncar_fork_of_doxygen
alperaltuntas Sep 17, 2019
e18a5b4
rm empty line
alperaltuntas Sep 17, 2019
ed59be3
Merge pull request #6 from alperaltuntas/create_ncar_fork_of_doxygen
alperaltuntas Sep 17, 2019
e44474c
changes for API page generation
alperaltuntas Sep 17, 2019
0b7f600
designate /mom_cap.F90 doxygen as subpage
alperaltuntas Sep 17, 2019
26c376c
move ncar files to ncar/ dir
alperaltuntas Sep 17, 2019
521c732
set EXTRACT_ALL to generate call graphs
alperaltuntas Sep 17, 2019
2bd130f
Merge pull request #124 from alperaltuntas/create_ncar_fork_of_doxygen
alperaltuntas Sep 17, 2019
7dc0fd0
Fix the NUOPC cap doxygen to use HTML style formatting for the import…
rsdunlapiv Sep 18, 2019
d1b0322
Move doxygen to end of module to be consistent with MOM6 conventions
rsdunlapiv Sep 19, 2019
d8a3886
Merge pull request #125 from NCAR/rsdunlapiv/cap_doc_fix
alperaltuntas Sep 19, 2019
0369959
Merge branch 'dev/ncar' into create_ncar_fork_of_doxygen
alperaltuntas Sep 19, 2019
3260a30
Merge branch 'dev/ncar' of https://github.com/NCAR/MOM6 into dev/ncar
alperaltuntas Sep 19, 2019
51a179a
Merge branch 'dev/ncar' into create_ncar_fork_of_doxygen
alperaltuntas Sep 19, 2019
900ad92
fix subroutine table
alperaltuntas Sep 19, 2019
de0777d
fix import/export field tables
alperaltuntas Sep 19, 2019
8648351
correct runoff units
alperaltuntas Sep 19, 2019
3b957a7
Merge pull request #126 from alperaltuntas/create_ncar_fork_of_doxygen
alperaltuntas Sep 20, 2019
be86d57
Merge branch 'dev/master' into dev-master-candidate-ncar-2019-10-02
gustavo-marques Oct 2, 2019
bccdf19
Restored comments documenting the dimensional rescaling of variables
gustavo-marques Oct 4, 2019
ec31391
Merge pull request #1013 from gustavo-marques/dev-master-candidate-nc…
marshallward Nov 7, 2019
100e92d
Merge remote-tracking branch 'GFDL/dev/master' into testnewdevmaster2…
JessicaMeixner-NOAA Nov 7, 2019
07481e4
updating mom_cap to add data override which was deleted in merge
JessicaMeixner-NOAA Nov 8, 2019
9a6f7f6
Merge NOAA-GFDL dev/master from 20191107
JessicaMeixner-NOAA Nov 13, 2019
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5 changes: 2 additions & 3 deletions config_src/mct_driver/mom_ocean_model_mct.F90
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,6 @@ module MOM_ocean_model_mct
use coupler_types_mod, only : coupler_type_set_diags, coupler_type_send_data
use mpp_domains_mod, only : domain2d, mpp_get_layout, mpp_get_global_domain
use mpp_domains_mod, only : mpp_define_domains, mpp_get_compute_domain, mpp_get_data_domain
use atmos_ocean_fluxes_mod, only : aof_set_coupler_flux
use fms_mod, only : stdout
use mpp_mod, only : mpp_chksum
use MOM_EOS, only : gsw_sp_from_sr, gsw_pt_from_ct
Expand Down Expand Up @@ -525,7 +524,7 @@ subroutine update_ocean_model(Ice_ocean_boundary, OS, Ocean_sfc, &
if (do_thermo) &
call shelf_calc_flux(OS%sfc_state, OS%fluxes, OS%Time, dt_coupling, OS%Ice_shelf_CSp)
if (do_dyn) &
call add_shelf_forces(OS%grid, OS%Ice_shelf_CSp, OS%forces)
call add_shelf_forces(OS%grid, OS%US, OS%Ice_shelf_CSp, OS%forces)
endif
if (OS%icebergs_alter_ocean) then
if (do_dyn) &
Expand Down Expand Up @@ -560,7 +559,7 @@ subroutine update_ocean_model(Ice_ocean_boundary, OS, Ocean_sfc, &
if (do_thermo) &
call shelf_calc_flux(OS%sfc_state, OS%flux_tmp, OS%Time, dt_coupling, OS%Ice_shelf_CSp)
if (do_dyn) &
call add_shelf_forces(OS%grid, OS%Ice_shelf_CSp, OS%forces)
call add_shelf_forces(OS%grid, OS%US, OS%Ice_shelf_CSp, OS%forces)
endif
if (OS%icebergs_alter_ocean) then
if (do_dyn) &
Expand Down
4 changes: 2 additions & 2 deletions config_src/mct_driver/mom_surface_forcing_mct.F90
Original file line number Diff line number Diff line change
Expand Up @@ -145,8 +145,8 @@ module MOM_surface_forcing_mct
!> Structure corresponding to forcing, but with the elements, units, and conventions
!! that exactly conform to the use for MOM-based coupled models.
type, public :: ice_ocean_boundary_type
real, pointer, dimension(:,:) :: rofl_flux =>NULL() !< liquid runoff [W/m2]
real, pointer, dimension(:,:) :: rofi_flux =>NULL() !< ice runoff [W/m2]
real, pointer, dimension(:,:) :: rofl_flux =>NULL() !< liquid runoff [kg/m2/s]
real, pointer, dimension(:,:) :: rofi_flux =>NULL() !< ice runoff [kg/m2/s]
real, pointer, dimension(:,:) :: u_flux =>NULL() !< i-direction wind stress [Pa]
real, pointer, dimension(:,:) :: v_flux =>NULL() !< j-direction wind stress [Pa]
real, pointer, dimension(:,:) :: t_flux =>NULL() !< sensible heat flux [W/m2]
Expand Down
18 changes: 12 additions & 6 deletions config_src/mct_driver/ocn_comp_mct.F90
Original file line number Diff line number Diff line change
Expand Up @@ -109,8 +109,9 @@ subroutine ocn_init_mct( EClock, cdata_o, x2o_o, o2x_o, NLFilename )
type(mct_aVect) , intent(inout) :: o2x_o !< Fluxes from ocean to coupler, computed by ocean
character(len=*), optional , intent(in) :: NLFilename !< Namelist filename

! local variables
type(time_type) :: time0 !< Model start time
! local variable
type(time_type) :: time0 !< Start time of coupled model's calendar.
type(time_type) :: time_start !< The time at which to initialize the ocean model
type(ESMF_time) :: time_var !< ESMF_time variable to query time
type(ESMF_time) :: time_in_ESMF !< Initial time for ocean
type(ESMF_timeInterval) :: ocn_cpl_interval !< Ocean coupling interval
Expand Down Expand Up @@ -202,11 +203,16 @@ subroutine ocn_init_mct( EClock, cdata_o, x2o_o, o2x_o, NLFilename )

call set_calendar_type(NOLEAP) !TODO: confirm this

! Get the initial time
call ESMF_ClockGet(EClock, currTime=time_var, rc=rc)
! Get start time
call ESMF_ClockGet(EClock, StartTime=time_var, rc=rc)
call ESMF_TimeGet(time_var, yy=year, mm=month, dd=day, h=hour, m=minute, s=seconds, rc=rc)
time0 = set_date(year, month, day, hour, minute, seconds, err_msg=err_msg)

! Get current time
call ESMF_ClockGet(EClock, currTime=time_var, rc=rc)
call ESMF_TimeGet(time_var, yy=year, mm=month, dd=day, h=hour, m=minute, s=seconds, rc=rc)
time_start = set_date(year, month, day, hour, minute, seconds, err_msg=err_msg)

! Debugging clocks
if (debug .and. is_root_pe()) then
write(glb%stdout,*) 'ocn_init_mct, current time: y,m,d-',year,month,day,'h,m,s=',hour,minute,seconds
Expand Down Expand Up @@ -279,7 +285,7 @@ subroutine ocn_init_mct( EClock, cdata_o, x2o_o, o2x_o, NLFilename )
runtype = get_runtype()
if (runtype == "initial") then
! startup (new run) - 'n' is needed below since we don't specify input_filename in input.nml
call ocean_model_init(glb%ocn_public, glb%ocn_state, time0, time0, input_restart_file = 'n')
call ocean_model_init(glb%ocn_public, glb%ocn_state, time0, time_start, input_restart_file = 'n')
else ! hybrid or branch or continuos runs
! get output path root
call seq_infodata_GetData( glb%infodata, outPathRoot=restartpath )
Expand All @@ -295,7 +301,7 @@ subroutine ocn_init_mct( EClock, cdata_o, x2o_o, o2x_o, NLFilename )
write(glb%stdout,*) 'Reading restart file: ',trim(restartfile)
end if
call shr_file_freeUnit(nu)
call ocean_model_init(glb%ocn_public, glb%ocn_state, time0, time0, input_restart_file=trim(restartfile))
call ocean_model_init(glb%ocn_public, glb%ocn_state, time0, time_start, input_restart_file=trim(restartfile))
endif
if (is_root_pe()) then
write(glb%stdout,'(/12x,a/)') '======== COMPLETED MOM INITIALIZATION ========'
Expand Down
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